Links:

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Results from PredictProtein for predict_h14099

TOC for file /home/ppuser/server/work/predict_h14099

The following information has been received by the server (TOC)
PROSITE motif search (A Bairoch; P Bucher and K Hofmann) (TOC)
ProDom domain search (E Sonnhammer, Corpet, Gouzy, D Kahn) (TOC)
PSI-BLAST alignment header (TOC)
MAXHOM alignment header (TOC)
MAXHOM alignment (TOC)
COILS prediction (A Lupas) (TOC)
DISULFIND (A. Vullo and P. Frasconi) (TOC)
PHD information about accuracy (TOC)
PHD predictions (TOC)
PROF predictions (TOC)
GLOBE prediction of globularity (TOC)
Ambivalent Sequence Predictor(Malin Young, Kent Kirshenbaum, Stefan Highsmith) (TOC)

END of TOC

BEG of results for file /home/ppuser/server/work/predict_h14099

The following information has been received by the server

reference predict_h14099 (Apr 10, 2005 15:59:02)
reference pred_h14099 (Apr 10, 2005 17:23:02)
PPhdr from: svik@smu.edu
PPhdr resp: MAIL
PPhdr orig: HTML
PPhdr want: HTML
PPhdr password(###)
prediction of: - default prediction of: - ProSite SEG ProDom
return msf format
ret store
ret html perline=60
# default: single protein sequence resfilename=gm5917ju  description=nuoB_printouts
MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLKGRGGAGFSTG
LKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAA
VNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSKPPFPATSGAW
GKPTCVNNVETLCNVPAILANGVEWYQNISKSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGG
MRDGLKFKAWQPGGAGTDFLTEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARES
CGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFE
AGIKQPFSNTHLINGIQPNLLKERW

PROSITE motif search (A Bairoch; P Bucher and K Hofmann)

TOP - BOTTOM - PROSITE

-------------------------------------------------------------
Pattern-ID: ASN_GLYCOSYLATION PS00001 PDOC00001
Pattern-DE: N-glycosylation site
Pattern:    N[^P][ST][^P]
   238      NISK

Pattern-ID: PKC_PHOSPHO_SITE PS00005 PDOC00005
Pattern-DE: Protein kinase C phosphorylation site
Pattern:    [ST].[RK]
   14       TWR
   98       TYK
   253      SGR
   269      TAR
   364      SVK

Pattern-ID: CK2_PHOSPHO_SITE PS00006 PDOC00006
Pattern-DE: Casein kinase II phosphorylation site
Pattern:    [ST].{2}[DE]
   46       SPDE
   98       TYKD
   163      TGFD
   269      TARE

Pattern-ID: MYRISTYL PS00008 PDOC00008
Pattern-DE: N-myristoylation site
Pattern:    G[^EDRKHPFYW].{2}[STAGCN][^P]
   37       GARKAL
   64       GAGFST
   70       GLKWSL
   115      GMLISA
   280      GMRDGL
   293      GGAGTD
   318      GSRLGT
   360      GLPWSV
   435      GIQPNL

Pattern-ID: AMIDATION PS00009 PDOC00009
Pattern-DE: Amidation site
Pattern:    .G[RK][RK]
   191      EGRR

Pattern-ID: COMPLEX1_51K_1 PS00644 PDOC00555
Pattern-DE: Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1
Pattern:    G[AM]G[AR]Y[LIVM]CG[DE]{2}[STA]{2}[LIM]{2}[EN]S
   174      GAGRYICGEETALINS

Pattern-ID: COMPLEX1_51K_2 PS00645 PDOC00555
Pattern-DE: Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2
Pattern:    ESCG.C.PCR.G
   349      ESCGWCTPCRDG

ProDom domain search (E Sonnhammer, Corpet, Gouzy, D Kahn)

TOP - BOTTOM - ProDom - MView

Identities computed with respect to: (query) prot
Colored by: consensus/70% and property

HSP processing: ranked

                   1 [        .         .         .         .         :         . 60 
  prot               MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLK    
1 PD002676           -------------------------LDDYLAHGGYEGLKKVLTTMSPEEIIEEVKQSGLR    
2 PD002895           ------------------------------------------------------------    
3 PD039184           MKNIIRTPETHPLTWRLRDDKQPVWLDE--------------------------------    
4 PD121821           ------------------------------------------------------------    
5 PD108468           ------------------------------------------------------------    
  consensus/100%     ............................................................    
  consensus/90%      ............................................................    
  consensus/80%      ............................................................    
  consensus/70%      ............................................................    

                  61          .         .         .         1         .         . 120
  prot               GRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISA    
1 PD002676           GRGGAGFPTGLKWSFMAKKDtsEPKYLICNADEGEPGTFKDRRLMRHDPHKIIEGMLIAA    
2 PD002895           ------------------------------------------------------------    
3 PD039184           ------------------------------------------------------------    
4 PD121821           ------------------------------------------------------------    
5 PD108468           ------------------------------------------------------------    
  consensus/100%     ............................................................    
  consensus/90%      ............................................................    
  consensus/80%      ............................................................    
  consensus/70%      ............................................................    

                 121          .         .         :         .         .         . 180
  prot               FALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYIC    
1 PD002676           YAIGANQGYIYIRGEYPQAVERLQRAIQEAREAGLLGKNILGSGFDFDIEIHRGAGAYVC    
2 PD002895           ------------------------------------------------------------    
3 PD039184           ------------------------------------------------------------    
4 PD121821           ------------------------------------------------------------    
5 PD108468           ------------------------------------------------------------    
  consensus/100%     ............................................................    
  consensus/90%      ............................................................    
  consensus/80%      ............................................................    
  consensus/70%      ............................................................    

                 181          .         2         .         .         .         . 240
  prot               GEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNIS    
1 PD002676           GEETALIESLEGKRGKPRLKPPFPAQSGLWGKPTVVNNVETIANVPTILRRGADWFASIG    
2 PD002895           ------------------------------------------------------------    
3 PD039184           ------------------------------------------------------------    
4 PD121821           ------------------------------------------------------------    
5 PD108468           ------------------------------------------------------------    
  consensus/100%     ............................................................    
  consensus/90%      ............................................................    
  consensus/80%      ............................................................    
  consensus/70%      ............................................................    

                 241          :         .         .         .         .         3 300
  prot               KSKDAGTKLMGFSGRVKNPGLWELPFGXTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL    
1 PD002676           TPNSKGTKLFSISGHVNNPGVIEVPMG---------------------------------    
2 PD002895           ------------------------------RELIEDYGGGVRGGWklKAVQPGGPSGGCL    
3 PD039184           ------------------------------------------------------------    
4 PD121821           ----------------------------TLRELL-DYAGGVRAGHRLKFWTPGGSSTPLL    
5 PD108468           ------------------------------------------------------------    
  consensus/100%     ........................... ................................    
  consensus/90%      ........................... ................................    
  consensus/80%      ........................... ................................    
  consensus/70%      ........................... ................................    

                 301          .         .         .         .         :         . 360
  prot               TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDG    
1 PD002676           ------------------------------------------------------------    
2 PD002895           PEKHldVPMDYDSLRAAGSMLGTGAIIVMDESTDMVEAVRRFMEFYKHESCGQCTPCREG    
3 PD039184           ------------------------------------------------------------    
4 PD121821           TDEHLDVPL---------------------------------------------------    
5 PD108468           ------------------------------------------------------------    
  consensus/100%     ............................................................    
  consensus/90%      ............................................................    
  consensus/80%      ............................................................    
  consensus/70%      ............................................................    

                 361          .         .         .         4         .         . 420
  prot               LPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFE    
1 PD002676           ------------------------------------------------------------    
2 PD002895           TKWLYKILERLVKGEATPEDIDMLQEISKMV-KGHSICGLGDAAPWPVQSTLRHFREEYE    
3 PD039184           ------------------------------------------------------------    
4 PD121821           ------------------------------------------------------------    
5 PD108468           ------------------------------------------------------------    
  consensus/100%     ............................................................    
  consensus/90%      ............................................................    
  consensus/80%      ............................... ............................    
  consensus/70%      ............................... ............................    

                 421          .         .    ] 445
  prot               AGIKQPFSNTHLINGIQPNLLKERW    
1 PD002676           -------------------------    
2 PD002895           ARIKE--------------------    
3 PD039184           -------------------------    
4 PD121821           -------------------------    
5 PD108468           -----PFSNTHLINGIQPNLLKERW    
  consensus/100%     .........................    
  consensus/90%      .........................    
  consensus/80%      .........................    
  consensus/70%      .........................

--- ------------------------------------------------------------
--- 
--- Again: these results were obtained based on the domain data-
--- base collected by Daniel Kahn and his coworkers in Toulouse.
--- 
--- PLEASE quote: 
---       F Corpet, J Gouzy, D Kahn (1998).  The ProDom database
---       of protein domain families. Nucleic Ac Res 26:323-326.
--- 
--- The general WWW page is on:
----      ---------------------------------------
---       http://www.toulouse.inra.fr/prodom.html
----      ---------------------------------------
--- 
--- For WWW graphic interfaces to PRODOM, in particular for your
--- protein family, follow the following links (each line is ONE
--- single link for your protein!!):
--- 
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD002676 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD002676
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD002676 ==> graphical output of all proteins having domain PD002676
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD002895 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD002895
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD002895 ==> graphical output of all proteins having domain PD002895
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD039184 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD039184
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD039184 ==> graphical output of all proteins having domain PD039184
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD121821 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD121821
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD121821 ==> graphical output of all proteins having domain PD121821
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD108468 ==> multiple alignment, consensus, PDB and PROSITE links of domain PD108468
http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD108468 ==> graphical output of all proteins having domain PD108468
--- 
--- NOTE: if you want to use the link, make sure the entire line
---       is pasted as URL into your browser!
--- 
--- END of PRODOM
--- ------------------------------------------------------------

PSI-BLAST alignment header

--- ------------------------------------------------------------
--- PSI-BLAST multiple sequence alignment
--- ------------------------------------------------------------
--- 
--- PSI-BLAST ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY
--- SEQLENGTH    : 445
--- ID           : identifier of aligned (homologous) protein
--- LSEQ2        : length of aligned sequence
--- IDE          : percentage of pairwise sequence identity
--- SIM          : percentage of similarity
--- LALI         : number of residues aligned
--- LGAP         : number of residues in all indels
--- BSCORE       : blast score (bits)
--- BEXPECT      : blast expectation value
--- OMIM         : OMIM (Online Mendelian Inheritance in Man) ID
--- PROTEIN      : one-line description of aligned protein
--- '!'          : indicates lower scoring alignment that is combined
---                with the higher scoring adjacent one
--- 
--- PSI-BLAST ALIGNMENT HEADER: SUMMARY

ID                          LSEQ2  IDE  SIM LALI LGAP BSCORE BEXPECT OMIM    PROTEIN                  
trembl|Q83QS7|Q83QS7          445   99   99  445    0    627   e-178         NADH dehydrogenase I chai
trembl|Q8XCX1|Q8XCX1          445   99   99  445    0    627   e-178         NADH dehydrogenase I chai
trembl|Q8FFJ8|Q8FFJ8          445   99  100  445    0    626   e-178         NADH dehydrogenase I chai
swiss|P31979|NUOF_ECOLI       445  100  100  445    0    625   e-178         NADH-quinone oxidoreducta
swiss|P33901|NUOF_SALTY       445   98   99  445    0    620   e-176         NADH-quinone oxidoreducta
trembl|Q5PN61|Q5PN61          445   98   99  445    0    620   e-176         NADH dehydrogenase I chai
trembl|Q8Z526|Q8Z526          445   98   99  445    0    617   e-175         NADH dehydrogenase I chai
trembl|Q7N2J1|Q7N2J1          454   88   92  445    3    606   e-172         NADH dehydrogenase I chai
trembl|Q6D2S1|Q6D2S1          449   88   92  444    3    605   e-172         NADH-quinone oxidoreducta
trembl|Q8ZDL1|Q8ZDL1          461   88   92  444    9    602   e-171         NADH dehydrogenase I chai
trembl|Q669A4|Q669A4          461   88   91  444    9    601   e-171         NADH dehydrogenase I chai
trembl|Q8EI33|Q8EI33          461   77   85  444    2    586   e-166         NADH dehydrogenase I, F s
trembl|Q88FH3|Q88FH3          453   75   83  436    7    569   e-161         NADH dehydrogenase I, F s
trembl|Q87ZQ5|Q87ZQ5          452   75   84  441    3    565   e-160         NADH dehydrogenase I, F s
trembl|Q9I0J7|Q9I0J7          448   79   87  422    2    563   e-159         NADH dehydrogenase I chai
swiss|Q8K9Y3|NUOF_BUCAP       447   70   82  439    2    560   e-158         NADH-quinone oxidoreducta
trembl|Q9KGW4|Q9KGW4          451   76   85  422    2    557   e-157         NADH dehydrogenase I subu
swiss|P57256|NUOF_BUCAI       444   67   81  440    5    556   e-157         NADH-quinone oxidoreducta
trembl|Q43840|Q43840          487   41   58  405   12    551   e-155         NADH dehydrogenase (EC 1.
trembl|Q9VMI3|Q9VMI3          474   41   59  402    4    551   e-155         CG9140-PA (GM14163p)     
trembl|Q9WXM5|Q9WXM5          607   38   59  431    3    549   e-155         NADP-reducing hydrogenase
swiss|Q9ZE33|NUOF_RICPR       421   44   61  394    3    548   e-155         NADH-quinone oxidoreducta
trembl|Q68XY3|Q68XY3          421   44   61  395    3    547   e-154         NADH dehydrogenase (Ubiqu
trembl|Q7PMH3|Q7PMH3          486   41   59  408    4    545   e-154         ENSANGP00000012416 (Fragm
swiss|Q91YT0|NUBM_MOUSE       464   41   59  407    4    545   e-154         NADH-ubiquinone oxidoredu
swiss|P56912|NUF1_RHIME       434   41   57  406    5    544   e-154         NADH-quinone oxidoreducta
swiss|P49821|NUBM_HUMAN       464   41   60  404    4    544   e-153 161015  NADH-ubiquinone oxidoredu
swiss|P25708|NUBM_BOVIN       464   42   60  401    4    543   e-153         NADH-ubiquinone oxidoredu
trembl|Q17880|Q17880          479   38   57  409   12    542   e-153         Hypothetical protein C09H
trembl|Q23923|Q23923          479   42   60  408    5    542   e-153         QinA                     
trembl|Q8RBC9|Q8RBC9          596   40   60  433    8    542   e-153         NADH:ubiquinone oxidoredu
trembl|Q9WY70|Q9WY70          545   42   60  428    3    541   e-153         NADP-reducing hydrogenase
trembl|Q61ZT2|Q61ZT2          479   38   57  409   12    541   e-153         Hypothetical protein CBG0
trembl|Q82DX6|Q82DX6          449   46   62  425    4    541   e-152         Putative NADH dehydrogena
swiss|P56913|NUF2_RHIME       421   49   66  418    2    541   e-152         NADH-quinone oxidoreducta
trembl|Q8GE74|Q8GE74          421   43   61  404    4    541   e-152         NADH dehydrogenase I chai
swiss|Q92JB2|NUOF_RICCN       421   43   61  404    4    540   e-152         NADH-quinone oxidoreducta
trembl|Q7PAQ6|Q7PAQ6          421   43   61  404    4    540   e-152         NADH dehydrogenase I chai
trembl|Q8HXQ9|Q8HXQ9          464   41   60  404    4    540   e-152         NADH dehydrogenase (Ubiqu
trembl|Q5ZRU3|Q5ZRU3          428   44   61  416    5    540   e-152         NADH dehydrogenase I, F s
trembl|Q5XIH3|Q5XIH3          464   40   60  404    4    540   e-152         NADH dehydrogenase (Ubiqu
trembl|Q73V10|Q73V10          453   47   63  419    9    539   e-152         NuoF                     
trembl|Q7WCU4|Q7WCU4          455   44   62  406    5    539   e-152         Respiratory-chain NADH de
trembl|Q7VZQ0|Q7VZQ0          455   44   62  406    5    539   e-152         Respiratory-chain NADH de
trembl|Q7W5B2|Q7W5B2          455   44   62  406    5    539   e-152         Respiratory-chain NADH de
trembl|Q5WT25|Q5WT25          425   44   61  416    5    538   e-152         NADH dehydrogenase I chai
trembl|Q5X1B2|Q5X1B2          425   44   61  416    5    538   e-152         NADH dehydrogenase I chai
trembl|Q8YGK5|Q8YGK5          435   40   56  406    5    538   e-152         NADH-QUINONE OXIDOREDUCTA
trembl|Q8H2T7|Q8H2T7          504   41   58  395   12    538   e-152         Putative NADH dehydrogena
trembl|Q6V9B2|Q6V9B2          484   41   58  409    4    538   e-152         NADH:ubiquinone oxidoredu
trembl|Q98KR0|Q98KR0          434   41   58  407    5    537   e-151         NADH-ubiquinone dehydroge
trembl|Q8G1B2|Q8G1B2          435   40   56  406    5    537   e-151         NADH dehydrogenase I, F s
trembl|Q44512|Q44512          535   39   59  414    4    537   e-151         Hydrogenase subunit      
swiss|P29913|NQO1_PARDE       431   41   60  408   12    537   e-151         NADH-quinone oxidoreducta
trembl|Q82TU8|Q82TU8          425   43   61  408    5    537   e-151         Respiratory-chain NADH de
trembl|Q8AVD7|Q8AVD7          471   38   56  423   32    537   e-151         Ndufv1-prov protein      
trembl|Q89KJ3|Q89KJ3          441   42   59  403    6    535   e-151         NADH ubiquinone oxidoredu
swiss|O07948|NUOF_RHOCA       431   42   58  404    4    535   e-151         NADH-quinone oxidoreducta
trembl|Q8XXQ6|Q8XXQ6          431   41   60  405    5    535   e-151         PROBABLE NADH DEHYDROGENA
trembl|Q7NZH6|Q7NZH6          431   43   63  407    5    534   e-151         NADH-ubiquinone oxidoredu
trembl|Q6AZA2|Q6AZA2          492   40   58  408    4    534   e-150         Zgc:86620                
trembl|Q5PAI3|Q5PAI3          430   39   58  413    5    534   e-150         NADH dehydrogenase chain 
trembl|Q8UFX2|Q8UFX2          434   40   58  405   13    533   e-150         NADH ubiquinone oxidoredu
trembl|Q9FNN5|Q9FNN5          486   41   58  395   12    533   e-150         NADH dehydrogenase (At5g0
trembl|Q9K1B8|Q9K1B8          433   43   62  405    5    533   e-150         NADH dehydrogenase I, F s
swiss|Q89AU2|NUOF_BUCBP       444   67   79  419    2    533   e-150         NADH-quinone oxidoreducta
trembl|Q5W1K6|Q5W1K6          462   41   58  405    4    532   e-150         NADH-quinone oxidoreducta
trembl|Q93SF8|Q93SF8          597   38   58  432    3    531   e-150         HymB protein             
swiss|Q9XAQ9|NUOF_STRCO       449   46   63  414    4    531   e-149         NADH-quinone oxidoreducta
swiss|P65568|NUOF_MYCBO       445   47   65  419   10    531   e-149         NADH-quinone oxidoreducta
swiss|P65567|NUOF_MYCTU       445   47   65  419   10    531   e-149         NADH-quinone oxidoreducta
trembl|Q9JX83|Q9JX83          433   44   62  405    5    530   e-149         NADH dehydrogenase I chai
trembl|Q8LAL7|Q8LAL7          486   41   58  395   12    530   e-149         NADH dehydrogenase       
trembl|Q7RV82|Q7RV82          493   42   60  394    6    530   e-149         NADH-ubiquinone oxidoredu
trembl|Q6N5M9|Q6N5M9          441   41   57  406    6    530   e-149         NADH-ubiquinone dehydroge
trembl|Q5ZHS2|Q5ZHS2          459   42   59  405    4    529   e-149         Hypothetical protein     
trembl|Q74GA3|Q74GA3          591   40   59  417    2    529   e-149         NADH dehydrogenase I, F s
trembl|Q83BR0|Q83BR0          422   41   62  417    5    528   e-148         NADH dehydrogenase I, F s
trembl|Q6G393|Q6G393          435   39   57  409   13    528   e-148         NADH dehydrogenase I, F s
trembl|Q6FE67|Q6FE67          443   66   79  416    4    527   e-148         NADH dehydrogenase I chai
trembl|Q5U0T0|Q5U0T0          702   41   58  404    4    527   e-148         AT08270p                 
trembl|Q9V852|Q9V852          702   41   58  404    4    526   e-148         CG11423-PA               
trembl|Q9A6X9|Q9A6X9          439   42   58  403    6    526   e-148         NADH dehydrogenase I, F s
swiss|P24917|NUBM_NEUCR       493   42   59  394    6    526   e-148         NADH-ubiquinone oxidoredu
trembl|Q608Y1|Q608Y1          427   60   77  413    1    525   e-148         NADH dehydrogenase I, F s
trembl|Q8YYU4|Q8YYU4          544   39   59  412    4    524   e-147         Hydrogenase subunit      
trembl|Q6BM47|Q6BM47          487   37   56  410   15    524   e-147         Similar to tr|Q96UX4 Cand
trembl|Q749M1|Q749M1          570   37   56  427    9    523   e-147         NAD-reducing hydrogenase,
trembl|Q6SGN3|Q6SGN3          431   56   72  424    7    523   e-147         NADH-quinone oxidoreducta
trembl|Q6FZY6|Q6FZY6          435   39   56  406   13    523   e-147         NADH dehydrogenase I, F s
trembl|Q67JG0|Q67JG0          618   40   57  435    2    522   e-147         Iron hydrogenase beta sub
trembl|Q73GH8|Q73GH8          417   42   61  389    5    521   e-146         NADH dehydrogenase I, F s
trembl|Q63VM8|Q63VM8          436   40   58  417   12    521   e-146         NADH dehydrogenase I chai
trembl|Q9U4M2|Q9U4M2          484   39   59  399    5    520   e-146         NADH dehydrogenase       
swiss|Q92406|NUBM_ASPNG       496   38   59  407   15    520   e-146         NADH-ubiquinone oxidoredu
trembl|Q62IP0|Q62IP0          436   40   58  417   12    519   e-146         NADH dehydrogenase I, F s
trembl|Q9UUU2|Q9UUU2          488   38   57  409    7    519   e-146         NUBM protein precursor (E
trembl|Q46507|Q46507          490   40   59  421    4    519   e-146         Potential NAD-reducing hy
trembl|Q8F7Q4|Q8F7Q4          443   46   62  406    3    519   e-146         NADH dehydrogenase I, F s
trembl|Q96UX4|Q96UX4          489   38   59  392    6    518   e-146         NADH dehydrogenase comple
trembl|Q5P1E5|Q5P1E5          437   44   60  406    6    518   e-145         NADH dehydrogenase I, cha
trembl|Q72NT3|Q72NT3          443   46   62  406    3    517   e-145         NADH dehydrogenase I F su
trembl|Q8PJ45|Q8PJ45          444   41   58  416    7    515   e-145         NADH-ubiquinone oxidoredu
trembl|Q6AL37|Q6AL37          550   37   57  430    2    515   e-145         Probable NADH dehydrogena
trembl|Q9AJC1|Q9AJC1          541   37   58  418    5    514   e-144         Hydrogenase diaphorase la
trembl|O52682|O52682          626   39   59  436   28    514   e-144         Fe-hydrogenase beta subun
trembl|Q8P7T7|Q8P7T7          444   41   57  416    7    513   e-144         NADH-ubiquinone oxidoredu
trembl|Q6MIR7|Q6MIR7          430   45   62  411    5    512   e-144         NADH dehydrogenase I, F s
trembl|Q5YWD2|Q5YWD2          441   47   63  415    7    512   e-144         Putative NADH dehydrogena
trembl|Q7X1N4|Q7X1N4          617   39   58  434    4    510   e-143         NADP-reducing hydrogenase
swiss|Q56222|NQO1_THETH       438   48   66  401    7    510   e-143         NADH-quinone oxidoreducta
trembl|Q5SM54|Q5SM54          438   48   66  401    7    510   e-143         NADH-quinone oxidoreducta
trembl|Q72GD3|Q72GD3          438   48   66  401    7    510   e-143         NADH-quinone oxidoreducta
trembl|Q8KX28|Q8KX28          534   38   58  417    2    508   e-143         Hydrogenase large diaphor
trembl|O27592|O27592          630   39   59  416    5    508   e-143         NADP-reducing hydrogenase
trembl|Q7VRV6|Q7VRV6          445   68   80  413    2    507   e-142         NADH dehydrogenase I chai
trembl|Q9PGJ0|Q9PGJ0          444   40   58  420    7    507   e-142         NADH-ubiquinone oxidoredu
trembl|Q8ABI5|Q8ABI5          635   39   57  438    7    507   e-142         NADH:ubiquinone oxidoredu
trembl|Q87EQ0|Q87EQ0          444   39   58  420    7    506   e-142         NADH-ubiquinone oxidoredu
trembl|Q79A13|Q79A13          533   39   60  401    2    505   e-142         Hydrogenase subunit      
trembl|P74024|P74024          533   39   60  401    2    505   e-142         Hydrogenase subunit      
trembl|Q6A6G3|Q6A6G3          444   47   66  411    7    503   e-141         NADH dehydrogenase I chai
trembl|Q67P17|Q67P17          425   45   62  397    9    499   e-140         NADH dehydrogenase I subu
trembl|Q6AQG1|Q6AQG1          634   37   55  412    4    496   e-139         Probable NADP-reducing hy
trembl|Q9RU92|Q9RU92          444   49   64  405    8    493   e-138         NADH dehydrogenase I, F s
trembl|Q6XQK4|Q6XQK4          536   37   57  417   13    489   e-137         HoxF                     
trembl|Q64C23|Q64C23          654   38   60  413    2    488   e-137         NADH-ubiquinone oxidoredu
trembl|Q89QJ1|Q89QJ1          518   37   55  415    3    487   e-136         NADH dehydrogenase I chai
trembl|Q6MDR1|Q6MDR1          432   48   65  402    3    486   e-136         Probable NADH-ubiquinone 
trembl|Q608U7|Q608U7          516   40   56  414    3    483   e-135         Formate dehydrogenase, be
trembl|Q746S7|Q746S7          423   50   66  417    4    481   e-135         NADH dehydrogenase I, F s
trembl|Q6NBU5|Q6NBU5          518   37   54  414    3    478   e-133         NAD-dependent formate deh
trembl|Q84FW2|Q84FW2          519   40   56  415    3    474   e-132         NAD-linked formate dehydr
trembl|Q7WMR8|Q7WMR8          526   39   56  415    4    473   e-132         NAD-dependent formate deh
swiss|O66841|NUOF_AQUAE       426   44   60  395   10    472   e-132         NADH-quinone oxidoreducta
trembl|Q7QNI1|Q7QNI1          366   78   86  363    2    471   e-132         ENSANGP00000000047       
trembl|Q92LN0|Q92LN0          518   37   55  414    3    471   e-131         PUTATIVE NAD-DEPENDENT FO
trembl|Q9Z353|Q9Z353          534   37   58  396    5    471   e-131         HoxF protein             
trembl|Q8U6U9|Q8U6U9          518   37   57  415    3    470   e-131         NADH dehydrogenase I chai
trembl|Q88KV5|Q88KV5          525   39   56  416    6    470   e-131         Formate dehydrogenase, be
trembl|Q96ID4|Q96ID4          354   42   62  341    3    468   e-131         Hypothetical protein (Fra
trembl|Q98BW8|Q98BW8          518   37   56  415    3    468   e-130         NAD-dependent formate deh
trembl|O87814|O87814          520   40   55  414    3    459   e-128         NAD-dependent formate deh
trembl|Q9UVT9|Q9UVT9          379   38   58  352    3    459   e-128         NADH:ubiquinone oxidoredu
trembl|Q5S7T0|Q5S7T0          429   38   56  385    6    459   e-128         Hydrogenosomal NADH dehyd
trembl|Q62M10|Q62M10          521   38   54  416    3    459   e-128         Formate dehydrogenase, be
trembl|Q63RZ2|Q63RZ2          521   38   54  416    3    459   e-128         NAD-dependent formate deh
trembl|Q9ZBV8|Q9ZBV8          646   44   56  391    9    445   e-124         Putative respiratory chai
trembl|Q82M25|Q82M25          607   42   57  394    9    436   e-121         Putative NADH dehydrogena
trembl|Q6N1Z2|Q6N1Z2          428   50   64  419    6    435   e-121         NADH-ubiquinone dehydroge
trembl|Q9V7A6|Q9V7A6          481   32   51  404   13    424   e-117         CG8102-PA, isoform A     
trembl|Q89ST4|Q89ST4          567   36   54  377   22    415   e-114         Blr2316 protein          
trembl|Q603S6|Q603S6          610   35   51  408   44    403   e-111         NAD-reducing hydrogenase,
trembl|Q604G6|Q604G6          561   35   53  380   18    401   e-110         Dehydrogenase subunit, pu
trembl|Q835I8|Q835I8          417   36   56  386    7    398   e-110         NAD-dependent formate deh
trembl|O94500|O94500          452   32   51  400    8    396   e-109         SPBC18E5.10 protein      
trembl|P72304|P72304          604   33   52  389   15    385   e-105         NAD-reducing hydrogenase 
trembl|Q8T495|Q8T495          462   29   47  385   32    384   e-105         AT08706p                 
swiss|P22317|HOXF_ALCEU       602   33   53  388   15    383   e-105         NAD-reducing hydrogenase 
trembl|Q8MLA3|Q8MLA3          462   29   47  385   32    383   e-105         CG8102-PB, isoform B     
trembl|Q8KTI8|Q8KTI8          572   36   54  375   22    382   e-104         Tungsten-containing forma
trembl|Q5P4U3|Q5P4U3          585   31   49  383   23    352   6e-96         Formate dehydrogenase, NA
trembl|Q742U7|Q742U7          436   27   44  390   27    312   1e-83         Hypothetical protein     
trembl|Q9EZD1|Q9EZD1          280   37   54  269    1    310   3e-83         NAD-dependent formate deh
trembl|Q51696|Q51696          401   31   46  374   16    303   6e-81         Hypothetical protein ORF2
trembl|Q67JR5|Q67JR5          394   32   46  378   23    292   9e-78         NADH dehydrogenase subuni
trembl|O96948|O96948         1206   27   43  344   30    279   9e-74         Hydrogenase (EC 1.18.99.1
trembl|Q9RDL3|Q9RDL3          524   25   42  372   18    273   7e-72         Putative oxidoreductase  
trembl|Q9ACZ1|Q9ACZ1          525   25   42  372   18    260   3e-68         Putative oxidoreductase  
trembl|Q82C68|Q82C68          524   24   42  372   18    259   7e-68         Putative oxidoreductase  
trembl|Q8FH95|Q8FH95          742   20   33  339   91    251   2e-65         Electron transport comple
trembl|Q87MX2|Q87MX2          869   18   32  314   82    251   2e-65         RnfC-related protein     
swiss|P77611|RNFC_ECOLI       740   20   33  339   91    251   2e-65         Electron transport comple
trembl|Q83RB9|Q83RB9          740   20   33  339   91    250   3e-65         Putative membrane protein
swiss|P58324|RNFC_ECO57       740   20   33  339   91    249   1e-64         Electron transport comple
swiss|Q8ZPM2|RNFC_SALTY       735   20   33  336   91    246   9e-64         Electron transport comple
trembl|Q8Z6Q9|Q8Z6Q9          673   20   33  336   91    245   1e-63         Putative NADH reducing de
trembl|Q83T35|Q83T35          673   20   33  336   91    245   1e-63         Putative NADH reducing de
trembl|Q5PIB9|Q5PIB9          735   20   33  336   91    244   2e-63         Putative NADH reducing de
swiss|Q9CNP2|RNFC_PASMU       835   18   31  355   86    244   2e-63         Electron transport comple
swiss|Q9KT88|RNFC_VIBCH       774   19   32  316   78    240   4e-62         Electron transport comple
trembl|Q65U33|Q65U33          723   18   32  341   81    239   6e-62         NqrA protein             
swiss|P71397|RNFC_HAEIN       819   18   33  343   83    239   1e-61         Electron transport comple
trembl|Q8SXT0|Q8SXT0          239   51   66  167    1    235   2e-60         RE33648p                 
trembl|Q7MM83|Q7MM83          885   18   32  315   80    234   3e-60         Predicted NADH:ubiquinone
trembl|Q8D888|Q8D888          919   18   32  315   80    234   3e-60         RnfC-related protein     
trembl|Q8RIJ6|Q8RIJ6          441   20   35  298   72    229   1e-58         Nitrogen fixation iron-su
trembl|Q7VNT4|Q7VNT4          702   18   32  351   86    224   3e-57         Putative iron-sulfur bind
trembl|Q5V638|Q5V638          507   23   38  349   35    221   2e-56         Putative NADH dehydrogena
trembl|Q7N4F9|Q7N4F9          852   19   32  313   78    217   4e-55         Electron transport comple
trembl|Q603B2|Q603B2          523   20   34  316   78    217   4e-55         Electron transport comple
trembl|Q896I5|Q896I5          449   20   36  305   83    217   4e-55         RnfC/nqrF                
trembl|Q6LP35|Q6LP35          761   17   31  315   79    217   4e-55         Putative NADH:ubiquinone 
trembl|Q8ZED0|Q8ZED0          620   18   32  310   78    208   2e-52         Putative iron-sulfur bind
trembl|Q66AG5|Q66AG5          659   18   32  310   78    208   2e-52         Putative iron-sulfur bind
trembl|Q8D0I9|Q8D0I9          659   18   32  310   78    208   2e-52         Putative membrane protein
trembl|Q74TT9|Q74TT9          659   18   32  310   78    207   2e-52         Putative iron-sulfur bind
trembl|Q8AA47|Q8AA47          445   21   37  263   61    207   5e-52         Na+-transporting NADH:ubi
trembl|Q9WY86|Q9WY86          451   21   35  291   74    205   1e-51         Electron transport comple
trembl|Q6D4W2|Q6D4W2          693   20   32  313   78    205   2e-51         Electron transport comple
trembl|Q64T32|Q64T32          445   19   36  287   66    204   2e-51         Electron transport comple
trembl|Q6AIQ7|Q6AIQ7          447   20   33  277   64    200   4e-50         Probable electron transfe
trembl|Q5P1B2|Q5P1B2          547   19   31  258   57    198   2e-49         Putative electron transpo
trembl|Q8VQW6|Q8VQW6          496   19   32  297   74    198   2e-49         RnfC                     
trembl|Q6AIR8|Q6AIR8          447   20   33  264   53    197   4e-49         Related to propanediol ut
swiss|Q52716|RNFC_RHOCA       519   19   33  305   72    196   9e-49         Electron transport comple
trembl|Q8EE79|Q8EE79          790   18   32  302   69    195   1e-48         Iron-sulfur cluster-bindi
trembl|Q9EVN5|Q9EVN5          487   18   30  301   74    194   3e-48         RnfC protein             
trembl|Q5P537|Q5P537          508   22   34  307   70    192   1e-47         Electron transport comple
trembl|Q7MXA5|Q7MXA5          443   21   37  262   61    191   3e-47         Electron transport comple
trembl|Q8XKI6|Q8XKI6          436   20   35  293   71    188   2e-46         Hypothetical protein CPE1
trembl|Q67R12|Q67R12          446   22   32  286   76    183   5e-45         Na+-transporting NADH-qui
trembl|Q5QUW0|Q5QUW0          556   17   32  313   79    182   1e-44         Predicted NADH:ubiquinone
trembl|Q6AQ74|Q6AQ74          438   21   35  292   69    180   5e-44         Probable electron transpo
trembl|Q603I4|Q603I4          495   19   33  308   76    180   6e-44         Electron transport comple
trembl|Q7P7D0|Q7P7D0          279   19   32  235   61    177   4e-43         Electron transport comple
trembl|Q73PG1|Q73PG1          480   19   33  318   69    168   2e-40         Na(+)-translocating NADH-
trembl|Q7BV74|Q7BV74          451   24   35  260   68    167   3e-40         PduS                     
trembl|Q9XDM9|Q9XDM9          451   24   35  260   68    167   3e-40         Propanediol utilization p
trembl|Q8Z5L1|Q8Z5L1          442   24   36  261   66    164   3e-39         Putative ferredoxin      
swiss|Q9HYB8|RNFC_PSEAE       774   21   32  256   56    162   2e-38         Electron transport comple
trembl|Q720T9|Q720T9          454   22   34  268   54    159   1e-37         PduS protein             
trembl|Q5PDR5|Q5PDR5          442   23   35  260   66    159   1e-37         Putative ferredoxin      
trembl|Q8Y7X7|Q8Y7X7          454   22   34  268   54    158   2e-37         Lmo1142 protein          
trembl|Q92CR5|Q92CR5          454   22   34  268   54    157   3e-37         Lin1106 protein          
swiss|P57215|RNFC_BUCAI       473   16   30  230   60    146   8e-34         Electron transport comple
trembl|Q9L4Q5|Q9L4Q5          402   21   40  219   48    145   1e-33         Electron transfer protein
swiss|Q89AW8|RNFC_BUCBP       505   17   32  281   69    140   8e-32         Electron transport comple
trembl|Q7XZ61|Q7XZ61          170   37   49   97    3    105   1e-21         NADH dehydrogenase (Fragm
trembl|Q72B66|Q72B66          673   23   40  124    1     98   3e-19         Pyridine nucleotide-disul
trembl|Q6NDH3|Q6NDH3          673   18   36  132    3     95   3e-18         Possible oxidoreductase  
trembl|Q7MBG7|Q7MBG7          649   17   38  128    8     94   4e-18         FORMATE DEHYDROGENASE, BE
trembl|Q73MB5|Q73MB5          609   26   43   94    1     88   2e-16         Pyridine nucleotide-disul
trembl|Q74FU5|Q74FU5          672   21   42  123    3     88   2e-16         Fe(III) reductase, beta s
trembl|Q65UM2|Q65UM2          612   23   41  101    1     88   3e-16         GltD protein             
trembl|P77907|P77907          707   21   41  118    7     75   2e-12         Formate dehydrogenase bet
trembl|Q8TSY4|Q8TSY4          447   17   29  262   64     61   3e-08         Na+-transporting NADH:ubi
trembl|Q73MW6|Q73MW6          428   16   40   67    8     44   0.005         Hypothetical protein     
trembl|Q87T50|Q87T50          889   19   31   66    0     38    0.28         OtnA protein             
trembl|Q727R3|Q727R3          401   13   26  217   76     38    0.35         Electron transport comple
trembl|O83187|O83187          514   22   40   70    7     37    0.62         Nitrogen fixation protein
---
--- PSI-BLAST ALIGNMENT

MAXHOM alignment header

--- ------------------------------------------------------------
--- MAXHOM multiple sequence alignment
--- ------------------------------------------------------------
--- 
--- MAXHOM ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY
--- ID           : identifier of aligned (homologous) protein
--- STRID        : PDB identifier (only for known structures)
--- IDE          : percentage of pairwise sequence identity
--- WSIM         : percentage of weighted similarity
--- LALI         : number of residues aligned
--- NGAP         : number of insertions and deletions (indels)
--- LGAP         : number of residues in all indels
--- LSEQ2        : length of aligned sequence
--- ACCNUM       : SwissProt accession number
--- OMIM         : OMIM (Online Mendelian Inheritance in Man) ID
--- NAME         : one-line description of aligned protein
--- 
--- MAXHOM ALIGNMENT HEADER: SUMMARY
ID         STRID  IDE WSIM LALI NGAP LGAP LSEQ2 ACCNUM OMIM    NAME                     
nuof_ecoli        100  100  445    0    0   445 P31979         OXIDOREDUCTASE CHAIN 6) (
nuof_salty         99   99  400    0    0   431 P33901         OXIDOREDUCTASE CHAIN 6) (
nuof_bucap         73   68  423    1    1   447 Q8K9Y3         oxidoreductase chain F). 
nuof_bucai         70   65  423    1    2   444 P57256         OXIDOREDUCTASE CHAIN F). 
nuof_bucbp         69   62  415    1    2   444 Q89AU2         I, chain F) (NDH-1, chain
nuof_aquae         56   45  234    1    2   426 O66841         OXIDOREDUCTASE CHAIN F). 
nqo1_theth         52   40  334    1    1   438 Q56222         DEHYDROGENASE 1, CHAIN 1)
nuf2_rhime         51   37  398    2    2   421 P56913         OXIDOREDUCTASE CHAIN F 2)
nuof_myctu         50   35  371    3    5   445 P95176         OXIDOREDUCTASE CHAIN F). 
nuof_mycbo         50   35  371    3    5   445 P65568         I, chain F) (NDH-1, chain
nuof_strco         49   33  391    4    4   449 Q9XAQ9         OXIDOREDUCTASE CHAIN F). 
nuof_riccn         48   32  315    2    2   421 Q92JB2         oxidoreductase chain F). 
nqo1_parde         47   32  328    2    2   431 P29913         DEHYDROGENASE 1, CHAIN 1)
nuof_ricpr         47   31  336    2    2   421 Q9ZE33         OXIDOREDUCTASE CHAIN F). 
hoxf_alceu         47   32  229    2    2   602 P22317         NAD-REDUCING HYDROGENASE 
nuof_rhoca         46   30  328    1    2   431 O07948         OXIDOREDUCTASE CHAIN F). 
nubm_bovin         45   26  373    3    3   464 P25708         (EC 1.6.99.3) (COMPLEX I-
nuf1_rhime         45   26  336    3    3   434 P56912         OXIDOREDUCTASE CHAIN F 1)
nubm_neucr         45   25  340    3    5   493 P24917         (EC 1.6.99.3) (COMPLEX I-
nubm_mouse         45   25  373    3    3   464 Q91YT0         (EC 1.6.5.3) (EC 1.6.99.3
nubm_human         44   25  373    3    3   464 P49821 161015  (EC 1.6.99.3) (COMPLEX I-
nubm_aspng         43   25  340    3    5   496 Q92406         (EC 1.6.99.3) (COMPLEX I-
--- 
--- MAXHOM ALIGNMENT: IN MSF FORMAT

--- 
--- Version of database searched for alignment:
--- SWISS-PROT release 41 (02/2003) with 122 564 proteins
---

MAXHOM alignment

TOP - BOTTOM - MaxHom - MView

Identities computed with respect to: (1) predict_h1400
Colored by: consensus/70% and property

                    1 [        .         .         .         .         :         . 60 
 1 predict_h1400      MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLK    
 2 nuof_ecoli         MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLK    
 3 nuof_salty         MKNVIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVSQVKDAGLK    
 4 nuof_bucap         MNNIIPTEETHPLTWRLRNDRETVWIEEYCKKNGYFSLKKALKTMCPEDVVHLIKESGLK    
 5 nuof_bucai         MNRILRISETHPLTWRLRDDQKTVWIKEYCDKNGYLSLKKALKEMLPEDVINIVKESGLK    
 6 nuof_bucbp         -----RTSETHPLTWRLNAQQDTVWIKEYKRKNGYRAFEKVVNHMTSEDVIDLIKQSGLK    
 7 nuof_aquae         --------------------------------------------MSPEEIIDWVDKSTLR    
 8 nqo1_theth         -------------------------LDYYLRHGGYETAKRVLKEKTPDEVIEEVKRSGLR    
 9 nuf2_rhime         -------------------------LSTYEAGGGYRALRKALGEYTPDEIVELVKESNLR    
10 nuof_myctu         ----------------------------------------------PDDVISIVKDSGLR    
11 nuof_mycbo         ----------------------------------------------PDDVISIVKDSGLR    
12 nuof_strco         -------------------------LDVYRRHEGYEGLRKALA-MAPDDLIAYVKESGLR    
13 nuof_riccn         -----------------------------------------------DFIVEEVKKSGLR    
14 nqo1_parde         -----------------------------------------------DKIIDEMKASGLR    
15 nuof_ricpr         -----------------------------------------------DFIIDEVKKSGLR    
16 hoxf_alceu         --------------------------------------------LKPEQVIETIVDSRLR    
17 nuof_rhoca         -----------------------------------------------DWIIEQVKASGLR    
18 nubm_bovin         ----------------------------------------------PDWILGEVKTSGLR    
19 nuf1_rhime         -----------------------------------------------DWIINEVKASGLR    
20 nubm_neucr         -----------------------------------------------DWIIGEVKASGLR    
21 nubm_mouse         ----------------------------------------------PDWILGEMKTSGLR    
22 nubm_human         ----------------------------------------------PDWILGEIKTSGLR    
23 nubm_aspng         -----------------------------------------------DWLISELKASGLR    
   consensus/100%     ...............................................-.llt.h.tutL+    
   consensus/90%      ...............................................-.llt.lKtusL+    
   consensus/80%      ...............................................-.llt.lKtSGL+    
   consensus/70%                               ......................D.lls.lKpSGLR    

                   61          .         .         .         1         .         . 120
 1 predict_h1400      GRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISA    
 2 nuof_ecoli         GRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISA    
 3 nuof_salty         GRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISA    
 4 nuof_bucap         GRGGAGFSTGLKWSLMSKDNSSKIRYLLCNADEMEPGTYKDRFLMENIPHQLIEGMLLSA    
 5 nuof_bucai         GRGGAGFSTGLKWSLMSQNHSYTReyLICNADEMEPGTYKDRLLIEKIPHQLIEGIILSA    
 6 nuof_bucbp         GRGGAGFLTGLKWSLMpnDEYGYTRYLLCNADEMEPGTYKDRFLMEKVPHQLLEGILISA    
 7 nuof_aquae         GRGGAGFPTGKKWKFAVQNPGP--RYFICNADESEPGTFKDRIIIERDPHLLIEGIIISS    
 8 nqo1_theth         GRGGAGFPTGLKWSFMPKDDGKQ-HYLICNADESEPGSFKDRYILEDVPHLLIEGMILAG    
 9 nuf2_rhime         GRGGAGFPTGMKWSFVPK-AAGKPKYLCCNADEGEPGTFKDRIIMERDPHQLIEGLAVSA    
10 nuof_myctu         GRGGAGFATGTKWSFIPQGdaAKPHYLVVNADESEPGTCKDIPLMLATPHVLIEGVIIAA    
11 nuof_mycbo         GRGGAGFATGTKWSFIPQGdaAKPHYLVVNADESEPGTCKDIPLMLATPHVLIEGVIIAA    
12 nuof_strco         GRGGAGFPTGMKWQFIPQGDG-KPHYLVVNADESEPGTCKDIPLLFANPHSLIEGIVIAC    
13 nuof_riccn         GRGGAGFSTGMKWSFMPKNLEKSC-YLVVNADESEPGTCKDRDILRFEPHKLIEGCLLAS    
14 nqo1_parde         GRGGAGFPTGMKWSFMPKESDGRPSYLVINADESEPATCKDREIMRHDPHTLIEGALIAS    
15 nuof_ricpr         GRGGAGFSTGMKWSFMPKN-SEKPCYLVVNADESEPGTCKDRDILRFEPHKLIEGCLIAS    
16 hoxf_alceu         GRGGAGFSTGLKWRLC-RDAESEQKYVICNADEGEPGTFKDRVLLTRAPKKVFVGMVIAA    
17 nuof_rhoca         GRGGAGFPTGLKWSFMPKQSDGRPSFLVINADESEPGTCKDREIMRHDPHTLIEGALIAG    
18 nubm_bovin         GRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEGEPGTCKDREIIRHDPHKLVEGCLVGG    
19 nuf1_rhime         GRGGAGFPTGLKWSFMPKESDGRPHYLVVNADESEPGTCKDRDIMRHDPHTLIEGCVIAS    
20 nubm_neucr         GRGGAGFPSGLKWSFmdWDKDDKPRYLVVNADEGEPGTCKDREIMRKDPHKLVEGCLVAG    
21 nubm_mouse         GRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEGEPGTCKDREIMRHDPHKLVEGCLVGG    
22 nubm_human         GRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEGEPGTCKDREILRHDPHKLLEGCLVGG    
23 nubm_aspng         GRGGAGFPSGLKYSFmdWDKDPRPRYLVVNADEGEPGTCKDREIMRKDPQKLIEGCLVVG    
   consensus/100%     GRGGAGF.oGhKaphh.........ahhhNADE.EPuohKDh.lh...Pp.lh.Ghhlss    
   consensus/90%      GRGGAGFsTGhKWphhsp..t.p.pYLlsNADE.EPGThKDh.lh.t.PH.LlEGhlluu    
   consensus/80%      GRGGAGFsTGhKWShhspsts.p.cYLlsNADE.EPGThKDR.lhct.PH.LlEGhlluu    
   consensus/70%      GRGGAGFsTGhKWShMspsps.p.+YLlsNADEuEPGThKDR.lhcp.PHhLlEGhlluu    

                  121          .         .         :         .         .         . 180
 1 predict_h1400      FALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYIC    
 2 nuof_ecoli         FALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYIC    
 3 nuof_salty         FALKAYRGYIFLRGEYIEAAVHLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYIC    
 4 nuof_bucap         FALNVSRGYIFLRGEYIKAEYILKKSIQEAINFGFIGSNILNSGFNFELFLHTGAGRYIC    
 5 nuof_bucai         YALNVSRAYIFLRGEYVQAEHILKQSIQEAINFGFIGLNILGSNFNIELVLHTGAGRYIC    
 6 nuof_bucbp         FALSVTKSYIFLRGEYVNTERILKQSIIEATNYGYLGKNVCGSNLTFEIFIHTGAGRYIC    
 7 nuof_aquae         YAIGANEAYIYIRGEYPAGYYILRDAIEEAKKKGFLGKNILGSGFDLEIYVARGAGAYIC    
 8 nqo1_theth         YAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAYIC    
 9 nuf2_rhime         YAIGAETAYVYIRGEYVTAIRRMEQAIAEAHENGYLGVGILGSKFNFMVHIHRGAGAYIC    
10 nuof_myctu         YAIRAHHAFVYVRGEVVPVLRRLHNAVAEAYAAGFLGRNIGGSGFDLELVVHAGAGAYIC    
11 nuof_mycbo         YAIRAHHAFVYVRGEVVPVLRRLHNAVAEAYAAGFLGRNIGGSGFDLELVVHAGAGAYIC    
12 nuof_strco         YAIRSSHAFIYLRGEVVPVLRRLHEAVREAYAAGFLGENILGSGLDLTLTVHAGAGAYIC    
13 nuof_riccn         FAIGANNCYIYIRGEFYNEASNIQRALDEAYKEGLIGKNSCGSGFDCNIYLHRGAGAYIC    
14 nqo1_parde         FAMGAHAAYIYIRGEFIREREALQAAIDECYDAGLLGRNAAGSGWDFDLYLHHGAGAYIC    
15 nuof_ricpr         FAIGANTCYIYIRGEFYNEASNMQRALDEAYKEGLIGKNACGSGFDCNIYLHRGAGAYIC    
16 hoxf_alceu         YAIGCRKGIVYLRGEYFYLKDYLERQLQELREDGLLGRAIGgaGFDFDIRIQMGAGAYIC    
17 nuof_rhoca         FAMGARAAYIYIRGEYVREKEALQAAIDECYEAGLIGKNACRSDYDFDVYLHHGAGAYIC    
18 nubm_bovin         RAMGARAAYIYIRGEFYNEASNLQVAIREAYEAGLIGKNACGSGYDFDVFVVRGAGAYIC    
19 nuf1_rhime         FAMGAHAAYIYVRGEFIREREALQAAIDECYEYGLLGKN-NKLGYDIDIYVHHGAGAYIC    
20 nubm_neucr         RAMNATAAYIYIRGEFIQEAAILQNAINEAYADGLIGKNACGSGYDFDVYLHRGAGAYVC    
21 nubm_mouse         RAMGARAAYIYIRGEFYNEASNLQVAIREAYEAGLIGKNACGSDYDFDVFVVRGAGAYIC    
22 nubm_human         RAMGARAAYIYIRGEFYNEASNLQVAIREAYEAGLIGKNACGSGYDFDVFVVRGAGAYIC    
23 nubm_aspng         RAMNANAAYMYIRGEFYQEATVLQRAINEAYEAGLIGKNACGTGYDFDVYIHRGMGAYVC    
   consensus/100%     hAhts..shhalRGEh......hp.tl.Ehht.GhlG.s..t.thsh.lhl.hGhGtYlC    
   consensus/90%      hAhts.tualalRGEhh.....lp.ultEsht.GhlGpNhhsosashplhlhtGAGtYIC    
   consensus/80%      hAhtuptuYlalRGEahtth..LptAltEAhttGhlG+NhhGosash-lhlppGAGtYIC    
   consensus/70%      aAhtAptuYIYlRGEahpttp.LppAItEAhptGhlG+NhhGoGaDh-lalHpGAGAYIC    

                  181          .         2         .         .         .         . 240
 1 predict_h1400      GEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNIS    
 2 nuof_ecoli         GEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNIS    
 3 nuof_salty         GEETALINSLEGRRANPRSKPPFPATSGVWGKPTCVNNVETLCNVPAILANGVEWYQNIS    
 4 nuof_bucap         GEETALINSLEGRRANPRAKPPFPAVFGLWGKPTCVNNVETLSNVPSIVLHGVNWYKKLS    
 5 nuof_bucai         GEETALINSLEGRRANPRSKPPFPAVFGLWGKPTCVNNVETLSNVPCIILNGVSWYKNLS    
 6 nuof_bucbp         GEETALINSLEGRRANPRFKPPFPAYVGLWGKPTCVNNVETLSNVPAIFLNGVKWYKGLS    
 7 nuof_aquae         GEETALIESLEGKRGHPRLKPPYPVQKGLWGKPTVVNNVETIANVPFIISMGWEEYRYIG    
 8 nqo1_theth         GEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQMG    
 9 nuf2_rhime         GEETAMLESLEGKRAQPRLKPPFPAVAGLYASPTVINNVETLACVPHIVMRGSAWFRGIG    
10 nuof_myctu         GEETALLDSLEGRRGQPRLRPPFPAVAGLYGCPTVINNVETIASVPSIILGGIDWFRSMG    
11 nuof_mycbo         GEETALLDSLEGRRGQPRLRPPFPAVAGLYGCPTVINNVETIASVPSIILGGIDWFRSMG    
12 nuof_strco         GEETALLDSLEGRRGQPRLRPPFPAVAGLYACPTVVNNVESIASVPAILNKGKDWFRSMG    
13 nuof_riccn         GEETALLESLEGKKGMPRLKPPFPAGFGLYGCPTTINNVESIAVVPTILRRGASWFAGIG    
14 nqo1_parde         GEETALLESLEGKKGMPRMKPPFPAGAGLYGCPTTVNNVESIAVVPTILRRGAEWFASFG    
15 nuof_ricpr         GEETALLESLEGKKGMPRLKPPFPAGFGLYGCPTTINNVESIAVVPTILRRGASWFAAIG    
16 hoxf_alceu         GDESALIESCEGKRGTPRVKPPFPVQQGYLGKPTSVNNVETFAAVSRIMEEGADWFRAMG    
17 nuof_rhoca         GEETALLESLEGKKGMPRMKPPFPAGSGLYGCPTTVNNVESIAVVPTILRRGGAWFAGIG    
18 nubm_bovin         GEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVANVETVAVSPTICRRGGAWFASFG    
19 nuf1_rhime         GEETALLESLEGKKGQPRLKPPFPANMGLYGCPTTVNNVESIAVTPTILRRGAGWYTSFG    
20 nubm_neucr         GEETSLIESLEGKPGKPRLKPPFPAAVGLFGCPSTVANVETAVVAPTICRRGGNWFAGFG    
21 nubm_mouse         GEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVANVETVAVSPTICRRGGTWFAGFG    
22 nubm_human         GEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVANVETVAVSPTICRRGGTWFAGFG    
23 nubm_aspng         GEETSLIESIEGKAGKPRLKPPFPAAVGLFGCPSTVTNVETVAVTPTIMRRGASWFSSFG    
   consensus/100%     G-EouhhpShEGh.u.PR.+PPaPs..GhhupPoslsNVEohssss.Ih..G.t.at.hu    
   consensus/90%      GEETALlpSlEG+pu.PR.+PPFPA..GhaGpPTslsNVEolsssPtIh.tGhtWatthu    
   consensus/80%      GEETALlpSlEG+pupPRhKPPFPAs.GlaGpPTslsNVEolussPsIhhpGspWatshu    
   consensus/70%      GEETALlpSLEG++upPRhKPPFPAshGlaGpPTsVNNVETlusVPsIhtpGssWatshG    

                  241          :         .         .         .         .         3 300
 1 predict_h1400      KSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL    
 2 nuof_ecoli         KSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL    
 3 nuof_salty         KSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL    
 4 nuof_bucap         KSTdtGTKLMGFSGKVNNPGVWELPFGTTAREILEDYARGMKSGLFLKSWQPGGAGTDFL    
 5 nuof_bucai         KSSDTGTKLMGFSGNVRNPGVWELPFGTTAREILEDYAHGMKSGFSLKAWQPGGAGTDFL    
 6 nuof_bucbp         KSLDTGTKMMGFSGSVKFPGIWELPFGITAREIFERYAGGMKNNKKLKVWQPGGASTSFL    
 7 nuof_aquae         PSDYAGPKLFPVSGKVKKPGVYELPMNTTLREVIFKYAGG--------------------    
 8 nqo1_theth         TEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPLPF    
 9 nuf2_rhime         PDRSPGPKLYCLSGQVRKPGLYELPMGISLRELVEEHAGGPLPGRKVKAVIPGGVSAPVI    
10 nuof_myctu         SEKSPGFTLYSLSGHVTRPGQYEAPLGITLRELL-DYAGGVRAGHRLKFWTPGGSSTPLL    
11 nuof_mycbo         SEKSPGFTLYSLSGHVTRPGQYEAPLGITLRELL-DYAGGVRAGHRLKFWTPGGSSTPLL    
12 nuof_strco         SEKSPGFTLYSLSGHVAGPGQYEAPLGITLRQLL-DMSGGMRPGHRLKFWTPGGSSTPMF    
13 nuof_riccn         KPNNTGTKIFCISGHVNKPCNVEEAMGISLKELIEKYAGGVRGGwnLKAIIPGGSSVPLL    
14 nqo1_parde         RPNNAGVKLFGLTGHVNTPCVVEEAMSIPMRELIEKHGGGIRGGWklKAVIPGGASCPVL    
15 nuof_ricpr         KPNNTGTKVFCISGHVNKPCNIEEVMGVPLKELIEKYAGGVRGGwnLKAIIPGGASVPLL    
16 hoxf_alceu         TPDSAGTRLLSVAGDCSKPGIYEVEWGVTLNEVL--------------------------    
17 nuof_rhoca         RPNNTGVKLFAMSGHVNTPCVVEEAMSISMKELIEKHGGGVRGGWKNLKAVIPGGASCPV    
18 nubm_bovin         RERNSGTKLFNISGHVNNPCTVEEEMSVPLKELIEKHAGGVTGGwnLLAVIPGGSSTPLI    
19 nuf1_rhime         RPNNHGTKLYSVSGHVNRPCTVEDAMSIPFHELIEKHCGGIRGGwnLLAVIPGGSSVPCV    
20 nubm_neucr         RERNQGTKLFCISGHVNNPCTVEEEMSIPMRELIDKHCGGVRGGwnLLAVIPGGSSTPIL    
21 nubm_mouse         RERNSGTKLFNISGHVNHPCTVEEEMSVPLKELIEKHAGGVTGGwnLLAVIPGGSSTPLI    
22 nubm_human         RERNSGTKLFNISGHVNHPCTVEEEMSVPLKELIEKHAGFVTGGWDylAVIPGGSSTPLI    
23 nubm_aspng         RERNAGTKLFCISGHVNNPCTVEEEMSISLRDVIDRHCGGVRGGwnLLAVIPGGSSTPVL    
   consensus/100%     .....G.phh.hsG.st.Ps.hE..hshshpplh..........................    
   consensus/90%      p.ps.GhplhshSGpVppPs.hE..huhsh+Ell.castG.h.sh..h....susss..h    
   consensus/80%      p.pssGsKLhshSGcVppPs.hE..huhsh+Ell.cauGGhpsGhphhhh.PGGuusshl    
   consensus/70%      pppssGsKLhshSG+VppPshhE.shuhsh+Ell-cauGGhpsGhphhhh.PGGuusshl    

                  301          .         .         .         .         :         . 360
 1 predict_h1400      TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDG    
 2 nuof_ecoli         TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDG    
 3 nuof_salty         TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEIGMVSLVRNLEEFFARESCGWCTPCRDG    
 4 nuof_bucap         IEKHLDLPMDFTSIAKAGSRLGTAIAMAVDNKTNMISLVCNIEKFFSRESCGLCTPCREG    
 5 nuof_bucai         LEEHLDLPMDFKNISQAGSRLGTALSMAVDNKTSMVSLVYNIEKFFSRESCGLCTPCRDG    
 6 nuof_bucbp         IDKHLDVPMDFVNIKKVGSRLGTALAMAVDDSVSIVSLVRNIEEFFSRESCGFCTPCRDG    
 7 nuof_aquae         ------------------------------------------------------------    
 8 nqo1_theth         TEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCREG    
 9 nuf2_rhime         PEGELEVGMDFDSLTAAGSMLGSAGVVVIDDSTCMVKLATRIIEFFHHESCGKCTPCREG    
10 nuof_myctu         TDEHLDVPLDYEGVGAAGSMLGTKALEIFDETTCVVRAVRRWTEFYKHESCGKCTPCREG    
11 nuof_mycbo         TDEHLDVPLDYEGVGAAGSMLGTKALEIFDETTCVVRAVRRWTEFYKHESCGKCTPCREG    
12 nuof_strco         TDEHLDVPLDYEGVGAAGSMLGTKALQCFDETTCVVRAVTRWTEFYAHESCGKCTPCREG    
13 nuof_riccn         PKSLCEVDMDFDSLRTAGSGLGTGGIIVMDQSTDIIYAIARLSKFYMHESCGQCTPCREG    
14 nqo1_parde         teQCENAIMDYDGMRDVRSSFGTACMIVMDQSTDVVKAIWRLSKFFKHESCGQCTPCREG    
15 nuof_ricpr         PKSLCEVEMDFDSLRTVGSGLGTGGIIVMDKSTDIIYAIARLSKFYMHESCGQCTPCREG    
16 hoxf_alceu         ------------------------------------------------------------    
17 nuof_rhoca         IPAHldAIMDYDGMREKQSSFGTACLIVMDQQTDIIKAIARLSKFFKHESCGQCTPCREG    
18 nubm_bovin         PKSVCevLMDFDALIQAQTGLGTAAVIVMDRSTDIVKAIARLIEFYKHESCGQCTPCREG    
19 nuf1_rhime         PGAQmdAIMDYDGLRELGSGLGTAAVIVMDKSTDIIKAIWRLSAFYKHESCGQCTPCREG    
20 nubm_neucr         PKHICDTqmDFDALKDSQSGLGTAALIVMDKSTDVVRAISRLSHFYRHESCGQCTPCREG    
21 nubm_mouse         PKSVCevLMDFDALVQAQTGLGTAAVIVMDRSTDIVKAIARLIEFYKHESCGQCTPCREG    
22 nubm_human         PKSVCevLMDFDALVQAQTGLGTAAVIVMDRSTDIVKAIARLIEFYKHESCGQCTPCREG    
23 nubm_aspng         PKTIcdQLMDFDALKDSQSGLGTAAVIVMDKSTDIVRAISRLSTFYKHESCGQCTPCREG    
   consensus/100%     ............................................................    
   consensus/90%      ..t..p..hpa.th.t.to.hGoth..hhspphshl.hh.ph.tFa.+ESCG.CTPCR-G    
   consensus/80%      .cthh-h.h-acslhthtohLGTthh.hhDpphshlphlhph.cFat+ESCG.CTPCR-G    
   consensus/70%      scthh-h.MDa-ulttstShLGTuhhhshDppsshlphltplpcFat+ESCG.CTPCR-G    

                  361          .         .         .         4         .         . 420
 1 predict_h1400      LPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFE    
 2 nuof_ecoli         LPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFE    
 3 nuof_salty         LPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAH--------------------    
 4 nuof_bucap         LPWIVKILESLEKKEGHKNDVKNLERLCLDLSPGKTFCAHAPGAVEPLQSAIKYFRLEFE    
 5 nuof_bucai         LPWIVKILKSLEQNKGHKNDVKNLEKLCSHLSPGKTFCAHAPGAIEPLQSAIKYFRSEFE    
 6 nuof_bucbp         LPWIVKILKVLEQKIGVPEDIEILEQLCEQLGPGRTFCAHAPGAIEPLKSALKYFRLEFE    
 7 nuof_aquae         ------------------------------------------------------------    
 8 nqo1_theth         ------------------------------------------------------------    
 9 nuf2_rhime         LDWTVKVLRRIEAGEGETGDLEQLEMLCKGIF-GNTFCALGDGAAMGLRAALKHFREEFV    
10 nuof_myctu         TFWLDKIYERLETGRGSHEDIDKLLDISDSI-LGKSFCALGDGAASPVMSSIKHFRDEY-    
11 nuof_mycbo         TFWLDKIYERLETGRGSHEDIDKLLDISDSI-LGKSFCALGDGAASPVMSSIKHFRDEY-    
12 nuof_strco         TYWLVQLLRDIEAGKGQMSDLDKLNDIADNIN-GKSFCALGDGAASPIFSSLKYFREEYE    
13 nuof_riccn         TGW---------------------------------------------------------    
14 nqo1_parde         TGWMMRVMERLVRGD---------------------------------------------    
15 nuof_ricpr         TGWMWRVMMRLVNGNAKKNEIDTL------------------------------------    
16 hoxf_alceu         ------------------------------------------------------------    
17 nuof_rhoca         TSWMWRVMERLVTGE---------------------------------------------    
18 nubm_bovin         VDWMNKVMARFVRGDARPAEIDSLWEISKQI-EGHTICALGDGAAWPVQGLIRHFRPELE    
19 nuf1_rhime         TGWMMRVMERMVQGRAQKREIDML------------------------------------    
20 nubm_neucr         SKWTEQIMKRFEKGQGREREIDMLQEL---------------------------------    
21 nubm_mouse         VDWMNKVMARFVKGDARPAEIDSLWEISKQI-EGHTICALGDGAAWPVQGLIRHFRPELE    
22 nubm_human         VDWMNKVMARFVRGDARPAEIDSLWEISKQI-EGHTICALGDGAAWPVQGLIRHFRPELE    
23 nubm_aspng         SKWTMHMMQRMEKGQAREREIDMLQEL---------------------------------    
   consensus/100%     ............................................................    
   consensus/90%      ............................................................    
   consensus/80%      ..W..phh..h.tt..............................................    
   consensus/70%      h.W..+lhtth.pspu..t-lc.L....................................    

                  421          .         .    ] 445
 1 predict_h1400      AGIKQPFSNTHLINGIQPNLLKERW    
 2 nuof_ecoli         AGIKQPFSNTHLINGIQPNLLKERW    
 3 nuof_salty         -------------------------    
 4 nuof_bucap         AGI----------------------    
 5 nuof_bucai         SGI----------------------    
 6 nuof_bucbp         -------------------------    
 7 nuof_aquae         -------------------------    
 8 nqo1_theth         -------------------------    
 9 nuf2_rhime         AHIEE--------------------    
10 nuof_myctu         -------------------------    
11 nuof_mycbo         -------------------------    
12 nuof_strco         -------------------------    
13 nuof_riccn         -------------------------    
14 nqo1_parde         -------------------------    
15 nuof_ricpr         -------------------------    
16 hoxf_alceu         -------------------------    
17 nuof_rhoca         -------------------------    
18 nubm_bovin         -------------------------    
19 nuf1_rhime         -------------------------    
20 nubm_neucr         -------------------------    
21 nubm_mouse         -------------------------    
22 nubm_human         -------------------------    
23 nubm_aspng         -------------------------    
   consensus/100%     .........................    
   consensus/90%      .....                        
   consensus/80%      ...                          
   consensus/70%

COILS prediction (A Lupas)

TOP - BOTTOM - SEG


--- COILS HEADER: SUMMARY

COILS version 2.2: R.B. Russell, A.N. Lupas, 1999
using MTIDK matrix.
weights: a,d=2.5 and b,c,e,f,g=1.0

For the threshold of 5 ( probability > 0.5):
>prot

window size = 14        14  residues in coiled coil domain
window size = 21         0  residues in coiled coil domain
window size = 28         0  residues in coiled coil domain

               .    :    .    :    .    :    .    :    .    5
seq        MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEI
frame-14   MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEI
frame-21   MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEI
frame-28   MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEI
prob-14    44455555555556666666666669999999999999999999999988
prob-21    33455555555555555666666689999999999999999999999999
prob-28    44444444455557777777777777777777777777777777777777
               .    :    .    :    .    :    .    :    .    10
seq        VNQVKDAGLKGRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYK
frame-14   VNQVKDAGLKGRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYK
frame-21   VNQVKDAGLKGRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYK
frame-28   VNQVKDAGLKGRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYK
prob-14    88777777777776666777777777788888899999999999999667
prob-21    99888777666666666666777777777777777777777777777777
prob-28    77777777777766666666666666666677777777777777777777
               .    :    .    :    .    :    .    :    .    15
seq        DRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEA
frame-14   DRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEA
frame-21   DRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEA
frame-28   DRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEA
prob-14    99999999999999999999999999999999999999999999999999
prob-21    77778888888888888888899999999999999999999999999999
prob-28    77778888888888888899999999999999999999999999999999
               .    :    .    :    .    :    .    :    .    20
seq        TEAGLLGKNIMGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSK
frame-14   TEAGLLGKNIMGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSK
frame-21   TEAGLLGKNIMGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSK
frame-28   TEAGLLGKNIMGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSK
prob-14    99999999999888886666666688888999999999999999998888
prob-21    99999999999998887777777777777888888888888888888888
prob-28    99999999999998887777777776666666666666666666666666
               .    :    .    :    .    :    .    :    .    25
seq        PPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNISKSKDAGTKLM
frame-14   PPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNISKSKDAGTKLM
frame-21   PPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNISKSKDAGTKLM
frame-28   PPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNISKSKDAGTKLM
prob-14    43334444666999999999999999999997888888888999999999
prob-21    44446666666666666777777788888888888888888888877777
prob-28    55555555555777777888888888888888888888888888877777
               .    :    .    :    .    :    .    :    .    30
seq        GFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL
frame-14   GFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL
frame-21   GFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL
frame-28   GFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL
prob-14    99999644444468888888999999999999998888888455558889
prob-21    77777766666668888888999999999999999999999666668889
prob-28    77777766666668888888888888888888888888888677777779
               .    :    .    :    .    :    .    :    .    35
seq        TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARES
frame-14   TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARES
frame-21   TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARES
frame-28   TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARES
prob-14    99999999999999999999999999999999999999999999999999
prob-21    99999999999999999999999999999999999999999999999998
prob-28    99999999999999999999999999999999999999999999999999
               .    :    .    :    .    :    .    :    .    40
seq        CGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAH
frame-14   CGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAH
frame-21   CGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAH
frame-28   CGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAH
prob-14    99555449999999999999999988888899999999999999666999
prob-21    88777777777777779999999999999999999999999999999999
prob-28    99888666677777778888888888888888888888888888777888
               .    :    .    :    .    :    .    :    .    45
seq        APGAVEPLQSAIKYFREEFEAGIKQPFSNTHLINGIQPNLLKERW
frame-14   APGAVEPLQSAIKYFREEFEAGIKQPFSNTHLINGIQPNLLKERW
frame-21   APGAVEPLQSAIKYFREEFEAGIKQPFSNTHLINGIQPNLLKERW
frame-28   APGAVEPLQSAIKYFREEFEAGIKQPFSNTHLINGIQPNLLKERW
prob-14    999999999999999999999888866677777777777777655
prob-21    999999999999999999999999966666655555555555544
prob-28    888888888888888888888888877777777776666666655
// End

DISULFIND (A. Vullo and P. Frasconi)

TOP - BOTTOM - DISULFIND

-------------------------------------------------------------------------------
              Cysteines Bonding State and Connectivity Predictor               
-------------------------------------------------------------------------------


0 = Not Bonded
1 = Bonded


Chain identifier: predict_h14099.fasta


                                                                               
                                                                               
                                                                               
                                                                               
.........10........20........30........40........50........60........70........
MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLKGRGGAGFSTGLKWSLMPKD
                                                                               

                                                                               
                                                                               
         +---------------------------------------------------------------------
         |                                                                     
80........90........100.......110.......120.......130.......140.......150......
ESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGK
         1                                                                     

                                                        +----------------------
                     +----------------------------------|----------------------
---------------------|----------------------------------|-------+              
                     |                                  |       |              
.160.......170.......180.......190.......200.......210.......220.......230.....
NIMGTGFDFELFVHTGAGRYICGEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQ
                     1                                  1       1              

-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
                                                                               
                                                                               
..240.......250.......260.......270.......280.......290.......300.......310....
NISKSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFLTEAHLDLPMEFESIGK
                                                                               

-------------------------------------+                                         
----------------------------------+  |                                         
                                  |  |                                         
                                  |  |                                         
...320.......330.......340.......350.......360.......370.......380.......390...
AGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGK
                                  1  1  0                              0       

                                                  
                                                  
                                                  
                                                  
....400.......410.......420.......430.......440...
TFCAHAPGAVEPLQSAIKYFREEFEAGIKQPFSNTHLINGIQPNLLKERW
  0                                               

-------------------------------------------------------------------------------
Please cite:

P. Frasconi, A. Passerini, and A. Vullo.
"A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines"
Proc. IEEE Workshop on Neural Networks for Signal Processing, pp. 25-34, 2002.

A.Ceroni, P.Frasconi, A.Passerini and A.Vullo.
"Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines"
Journal of VLSI Signal Processing, 35, 287-295, 2003.

A. Vullo and P. Frasconi.
"Disulfide Connectivity Prediction using Recursive Neural Networks and Evolutionary Information"
Bioinformatics, 20, 653-659, 2004.

Questions and comments are very appreciated.
Please, send email to: cystein@dsi.unifi.it

Created by members of the Machine Learning and
Neural Network Group, Universita' di Firenze

The server is hosted at the Department of Systems and
Computer Science (DSI), Faculty of Engineering,
Universita' di Firenze, Italy
-------------------------------------------------------------------------------

PHD information about accuracy

****************************************************************************
*                                                                          *
*    PHD: Profile fed neural network systems from HeiDelberg               *
*    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~               *
*                                                                          *
*    Prediction of:			                                   *
* 	secondary structure,   			   by PHDsec		   *
* 	solvent accessibility, 			   by PHDacc		   *
* 	and helical transmembrane regions, 	   by PHDhtm		   *
*                                                                          *
*    Author:             						   *
*	Burkhard Rost							   *
*       EMBL, 69012 Heidelberg, Germany					   *
*       Internet: Rost@EMBL-Heidelberg.DE				   *
*                                                                          *
*    All rights reserved.                                                  *
*                                                                          *
****************************************************************************
*                                                                          *
*    The network systems are described in:   	                     	   *
*                                                                          *
*    PHDsec:    B Rost & C Sander: JMB, 1993, 232, 584-599.		   *
*    		B Rost & C Sander: Proteins, 1994, 19, 55-72.		   *
*    PHDacc:  	B Rost & C Sander: Proteins, 1994, 20, 216-226.		   *
*    PHDhtm:  	B Rost et al.: 	   Prot. Science, 1995, 4, 521-533.	   *
*                                                                          *
****************************************************************************

PHD predictions for predict_h14099

Contents:

SYNOPSIS of prediction

transmembrane helices

HEADER information

about protein
about alignment
residue composition
about method used
please quote
copyright & contact
abbreviations used

BODY with predictions
Different levels of data:

PHD brief
PHD normal

SYNOPSIS of prediction

PHDhtm summary
- NHTM=1
  PHDhtm detected 1 membrane helix for the best model.The second best model contained 0 helix.
- TOP=out
  PHDhtm predicted the topology out, i.e. the first loop region is out (Note: this prediction may be problematic when the sequence you sent starts or ends with a region predicted in a membrane helix!)
- Reliability of best model=1 (0 is low, 9 is high)
- Zscore for best model=0.000
- Difference of positive charges (K+R) inside - outside=6.000 (the higher the value, the more reliable)
- Reliability of topology prediction =6 (0 is low, 9 is high)
- Details of the strength of each predicted membrane helix:
  (sorted by strength, strongest first)
  
  N HTM Total score Best HTM c-N
  
  1 0.9679 0.7048 114 - 131
- Overview over transmembrane segments:
  
  Positions Segments Explain
  
  1- 113 o1 outside region 1
  
  114- 131 T1 ?=error 1
  
  132- 445 i1 inside region 1

HEADER information

About your protein:

About the alignment used:

Residue composition for your protein:

%A: 8.5 %C: 2.0 %D: 3.8 %E: 8.5 %F: 4.3

%G: 10.8 %H: 1.6 %I: 4.9 %K: 5.6 %L: 10.8

%M: 2.7 %N: 4.5 %P: 5.6 %Q: 2.2 %R: 6.3

%S: 4.3 %T: 5.2 %V: 3.6 %W: 2.2 %Y: 2.5

About the PHD methods used:

Please quote:
1. PHD: B Rost (1996) Methods in Enzymology, 266:525-539
2. PHDhtm: B Rost, P Fariselli & R Casadio (1996) Prot Science, 7:1704-1718

Copyright & Contact:
- Burkhard Rost, CUBIC NYC / LION Heidelberg
- Email: rost@columbia.edu
- WWW: http://cubic.bioc.columbia.edu
- Fax: +1-212-305 3773

ABBREVIATIONS used:

AA :	amino acid sequence
pH_sec:	'probability' for assigning helix (1=high, 0=low)
pL_sec:	'probability' for assigning neither helix, nor strand (1=high, 0=low)
PHD_htm:	PHD predicted membrane helix: M=helical transmembrane region, blank=non-membrane PHD = PHD: Profile network prediction HeiDelberg
Rel_htm:	reliability index for PHDhtm prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_htm:	subset of the PHDhtm prediction, for all residues with an expected average accuracy > 98% (tables in header) NOTE: for this subset the following symbols are used: N: is non-membrane region (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 7

PHDrhtm:	refined PHD prediction: M=helical transmembrane region, blank=non-membrane
PiMohtm:	PHD prediction of membrane topology: T=helical transmembrane region, i=inside of membrane, o=outside of membrane
pT_htm:	'probability' for assigning transmembrane helix
pN_htm:	'probability' for assigning globular region

phd_skip:	note: sequence stretches with less than 9 are not predicted, the symbol '*' is used!

....,....1....,....2....,....3....,....4....,....5....,....6 AA MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLK PHD_htm Rel_htm ************************************************************ PiMohtm oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo ....,....7....,....8....,....9....,....10...,....11...,....12 AA GRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISA PHD_htm MMMMM Rel_htm **************************************************** PiMohtm oooooooooooooooooooooooooooooooooooooooooooooooooooooTTTTTTT ....,....13...,....14...,....15...,....16...,....17...,....18 AA FALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYIC PHD_htm MMMMMMMMMM Rel_htm *** *********************************************** PiMohtm TTTTTTTTTTTiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii ....,....19...,....20...,....21...,....22...,....23...,....24 AA GEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNIS PHD_htm Rel_htm ************************************** **** ************ PiMohtm iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii ....,....25...,....26...,....27...,....28...,....29...,....30 AA KSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL PHD_htm Rel_htm ************************************************************ PiMohtm iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii ....,....31...,....32...,....33...,....34...,....35...,....36 AA TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDG PHD_htm Rel_htm ************************************************************ PiMohtm iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii ....,....37...,....38...,....39...,....40...,....41...,....42 AA LPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFE PHD_htm Rel_htm ************************************************************ PiMohtm iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii ....,....43...,....44...,....45 AA AGIKQPFSNTHLINGIQPNLLKERW PHD_htm Rel_htm ************************* PiMohtm iiiiiiiiiiiiiiiiiiiiiiiii

PHD results (normal)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLK PHD_htm Rel_htm 999999999999999999999999999999999999999999999999999999999999 SUB_htm NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN PHDrhtm PiMohtm oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo ....,....7....,....8....,....9....,....10...,....11...,....12 AA GRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISA PHD_htm MMMMM Rel_htm 999999999999999999999999999999999999999999999999999864024556 SUB_htm NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN........ PHDrhtm MMMMMMM PiMohtm oooooooooooooooooooooooooooooooooooooooooooooooooooooTTTTTTT ....,....13...,....14...,....15...,....16...,....17...,....18 AA FALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYIC PHD_htm MMMMMMMMMM Rel_htm 777665543013678999999999999999999999999999999999999999999999 SUB_htm MMM..........NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN PHDrhtm MMMMMMMMMMM PiMohtm TTTTTTTTTTTiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii ....,....19...,....20...,....21...,....22...,....23...,....24 AA GEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNIS PHD_htm Rel_htm 999999999999999999999999999999999999875556777766788899999999 SUB_htm NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN....NNNN..NNNNNNNNNNNN PHDrhtm PiMohtm iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii ....,....25...,....26...,....27...,....28...,....29...,....30 AA KSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL PHD_htm Rel_htm 999999999999999999999999999999999999999999999999999999999999 SUB_htm NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN PHDrhtm PiMohtm iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii ....,....31...,....32...,....33...,....34...,....35...,....36 AA TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDG PHD_htm Rel_htm 999999999999999999988888777789999999999999999999999999999999 SUB_htm NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN PHDrhtm PiMohtm iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii ....,....37...,....38...,....39...,....40...,....41...,....42 AA LPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFE PHD_htm Rel_htm 999999999999999999999999999999999999999999888778899999999999 SUB_htm NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN PHDrhtm PiMohtm iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii ....,....43...,....44...,....45 AA AGIKQPFSNTHLINGIQPNLLKERW PHD_htm Rel_htm 9999999999999999999999999 SUB_htm NNNNNNNNNNNNNNNNNNNNNNNNN PHDrhtm PiMohtm iiiiiiiiiiiiiiiiiiiiiiiii

PROF predictions

TOP - BOTTOM - PROF

Bottom - Summary - Details - PredictProtein

PROF predictions for query

Contents:

SYNOPSIS of prediction for query

secondary structure class
secondary structure composition
surface/core ratio

HEADER information

about protein
about alignment
residue composition
about method used
please quote
copyright & contact
abbreviations used

BODY with predictions
Different levels of data:

PROF normal
PROF detail

SYNOPSIS of prediction for query

PROFsec summary overall your protein can be classified as:
mixed given the following classes:
- 'all-alpha': %H > 45% AND %E < 5%
- 'all-beta': %H < 5% AND %E > 45%
- 'alpha-beta': %H > 30% AND %E > 20%
- 'mixed': all others

Predicted secondary structure composition for your protein:

sec str type H E L

% in protein 37.08 12.13 50.79

Predicted solvent accessibility composition (core/surface ratio) for your protein:
Classes used:
- e: residues exposed with more than 16% of their surface
- b: all other residues.
accessib type b e

% in protein 56.40 43.60

HEADER information

About your protein:

prot_id query

prot_nres 445

prot_nali 134

prot_nchn 1

prot_nfar 92

About the alignment used:

ali_orig /home/ppuser/server/work/predict_h14099.hsspPsiFil

Residue composition for your protein:

%A: 8.5 %C: 2.0 %D: 3.8 %E: 8.5 %F: 4.3

%G: 10.8 %H: 1.6 %I: 4.9 %K: 5.6 %L: 10.8

%M: 2.7 %N: 4.5 %P: 5.6 %Q: 2.2 %R: 6.3

%S: 4.3 %T: 5.2 %V: 3.6 %W: 2.2 %Y: 2.5

About the PROF methods used:

prof_fpar acc=/home/ppuser/server/pub/prof/net/PROFboth_best.par

prof_nnet acc=6

Please quote:
1. PROF: B Rost & C Sander (1993) J Mol Biol, 232:584-599
2. PROFhtm: B Rost, P Fariselli & R Casadio (1996) Prot Science, 7:1704-1718

Copyright & Contact:
- Burkhard Rost, CUBIC NYC / LION Heidelberg
- Email: rost@columbia.edu
- WWW: http://cubic.bioc.columbia.edu
- Fax: +1-212-305 3773

ABBREVIATIONS used:

AA :	amino acid sequence
OBS_sec:	observed secondary structure: H=helix, E=extended (sheet), blank=other (loop)
PROF_sec:	PROF predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop) PROF = PROF: Profile network prediction HeiDelberg
Rel_sec:	reliability index for PROFsec prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_sec:	subset of the PROFsec prediction, for all residues with an expected average accuracy > 82% (tables in header) NOTE: for this subset the following symbols are used: L: is loop (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 5

pH_sec:	'probability' for assigning helix (1=high, 0=low)
pE_sec:	'probability' for assigning strand (1=high, 0=low)
pL_sec:	'probability' for assigning neither helix, nor strand (1=high, 0=low)
O_2_acc:	observerd relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%.
P_2_acc:	PROF predicted relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%.
O_3_acc:	observerd relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
P_3_acc:	PROF predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
OBS_acc:	observed relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between nn % and (n+1)(n+1) % (e.g. for n=5: 16-25%).
PROF_acc:	PROF predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between nn % and (n+1)(n+1) % (e.g. for n=5: 16-25%).
Rel_acc:	reliability index for PROFacc prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_acc:	subset of the PROFacc prediction, for all residues with an expected average correlation > 0.69 (tables in header) NOTE: for this subset the following symbols are used: I: is intermediate (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 4


ali_orig:	input file
prof_fpar:	name of parameter file, used [w]
prof_nnet:	number of networks used for prediction [d]
prof_skip:	note: sequence stretches with less than 9 are not predicted, the symbol '*' is used!

BODY with predictions for query

PROF results (normal)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLK OBS_sec PROF_sec EEEEE HHHHHHHH HHHHHHHH HHHHHHHHHH Rel_sec 942236776664057752787730145643125705788887207948898898762773 SUB_sec L....LLLLLL..EEEE.LLLL....HH....LL.HHHHHHH..LL.HHHHHHHHH.LL. O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc eee e eee bbb b eee eebbe beeeeb ebb ebbee e e bbe bee bb Rel_acc 414211213232214334225112014333402013083424434424391649441021 SUB_acc e.e...........b..i..e.....e...e......b.e.be.ie.e.b.eibee.... ....,....7....,....8....,....9....,....10.1.,....11.1.,....1 AA GRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISA OBS_sec PROF_sec EEE EEEEEE HHHHHH HHHHHHHHHHH Rel_sec 213355534331000344567862378872676776643204555105324565788888 SUB_sec ....LLL...........LLLLL..EEEE.LLLLLLL.....HHH..L...HHHHHHHHH O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc b bbbbbbbbbeb eeeeeeb bbbbbb e e beb bbeebb bbbbbbbbb Rel_acc 322242211102110022253123419984311020100200213311022671996997 SUB_acc ....b..............e....i.bbbb.....................bb.bbbbbb ....,....13.1.,....14.1.,....15.1.,....16.1.,....17.1.,....1 AA FALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYIC OBS_sec PROF_sec HH EEEEEEE HHHHHHHHHHHHHHHH EEEEEEE Rel_sec 850364137987245357888888888888761775422024554203788614541002 SUB_sec HH..L...EEEE..L.HHHHHHHHHHHHHHHH.LLL......LL....EEEE..L..... O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc bbb b bbbbbb ebbe b ebbe b e bbbb bbb beb b bb bbbbbbb Rel_acc 261112183969002303652393489549233110110101003223838011012112 SUB_acc .b.....b.bbb......bb..b.ebbeib..................b.b......... ....,....19.1.,....20.1.,....21.1.,....22.1.,....23.1.,....2 AA GEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNIS OBS_sec PROF_sec HHHHHHHHH EEE HHHHHHHHHHHHH HHHHH Rel_sec 531478875504547767666655312334664211044458778888760102331057 SUB_sec L...HHHHHH..L.LLLLLLLLLL......LL........HHHHHHHHHH........LL O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc b b bbb bbe e eee bbbbbbbbb bbbbbbb bbbbbb bbe bbe bee Rel_acc 220135322430241211021001101221121133223235339426823803061310 SUB_acc .....b...b...e...........................b..bb.bb..b...b.... ....,....25.1.,....26.1.,....27.1.,....28.1.,....29.1.,....3 AA KSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL OBS_sec PROF_sec EEEEEEEEE EEEE HHHHHHHH EEEEE Rel_sec 776776247887533136633664036657889976157745554014663044442325 SUB_sec LLLLLL..EEEEE....LL..EE...LLLHHHHHHH.LLL.LLL....EE.........L O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc eeeeee bbbbbb beee b bbbbbbb bbeebbe b ee eb bbbbbbbbbbbb Rel_acc 033301223657243231110023011007237833002100212233443233101000 SUB_acc .........bbb.b...............b..bb..............bb.......... ....,....31.1.,....32.1.,....33.1.,....34.1.,....35.1.,....3 AA TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDG OBS_sec PROF_sec HHHHHHH EEEEE HHHHHHHHHHHHHHH Rel_sec 631023454724564401335630478861675568888877554322114535553134 SUB_sec L......L.L..HH......LL...EEEE.LLLLHHHHHHHHHH.......L.LLL.... O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc ee e bb bebb e bb bbbbbbbbb bb bb bbebb bbb bbbb eb Rel_acc 221010000224072202011224899970201033269325140322101010001100 SUB_acc ...........e.b.........bbbbbb........bb..b.e................ ....,....37.1.,....38.1.,....39.1.,....40.1.,....41.1.,....4 AA LPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFE OBS_sec PROF_sec HHHHHHHHHHH HHHHHHHHHHHHHH HHHHHHHHHHHHHH Rel_sec 515888998876177881137889988886303754011250231047888887578888 SUB_sec L.HHHHHHHHHH.LLLL...HHHHHHHHHH...LL.....L......HHHHHHHHHHHHH O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc b bb bbe beeeeeeee be b ebbe bee bbbbbbbbbb bbbbbbe b e b Rel_acc 020712693332313232511439436350333021243210031129138633935373 SUB_acc ...b..bb..........e..e.bi.b.e........b.........b..bb..b.e.b. ....,....43.1.,....44.1., AA AGIKQPFSNTHLINGIQPNLLKERW OBS_sec PROF_sec HHHH HHHH Rel_sec 7620445754111026731320248 SUB_sec HH....LLL......LL.......L O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc e beee eee eebeee beeee Rel_acc 5314310320000321233016303 SUB_acc e..e.................e...

PROF results (detail)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MKNIIRTPETHPLTWRLRDDKQPVWLDEYRSKNGYEGARKALTGLSPDEIVNQVKDAGLK pH_sec .... ....... 1.0 pH_sec . ...... ......... 0.9 pH_sec .... ....... .......... 0.8 pH_sec ..... ........ .......... 0.7 pH_sec ....... ........ .......... 0.6 pH_sec ........ .......... .......... 0.5 pH_sec ......... .......... ........... 0.4 pH_sec .......... .......... ........... 0.3 pH_sec . .. ........................ ............ 0.2 ------------------------------------------------------------ pE_sec 1.0 pE_sec .. 0.9 pE_sec .... 0.8 pE_sec .... 0.7 pE_sec ..... 0.6 pE_sec ..... 0.5 pE_sec ... ...... . 0.4 pE_sec .... ....... . 0.3 pE_sec ..... ......... . . 0.2 ------------------------------------------------------------ pL_sec . . . 1.0 pL_sec . .. . .... . .. .. 0.9 pL_sec . ....... .... .. .. .. 0.8 pL_sec .. ........ ..... .. .. .... 0.7 pL_sec ............ ...... ... ... .... 0.6 pL_sec ............. ....... .... ... .... 0.5 pL_sec ............. ........ ...... .... .... 0.4 pL_sec .............. ........... ........ ..... .... 0.3 pL_sec ..................................... ...... ...... 0.2 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc . . . . 100% PROF_acc . . .. ... . . . . . 81% PROF_acc . . . ... ... . . . . .. . . . 64% PROF_acc ... . ... ... .. . .... . . .. . . . .. 49% PROF_acc ... ...... . ....... .. .... . .. .. .... . .. . 36% PROF_acc ... ...... . . ....... .. .... . .. .. .... .. .. . 25% PROF_acc ............ . ....... .. .... .. .. ....... .. ... . 16% PROF_acc ............ . ....... .. .... .. .. ....... .. ... . 9% PROF_acc ............. . ....... .. .... .. .. ....... .. ... .. 4% ------------------------------------------------------------ ....,....7....,....8....,....9....,....10.1.,....11.1.,....1 AA GRGGAGFSTGLKWSLMPKDESMNIRYLLCNADEMEPGTYKDRLLMEQLPHLLVEGMLISA pH_sec ..... 1.0 pH_sec . ...... 0.9 pH_sec ... .......... 0.8 pH_sec .... ........... 0.7 pH_sec ..... ........... 0.6 pH_sec ....... ........... 0.5 pH_sec ....... ............ 0.4 pH_sec ... ........ ............ 0.3 pH_sec .......... ... .. ...................... 0.2 ------------------------------------------------------------ pE_sec .. 1.0 pE_sec .... 0.9 pE_sec .... 0.8 pE_sec ..... 0.7 pE_sec ...... 0.6 pE_sec .... ...... 0.5 pE_sec ... ..... ....... 0.4 pE_sec .... ....... ....... .. 0.3 pE_sec ................... ........... . .... 0.2 ------------------------------------------------------------ pL_sec 1.0 pL_sec .... . ... 0.9 pL_sec .. ..... ....... . 0.8 pL_sec ....... . ........ ........ .. 0.7 pL_sec ........... ......... .......... ... 0.6 pL_sec ........... .......... ........... .... 0.5 pL_sec ......................... ............ ..... 0.4 pL_sec ......................... ............. ....... . 0.3 pL_sec .......................... ........................... 0.2 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc ..... . 100% PROF_acc ..... . 81% PROF_acc ..... . . 64% PROF_acc . ...... . . . .. 49% PROF_acc . . ....... .. ... . . .. . 36% PROF_acc . . . ....... . .. ... . . .. .. 25% PROF_acc . . .......... . ....... . .. .. .. 16% PROF_acc . . ............ ....... . .. ... .. 9% PROF_acc . .............. ....... . .. ... .. 4% ------------------------------------------------------------ ....,....13.1.,....14.1.,....15.1.,....16.1.,....17.1.,....1 AA FALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHTGAGRYIC pH_sec ............ 1.0 pH_sec . ............... 0.9 pH_sec .. ................ 0.8 pH_sec .. ................ 0.7 pH_sec .. ................ 0.6 pH_sec ... ................. 0.5 pH_sec ... ................. 0.4 pH_sec .... .................. .. 0.3 pH_sec ...... ........................... . ... 0.2 ------------------------------------------------------------ pE_sec .. .. 1.0 pE_sec .... .... 0.9 pE_sec .... .... 0.8 pE_sec ..... ..... 0.7 pE_sec ....... ...... . 0.6 pE_sec ....... ....... .. 0.5 pE_sec ....... .. ........ .... 0.4 pE_sec ......... ..... ................ 0.3 pE_sec .......... .......................... 0.2 ------------------------------------------------------------ pL_sec 1.0 pL_sec .. 0.9 pL_sec . . .. .. .. 0.8 pL_sec ... ... .... .... ... 0.7 pL_sec .... ... ..... . ...... ... . 0.6 pL_sec .... ... ............... ...... . 0.5 pL_sec ...... .... ............... ........ 0.4 pL_sec ...... ..... ................ ........ 0.3 pL_sec ........ ....... .................. ......... 0.2 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc . 100% PROF_acc . 81% PROF_acc . 64% PROF_acc . . . . . . 49% PROF_acc . . . . . . .. ... . . . 36% PROF_acc . .. ... . .. .. .. ... . . . . . . 25% PROF_acc . .. ..... .. .. .. ... .. .. . . . . 16% PROF_acc . .. ..... .. .. .. ... . .. .... . . . 9% PROF_acc . .. ..... .. .. .. ... . .. .... . . . . 4% ------------------------------------------------------------ ....,....19.1.,....20.1.,....21.1.,....22.1.,....23.1.,....2 AA GEETALINSLEGRRANPRSKPPFPATSGAWGKPTCVNNVETLCNVPAILANGVEWYQNIS pH_sec . .... 1.0 pH_sec .... ......... 0.9 pH_sec ....... ............ 0.8 pH_sec ....... ............ ... 0.7 pH_sec ......... ............ .... 0.6 pH_sec ......... .................... 0.5 pH_sec ......... .................... 0.4 pH_sec ........... .... ... .................... 0.3 pH_sec .............. ....... ........................... 0.2 ------------------------------------------------------------ pE_sec 1.0 pE_sec 0.9 pE_sec 0.8 pE_sec 0.7 pE_sec 0.6 pE_sec ... 0.5 pE_sec . ... 0.4 pE_sec . ...... .... 0.3 pE_sec .. .... .................... 0.2 ------------------------------------------------------------ pL_sec 1.0 pL_sec ..... . . 0.9 pL_sec . .. ......... .. .. 0.8 pL_sec .. .............. .... . .. 0.7 pL_sec .. .............. ....... . . .. 0.6 pL_sec .. ........................ . ... .... 0.5 pL_sec ... ......................... .. .... ..... 0.4 pL_sec .... ............................... .......... 0.3 pL_sec ..... .................................. . ........... 0.2 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc . 100% PROF_acc ... 81% PROF_acc . . ... . . 64% PROF_acc . . ... . . .. 49% PROF_acc . . .... ..... .. . .. . 36% PROF_acc . . . .... ..... . . .. . .. . 25% PROF_acc . . . ............ . . . .. .. .... 16% PROF_acc . . . ............ . . . .. .. .... 9% PROF_acc . . . ............ . . . . .. .. .... 4% ------------------------------------------------------------ ....,....25.1.,....26.1.,....27.1.,....28.1.,....29.1.,....3 AA KSKDAGTKLMGFSGRVKNPGLWELPFGTTAREILEDYAGGMRDGLKFKAWQPGGAGTDFL pH_sec .... 1.0 pH_sec ....... 0.9 pH_sec ....... 0.8 pH_sec ....... 0.7 pH_sec ........ 0.6 pH_sec ........ 0.5 pH_sec ........ . 0.4 pH_sec ......... ... 0.3 pH_sec .. .......... ...... ..... 0.2 ------------------------------------------------------------ pE_sec .. 1.0 pE_sec .... .. . 0.9 pE_sec ..... .. .. 0.8 pE_sec ........ .... .... 0.7 pE_sec ......... .... ..... 0.6 pE_sec ......... ..... ....... 0.5 pE_sec ........... ....... ....... 0.4 pE_sec ........... ....... .......... .. 0.3 pE_sec ....................... .. ................ 0.2 ------------------------------------------------------------ pL_sec 1.0 pL_sec ..... .. 0.9 pL_sec ...... .. ... ....... . . 0.8 pL_sec ....... .... .... ........ .... . 0.7 pL_sec ....... .... .... ........ ......... 0.6 pL_sec ....... ..... ..... ......... ......... 0.5 pL_sec ....... . ...... ..... ........... .......... 0.4 pL_sec ........ ......... ...... ............ .......... 0.3 pL_sec ......... .................. .......................... 0.2 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc . . 100% PROF_acc ... . . .. 81% PROF_acc ... . . . . .. 64% PROF_acc ...... ... .. . .. . 49% PROF_acc ...... . . .... . .. .. . ... . . 36% PROF_acc ........ . .... . .. .. .. ..... . 25% PROF_acc ........ . ..... . .. .. .. ..... . 16% PROF_acc ........ . ..... . .. .. .. ..... . 9% PROF_acc ........ . ..... . .. .. .......... 4% ------------------------------------------------------------ ....,....31.1.,....32.1.,....33.1.,....34.1.,....35.1.,....3 AA TEAHLDLPMEFESIGKAGSRLGTALAMAVDHEINMVSLVRNLEEFFARESCGWCTPCRDG pH_sec ..... 1.0 pH_sec . ........ 0.9 pH_sec .... ........... 0.8 pH_sec ...... ............. 0.7 pH_sec ...... ............... 0.6 pH_sec . ....... ............... 0.5 pH_sec .. ........ ................ .. 0.4 pH_sec .... .......... ................. .... 0.3 pH_sec ....... ........... ...................... ..... 0.2 ------------------------------------------------------------ pE_sec . 1.0 pE_sec ... 0.9 pE_sec .... 0.8 pE_sec ..... 0.7 pE_sec ..... 0.6 pE_sec ....... 0.5 pE_sec ....... 0.4 pE_sec .... ........ .. 0.3 pE_sec . ...... ............. . ..... . 0.2 ------------------------------------------------------------ pL_sec 1.0 pL_sec . .. 0.9 pL_sec . . . .... . ... 0.8 pL_sec .. ..... . ... .... .. .... .. 0.7 pL_sec ... ...... ....... ..... ........... 0.6 pL_sec .......... ........ ..... ............ 0.5 pL_sec ........... ........ ..... ............... 0.4 pL_sec ............. ........... ..... .................. 0.3 pL_sec .......................... ....... ................... 0.2 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc 100% PROF_acc .. . 81% PROF_acc .. . . . 64% PROF_acc .. . . . . . 49% PROF_acc .... . . . .. . .. . ... . 36% PROF_acc .... . . . .. . .. . .. . ... . . 25% PROF_acc ....... . . ... . ..... . .. . ... . .. 16% PROF_acc ....... ... ... . ..... . .. . ... . .. 9% PROF_acc ....... ... ... . ..... . .. . ... . .. 4% ------------------------------------------------------------ ....,....37.1.,....38.1.,....39.1.,....40.1.,....41.1.,....4 AA LPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQSAIKYFREEFE pH_sec ....... ....... ..... .... 1.0 pH_sec ......... .......... ....... ..... 0.9 pH_sec .......... .......... .............. 0.8 pH_sec .......... ............ .............. 0.7 pH_sec ........... .............. .............. 0.6 pH_sec ........... ............... . ................ 0.5 pH_sec ............ ................ . . .. ................ 0.4 pH_sec ............ ................ ........................ 0.3 pH_sec .............. ........................................... 0.2 ------------------------------------------------------------ pE_sec 1.0 pE_sec 0.9 pE_sec 0.8 pE_sec 0.7 pE_sec 0.6 pE_sec 0.5 pE_sec 0.4 pE_sec ... 0.3 pE_sec ...... .. 0.2 ------------------------------------------------------------ pL_sec ... 1.0 pL_sec .... . 0.9 pL_sec . .... . . 0.8 pL_sec . .... .... . . 0.7 pL_sec . ..... .... .. .... 0.6 pL_sec . ..... ..... ......... 0.5 pL_sec .. ........ ................ 0.4 pL_sec ... ........ ................. . 0.3 pL_sec ... .......... .................. ... 0.2 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc . . 100% PROF_acc .... 81% PROF_acc .... .. . . .. . . 64% PROF_acc . ........ . . . .. . . 49% PROF_acc . . . ........ .. .. . .. . .. .. . 36% PROF_acc . . .. ......... .. .. . .. . .. ... . 25% PROF_acc .. . .. ......... .. .. .. .... . .. ... . 16% PROF_acc .. . .. ......... .. .. .. .... . .. ... . 9% PROF_acc .. . .. ......... .. .. .. .... . .. ... . 4% ------------------------------------------------------------ ....,....43.1.,....44.1., AA AGIKQPFSNTHLINGIQPNLLKERW pH_sec . 1.0 pH_sec .. 0.9 pH_sec .. 0.8 pH_sec ... . 0.7 pH_sec .... ... 0.6 pH_sec .... .... 0.5 pH_sec .... ..... ...... 0.4 pH_sec ...... ...... ....... 0.3 pH_sec ....... ........ ....... 0.2 ------------------------- pE_sec 1.0 pE_sec 0.9 pE_sec 0.8 pE_sec 0.7 pE_sec 0.6 pE_sec 0.5 pE_sec 0.4 pE_sec . 0.3 pE_sec . ...... . 0.2 ------------------------- pL_sec . 1.0 pL_sec . . . 0.9 pL_sec .... .. . 0.8 pL_sec ...... ... .. 0.7 pL_sec ...... .... ... 0.6 pL_sec ................ .... 0.5 pL_sec ....................... 0.4 pL_sec ....................... 0.3 pL_sec ........................ 0.2 ------------------------- OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------- PROF_acc . . 100% PROF_acc ... .. . . .... 81% PROF_acc . ... .. .. .. .... 64% PROF_acc . ... ... .. ... .... 49% PROF_acc . .... ... .. ... .... 36% PROF_acc .. .... ... .. ... .... 25% PROF_acc .. ............ .... .... 16% PROF_acc .. ................. .... 9% PROF_acc .. ................. .... 4% -------------------------

Top - Summary - Details - PredictProtein

GLOBE prediction of globularity

--- 
--- GLOBE: prediction of protein globularity
--- 
--- nexp =   194    (number of predicted exposed residues)
--- nfit =   174    (number of expected exposed residues
--- diff =    20.00 (difference nexp-nfit)
--- =====> your protein appears as compact, as a globular domain
--- 
--- 
--- GLOBE: further explanations preliminaryily in:
---        http://cubic.bioc.columbia.edu/papers/1999_globe/paper.html
--- 
--- END of GLOBE

Ambivalent Sequence Predictor(Malin Young, Kent Kirshenbaum, Stefan Highsmith)

TOP - BOTTOM - A conformational switch prediction program



Ambivalent Sequence Predictor (ASP v1.0) mmy


Parameters:
	Window size	:	5
	Min mu dPr	:	9
	Z-score cutoff	:	-1.75

	Mean dPr score=13.250, Standard deviation=2.866


Please note: ASP was designed to identify the location of conformational 
switches in amino acid sequences. It is NOT designed to predict whether 
a given sequence does or does not contain a switch.  For best results,
ASP should be used on sequences of length >150 amino acids with >10 
sequence homologues in the SWISS-PROT data bank. 
ASP has been validated against a set of globular proteins and may not 
be generally applicable. Please see Young et al., Protein Science 
8(9):1852-64. 1999. for details and for how best to interpret this 
output.  We consider ASP to be experimental at this time, and would 
appreciate any feedback from our users.

END of results for file predict_h14099

Quotes for methods

PredictProtein: B Rost,G Yachdav and J Liu (2004) The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326.
- Author: B Rost
- Contact: yachdav@maple.bioc.columbia.edu
- URL: http://cubic.bioc.columbia.edu
- Version: 10.20.04
- Description: PredictProtein is the acronym for all prediction programs run.
PROSITE: A Bairoch, P Bucher & K Hofmann (1997) Nucleic Acids Research, 25:217-221
- Author: A Bairoch, bairoch@cmu.unige.ch P Bucher & K Hofmann
- Contact: bairoch@cmu.unige.ch
- URL: http://www.expasy.ch/prosite
- Version: 99.07
- Description: PROSITE is a database of functional motifs. ScanProsite, finds all functional motifs in your sequence that are annotated in the ProSite db.
SEG: J C Wootton & S Federhen (1996) Methods in Enzymology, 266:554-571
- Author: J C Wootton & S Federhen, wootton@ncbi.nlm.nih.gov
- Contact: rost@columbia.edu
- URL: wootton@ncbi.nlm.nih.gov
- Version: 1994
- Description: SEG divides sequences into regions of low-, and high-complexity. Low-complexity regions typically correspond to 'simple sequences' or 'compositionally-biased' regions.
ProDom: ELL Sonnhammer & D Kahn (1994) Protein Science, 3:482-492
- Author: LL Sonnhammer; J Gouzy, F Corpet, F Servant, D Kahn, dkahn@zyx.toulouse.inra.fr
- Contact: dkahn@zyx.toulouse.inra.fr
- URL: http://protein.toulouse.inra.fr/prodom.html
- Version: 2000.1
- Description: ProDom is a database of putative protein domains. The database is searched with BLAST for domains corresponding to your protein.
MaxHom: MaxHom: C Sander R Schneider (1991) Proteins, 9:56-68
- Author: C Sander & R Schneider, schneider@lion-ag.de
- Contact: schneider@lion-ag.de
- Version: 1.99.04
- Description: MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
MView: MView: N P Brown, C Leroy & C Sander (1998) Bioinformatics, 14:380-381
- Author: N Brown, nbrown@nimr.mrc.ac.uk
- URL: http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/
- Copyright: Copyright (C) Nigel P. Brown, 1997-1998. All rights reserved.
- Version: 1.40.2
- Description: MView is a program converting multiple sequence alignments into fancy HTML formatted output.
PHD: B Rost (1996) Methods in Enzymology, 266:525-539
- Author: B Rost
- Contact: rost@columbia.edu
- URL: http://cubic.bioc.columbia.edu
- Version: 1.96
- Description: PHD is a suite of programs predicting 1D structure (secondary structure, solvent accessibility) from multiple sequence alignments.
PHDsec: B Rost & C Sander (1993) J. of Molecular Biology, 232:584-599
- Author: B Rost
- Contact: rost@columbia.edu
- URL: http://cubic.bioc.columbia.edu
- Version: 1.96
- Description: PHDsec predicts secondary structure from multiple sequence alignments.
PHDacc: B Rost & C Sander (1994) Proteins, 20:216-226
- Author: B Rost
- Contact: rost@columbia.edu
- Version: 1.96
- Description: PHDacc predicts per residue solvent accessibility

Positions	Segments	Explain
1- 113	o1	outside region 1
114- 131	T1	?=error 1
132- 445	i1	inside region 1

%A: 8.5	%C: 2.0	%D: 3.8	%E: 8.5	%F: 4.3
%G: 10.8	%H: 1.6	%I: 4.9	%K: 5.6	%L: 10.8
%M: 2.7	%N: 4.5	%P: 5.6	%Q: 2.2	%R: 6.3
%S: 4.3	%T: 5.2	%V: 3.6	%W: 2.2	%Y: 2.5

prof_fpar	acc=/home/ppuser/server/pub/prof/net/PROFboth_best.par
prof_nnet	acc=6

N HTM	Total score	Best HTM	c-N
1	0.9679	0.7048	114 - 131

sec str type	H	E	L
% in protein	37.08	12.13	50.79

accessib type	b	e
% in protein	56.40	43.60