YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|241907414, gi...
Organism:	Desulfovibrio vulgaris RCH1
Length:	397 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for gi|241907414, gi....

Description	E-value	Query Range	Subject Range
gi\|190902162, gi... - gi\|75229050\|ref\|ZP_00715634.1\| COG0582: Integrase [Escherichia coli B7A], gi\|191167819\|ref\|ZP_030296...	3.0E-68	[2..393]	[3..392]
gi\|77962153, gi\|... - gi\|77962153\|ref\|ZP_00825977.1\| COG0582: Integrase [Yersinia mollaretii ATCC 43969], gi\|238795435\|ref...	3.0E-67	[2..393]	[3..392]
gi\|77974232, gi\|... - gi\|77974232\|ref\|ZP_00829773.1\| COG0582: Integrase [Yersinia frederiksenii ATCC 33641], gi\|238790928\|...	3.0E-67	[2..390]	[3..389]
gi\|253975488, gi... - gi\|254163587\|ref\|YP_003046695.1\| Int [Escherichia coli B str. REL606], gi\|253975488\|gb\|ACT41159.1\| I... gi\|194435929, gi... - gi\|83588494\|ref\|ZP_00927118.1\| COG0582: Integrase [Escherichia coli 101-1], gi\|194435929\|ref\|ZP_0306... gi\|57545625 - gi\|57545625\|gb\|AAW51716.1\| Int [Escherichia coli] gi\|26250313, gi\|... - gi\|26250313\|ref\|NP_756353.1\| putative prophage integrase [Escherichia coli CFT073], gi\|26110743\|gb\|A... gi\|251786909, gi... - gi\|251786909\|ref\|YP_003001213.1\| hypothetical protein B21_03468 [Escherichia coli BL21], gi\|24237918... gi\|254290337, gi... - gi\|254290337\|ref\|YP_003056085.1\| Int [Escherichia coli BL21(DE3)], gi\|253979644\|gb\|ACT45314.1\| Int [...	3.0E-67	[2..394]	[3..393]
gi\|14252927 - gi\|14252927\|emb\|CAC39282.1\| integrase [Escherichia coli]	5.0E-67	[2..394]	[3..393]
gi\|75194504, gi\|... - gi\|75194504\|ref\|ZP_00704574.1\| COG0582: Integrase [Escherichia coli HS], gi\|157159783\|ref\|YP_0014571...	6.0E-67	[2..393]	[3..392]
gi\|24114927, gi\|... - gi\|24114927\|ref\|NP_709437.1\| putative integrase [Shigella flexneri 2a str. 301], gi\|24054171\|gb\|AAN4... gi\|30065067, gi\|... - gi\|30065067\|ref\|NP_839238.1\| putative integrase [Shigella flexneri 2a str. 2457T], gi\|30043328\|gb\|AA... gi\|5880470 - gi\|5880470\|gb\|AAD54663.1\|AF097520_1 Sai integrase [Shigella flexneri]	1.0E-66	[2..394]	[12..402]
gi\|74314106, gi\|... - gi\|74314106\|ref\|YP_312525.1\| putative integrase [Shigella sonnei Ss046], gi\|73857583\|gb\|AAZ90290.1\| ...	1.0E-66	[2..394]	[3..393]
gi\|110617213, gi... - gi\|110807665\|ref\|YP_691185.1\| putative integrase [Shigella flexneri 5 str. 8401], gi\|110617213\|gb\|AB... gi\|11278380, gi\|... - gi\|5532446\|gb\|AAD44730.1\|AF141323_1 Int [Shigella flexneri], pir\|\|T44463 integrase int [imported] - ...	2.0E-66	[2..394]	[3..393]
gi\|186700420, gi... - gi\|186897394\|ref\|YP_001874506.1\| integrase family protein [Yersinia pseudotuberculosis PB1/+], gi\|18... gi\|51591453, gi\|... - gi\|51598171\|ref\|YP_072362.1\| putative integrase [Yersinia pseudotuberculosis IP 32953], gi\|51591453\|... Q663Y8\|Q663Y8_YERPS - Putative integrase - Yersinia pseudotuberculosis	8.0E-66	[2..394]	[3..393]

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Predicted Domain #1

Region A:
Residues: [1-397]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLTDIKARAA KPAEKVYRLY DGGGMYLEVP PSGNKRWRLK YRVNGKEKRL SLGVYPNVGL  60
   61 KEAREKRDEL RRLIAEGIDP AAQRCPQKVA PTADSFEMVA REWMDLRSPA WAPRHLSTTC 120
  121 QRLEAYIFPH IGPLPIDQIG PLDVLNALRI VEKRGAVEAA RKTLSICSQV FRYAVASARI 180
  181 QSDPCRDLRG ALKTRQPGHY AAIVDPKDVG ALMRAIDGYS GAMVVRCALR FLALTFVRPG 240
  241 ELRAAEWNEF DMERRIWTIP AHKMKKRREH IVPLSTQALA VLRDVRATAP RLNSPMVFQS 300
  301 VRLRSDRGLS ENTLLVALRS LGYGQGTMTA HGFRAMASSL LNGLGYNPDV IERQLAHIEG 360
  361 NKIRAAYHRT EYLEERTAMM QAYADYLDSL RDSMPPR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	30.0
Match:	1z1bA
Description:	Crystal structure of a lambda integrase dimer bound to a COC' core site
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
structure-specific DNA binding	2.96794540657137	bayes_pls_golite062009
chromatin binding	2.66956311972752	bayes_pls_golite062009
catalytic activity	1.85476765215403	bayes_pls_golite062009
double-stranded DNA binding	1.47056442077417	bayes_pls_golite062009
DNA binding	1.08208472364243	bayes_pls_golite062009
nucleic acid binding	1.01945666037816	bayes_pls_golite062009
sequence-specific DNA binding	0.88630365094839	bayes_pls_golite062009
binding	0.849061082531999	bayes_pls_golite062009
methyl-CpG binding	0.644006146507516	bayes_pls_golite062009
transcription regulator activity	0.433129028335043	bayes_pls_golite062009
protein binding	0.391840757563427	bayes_pls_golite062009
DNA secondary structure binding	0.32168641878414	bayes_pls_golite062009
transcription factor activity	0.135216468398819	bayes_pls_golite062009
transcription factor binding	0.0858654055973298	bayes_pls_golite062009
four-way junction DNA binding	0.0788334929658094	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: