YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24374538, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	419 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|24374538, gi|....

Description	E-value	Query Range	Subject Range
gi\|28872456, gi\|... - gi\|28872456\|ref\|NP_795075.1\| phage integrase family site specific recombinase [Pseudomonas syringae ... tr\|Q87UF4\|Q87UF4... - Site-specific recombinase, phage integrase family OS=Pseudomonas syringae pv. tomato (strain DC3000)...	226.0	[0..1]	[417..1]
gi\|67156550 - gi\|67156550\|ref\|ZP_00418143.1\| Phage integrase [Azotobacter vinelandii AvOP] gi\|67156550, gi\|... - gi\|67156550\|ref\|ZP_00418143.1\| Phage integrase [Azotobacter vinelandii AvOP], gi\|67086309\|gb\|EAM0577...	224.0	[0..1]	[418..1]
gi\|77974232, gi\|... - gi\|77974232\|ref\|ZP_00829773.1\| COG0582: Integrase [Yersinia frederiksenii ATCC 33641], gi\|238790928\|...	219.0	[0..1]	[412..1]
gi\|75194504, gi\|... - gi\|75194504\|ref\|ZP_00704574.1\| COG0582: Integrase [Escherichia coli HS], gi\|157159783\|ref\|YP_0014571...	217.0	[0..1]	[402..1]
gi\|77962153, gi\|... - gi\|77962153\|ref\|ZP_00825977.1\| COG0582: Integrase [Yersinia mollaretii ATCC 43969], gi\|238795435\|ref...	217.0	[0..1]	[405..1]
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 [...	216.0	[0..1]	[408..1]
gi\|14252927 - gi\|14252927\|emb\|CAC39282.1\| integrase [Escherichia coli]	216.0	[0..1]	[408..1]
gi\|190902162, gi... - gi\|75229050\|ref\|ZP_00715634.1\| COG0582: Integrase [Escherichia coli B7A], gi\|191167819\|ref\|ZP_030296...	216.0	[0..1]	[408..1]
gi\|126194866, gi... - gi\|254241488\|ref\|ZP_04934810.1\| hypothetical protein PA2G_02184 [Pseudomonas aeruginosa 2192], gi\|19... gi\|24461523 - gi\|24461523\|gb\|AAN62094.1\|AF440523_1 putative integrase [Pseudomonas aeruginosa]	215.0	[0..1]	[417..1]
gi\|74314106, gi\|... - gi\|74314106\|ref\|YP_312525.1\| putative integrase [Shigella sonnei Ss046], gi\|73857583\|gb\|AAZ90290.1\| ...	215.0	[0..1]	[408..1]

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Predicted Domain #1

Region A:
Residues: [1-419]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MALSDSWLKA NLNKVADKPY EKADRDGLSV RVSAKGAITF QMRYRWASNA ARVDIGPYPL  60
   61 LSLKEAREQC EAYRKLLLDN QDPREYKRDK AAKAVSNEGS VEQVFRAWHK SQFSDGRASV 120
  121 KDSTAHEYLR ALEINVFPVL GKKQVDQVTL HQWLDLFESI AAKKPTITNL TLTVSRRALK 180
  181 WAVRRRIIST NELMGIESKE DLNISRKSRK RTLSDDELKI ILQAIDNAKR QRLGNRIMVF 240
  241 MALFFGCRIG ELRLAQKAHF DFTKMIWTVP VENHKTGYKM QRPLLRPIID EIVPLLELAF 300
  301 SLSPNELVFP TEKGGIYSQA ATTRMSNPIN TWAKLNGTPL NEWYLHDLRR TQRTNMSKIT 360
  361 TTEVAETMLG HKLSGIQSIY DHYDYLEEQA KAYRIWWQKL QRLKDPAAYH NVVELKAAQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	24.0
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: