YRC Public Data Repository - Protein Structure Prediction

Protein:	SO1471
Organism:	Shewanella oneidensis
Length:	415 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 SO1471.

Description	E-value	Query Range	Subject Range
gi\|77974232, gi\|... - gi\|77974232\|ref\|ZP_00829773.1\| COG0582: Integrase [Yersinia frederiksenii ATCC 33641], gi\|238790928\|...	274.0	[0..6]	[398..1]
gi\|77962153, gi\|... - gi\|77962153\|ref\|ZP_00825977.1\| COG0582: Integrase [Yersinia mollaretii ATCC 43969], gi\|238795435\|ref...	273.0	[0..6]	[399..1]
INTA_ECOLI - Prophage CP4-57 integrase - Escherichia coli EG11783 - CP4-57 prophage; integrase / Integrase gene, CP4-57 putative defective prophage gi\|89109421, gi\|... - gi\|89109421\|ref\|AP_003201.1\| integrase [Escherichia coli str. K-12 substr. W3110], gi\|85675485\|dbj\|B... gi\|238901780, gi... - gi\|238901780\|ref\|YP_002927576.1\| CP4-57 prophage; integrase [Escherichia coli BW2952], gi\|238860623\|... EG11783 - CP4-57 prophage; integrase / Integrase gene, CP4-57 putative defective prophage	273.0	[0..1]	[413..1]
gi\|9655299, gi\|1... - gi\|9655299\|gb\|AAF94009.1\| integrase, phage family [Vibrio cholerae O1 biovar El Tor str. N16961], gi... gi\|1100883, gi\|4... - gi\|498253\|gb\|AAC44230.1\| integrase, gi\|13377568\|gb\|AAK20803.1\|AF325734_29 integrase [Vibrio cholerae... gi\|229344622, gi... - gi\|229517907\|ref\|ZP_04407351.1\| phage integrase [Vibrio cholerae RC9], gi\|229344622\|gb\|EEO09596.1\| p... gi\|498253, gi\|14... - gi\|498253\|gb\|AAC44230.1\| integrase, gi\|227117217\|ref\|YP_002819113.1\| integrase, phage family [Vibrio... gi\|121550043, gi... - gi\|121585680\|ref\|ZP_01675475.1\| integrase, phage family [Vibrio cholerae 2740-80], gi\|121550043\|gb\|E... gi\|153224615, gi... - gi\|153224615\|ref\|ZP_01954522.1\| integrase, phage family [Vibrio cholerae MAK 757], gi\|124117544\|gb\|E... gi\|121631470, gi... - gi\|121725988\|ref\|ZP_01679287.1\| integrase, phage family [Vibrio cholerae V52], gi\|121631470\|gb\|EAX63... gi\|153818037, gi... - gi\|153818037\|ref\|ZP_01970704.1\| integrase, phage family [Vibrio cholerae NCTC 8457], gi\|126511383\|gb... gi\|254843689, gi... - gi\|254847984\|ref\|ZP_05237334.1\| integrase [Vibrio cholerae MO10], gi\|254843689\|gb\|EET22103.1\| integr... gi\|227081023, gi... - gi\|227081023\|ref\|YP_002809574.1\| integrase, phage family [Vibrio cholerae M66-2], gi\|227008911\|gb\|AC... gi\|229350751, gi... - gi\|229510786\|ref\|ZP_04400265.1\| phage integrase [Vibrio cholerae B33], gi\|229350751\|gb\|EEO15692.1\| p... gi\|229357766, gi... - gi\|229505543\|ref\|ZP_04395053.1\| phage integrase [Vibrio cholerae BX 330286], gi\|229357766\|gb\|EEO2268...	272.0	[0..1]	[405..1]
gi\|37197485, gi\|... - gi\|37678744\|ref\|NP_933353.1\| phage integrase [Vibrio vulnificus YJ016], gi\|37197485\|dbj\|BAC93324.1\| ...	272.0	[0..1]	[406..1]
tr\|D7HF28\|D7HF28... - Integrase OS=Vibrio cholerae RC385 GN=VCRC385_00574 PE=4 SV=1 gi\|150421294, gi... - gi\|75822961\|ref\|ZP_00752506.1\| COG0582: Integrase [Vibrio cholerae RC385], gi\|254222126\|ref\|ZP_04915...	271.0	[0..1]	[413..1]
gi\|127512199, gi... - gi\|78366488\|ref\|ZP_00836768.1\| Phage integrase [Shewanella sp. PV-4], gi\|78361533\|gb\|EAP03357.1\| Pha...	269.0	[0..1]	[403..1]
gi\|75194504, gi\|... - gi\|75194504\|ref\|ZP_00704574.1\| COG0582: Integrase [Escherichia coli HS], gi\|157159783\|ref\|YP_0014571...	269.0	[0..6]	[407..1]
gi\|82496810, gi\|... - gi\|82496810\|ref\|ZP_00882374.1\| phage integrase [Shewanella sp. MR-4], gi\|82405219\|gb\|EAP45895.1\| pha...	269.0	[0..1]	[410..1]
gi\|78685056, gi\|... - gi\|78685056\|ref\|ZP_00849837.1\| phage integrase [Shewanella sp. ANA-3], gi\|78507280\|gb\|EAP20792.1\| ph...	268.0	[0..1]	[410..1]

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Predicted Domain #1

Region A:
Residues: [1-415]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MARLTKPLSD TEIKTAKPKD KEYNLADGGG LQIRIKPNGS KLWLLNYSHP ITKKRQNLSL  60
   61 GTYPDISLLS ARKLAQEART LLAHGTDPKA HREAQIAAKA AIIEHTFGKI AAEWFERKKD 120
  121 EVTEDHAAAT WRSFKLHLLP SLKDIPISQI TAPMVIEFLR PIEAKGNLET VKRLTQRLNE 180
  181 VMIYAVNTGL IHANPLSGIK AIFKKPRKEH LAALKPDELP ELMQAIANAS IKKVTRFLIE 240
  241 WQLHTMTRPN EAAAARWDEI NFDERIWLIP AARMKMRRDH QIPLTEQTLA LLAAIKPISG 300
  301 HREYIFPADR DPKTHSNVQT ANAALKRMGL KDRTTAHGFR SLASTTLNEQ GFDPDVIEAA 360
  361 LAHTDKNQVR SAYNRSIYLD RRREMMTWWS NYIVEAAKGN VSLAHNARNL RLVAQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	25.221849
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: