YRC Public Data Repository - Protein Structure Prediction

Protein:	rim1
Organism:	Schizosaccharomyces pombe
Length:	150 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 rim1.

Description	E-value	Query Range	Subject Range
gi\|83648823, gi\|... - gi\|83648823\|ref\|YP_437258.1\| single-stranded DNA-binding protein [Hahella chejuensis KCTC 2396], gi\|...	163.0	[0..21]	[150..1]
SSB_CUPNH - Single-stranded DNA-binding protein OS=Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stan... SSB_ALCEU - (P59927) Single-strand binding protein (SSB) (Helix-destabilizing protein) SSB_RALEU - (P59927) Single-stranded DNA-binding protein (SSB) (Helix-destabilizing protein)	161.0	[0..21]	[149..1]
gi\|88818879, gi\|... - gi\|88858653\|ref\|ZP_01133294.1\| Single-strand binding protein (SSB) (Helix-destabilizing protein) [Ps...	160.0	[0..21]	[143..1]
gi\|88812721, gi\|... - gi\|88812721\|ref\|ZP_01127967.1\| Single-strand binding protein [Nitrococcus mobilis Nb-231], gi\|887899...	159.0	[0..21]	[149..1]
gi\|84780626, gi\|... - gi\|85060106\|ref\|YP_455808.1\| single-strand DNA-binding protein [Sodalis glossinidius str. 'morsitans...	159.0	[0..20]	[149..1]
gi\|194684063, gi... - gi\|197286576\|ref\|YP_002152448.1\| single-strand binding protein [Proteus mirabilis HI4320], gi\|194684... SSB_PROMI - Single-stranded DNA-binding protein OS=Proteus mirabilis GN=ssb PE=1 SV=2	159.0	[0..20]	[133..1]
gi\|3851548 - gi\|3851548\|gb\|AAC72352.1\| single strand DNA-binding protein; SSB [Vibrio cholerae]	159.0	[0..7]	[149..2]
SO4028 - single-strand binding protein SSB_SHEON - Single-stranded DNA-binding protein OS=Shewanella oneidensis (strain MR-1) GN=ssb PE=3 SV=1	158.0	[0..20]	[149..1]
gi\|77544340, gi\|... - gi\|77918257\|ref\|YP_356072.1\| ssDNA-binding protein [Pelobacter carbinolicus DSM 2380], gi\|77544340\|g...	158.0	[0..23]	[150..1]
gi\|207088673 - gi\|207088673\|gb\|EDZ65945.1\| single-strand binding protein [Nitrosococcus oceani AFC27] gi\|224409019, gi... - gi\|254435562\|ref\|ZP_05049069.1\| single-strand binding protein [Nitrosococcus oceani AFC27], gi\|22440... gi\|77166470, gi\|... - gi\|77166470\|ref\|YP_344995.1\| single-strand binding protein [Nitrosococcus oceani ATCC 19707], gi\|768...	158.0	[0..20]	[144..1]

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Predicted Domain #1

Region A:
Residues: [1-150]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLFLKSSRAF SKRLFSSSTV RYRDIQRLTL TGNLTKDVER LQSQKGNEYM RYTVASNNGK  60
   61 DVAPTFHSVY VFDSYNFDRL QTILRKGTRV YVEADAVWRS VPAGNEGSQA KMSLRHVSAD 120
  121 VLFYPRNKNG DESGEETHPE LDADPMINSF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	38.0
Match:	1kawA
Description:	ssDNA-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	2.69275272183315	bayes_pls_golite062009
single-stranded DNA binding	2.3572495084765	bayes_pls_golite062009
structure-specific DNA binding	2.34831682853439	bayes_pls_golite062009
binding	2.25744085310968	bayes_pls_golite062009
DNA binding	1.97161900822354	bayes_pls_golite062009
structural constituent of ribosome	1.39029069959347	bayes_pls_golite062009
structural molecule activity	1.10843643894126	bayes_pls_golite062009
nucleotidyltransferase activity	0.377540062296145	bayes_pls_golite062009
protein binding	0.360033745054291	bayes_pls_golite062009
ribonuclease activity	0.35415853560434	bayes_pls_golite062009
translation regulator activity	0.31332179848255	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.263197317040851	bayes_pls_golite062009
nuclease activity	0.192509675054684	bayes_pls_golite062009
transcription regulator activity	0.157816897728538	bayes_pls_golite062009
DNA-directed RNA polymerase activity	0.1542034177713	bayes_pls_golite062009
RNA polymerase activity	0.1542034177713	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: