YRC Public Data Repository - Protein Structure Prediction

Protein:	RS1_ECOLI
Organism:	Escherichia coli
Length:	557 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 RS1_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|67665375, gi\|... - gi\|67665375\|ref\|ZP_00462639.1\| Ribosomal protein S1 [Burkholderia cenocepacia HI2424], gi\|67101075\|g... gi\|67659525, gi\|... - gi\|67659525\|ref\|ZP_00456886.1\| Ribosomal protein S1 [Burkholderia cenocepacia AU 1054], gi\|67092904\|...	508.0	[0..2]	[556..77]
gi\|59480467, gi\|... - gi\|59712366\|ref\|YP_205142.1\| 30S ribosomal protein S1 [Vibrio fischeri ES114], gi\|59480467\|gb\|AAW862... gi\|197334803, gi... - gi\|197334803\|ref\|YP_002156581.1\| ribosomal protein S1 [Vibrio fischeri MJ11], gi\|197316293\|gb\|ACH657...	499.0	[0..1]	[557..1]
gi\|11275272 - pir\|\|B82141 ribosomal protein S1 VC1915 [imported] - Vibrio cholerae (strain N16961 serogroup O1) gi\|229337516, gi... - gi\|229523935\|ref\|ZP_04413340.1\| SSU ribosomal protein S1p [Vibrio cholerae bv. albensis VL426], gi\|2... gi\|229529059, gi... - gi\|229529059\|ref\|ZP_04418449.1\| SSU ribosomal protein S1p [Vibrio cholerae 12129(1)], gi\|229332833\|g... gi\|229607535, gi... - gi\|229607535\|ref\|YP_002878183.1\| SSU ribosomal protein S1p [Vibrio cholerae MJ-1236], gi\|229370190\|g... gi\|254844708, gi... - gi\|254849003\|ref\|ZP_05238353.1\| ribosomal protein S1 [Vibrio cholerae MO10], gi\|254844708\|gb\|EET2312... gi\|9656450, gi\|1... - gi\|9656450\|gb\|AAF95063.1\| ribosomal protein S1 [Vibrio cholerae O1 biovar El Tor str. N16961], gi\|15... gi\|197751726, gi... - gi\|254286724\|ref\|ZP_04961678.1\| ribosomal protein S1 [Vibrio cholerae AM-19226], gi\|197751726\|ref\|YP... gi\|227118363, gi... - gi\|75827237\|ref\|ZP_00756672.1\| COG0539: Ribosomal protein S1 [Vibrio cholerae O395], gi\|227118363\|re... gi\|227082045, gi... - gi\|227082045\|ref\|YP_002810596.1\| ribosomal protein S1 [Vibrio cholerae M66-2], gi\|227009933\|gb\|ACP06... gi\|229507989, gi... - gi\|229507989\|ref\|ZP_04397494.1\| SSU ribosomal protein S1p [Vibrio cholerae BX 330286], gi\|229355494\|... gi\|229515301, gi... - gi\|229515301\|ref\|ZP_04404761.1\| SSU ribosomal protein S1p [Vibrio cholerae TMA 21], gi\|229348006\|gb\|... gi\|229343600, gi... - gi\|229518911\|ref\|ZP_04408354.1\| SSU ribosomal protein S1p [Vibrio cholerae RC9], gi\|229343600\|gb\|EEO... gi\|229521837, gi... - gi\|229521837\|ref\|ZP_04411254.1\| SSU ribosomal protein S1p [Vibrio cholerae TM 11079-80], gi\|22934076...	496.0	[0..1]	[557..1]
gi\|67531905, gi\|... - gi\|67546802\|ref\|ZP_00424712.1\| Ribosomal protein S1 [Burkholderia vietnamiensis G4], gi\|67531905\|gb\|...	496.0	[0..2]	[556..36]
gi\|50121515, gi\|... - gi\|50121515\|ref\|YP_050682.1\| 30S ribosomal protein S1 [Pectobacterium atrosepticum SCRI1043], gi\|496...	495.0	[0..1]	[557..1]
gi\|27366257, gi\|... - gi\|27366257\|ref\|NP_761785.1\| 30S ribosomal protein S1 [Vibrio vulnificus CMCP6], gi\|27362458\|gb\|AAO1...	494.0	[0..1]	[557..1]
gi\|28807023 - gi\|28807023\|dbj\|BAC60293.1\| ribosomal protein S1 [Vibrio parahaemolyticus RIMD 2210633] gi\|28898804, gi\|... - gi\|28898804\|ref\|NP_798409.1\| 30S ribosomal protein S1 [Vibrio parahaemolyticus RIMD 2210633], gi\|288...	493.0	[0..1]	[557..1]
gi\|37198228, gi\|... - gi\|37679484\|ref\|NP_934093.1\| 30S ribosomal protein S1 [Vibrio vulnificus YJ016], gi\|37198228\|dbj\|BAC...	493.0	[0..1]	[557..1]
gi\|78700811, gi\|... - gi\|78700811\|ref\|ZP_00865266.1\| Ribosomal protein S1 [Alkalilimnicola ehrlichei MLHE-1], gi\|78521841\|...	492.0	[0..1]	[557..1]
gi\|56475922, gi\|... - gi\|56475922\|ref\|YP_157511.1\| 30S ribosomal protein S1 [Azoarcus sp. EbN1], gi\|56311965\|emb\|CAI06610....	492.0	[0..3]	[557..34]

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Predicted Domain #1

Region A:
Residues: [1-274]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTESFAQLFE ESLKEIETRP GSIVRGVVVA IDKDVVLVDA GLKSESAIPA EQFKNAQGEL  60
   61 EIQVGDEVDV ALDAVEDGFG ETLLSREKAK RHEAWITLEK AYEDAETVTG VINGKVKGGF 120
  121 TVELNGIRAF LPGSLVDVRP VRDTLHLEGK ELEFKVIKLD QKRNNVVVSR RAVIESENSA 180
  181 ERDQLLENLQ EGMEVKGIVK NLTDYGAFVD LGGVDGLLHI TDMAWKRVKH PSEIVNVGDE 240
  241 ITVKVLKFDR ERTRVSLGLK QLGEDPWVAI AKRY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	38.154902
Match:	2oceA
Description:	No description for 2oceA was found.

Predicted functions:

Term	Confidence	Notes
structural constituent of ribosome	7.45319063235379	bayes_pls_golite062009
structural molecule activity	6.87843523680097	bayes_pls_golite062009
nucleic acid binding	2.61313484113692	bayes_pls_golite062009
DNA binding	1.87254683997276	bayes_pls_golite062009
binding	1.81248034004657	bayes_pls_golite062009
RNA binding	1.76502371106766	bayes_pls_golite062009
translation regulator activity	1.46320772716954	bayes_pls_golite062009
translation factor activity, nucleic acid binding	1.40718318783582	bayes_pls_golite062009
endodeoxyribonuclease activity	1.40144679199104	bayes_pls_golite062009
translation initiation factor activity	1.27539679024898	bayes_pls_golite062009
deoxyribonuclease activity	1.08938787733248	bayes_pls_golite062009
structure-specific DNA binding	0.83151863389272	bayes_pls_golite062009
endonuclease activity	0.795396479988128	bayes_pls_golite062009
excinuclease ABC activity	0.78903017411423	bayes_pls_golite062009
single-stranded DNA binding	0.72238927168323	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.562603623565981	bayes_pls_golite062009
exoribonuclease activity	0.51569543713363	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	0.474251377131502	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	0.47336621289748	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	0.47336621289748	bayes_pls_golite062009
3'-5' exonuclease activity	0.32253752994732	bayes_pls_golite062009
3'-5'-exoribonuclease activity	0.22548557495593	bayes_pls_golite062009
transcription regulator activity	0.0185639841733248	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [275-438]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PEGTKLTGRV TNLTDYGCFV EIEEGVEGLV HVSEMDWTNK NIHPSKVVNV GDVVEVMVLD  60
   61 IDEERRRISL GLKQCKANPW QQFAETHNKG DRVEGKIKSI TDFGIFIGLD GGIDGLVHLS 120
  121 DISWNVAGEE AVREYKKGDE IAAVVLQVDA ERERISLGVK QLAE

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	4.44
Match:	1q46A
Description:	crystal structure of the eIF2 alpha subunit from saccharomyces cerevisia
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
structural constituent of ribosome	7.25865887570075	bayes_pls_golite062009
structural molecule activity	6.71426355916788	bayes_pls_golite062009
nucleic acid binding	2.40696086435588	bayes_pls_golite062009
binding	1.72974613190175	bayes_pls_golite062009
DNA binding	1.70531530032581	bayes_pls_golite062009
RNA binding	1.63018000615308	bayes_pls_golite062009
translation regulator activity	1.22002670068528	bayes_pls_golite062009
translation factor activity, nucleic acid binding	1.16348298918189	bayes_pls_golite062009
translation initiation factor activity	0.994761133382189	bayes_pls_golite062009
structure-specific DNA binding	0.518801208827569	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	0.369610293193347	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	0.368886987688918	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	0.368886987688918	bayes_pls_golite062009
single-stranded DNA binding	0.347963475301706	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.262871056043292	bayes_pls_golite062009
exoribonuclease activity	0.218369788111831	bayes_pls_golite062009
3'-5' exonuclease activity	0.0741372160493743	bayes_pls_golite062009
transcription regulator activity	0.0490728527880692	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [439-557]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DPFNNWVALN KKGAIVTGKV TAVDAKGATV ELADGVEGYL RASEASRDRV EDATLVLSVG  60
   61 DEVEAKFTGV DRKNRAISLS VRAKDEADEK DAIATVNKQE DANFSNNAMA EAFKAAKGE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	18.221849
Match:	1yz6A
Description:	Crystal structure of intact alpha subunit of aIF2 from Pyrococcus abyssi
Matching Structure (courtesy of the PDB):

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:

Predicted functions: