YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24053639, gi\|...
Organism:	Shigella flexneri 2a str. 301
Length:	139 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|24053639, gi|....

Description	E-value	Query Range	Subject Range
RBFA_ECOUT - Ribosome-binding factor A OS=Escherichia coli (strain UTI89 / UPEC) GN=rbfA PE=3 SV=2 RBFA_ECOLC - Ribosome-binding factor A OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=rbfA PE=3 SV... RBFA_ECOL6 - Ribosome-binding factor A OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=rbfA PE=... EG11178 - 30s ribosome binding factor / Ribosome binding factor required for efficient processing of 16s rRNA;... RBFA_ECOK1 - Ribosome-binding factor A OS=Escherichia coli O1:K1 / APEC GN=rbfA PE=3 SV=1 gi\|124525925, gi... - gi\|124525925\|ref\|ZP_01697930.1\| ribosome-binding factor A [Escherichia coli B], gi\|124502029\|gb\|EAY4... RBFA_ECOLI - Ribosome-binding factor A (Protein P15B) - Escherichia coli gi\|30042766, gi\|... - gi\|30064507\|ref\|NP_838678.1\| ribosome-binding factor A [Shigella flexneri 2a str. 2457T], gi\|3004276... RBFA_ECO57 - Ribosome-binding factor A OS=Escherichia coli O157:H7 GN=rbfA PE=3 SV=2 EG11178 - 30s ribosome binding factor / Ribosome binding factor required for efficient processing of 16s rRNA;... gi\|15803709, gi\|... - gi\|15803709\|ref\|NP_289743.1\| ribosome-binding factor A [Escherichia coli O157:H7 EDL933], gi\|1251777... gi\|89109932, gi\|... - gi\|89109932\|ref\|AP_003712.1\| 30s ribosome binding factor [Escherichia coli str. K-12 substr. W3110],... gi\|56480279, gi\|... - gi\|56480279\|ref\|NP_708968.2\| ribosome-binding factor A [Shigella flexneri 2a str. 301], gi\|56383830\|... RBFA_SHIDS - Ribosome-binding factor A OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=rbfA PE=3 SV=1 RBFA_SHIBS - Ribosome-binding factor A OS=Shigella boydii serotype 4 (strain Sb227) GN=rbfA PE=3 SV=1 gi\|75239263, gi\|... - gi\|75239263\|ref\|ZP_00723234.1\| COG0858: Ribosome-binding factor A [Escherichia coli E110019], gi\|193... gi\|75240808, gi\|... - gi\|75240808\|ref\|ZP_00724706.1\| COG0858: Ribosome-binding factor A [Escherichia coli F11], gi\|1911722... gi\|75211118, gi\|... - gi\|75211118\|ref\|ZP_00711231.1\| COG0858: Ribosome-binding factor A [Escherichia coli B171], gi\|194427... gi\|75228774, gi\|... - gi\|75228774\|ref\|ZP_00715383.1\| COG0858: Ribosome-binding factor A [Escherichia coli B7A], gi\|1911680... RBFA_SHISS - Ribosome-binding factor A OS=Shigella sonnei (strain Ss046) GN=rbfA PE=3 SV=1 gi\|227887890, gi... - gi\|227887890\|ref\|ZP_04005695.1\| ribosome binding factor A [Escherichia coli 83972], gi\|227835286\|gb\|... RBFA_ECOL6 - Ribosome-binding factor A OS=Escherichia coli O6 GN=rbfA PE=3 SV=2 RBFA_ECOBW - Ribosome-binding factor A OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=rbfA PE=3 SV=1 gi\|193062103, gi... - gi\|75260097\|ref\|ZP_00731375.1\| COG0858: Ribosome-binding factor A [Escherichia coli E22], gi\|1930621... gi\|251786439, gi... - gi\|251786439\|ref\|YP_003000743.1\| hypothetical protein B21_02985 [Escherichia coli BL21], gi\|24237871... gi\|75513382, gi\|... - gi\|75513382\|ref\|ZP_00735806.1\| COG0858: Ribosome-binding factor A [Escherichia coli 53638], gi\|18849... gi\|253771997, gi... - gi\|254289861\|ref\|YP_003055609.1\| ribosome-binding factor A [Escherichia coli BL21(DE3)], gi\|25397916... gi\|253975012, gi... - gi\|254163111\|ref\|YP_003046219.1\| ribosome-binding factor A [Escherichia coli B str. REL606], gi\|2539... gi\|254594518, gi... - gi\|254795118\|ref\|YP_003079955.1\| 30s ribosome binding factor [Escherichia coli O157:H7 str. TW14359]... RBFA_ECO24 - Ribosome-binding factor A OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=rbfA PE=3 SV=1 RBFA_ECOHS - Ribosome-binding factor A OS=Escherichia coli O9:H4 (strain HS) GN=rbfA PE=3 SV=1 gi\|83585808, gi\|... - gi\|83585808\|ref\|ZP_00924449.1\| COG0858: Ribosome-binding factor A [Escherichia coli 101-1], gi\|19443... RBFA_SHIFL - Ribosome-binding factor A OS=Shigella flexneri GN=rbfA PE=3 SV=2 RBFA_SHIB3 - Ribosome-binding factor A OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=rbfA PE=3 S... RBFA_ECOSM - Ribosome-binding factor A OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=rbfA PE=3 SV=1 RBFA_ECODH - Ribosome-binding factor A OS=Escherichia coli (strain K12 / DH10B) GN=rbfA PE=3 SV=1 gi\|195938387 - gi\|195938387\|ref\|ZP_03083769.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC4024] gi\|194418048, gi... - gi\|194433785\|ref\|ZP_03066060.1\| ribosome-binding factor A [Shigella dysenteriae 1012], gi\|194418048\|... gi\|208814431, gi... - gi\|208814431\|ref\|ZP_03255760.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC4045], gi... gi\|208807175, gi... - gi\|208807175\|ref\|ZP_03249512.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC4206], gi... RBFA_ECO5E - Ribosome-binding factor A OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=rbfA PE=3 SV=1 gi\|208739563, gi... - gi\|208819440\|ref\|ZP_03259760.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC4042], gi... gi\|168754148, gi... - gi\|189358437\|gb\|EDU76856.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC4401], gi\|168... gi\|168749237, gi... - gi\|188016404\|gb\|EDU54526.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC4113], gi\|168... gi\|189361487, gi... - gi\|189361487\|gb\|EDU79906.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC4486], gi\|168... gi\|189367587, gi... - gi\|189367587\|gb\|EDU86003.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC4501], gi\|168... gi\|189001131, gi... - gi\|189001131\|gb\|EDU70117.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC4076], gi\|168... gi\|187770833, gi... - gi\|187770833\|gb\|EDU34677.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC4196], gi\|168... gi\|189379719, gi... - gi\|189379719\|gb\|EDU98135.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC508], gi\|1687... gi\|168786052, gi... - gi\|189373921\|gb\|EDU92337.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. EC869], gi\|1687... RBFA_ECOLU - Ribosome-binding factor A OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=rbfA PE=3 SV=1 gi\|13363521, gi\|... - gi\|15833302\|ref\|NP_312075.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. Sakai], gi\|133... gi\|217320105, gi... - gi\|217327738\|ref\|ZP_03443821.1\| ribosome-binding factor A [Escherichia coli O157:H7 str. TW14588], g... RBFA_ECOSE - Ribosome-binding factor A OS=Escherichia coli (strain SE11) GN=rbfA PE=3 SV=1 RBFA_ECO8A - Ribosome-binding factor A OS=Escherichia coli O8 (strain IAI1) GN=rbfA PE=3 SV=1 RBFA_ESCF3 - Ribosome-binding factor A OS=Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73) GN... RBFA_ECOL5 - Ribosome-binding factor A OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=rbfA PE=3 SV=1 RBFA_ECO81 - Ribosome-binding factor A OS=Escherichia coli O81 (strain ED1a) GN=rbfA PE=3 SV=1 RBFA_SHIF8 - Ribosome-binding factor A OS=Shigella flexneri serotype 5b (strain 8401) GN=rbfA PE=3 SV=1 RBFA_ECO45 - Ribosome-binding factor A OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=rbfA PE=3 SV=1 RBFA_ECO7I - Ribosome-binding factor A OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=rbfA PE=3 SV=1 RBFA_ECO55 - Ribosome-binding factor A OS=Escherichia coli (strain 55989 / EAEC) GN=rbfA PE=3 SV=1	168.0	[0..7]	[139..1]
RBFA_SALPA - Ribosome-binding factor A OS=Salmonella paratyphi A GN=rbfA PE=3 SV=1 gi\|238910080 - gi\|238910080\|ref\|ZP_04653917.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... gi\|214000925 - gi\|214000925\|ref\|ZP_03411660.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... RBFA_SALTI - Ribosome-binding factor A OS=Salmonella typhi GN=rbfA PE=3 SV=1 gi\|213980442 - gi\|213980442\|ref\|ZP_03407701.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... gi\|213852745 - gi\|213852745\|ref\|ZP_03382277.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... gi\|213646147 - gi\|213646147\|ref\|ZP_03376200.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... gi\|29143539, gi\|... - gi\|29143539\|ref\|NP_806881.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serovar ... gi\|16762050 - gi\|16762050\|ref\|NP_457667.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serovar ... RBFA_SALPC - Ribosome-binding factor A OS=Salmonella paratyphi C (strain RKS4594) GN=rbfA PE=3 SV=1 RBFA_SALCH - Ribosome-binding factor A OS=Salmonella choleraesuis (strain SC-B67) GN=rbfA PE=3 SV=1 RBFA_SALPA - Ribosome-binding factor A OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=rbfA PE=3 SV=1 RBFA_SALPB - Ribosome-binding factor A OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=rbfA PE=3 SV=1 RBFA_SALTI - Ribosome-binding factor A OS=Salmonella typhi GN=rbfA PE=3 SV=1 RBFA_SALCH - Ribosome-binding factor A OS=Salmonella choleraesuis GN=rbfA PE=3 SV=1 RBFA_SALPB - Ribosome-binding factor A OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=rbfA PE=3 SV=1 RBFA_SALCH - Ribosome-binding factor A OS=Salmonella choleraesuis GN=rbfA PE=3 SV=1 gi\|213052980 - gi\|213052980\|ref\|ZP_03345858.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... gi\|213029804 - gi\|213029804\|ref\|ZP_03344251.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... gi\|204928299, gi... - gi\|204928299\|ref\|ZP_03219499.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... RBFA_SALPK - Ribosome-binding factor A OS=Salmonella paratyphi A (strain AKU_12601) GN=rbfA PE=3 SV=1 gi\|213620436 - gi\|213620436\|ref\|ZP_03373262.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... gi\|213582314 - gi\|213582314\|ref\|ZP_03364140.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... gi\|213425435 - gi\|213425435\|ref\|ZP_03358185.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... gi\|213416951 - gi\|213416951\|ref\|ZP_03350095.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... RBFA_SALA4 - Ribosome-binding factor A OS=Salmonella agona (strain SL483) GN=rbfA PE=3 SV=1 gi\|205343329, gi... - gi\|205343329\|gb\|EDZ30093.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serovar W...	168.0	[0..7]	[139..1]
gi\|199604215, gi... - gi\|200387117\|ref\|ZP_03213729.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... RBFA_SALTY - Ribosome-binding factor A OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=rbfA PE... RBFA_SALDC - Ribosome-binding factor A OS=Salmonella dublin (strain CT_02021853) GN=rbfA PE=3 SV=1 gi\|194470716, gi... - gi\|194470716\|ref\|ZP_03076700.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serov... lcl\|NC_016856.1_... - [gene=rbfA] [protein=ribosome-binding factor A] [protein_id=YP_005239463.1] [location=complement(346... gi\|205333937, gi... - gi\|205333937\|gb\|EDZ20701.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serovar K... RBFA_SALTY - Ribosome-binding factor A OS=Salmonella typhimurium GN=rbfA PE=3 SV=1 RBFA_SALTY - Ribosome-binding factor A OS=Salmonella typhimurium GN=rbfA PE=3 SV=1 RBFA_SALEP - Ribosome-binding factor A OS=Salmonella enteritidis PT4 (strain P125109) GN=rbfA PE=3 SV=1 RBFA_SALG2 - Ribosome-binding factor A OS=Salmonella gallinarum (strain 287/91 / NCTC 13346) GN=rbfA PE=3 SV=1 gi\|167990150, gi... - gi\|205331145\|gb\|EDZ17909.1\| ribosome-binding factor A [Salmonella enterica subsp. enterica serovar 4...	167.0	[0..7]	[139..1]
gi\|49077912 - gi\|49077912\|gb\|AAT49730.1\| PA4743 [synthetic construct]	156.0	[0..7]	[136..1]
RBFA_PSEA8 - Ribosome-binding factor A OS=Pseudomonas aeruginosa (strain LESB58) GN=rbfA PE=3 SV=1 gi\|194555340, gi... - gi\|84323600\|ref\|ZP_00971669.1\| COG0858: Ribosome-binding factor A [Pseudomonas aeruginosa 2192], gi\|... gi\|107103842 - gi\|107103842\|ref\|ZP_01367760.1\| hypothetical protein PaerPA_01004913 [Pseudomonas aeruginosa PACS2]	155.0	[0..7]	[137..1]
RBFA_PSEAB - Ribosome-binding factor A OS=Pseudomonas aeruginosa (strain UCBPP-PA14) GN=rbfA PE=3 SV=1 RBFA_PSEAE - Ribosome-binding factor A OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 1... RBFA_PSEAE - Ribosome-binding factor A OS=Pseudomonas aeruginosa GN=rbfA PE=3 SV=1	155.0	[0..7]	[136..1]
gi\|22124603, gi\|... - gi\|22124603\|ref\|NP_668026.1\| ribosome-binding factor A [Yersinia pestis KIM], gi\|21957407\|gb\|AAM8427... gi\|45440442, gi\|... - gi\|45440442\|ref\|NP_991981.1\| ribosome-binding factor A [Yersinia pestis biovar Microtus str. 91001],...	155.0	[0..7]	[138..19]
RBFA_ERWCT - Ribosome-binding factor A OS=Erwinia carotovora subsp. atroseptica GN=rbfA PE=3 SV=1 RBFA_PECAS - Ribosome-binding factor A OS=Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) GN=rbfA P... gi\|254987507, gi... - gi\|255056670\|ref\|ZP_05308877.1\| ribosome-binding factor A [Pectobacterium wasabiae WPP163], gi\|25498...	155.0	[0..7]	[139..1]
RBFA_PASMU - Ribosome-binding factor A OS=Pasteurella multocida (strain Pm70) GN=rbfA PE=3 SV=1 RBFA_PASMU - Ribosome-binding factor A OS=Pasteurella multocida GN=rbfA PE=3 SV=1	154.0	[0..7]	[138..1]
gi\|213928496, gi... - gi\|213966646\|ref\|ZP_03394797.1\| ribosome-binding factor A [Pseudomonas syringae pv. tomato T1], gi\|2... RBFA_PSESM - Ribosome-binding factor A OS=Pseudomonas syringae pv. tomato GN=rbfA PE=3 SV=1 RBFA_PSESM - Ribosome-binding factor A OS=Pseudomonas syringae pv. tomato (strain DC3000) GN=rbfA PE=3 SV=1	153.0	[0..7]	[137..1]

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Predicted Domain #1

Region A:
Residues: [1-139]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSGEFIMAKE FGRPQRVAQE MQKEIALILQ REIKDPRLGM MTTVSGVEMS RDLAYAKVYV  60
   61 TFLNDKDEDA VKAGIKALQE ASGFIRSLLG KAMRLRIVPE LTFFYDNSLV EGMRMSNLVT 120
  121 SVVKHDEERR VNPDDSKED

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.0
Match:	1kkgA
Description:	Ribosome-binding factor A, RbfA
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	1.78763405231681	bayes_pls_golite062009
nucleic acid binding	0.83586229977035	bayes_pls_golite062009
catalytic activity	0.640244199484628	bayes_pls_golite062009
binding	0.519389427071401	bayes_pls_golite062009
rRNA binding	0.22053492547658	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: