YRC Public Data Repository - Protein Structure Prediction

Protein:	SSRP_ECOLI
Organism:	Escherichia coli
Length:	160 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 SSRP_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|77958609, gi\|... - gi\|77958609\|ref\|ZP_00822640.1\| COG0691: tmRNA-binding protein [Yersinia bercovieri ATCC 43970], gi\|2...	257.0	[0..1]	[160..5]
gi\|238793792, gi... - gi\|77978429\|ref\|ZP_00833858.1\| COG0691: tmRNA-binding protein [Yersinia intermedia ATCC 29909], gi\|2...	257.0	[0..1]	[160..5]
gi\|204929524, gi... - gi\|204929524\|ref\|ZP_03220598.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Ja... gi\|197940299, gi... - gi\|198245783\|ref\|YP_002216696.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar D... gi\|197301208, gi... - gi\|197301208\|ref\|ZP_02664518.2\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Sc... gi\|195633702, gi... - gi\|195873630\|ref\|ZP_02698054.2\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Ne... gi\|161615620, gi... - gi\|161615620\|ref\|YP_001589585.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar P... gi\|62128891, gi\|... - gi\|62181258\|ref\|YP_217675.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Chole...	256.0	[0..1]	[160..16]
gi\|238796717, gi... - gi\|77963356\|ref\|ZP_00827166.1\| COG0691: tmRNA-binding protein [Yersinia mollaretii ATCC 43969], gi\|2...	256.0	[0..1]	[160..5]
SSRP_ECOL5 - SsrA-binding protein OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=smpB PE=3 SV=1	254.0	[0..1]	[160..1]
gi\|45440889, gi\|... - gi\|45440889\|ref\|NP_992428.1\| SsrA-binding protein [Yersinia pestis biovar Microtus str. 91001], gi\|4... gi\|108806576, gi... - gi\|108806576\|ref\|YP_650492.1\| SsrA-binding protein [Yersinia pestis Antiqua], gi\|108778489\|gb\|ABG125... gi\|89105214 - gi\|89105214\|ref\|ZP_01177738.1\| COG0691: tmRNA-binding protein [Yersinia pestis biovar Orientalis str... gi\|145211557, gi... - gi\|145599861\|ref\|YP_001163937.1\| SsrA-binding protein [Yersinia pestis Pestoides F], gi\|145211557\|gb... gi\|22126955, gi\|... - gi\|22126955\|ref\|NP_670378.1\| SsrA-binding protein [Yersinia pestis KIM], gi\|21959996\|gb\|AAM86629.1\|A... gi\|108813057, gi... - gi\|108813057\|ref\|YP_648824.1\| SsrA-binding protein [Yersinia pestis Nepal516], gi\|108776705\|gb\|ABG19... gi\|77632094, gi\|... - gi\|77632094\|ref\|ZP_00794680.1\| COG0691: tmRNA-binding protein [Yersinia pseudotuberculosis IP 31758]... gi\|170025202, gi... - gi\|170025202\|ref\|YP_001721707.1\| SsrA-binding protein [Yersinia pseudotuberculosis YPIII], gi\|169751... gi\|162354036, gi... - gi\|77636440\|ref\|ZP_00798514.1\| COG0691: tmRNA-binding protein [Yersinia pestis Angola], gi\|162421221... gi\|167057066, gi... - gi\|167424217\|ref\|ZP_02315970.1\| SsrA-binding protein [Yersinia pestis biovar Mediaevalis str. K19730... gi\|186894532, gi... - gi\|186894532\|ref\|YP_001871644.1\| SsrA-binding protein [Yersinia pseudotuberculosis PB1/+], gi\|186697...	253.0	[0..1]	[160..5]
SSRP_SALPC - SsrA-binding protein OS=Salmonella paratyphi C (strain RKS4594) GN=smpB PE=3 SV=1 gi\|213650040 - gi\|213650040\|ref\|ZP_03380093.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Ty... gi\|213424852 - gi\|213424852\|ref\|ZP_03357602.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Ty... SSRP_SALPB - SsrA-binding protein OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=smpB PE=3 SV=2 SSRP_SALPA - SsrA-binding protein OS=Salmonella paratyphi A GN=smpB PE=3 SV=1 SSRP_SALCH - SsrA-binding protein OS=Salmonella choleraesuis GN=smpB PE=3 SV=2 SSRP_SALTI - SsrA-binding protein OS=Salmonella typhi GN=smpB PE=3 SV=2 gi\|29143011, gi\|... - gi\|29143011\|ref\|NP_806353.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Typhi... gi\|16761540 - gi\|16761540\|ref\|NP_457157.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Typhi... SSRP_SALTI - SsrA-binding protein OS=Salmonella typhi GN=smpB PE=3 SV=2 SSRP_SALCH - SsrA-binding protein OS=Salmonella choleraesuis (strain SC-B67) GN=smpB PE=3 SV=2 SSRP_SALTY - SsrA-binding protein OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=smpB PE=3 SV... lcl\|NC_016856.1_... - [gene=smpB] [protein=SsrA-binding protein] [protein_id=YP_005238813.1] [location=2880401..2880883] SSRP_SALCH - SsrA-binding protein OS=Salmonella choleraesuis GN=smpB PE=3 SV=2 gi\|205331835, gi... - gi\|205331835\|gb\|EDZ18599.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Kentuc... gi\|238909530 - gi\|238909530\|ref\|ZP_04653367.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Te... gi\|205329322, gi... - gi\|205329322\|gb\|EDZ16086.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar 4,[5],... SSRP_SALPB - SsrA-binding protein OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=smpB PE=3 SV=2 gi\|205322056, gi... - gi\|205322056\|gb\|EDZ09895.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Saintp... SSRP_SALG2 - SsrA-binding protein OS=Salmonella gallinarum (strain 287/91 / NCTC 13346) GN=smpB PE=3 SV=1 gi\|200387705, gi... - gi\|200387705\|ref\|ZP_03214317.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Vi... SSRP_SALPK - SsrA-binding protein OS=Salmonella paratyphi A (strain AKU_12601) GN=smpB PE=3 SV=1 gi\|197241716, gi... - gi\|197263461\|ref\|ZP_03163535.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Sa... gi\|213416794 - gi\|213416794\|ref\|ZP_03349938.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Ty... gi\|213052721 - gi\|213052721\|ref\|ZP_03345599.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Ty... gi\|213027768 - gi\|213027768\|ref\|ZP_03342215.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Ty... SSRP_SALEP - SsrA-binding protein OS=Salmonella enteritidis PT4 (strain P125109) GN=smpB PE=3 SV=1 SSRP_SALNS - SsrA-binding protein OS=Salmonella newport (strain SL254) GN=smpB PE=3 SV=1 gi\|205340643, gi... - gi\|205340643\|gb\|EDZ27407.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Weltev... gi\|168262137, gi... - gi\|205349260\|gb\|EDZ35891.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Hadar ... gi\|168244713, gi... - gi\|205336461\|gb\|EDZ23225.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Heidel... SSRP_SALPA - SsrA-binding protein OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=smpB PE=3 SV=1 SSRP_SALA4 - SsrA-binding protein OS=Salmonella agona (strain SL483) GN=smpB PE=3 SV=1 SSRP_SALTY - SsrA-binding protein OS=Salmonella typhimurium GN=smpB PE=3 SV=2 SSRP_SALSV - SsrA-binding protein OS=Salmonella schwarzengrund (strain CVM19633) GN=smpB PE=3 SV=1 gi\|194456408, gi... - gi\|194470044\|ref\|ZP_03076028.1\| SsrA-binding protein [Salmonella enterica subsp. enterica serovar Ke... SSRP_SALTY - SsrA-binding protein OS=Salmonella typhimurium GN=smpB PE=3 SV=2 SSRP_SALHS - SsrA-binding protein OS=Salmonella heidelberg (strain SL476) GN=smpB PE=3 SV=1	251.0	[0..1]	[160..1]
gi\|115346880, gi... - gi\|218928269\|ref\|YP_002346144.1\| SsrA-binding protein [Yersinia pestis CO92], gi\|16121401\|ref\|NP_404... SSRP_YERPS - SsrA-binding protein OS=Yersinia pseudotuberculosis serotype I (strain IP32953) GN=smpB PE=3 SV=1 gi\|166962642, gi... - gi\|167419901\|ref\|ZP_02311654.1\| SsrA-binding protein [Yersinia pestis biovar Orientalis str. MG05-10... gi\|166207310, gi... - gi\|166211539\|ref\|ZP_02237574.1\| SsrA-binding protein [Yersinia pestis biovar Antiqua str. B42003004]... SSRP_YERPP - SsrA-binding protein OS=Yersinia pestis (strain Pestoides F) GN=smpB PE=3 SV=2 SSRP_YERPN - SsrA-binding protein OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=smpB PE=3 SV=2 SSRP_YERPA - SsrA-binding protein OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=smpB PE=3 SV=2 gi\|165989536, gi... - gi\|166011588\|ref\|ZP_02232486.1\| SsrA-binding protein [Yersinia pestis biovar Antiqua str. E1979001],... SSRP_YERPS - SsrA-binding protein OS=Yersinia pseudotuberculosis GN=smpB PE=3 SV=1 gi\|165913729, gi... - gi\|165938351\|ref\|ZP_02226909.1\| SsrA-binding protein [Yersinia pestis biovar Orientalis str. IP275],... gi\|165924594, gi... - gi\|165924594\|ref\|ZP_02220426.1\| SsrA-binding protein [Yersinia pestis biovar Orientalis str. F199101... gi\|149366899, gi... - gi\|149366899\|ref\|ZP_01888933.1\| SsrA-binding protein (small protein B) [Yersinia pestis CA88-4125], ... gi\|229841036, gi... - gi\|229841036\|ref\|ZP_04461195.1\| trans-translation protein [Yersinia pestis biovar Orientalis str. PE... SSRP_YERPE - SsrA-binding protein OS=Yersinia pestis GN=smpB PE=3 SV=3 gi\|229703863, gi... - gi\|229893978\|ref\|ZP_04509164.1\| trans-translation protein [Yersinia pestis Pestoides A], gi\|22970386... SSRP_YERP3 - SsrA-binding protein OS=Yersinia pseudotuberculosis serotype O:1b (strain IP 31758) GN=smpB PE=3 SV=... gi\|229689487, gi... - gi\|229843140\|ref\|ZP_04463286.1\| trans-translation protein [Yersinia pestis biovar Orientalis str. In...	250.0	[0..1]	[160..1]
gi\|188494999, gi... - gi\|75513225\|ref\|ZP_00735667.1\| COG0691: tmRNA-binding protein [Escherichia coli 53638], gi\|188494999...	250.0	[0..1]	[160..1]
SSRP_ERWCT - SsrA-binding protein OS=Erwinia carotovora subsp. atroseptica GN=smpB PE=3 SV=1 SSRP_PECAS - SsrA-binding protein OS=Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) GN=smpB PE=3 S...	250.0	[0..1]	[160..1]

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Predicted Domain #1

Region A:
Residues: [1-160]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTKKKAHKPG SATIALNKRA RHEYFIEEEF EAGLALQGWE VKSLRAGKAN ISDSYVLLRD  60
   61 GEAFLFGANI TPMAVASTHV VCDPTRTRKL LLNQRELDSL YGRVNREGYT VVALSLYWKN 120
  121 AWCKVKIGVA KGKKQHDKRS DIKEREWQVD KARIMKNAHR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	49.522879
Match:	1p6vA
Description:	Crystal structure of the tRNA domain of transfer-messenger RNA in complex with SmpB
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	3.32492468545684	bayes_pls_golite062009
binding	2.51918663753466	bayes_pls_golite062009
RNA binding	2.15601096339293	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: