YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24372001, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	421 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|24372001, gi|....

Description	E-value	Query Range	Subject Range
gi\|124498664, gi... - gi\|124531287\|ref\|ZP_01701623.1\| transcription termination factor Rho [Escherichia coli B], gi\|124498... gi\|117626043, gi... - gi\|117626043\|ref\|YP_859366.1\| transcription termination factor Rho [Escherichia coli APEC O1], gi\|11... gi\|110644109, gi... - gi\|110644109\|ref\|YP_671839.1\| transcription termination factor Rho [Escherichia coli 536], gi\|110345... tr\|A0A0G3HTJ8\|A0... - Transcription termination factor Rho OS=Escherichia coli (strain K12) GN=rho PE=3 SV=2 gi\|91074878, gi\|... - gi\|91213304\|ref\|YP_543290.1\| transcription termination factor Rho [Escherichia coli UTI89], gi\|91074... gi\|26110951, gi\|... - gi\|26250521\|ref\|NP_756561.1\| transcription termination factor Rho [Escherichia coli CFT073], gi\|2611... gi\|237702792, gi... - gi\|237702792\|ref\|ZP_04533273.1\| transcription termination factor rho [Escherichia sp. 3_2_53FAA], gi... gi\|24115076, gi\|... - ref\|NP_709586.1\| transcription termination factor Rho [Shigella flexneri 2a str. 301], gb\|AAN45293.... gi\|226838685, gi... - gi\|254038994\|ref\|ZP_04873045.1\| transcription termination factor rho [Escherichia sp. 1_1_43], gi\|22... gi\|110617076, gi... - gi\|110807528\|ref\|YP_691048.1\| transcription termination factor Rho [Shigella flexneri 5 str. 8401], ...	535.0	[0..1]	[418..25]
RHO_ECOL6 - Transcription termination factor Rho OS=Escherichia coli O6 GN=rho PE=3 SV=1 gi\|75512657, gi\|... - gi\|75512657\|ref\|ZP_00735169.1\| COG1158: Transcription termination factor [Escherichia coli 53638], g... gi\|73857774, gi\|... - gi\|74314297\|ref\|YP_312716.1\| transcription termination factor Rho [Shigella sonnei Ss046], gi\|738577... gi\|190905288, gi... - gi\|75236536\|ref\|ZP_00720626.1\| COG1158: Transcription termination factor [Escherichia coli F11], gi\|... gi\|75255787, gi\|... - gi\|75255787\|ref\|ZP_00727541.1\| COG1158: Transcription termination factor [Escherichia coli E22], gi\|... gi\|85676265, gi\|... - gi\|89110234\|ref\|AP_004014.1\| transcription termination factor [Escherichia coli str. K-12 substr. W3... gi\|56383986, gi\|... - gi\|56480435\|ref\|NP_709586.2\| transcription termination factor Rho [Shigella flexneri 2a str. 301], g... gi\|82779036, gi\|... - gi\|82779036\|ref\|YP_405385.1\| transcription termination factor Rho [Shigella dysenteriae Sd197], gi\|8... gi\|81247548, gi\|... - gi\|82546137\|ref\|YP_410084.1\| transcription termination factor Rho [Shigella boydii Sb227], gi\|812475... gi\|187429447, gi... - gi\|75177653\|ref\|ZP_00697718.1\| COG1158: Transcription termination factor [Shigella boydii BS512], gi... gi\|157077943, gi... - gi\|75188529\|ref\|ZP_00701796.1\| COG1158: Transcription termination factor [Escherichia coli E24377A],... gi\|194417149, gi... - gi\|83569038\|ref\|ZP_00920500.1\| COG1158: Transcription termination factor [Shigella dysenteriae 1012]... gi\|194438677, gi... - gi\|83585965\|ref\|ZP_00924604.1\| COG1158: Transcription termination factor [Escherichia coli 101-1], g... gi\|191166125, gi... - gi\|75230748\|ref\|ZP_00717211.1\| COG1158: Transcription termination factor [Escherichia coli B7A], gi\|... gi\|192955625, gi... - gi\|75234077\|ref\|ZP_00718490.1\| COG1158: Transcription termination factor [Escherichia coli E110019],... gi\|157068936, gi... - gi\|75197670\|ref\|ZP_00707740.1\| COG1158: Transcription termination factor [Escherichia coli HS], gi\|1... gi\|75208997, gi\|... - gi\|75208997\|ref\|ZP_00709261.1\| COG1158: Transcription termination factor [Escherichia coli B171], gi... gi\|218434516, gi... - gi\|218707419\|ref\|YP_002414938.1\| transcription termination factor Rho [Escherichia coli UMN026], gi\|... gi\|189365819, gi... - gi\|189365819\|gb\|EDU84235.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. EC45... gi\|168753676, gi... - gi\|189359221\|gb\|EDU77640.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. EC44... gi\|168775670, gi... - gi\|187768863\|gb\|EDU32707.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. EC41... gi\|168768060, gi... - gi\|189362557\|gb\|EDU80976.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. EC44... gi\|168786617, gi... - gi\|189373337\|gb\|EDU91753.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. EC86... gi\|189001536, gi... - gi\|189001536\|gb\|EDU70522.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. EC40... gi\|170022190, gi... - gi\|170022190\|ref\|YP_001727144.1\| transcription termination factor Rho [Escherichia coli ATCC 8739], ... gi\|189376810, gi... - gi\|189376810\|gb\|EDU95226.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. EC50... EG10845 - transcription termination factor / Transcription termination factor Rho; hexameric; RNA-dependent AT... gi\|188014278, gi... - gi\|188014278\|gb\|EDU52400.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. EC41... gi\|215267183, gi... - gi\|215489111\|ref\|YP_002331542.1\| transcription termination factor Rho [Escherichia coli O127:H6 str.... gi\|209921256, gi... - gi\|209921256\|ref\|YP_002295340.1\| transcription termination factor Rho [Escherichia coli SE11], gi\|20... gi\|218550993, gi... - gi\|218550993\|ref\|YP_002384784.1\| transcription termination factor Rho [Escherichia fergusonii ATCC 3... gi\|15833970, gi\|... - gi\|15833970\|ref\|NP_312743.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. Sak... gi\|217324419, gi... - gi\|217324419\|ref\|ZP_03440503.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. ... gi\|218560849, gi... - gi\|218560849\|ref\|YP_002393762.1\| transcription termination factor Rho [Escherichia coli S88], gi\|218... gi\|218363114, gi... - gi\|218556345\|ref\|YP_002389259.1\| transcription termination factor Rho [Escherichia coli IAI1], gi\|21... gi\|218697500, gi... - gi\|218697500\|ref\|YP_002405167.1\| transcription termination factor Rho [Escherichia coli 55989], gi\|2... gi\|218692062, gi... - gi\|218692062\|ref\|YP_002400274.1\| transcription termination factor Rho [Escherichia coli ED1a], gi\|21... gi\|170683673, gi... - gi\|170683673\|ref\|YP_001746101.1\| transcription termination factor Rho [Escherichia coli SMS-3-5], gi... gi\|170083270, gi... - gi\|170083270\|ref\|YP_001732590.1\| transcription termination factor [Escherichia coli str. K-12 substr... gi\|195938071 - gi\|195938071\|ref\|ZP_03083453.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. ... gi\|170121255, gi... - gi\|170769817\|ref\|ZP_02904270.1\| transcription termination factor Rho [Escherichia albertii TW07627],... gi\|208812033, gi... - gi\|208812033\|ref\|ZP_03253362.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. ... gi\|208729225, gi... - gi\|208809424\|ref\|ZP_03251761.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. ... gi\|209162058, gi... - gi\|209400658\|ref\|YP_002273300.1\| transcription termination factor Rho [Escherichia coli O157:H7 str.... gi\|208819558, gi... - gi\|208819558\|ref\|ZP_03259878.1\| transcription termination factor Rho [Escherichia coli O157:H7 str. ... EG10845 - transcription termination factor / Transcription termination factor Rho; hexameric; RNA-dependent AT... RHO_ECOL6 - Transcription termination factor Rho OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) ... gi\|227888634, gi... - gi\|227888634\|ref\|ZP_04006439.1\| transcription termination factor Rho [Escherichia coli 83972], gi\|22... gi\|238863679, gi... - gi\|238902863\|ref\|YP_002928659.1\| transcription termination factor [Escherichia coli BW2952], gi\|2388... RHO_ECOLI - Transcription termination factor rho (EC 3.6.1.-) (ATP-dependent helicase rho) - Escherichia coli gi\|254795780, gi... - gi\|254795780\|ref\|YP_003080617.1\| transcription termination factor [Escherichia coli O157:H7 str. TW1... RHO_SHIFL - Transcription termination factor Rho OS=Shigella flexneri GN=rho PE=3 SV=1 gi\|30064922, gi\|... - gi\|30064922\|ref\|NP_839093.1\| transcription termination factor Rho [Shigella flexneri 2a str. 2457T],... RHO_ECO57 - Transcription termination factor Rho OS=Escherichia coli O157:H7 GN=rho PE=3 SV=1	533.0	[0..1]	[418..1]
gi\|37528480, gi\|... - gi\|37528480\|ref\|NP_931825.1\| transcription termination factor Rho [Photorhabdus luminescens subsp. l...	532.0	[0..1]	[418..1]
gi\|62130025, gi\|... - gi\|62182392\|ref\|YP_218809.1\| transcription termination factor Rho [Salmonella enterica subsp. enteri...	532.0	[0..1]	[418..25]
gi\|85060364, gi\|... - gi\|85060364\|ref\|YP_456066.1\| transcription termination factor Rho [Sodalis glossinidius str. 'morsit...	531.0	[0..1]	[418..1]
gi\|37200117, gi\|... - gi\|37681365\|ref\|NP_935974.1\| transcription termination factor Rho [Vibrio vulnificus YJ016], gi\|3720...	531.0	[0..1]	[419..9]
gi\|27364379, gi\|... - gi\|27364379\|ref\|NP_759907.1\| transcription termination factor Rho [Vibrio vulnificus CMCP6], gi\|2736...	530.0	[0..1]	[419..1]
gi\|194444899, gi... - gi\|194444899\|ref\|YP_002043154.1\| transcription termination factor Rho [Salmonella enterica subsp. en... RHO_SALTY - Transcription termination factor Rho OS=Salmonella typhimurium GN=rho PE=3 SV=1 gi\|205340701, gi... - gi\|205340701\|gb\|EDZ27465.1\| transcription termination factor Rho [Salmonella enterica subsp. enteric... lcl\|NC_016856.1_... - [gene=rho] [protein=transcription termination factor Rho] [protein_id=YP_005240179.1] [location=4139... gi\|168467667, gi... - gi\|195630005\|gb\|EDX48665.1\| transcription termination factor Rho [Salmonella enterica subsp. enteric... gi\|168263192, gi... - gi\|205348063\|gb\|EDZ34694.1\| transcription termination factor Rho [Salmonella enterica subsp. enteric... gi\|197249760, gi... - gi\|197249760\|ref\|YP_002148846.1\| transcription termination factor Rho [Salmonella enterica subsp. en... gi\|194736430, gi... - gi\|194736430\|ref\|YP_002116852.1\| transcription termination factor Rho [Salmonella enterica subsp. en... RHO_SALTY - Transcription termination factor rho OS=Salmonella typhimurium GN=rho PE=3 SV=1 gi\|194469338, gi... - gi\|194469338\|ref\|ZP_03075322.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|194450354, gi... - gi\|194450354\|ref\|YP_002047937.1\| transcription termination factor Rho [Salmonella enterica subsp. en... gi\|205322225, gi... - gi\|205322225\|gb\|EDZ10064.1\| transcription termination factor Rho [Salmonella enterica subsp. enteric... gi\|161617034, gi... - gi\|161617034\|ref\|YP_001590999.1\| transcription termination factor Rho [Salmonella enterica subsp. en... gi\|160866913, gi... - gi\|161505566\|ref\|YP_001572678.1\| transcription termination factor Rho [Salmonella enterica subsp. ar... gi\|205336257, gi... - gi\|205336257\|gb\|EDZ23021.1\| transcription termination factor Rho [Salmonella enterica subsp. enteric... gi\|168238373, gi... - gi\|197288790\|gb\|EDY28165.1\| transcription termination factor Rho [Salmonella enterica subsp. enteric... gi\|168234237, gi... - gi\|205331810\|gb\|EDZ18574.1\| transcription termination factor Rho [Salmonella enterica subsp. enteric... gi\|167994612, gi... - gi\|205327557\|gb\|EDZ14321.1\| transcription termination factor Rho [Salmonella enterica subsp. enteric... gi\|213856932 - gi\|213856932\|ref\|ZP_03384172.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|213648369 - gi\|213648369\|ref\|ZP_03378422.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|213426567 - gi\|213426567\|ref\|ZP_03359317.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|213051687 - gi\|213051687\|ref\|ZP_03344565.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|238912926 - gi\|238912926\|ref\|ZP_04656763.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|224585739, gi... - gi\|224585739\|ref\|YP_002639538.1\| transcription termination factor Rho [Salmonella enterica subsp. en... gi\|214000864 - gi\|214000864\|ref\|ZP_03411599.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|200388193, gi... - gi\|200388193\|ref\|ZP_03214805.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|198243711, gi... - gi\|198243711\|ref\|YP_002217854.1\| transcription termination factor Rho [Salmonella enterica subsp. en... gi\|197364706, gi... - gi\|197364706\|ref\|YP_002144343.1\| transcription termination factor Rho [Salmonella enterica subsp. en... gi\|197264201, gi... - gi\|197264201\|ref\|ZP_03164275.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|213021585 - gi\|213021585\|ref\|ZP_03336032.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|207859128, gi... - gi\|207859128\|ref\|YP_002245779.1\| transcription termination factor Rho [Salmonella enterica subsp. en... gi\|205274294, gi... - gi\|205354513\|ref\|YP_002228314.1\| transcription termination factor Rho [Salmonella enterica subsp. en... gi\|204930193, gi... - gi\|204930193\|ref\|ZP_03221170.1\| transcription termination factor Rho [Salmonella enterica subsp. ent... gi\|16762213 - gi\|16762213\|ref\|NP_457830.1\| transcription termination factor Rho [Salmonella enterica subsp. enteri... RHO_SALTY - Transcription termination factor Rho OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)... gi\|29143702, gi\|... - gi\|29143702\|ref\|NP_807044.1\| transcription termination factor Rho [Salmonella enterica subsp. enteri... gi\|56415776, gi\|... - gi\|56415776\|ref\|YP_152851.1\| transcription termination factor Rho [Salmonella enterica subsp. enteri... RHO_SALTI - Transcription termination factor rho OS=Salmonella typhi GN=rho PE=3 SV=1 RHO_SALTI - Transcription termination factor Rho OS=Salmonella typhi GN=rho PE=3 SV=1	530.0	[0..1]	[418..1]
gi\|49363\|emb\|CAA... - Rho Factor [Salmonella typhimurium] gi\|1073691, gi\|49363 - gi\|49363\|emb\|CAA79852.1\| Rho Factor [Salmonella typhimurium], pir\|\|B49917 transcription termination ...	530.0	[0..1]	[418..1]
gi\|49613657, gi\|... - gi\|50123131\|ref\|YP_052298.1\| transcription termination factor Rho [Pectobacterium atrosepticum SCRI1...	529.0	[0..1]	[418..1]

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Predicted Domain #1

Region A:
Residues: [1-421]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNLTELKDTP ISDLVSLAEN MKLENMARAR KQDIIFSILK AHAKSGEDIF GGGVLEILQD  60
   61 GFGFLRSADG SYLAGPDDIY VSPSQIRRFN MRTGDTIFGK IRPPKEGERY FALLKVNEVN 120
  121 FDKPENSRNK ILFENLTPLH AEERMRMERG NGSTEDITAR ILDLCSPIGK GQRGLIVAPP 180
  181 KAGKTLLLQN IAQSITYNNP EVVLMVLLID ERPEEVTEMQ RLVKGEVIAS TFDEPASRHV 240
  241 QVAEMVIEKA KRLVEHKKDV VILLDSITRL ARAYNTVIPS SGKVLTGGVD ANALHRPKRF 300
  301 FGAARNIENG GSLTIIATAL VDTGSKMDEV IYEEFKGTGN QELHLSRKAA EKRVFPAIDF 360
  361 NRSGTRREEK LTNPDELQKM WILRKILNPM DEVSAMEFLI DKLAMTKTND EFFTAMKRAK 420
  421 S

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	152.0
Match:	1pv4A
Description:	Rho termination factor, N-terminal domain; Rho termination factor, RNA-binding domain; Transcription termination factor Rho, ATPase domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	2.52864900707835	bayes_pls_golite062009
transcription termination factor activity	1.46620917553746	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
nucleic acid binding	0.991157380393447	bayes_pls_golite062009
transcription regulator activity	0.834867065912847	bayes_pls_golite062009
DNA binding	0.686733725554901	bayes_pls_golite062009
protein binding	0.378225828131122	bayes_pls_golite062009
nucleotide binding	0.114848452385726	bayes_pls_golite062009
purine nucleotide binding	0.10713474095071	bayes_pls_golite062009
purine ribonucleotide binding	0.0916519414118148	bayes_pls_golite062009
ribonucleotide binding	0.0915913646217636	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: