YRC Public Data Repository - Protein Structure Prediction

Protein:	RPOB_SALPK
Organism:	Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601
Length:	1342 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 RPOB_SALPK.

Description	E-value	Query Range	Subject Range
RPOB_SHIDS - DNA-directed RNA polymerase subunit beta OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=rpoB P...	0.0	[1..1342]	[1..1342]
gi\|75514754 - gi\|75514754\|ref\|ZP_00736983.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Es... gi\|227885483, gi... - gi\|227885483\|ref\|ZP_04003288.1\| DNA-directed RNA polymerase subunit beta [Escherichia coli 83972], g... gi\|26250758, gi\|... - gi\|26250758\|ref\|NP_756798.1\| DNA-directed RNA polymerase subunit beta [Escherichia coli CFT073], gi\|... gi\|226903068, gi... - gi\|237702755\|ref\|ZP_04533236.1\| RNA polymerase beta subunit [Escherichia sp. 3_2_53FAA], gi\|22690306... gi\|24054565, gi\|... - ref\|NP_709782.1\| RNA polymerase beta subunit [Shigella flexneri 2a str. 301], gb\|AAN45489.1\| RNA po... gi\|254039244, gi... - gi\|254039244\|ref\|ZP_04873293.1\| RNA polymerase beta subunit [Escherichia sp. 1_1_43], gi\|226838479\|g... gi\|75179655 - gi\|75179655\|ref\|ZP_00699659.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Sh... gi\|75188717 - gi\|75188717\|ref\|ZP_00701984.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Es... gi\|91212806, gi\|... - gi\|91212806\|ref\|YP_542792.1\| DNA-directed RNA polymerase subunit beta [Escherichia coli UTI89], gi\|9... gi\|75197851 - gi\|75197851\|ref\|ZP_00707921.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Es... gi\|75208785 - gi\|75208785\|ref\|ZP_00709071.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Es... gi\|75228142 - gi\|75228142\|ref\|ZP_00714811.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Es... gi\|75236717 - gi\|75236717\|ref\|ZP_00720790.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Es... gi\|75238528 - gi\|75238528\|ref\|ZP_00722517.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Es... gi\|75255484 - gi\|75255484\|ref\|ZP_00727283.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Es... gi\|115515374, gi... - gi\|117626250\|ref\|YP_859573.1\| DNA-directed RNA polymerase subunit beta [Escherichia coli APEC O1], g... gi\|83569000 - gi\|83569000\|ref\|ZP_00920463.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Sh... gi\|83584817 - gi\|83584817\|ref\|ZP_00923477.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [Es...	0.0	[1..1342]	[12..1353]
gi\|85676083, gi\|... - gi\|89110052\|ref\|AP_003832.1\| RNA polymerase, beta subunit [Escherichia coli str. K-12 substr. W3110]... gi\|56384051, gi\|... - gi\|56480500\|ref\|NP_709782.2\| DNA-directed RNA polymerase subunit beta [Shigella flexneri 2a str. 301... RPOB_ECOK1 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O1:K1 / APEC GN=rpoB PE=3 SV=2 RPOB_ECODH - DNA-directed RNA polymerase subunit beta OS=Escherichia coli (strain K12 / DH10B) GN=rpoB PE=3 SV=1 RPOB_ECOSM - DNA-directed RNA polymerase subunit beta OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=rpoB PE=3 S... RPOB_SHIB3 - DNA-directed RNA polymerase subunit beta OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)... gi\|188495017, gi... - gi\|188495017\|ref\|ZP_03002287.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli 53638], ... gi\|168777402, gi... - gi\|187767357\|gb\|EDU31201.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 str.... gi\|168780370, gi... - gi\|189001730\|gb\|EDU70716.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 str.... gi\|189370171, gi... - gi\|189370171\|gb\|EDU88587.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 str.... gi\|189379158, gi... - gi\|189379158\|gb\|EDU97574.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 str.... gi\|189354590, gi... - gi\|189354590\|gb\|EDU73009.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 str.... gi\|168764565, gi... - gi\|189365467\|gb\|EDU83883.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 str.... gi\|189359774, gi... - gi\|189359774\|gb\|EDU78193.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 str.... gi\|124498587, gi... - gi\|124531373\|ref\|ZP_01701683.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli B], gi\|1... gi\|254290678, gi... - gi\|254290678\|ref\|YP_003056426.1\| DNA-directed RNA polymerase subunit beta [Escherichia coli BL21(DE3... gi\|254163928, gi... - gi\|254163928\|ref\|YP_003047036.1\| DNA-directed RNA polymerase subunit beta [Escherichia coli B str. R... RPOB_ECOBW - DNA-directed RNA polymerase subunit beta OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=rpoB ... gi\|251787244, gi... - gi\|251787244\|ref\|YP_003001548.1\| hypothetical protein B21_03816 [Escherichia coli BL21], gi\|24237951... RPOB_SHIFL - DNA-directed RNA polymerase subunit beta OS=Shigella flexneri GN=rpoB PE=3 SV=1 gi\|22774032 - gi\|22774032\|gb\|AAN07182.1\| RNA polymerase beta subunit [Cloning vector pIA423] sp\|B7UPE2\|RPOB_ECO27 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=rpo... gi\|254595385, gi... - gi\|254795985\|ref\|YP_003080822.1\| RNA polymerase, beta subunit [Escherichia coli O157:H7 str. TW14359... EG10894 - RNA polymerase, beta subunit / RNA polymerase, beta subunit; binds Zn(II) gi\|30042990, gi\|... - gi\|30064730\|ref\|NP_838901.1\| DNA-directed RNA polymerase subunit beta [Shigella flexneri 2a str. 245... RPOB_ECO57 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O157:H7 GN=rpoB PE=3 SV=1 EG10894 - RNA polymerase, beta subunit / RNA polymerase, beta subunit; binds Zn(II) RPOB_ECOL6 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O6 GN=rpoB PE=3 SV=1 RPOB_ECOL6 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UP... RPOB_ECOSE - DNA-directed RNA polymerase subunit beta OS=Escherichia coli (strain SE11) GN=rpoB PE=3 SV=1 RPOB_ECO27 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=rpo... gi\|217325660, gi... - gi\|217325660\|ref\|ZP_03441744.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 ... RPOB_ECO8A - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O8 (strain IAI1) GN=rpoB PE=3 SV=1 gi\|208808239, gi... - gi\|208808239\|ref\|ZP_03250576.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 ... gi\|208814392, gi... - gi\|208814392\|ref\|ZP_03255721.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 ... gi\|208820515, gi... - gi\|208820515\|ref\|ZP_03260835.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli O157:H7 ... RPOB_ECO5E - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=rpoB ... gi\|194412004, gi... - gi\|194429975\|ref\|ZP_03062484.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli B171], g... gi\|194416989, gi... - gi\|194434765\|ref\|ZP_03067016.1\| DNA-directed RNA polymerase, beta subunit [Shigella dysenteriae 1012... gi\|194439780, gi... - gi\|194439780\|ref\|ZP_03071847.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli 101-1], ... gi\|195939612 - gi\|195939612\|ref\|ZP_03084994.1\| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H7 s... gi\|13364386, gi\|... - gi\|15834164\|ref\|NP_312937.1\| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H7 str.... RPOB_ECOLC - DNA-directed RNA polymerase subunit beta OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) ... gi\|191168659, gi... - gi\|191168659\|ref\|ZP_03030440.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli B7A], gi... gi\|190905431, gi... - gi\|191174299\|ref\|ZP_03035807.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli F11], gi... gi\|193066419, gi... - gi\|193066419\|ref\|ZP_03047466.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli E22], gi... gi\|193067811, gi... - gi\|193067811\|ref\|ZP_03048777.1\| DNA-directed RNA polymerase, beta subunit [Escherichia coli E110019]... RPOB_ECOLI - DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (RNAP beta subunit) (Transcriptase beta chain) (... RPOB_SHIBS - DNA-directed RNA polymerase subunit beta OS=Shigella boydii serotype 4 (strain Sb227) GN=rpoB PE=3 S... RPOB_ECOUT - DNA-directed RNA polymerase subunit beta OS=Escherichia coli (strain UTI89 / UPEC) GN=rpoB PE=3 SV=2 RPOB_SHISS - DNA-directed RNA polymerase subunit beta OS=Shigella sonnei (strain Ss046) GN=rpoB PE=3 SV=1 RPOB_ECOHS - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O9:H4 (strain HS) GN=rpoB PE=3 SV=1 RPOB_ECO24 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=rpo... RPOB_ECO45 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=rpoB PE=... RPOB_ECO55 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli (strain 55989 / EAEC) GN=rpoB PE=3 SV=1 RPOB_ECO7I - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=rpoB PE... RPOB_ECOLU - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=...	0.0	[1..1342]	[1..1342]
RPOB_ECOL5 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=rpoB ...	0.0	[1..1342]	[1..1342]
gi\|15804577, gi\|... - gi\|15804577\|ref\|NP_290618.1\| DNA-directed RNA polymerase subunit beta [Escherichia coli O157:H7 EDL9... gi\|25288387 - gi\|25288387\|pir\|\|C86090 RNA polymerase, beta subunit [imported] - Escherichia coli (strain O157:H7,...	0.0	[1..1342]	[1..1342]
gi\|62182607, gi\|... - gi\|62182607\|ref\|YP_219024.1\| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp. en...	0.0	[1..1342]	[39..1380]
RPOB_SALTY - DNA-directed RNA polymerase subunit beta OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700... lcl\|NC_016856.1_... - [gene=rpoB] [protein=DNA-directed RNA polymerase subunit beta] [protein_id=YP_005240432.1] [location... RPOB_SALTY - DNA-directed RNA polymerase subunit beta OS=Salmonella typhimurium GN=rpoB PE=3 SV=2 RPOB_SALTY - DNA-directed RNA polymerase subunit beta OS=Salmonella typhimurium GN=rpoB PE=3 SV=2	0.0	[1..1342]	[1..1342]
RPOB_SALCH - DNA-directed RNA polymerase subunit beta OS=Salmonella choleraesuis GN=rpoB PE=3 SV=2 RPOB_SALCH - DNA-directed RNA polymerase subunit beta OS=Salmonella choleraesuis GN=rpoB PE=3 SV=2 RPOB_SALCH - DNA-directed RNA polymerase subunit beta OS=Salmonella choleraesuis (strain SC-B67) GN=rpoB PE=3 SV=...	0.0	[1..1342]	[1..1342]
gi\|47919, gi\|66968 - pir\|\|RNEBBT DNA-directed RNA polymerase (EC 2.7.7.6) beta chain - Salmonella typhimurium, gi\|47919\|e... gi\|47919\|emb\|CAA... - unnamed protein product [Salmonella typhimurium]	0.0	[1..1342]	[1..1342]
gi\|42818, gi\|223... - gi\|42821\|emb\|CAA23627.1\| unnamed protein product [Escherichia coli], gi\|42818\|emb\|CAA23625.1\| rpoB [...	0.0	[1..1342]	[1..1342]

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Predicted Domain #1

Region A:
Residues: [1-189]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ  60
   61 SYSGNSELQY VSYRLGEPVF DVQECQIRGV TYSAPLRVKL RLVIYEREAP EGTVKDIKEQ 120
  121 EVYMGEIPLM TDNGTFVING TERVIVSQLH RSPGVFFDSD KGKTHSSGKV LYNARIIPYR 180
  181 GSWLDFEFD

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	9.142668
Match:	PF04563.6
Description:	No description for PF04563.6 was found.

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [190-1086]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PKDNLFVRID RRRKLPATII LRALNYTTEQ ILDLFFEKVV FEIRDNKLQM ELIPERLRGE  60
   61 TASFDIEANG KVYVEKGRRI TARHIRQLEK DDIKHIEVPV EYIAGKVVSK DYVDESTGEL 120
  121 ICAANMELSL DLLAKLSQSG HKRIETLFTN DLDHGPYISE TVRVDPTNDR LSALVEIYRM 180
  181 MRPGEPPTRE AAESLFENLF FSEDRYDLSA VGRMKFNRSL LRDEIEGSGI LSKDDIIDVM 240
  241 KKLIDIRNGK GEVDDIDHLG NRRIRSVGEM AENQFRVGLV RVERAVKERL SLGDLDTLMP 300
  301 QDMINAKPIS AAVKEFFGSS QLSQFMDQNN PLSEITHKRR ISALGPGGLT RERAGFEVRD 360
  361 VHPTHYGRVC PIETPEGPNI GLINSLSVYA QTNEYGFLET PYRRVVDGVV TDEIHYLSAI 420
  421 EEGNYVIAQA NSNLDDEGHF VEDLVTCRSK GESSLFSRDQ VDYMDVSTQQ VVSVGASLIP 480
  481 FLEHDDANRA LMGANMQRQA VPTLRADKPL VGTGMERAVA VDSGVTAVAK RGGTVQYVDA 540
  541 SRIVIKVNED EMYPGEAGID IYNLTKYTRS NQNTCINQMP CVSLGEPVER GDVLADGPST 600
  601 DLGELALGQN MRVAFMPWNG YNFEDSILVS ERVVQEDRFT TIHIQELACV SRDTKLGPEE 660
  661 ITADIPNVGE AALSKLDESG IVYIGAEVTG GDILVGKVTP KGETQLTPEE KLLRAIFGEK 720
  721 ASDVKDSSLR VPNGVSGTVI DVQVFTRDGV EKDKRALEIE EMQLKQAKKD LSEELQILEA 780
  781 GLFSRIRAVL VSGGVEAEKL DKLPRDRWLE LGLTDEEKQN QLEQLAEQYD ELKHEFEKKL 840
  841 EAKRRKITQG DDLAPGVLKI VKVYLAVKRR IQPGDKMAGR HGNKGVISKI NPIEDMP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.0
Match:	1ynjC
Description:	Taq RNA polymerase-Sorangicin complex
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA-directed RNA polymerase activity	10.2021663255698	bayes_pls_golite062009
RNA polymerase activity	10.2021663255698	bayes_pls_golite062009
nucleotidyltransferase activity	7.6240729546188	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	5.44374972993429	bayes_pls_golite062009
transferase activity	4.83218811360621	bayes_pls_golite062009
binding	1.61743849829314	bayes_pls_golite062009
catalytic activity	1.36406839864424	bayes_pls_golite062009
transcription regulator activity	1.30860843987842	bayes_pls_golite062009
DNA binding	1.06504127306982	bayes_pls_golite062009
nucleic acid binding	1.04375863237637	bayes_pls_golite062009
protein binding	0.251709363216351	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [1087-1280]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YDENGTPVDI VLNPLGVPSR MNIGQILETH LGMAAKGIGD KINAMLKQQQ EVAKLREFIQ  60
   61 RAYDLGADVR QKVDLSTFSD DEVLRLAENL RKGMPIATPV FDGAKEAEIK ELLKLGDLPT 120
  121 SGQITLFDGR TGEQFERPVT VGYMYMLKLN HLVDDKMHAR STGSYSLVTQ QPLGGKAQFG 180
  181 GQRFGEMEVW ALEA

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	7.366532
Match:	PF00562.19
Description:	No description for PF00562.19 was found.

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #4

Region A:
Residues: [1281-1342]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YGAAYTLQEM LTVKSDDVNG RTKMYKNIVD GNHQMEPGMP ESFNVLLKEI RSLGINIELE  60
   61 DE

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	51.327902
Match:	PF04560.11
Description:	No description for PF04560.11 was found.

Shown below is our most confident prediction for this domain.
Click here to view all matches.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.864	0.015	DNA-directed RNA polymerase activity	d.45.1	ClpS-like

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: