YRC Public Data Repository - Protein Structure Prediction

Protein:	RPOB_ECOLI
Organism:	Escherichia coli
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_ECOLI.

Description	E-value	Query Range	Subject Range
RPOB_SALPB - DNA-directed RNA polymerase subunit beta OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=... gi\|238913732 - gi\|238913732\|ref\|ZP_04657569.1\| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.... gi\|226358427, gi... - gi\|226358431\|gb\|ACO51078.1\| RNA polymerase beta-subunit [Salmonella enterica subsp. enterica serovar... RPOB_SALPC - DNA-directed RNA polymerase subunit beta OS=Salmonella paratyphi C (strain RKS4594) GN=rpoB PE=3 SV=... gi\|214001621 - gi\|214001621\|ref\|ZP_03412356.1\| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.... gi\|213650888 - gi\|213650888\|ref\|ZP_03380941.1\| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp.... RPOB_SALPK - DNA-directed RNA polymerase subunit beta OS=Salmonella paratyphi A (strain AKU_12601) GN=rpoB PE=3 S... gi\|197242949, gi... - gi\|197264694\|ref\|ZP_03164768.1\| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp... RPOB_SALA4 - DNA-directed RNA polymerase subunit beta OS=Salmonella agona (strain SL483) GN=rpoB PE=3 SV=1 RPOB_SALPA - DNA-directed RNA polymerase subunit beta OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=rp... RPOB_SALSV - DNA-directed RNA polymerase subunit beta OS=Salmonella schwarzengrund (strain CVM19633) GN=rpoB PE=3... RPOB_SALPA - DNA-directed RNA polymerase subunit beta OS=Salmonella paratyphi A GN=rpoB PE=3 SV=1 RPOB_SALEP - DNA-directed RNA polymerase subunit beta OS=Salmonella enteritidis PT4 (strain P125109) GN=rpoB PE=3... gi\|204319880, gi... - gi\|204931265\|ref\|ZP_03222025.1\| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp... gi\|199604260, gi... - gi\|200387162\|ref\|ZP_03213774.1\| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp... RPOB_SALDC - DNA-directed RNA polymerase subunit beta OS=Salmonella dublin (strain CT_02021853) GN=rpoB PE=3 SV=1 gi\|168264592, gi... - gi\|205346980\|gb\|EDZ33611.1\| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp. en... RPOB_SALPB - DNA-directed RNA polymerase subunit beta OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=... gi\|29143788, gi\|... - gi\|29143788\|ref\|NP_807130.1\| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp. en... RPOB_SALAR - DNA-directed RNA polymerase subunit beta OS=Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / R... gi\|194470339, gi... - gi\|194470339\|ref\|ZP_03076323.1\| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp... RPOB_SALHS - DNA-directed RNA polymerase subunit beta OS=Salmonella heidelberg (strain SL476) GN=rpoB PE=3 SV=1 RPOB_SALNS - DNA-directed RNA polymerase subunit beta OS=Salmonella newport (strain SL254) GN=rpoB PE=3 SV=1 gi\|195629014, gi... - gi\|195629014\|gb\|EDX48406.1\| DNA-directed RNA polymerase, beta subunit [Salmonella enterica subsp. en...	1673.0	[0..1]	[1342..1]
gi\|62182607, gi\|... - gi\|62182607\|ref\|YP_219024.1\| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp. en...	1673.0	[0..1]	[1342..39]
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	1672.0	[0..1]	[1342..1]
RPOB_ECOL5 - DNA-directed RNA polymerase subunit beta OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=rpoB ...	1672.0	[0..1]	[1342..1]
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...	1672.0	[0..1]	[1342..12]
RPOB_SHIDS - DNA-directed RNA polymerase subunit beta OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=rpoB P...	1672.0	[0..1]	[1342..1]
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=...	1671.0	[0..1]	[1342..1]
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,...	1671.0	[0..1]	[1342..1]
RPOB_SALTI - DNA-directed RNA polymerase subunit beta OS=Salmonella typhi GN=rpoB PE=3 SV=1 gi\|16762300 - gi\|16762300\|ref\|NP_457917.1\| DNA-directed RNA polymerase subunit beta [Salmonella enterica subsp. en... RPOB_SALTI - DNA-directed RNA polymerase subunit beta OS=Salmonella typhi GN=rpoB PE=3 SV=1	1671.0	[0..1]	[1342..1]
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]	1670.0	[0..1]	[1342..1]

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Predicted Domain #1

Region A:
Residues: [1-191]

      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 GSWLDFEFDP K

[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 are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [192-1101]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DNLFVRIDRR RKLPATIILR ALNYTTEQIL DLFFEKVIFE IRDNKLQMEL VPERLRGETA  60
   61 SFDIEANGKV YVEKGRRITA RHIRQLEKDD VKLIEVPVEY IAGKVVAKDY IDESTGELIC 120
  121 AANMELSLDL LAKLSQSGHK RIETLFTNDL DHGPYISETL RVDPTNDRLS ALVEIYRMMR 180
  181 PGEPPTREAA ESLFENLFFS EDRYDLSAVG RMKFNRSLLR EEIEGSGILS KDDIIDVMKK 240
  241 LIDIRNGKGE VDDIDHLGNR RIRSVGEMAE NQFRVGLVRV ERAVKERLSL GDLDTLMPQD 300
  301 MINAKPISAA VKEFFGSSQL SQFMDQNNPL SEITHKRRIS ALGPGGLTRE RAGFEVRDVH 360
  361 PTHYGRVCPI ETPEGPNIGL INSLSVYAQT NEYGFLETPY RKVTDGVVTD EIHYLSAIEE 420
  421 GNYVIAQANS NLDEEGHFVE DLVTCRSKGE SSLFSRDQVD YMDVSTQQVV SVGASLIPFL 480
  481 EHDDANRALM GANMQRQAVP TLRADKPLVG TGMERAVAVD SGVTAVAKRG GVVQYVDASR 540
  541 IVIKVNEDEM YPGEAGIDIY NLTKYTRSNQ NTCINQMPCV SLGEPVERGD VLADGPSTDL 600
  601 GELALGQNMR VAFMPWNGYN FEDSILVSER VVQEDRFTTI HIQELACVSR DTKLGPEEIT 660
  661 ADIPNVGEAA LSKLDESGIV YIGAEVTGGD ILVGKVTPKG ETQLTPEEKL LRAIFGEKAS 720
  721 DVKDSSLRVP NGVSGTVIDV QVFTRDGVEK DKRALEIEEM QLKQAKKDLS EELQILEAGL 780
  781 FSRIRAVLVA GGVEAEKLDK LPRDRWLELG LTDEEKQNQL EQLAEQYDEL KHEFEKKLEA 840
  841 KRRKITQGDD LAPGVLKIVK VYLAVKRRIQ PGDKMAGRHG NKGVISKINP IEDMPYDENG 900
  901 TPVDIVLNPL

[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: [1102-1276]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GVPSRMNIGQ ILETHLGMAA KGIGDKINAM LKQQQEVAKL REFIQRAYDL GADVRQKVDL  60
   61 STFSDEEVMR LAENLRKGMP IATPVFDGAK EAEIKELLKL GDLPTSGQIR LYDGRTGEQF 120
  121 ERPVTVGYMY MLKLNHLVDD KMHARSTGSY SLVTQQPLGG KAQFGGQRFG EMEVW

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	6.958607
Match:	PF00562.19
Description:	No description for PF00562.19 was found.

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #4

Region A:
Residues: [1277-1342]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ALEAYGAAYT LQEMLTVKSD DVNGRTKMYK NIVDGNHQME PGMPESFNVL LKEIRSLGIN  60
   61 IELEDE

[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 are all of our structure predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.819	0.033	DNA-directed RNA polymerase activity	f.14.1	Voltage-gated potassium channels
View	Download	0.681	0.016	DNA-directed RNA polymerase activity	d.58.18	Regulatory domain in the aminoacid metabolism
View	Download	0.603	0.014	DNA-directed RNA polymerase activity	a.24.4	Hemerythrin
View	Download	0.602	0.004	DNA-directed RNA polymerase activity	d.58.49	YajQ-like
View	Download	0.595	N/A	N/A	f.14.1	Voltage-gated potassium channels

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: