YRC Public Data Repository - Protein Structure Prediction

Protein:	RP54_ECOLI
Organism:	Escherichia coli
Length:	477 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 RP54_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|82545560, gi\|... - gi\|82545560\|ref\|YP_409507.1\| RNA polymerase factor sigma-54 [Shigella boydii Sb227], gi\|81246971\|gb\|...	696.0	[0..1]	[477..1]
gi\|189361831, gi... - gi\|189361831\|gb\|EDU80250.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC4486], g... gi\|187767471, gi... - gi\|187767471\|gb\|EDU31315.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC4196], g... gi\|189000994, gi... - gi\|189000994\|gb\|EDU69980.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC4076], g... gi\|189374176, gi... - gi\|189374176\|gb\|EDU92592.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC869], gi... gi\|168800916, gi... - gi\|189376847\|gb\|EDU95263.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC508], gi... gi\|170018548, gi... - gi\|170018548\|ref\|YP_001723502.1\| RNA polymerase factor sigma-54 [Escherichia coli ATCC 8739], gi\|169... gi\|170684031, gi... - gi\|170684031\|ref\|YP_001745474.1\| RNA polymerase sigma-54 factor [Escherichia coli SMS-3-5], gi\|17052... gi\|195940058 - gi\|195940058\|ref\|ZP_03085440.1\| RNA polymerase factor sigma-54 [Escherichia coli O157:H7 str. EC4024... gi\|227835319, gi... - gi\|227887923\|ref\|ZP_04005728.1\| RNA polymerase factor sigma-54 [Escherichia coli 83972], gi\|22783531... gi\|237706046, gi... - gi\|237706046\|ref\|ZP_04536527.1\| RNA polymerase sigma-54 factor [Escherichia sp. 3_2_53FAA], gi\|22689... gi\|188014376, gi... - gi\|188014376\|gb\|EDU52498.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC4113], g... gi\|251786472, gi... - gi\|251786472\|ref\|YP_003000776.1\| hypothetical protein B21_03018 [Escherichia coli BL21], gi\|24237874... gi\|189358593, gi... - gi\|189358593\|gb\|EDU77012.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC4401], g... gi\|253771964, gi... - gi\|254289894\|ref\|YP_003055642.1\| DNA-directed RNA polymerase subunit N [Escherichia coli BL21(DE3)],... gi\|168763739, gi... - gi\|189366137\|gb\|EDU84553.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC4501], g... gi\|253975045, gi... - gi\|254163144\|ref\|YP_003046252.1\| DNA-directed RNA polymerase subunit N [Escherichia coli B str. REL6... gi\|218701971, gi... - gi\|218701971\|ref\|YP_002409600.1\| RNA polymerase factor sigma-54 [Escherichia coli IAI39], gi\|2183719... gi\|254795151, gi... - gi\|254795151\|ref\|YP_003079988.1\| RNA polymerase, sigma 54 (sigma N) factor [Escherichia coli O157:H7... gi\|218706822, gi... - gi\|218706822\|ref\|YP_002414341.1\| RNA polymerase factor sigma-54 [Escherichia coli UMN026], gi\|218433... gi\|208808618, gi... - gi\|208808618\|ref\|ZP_03250955.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC4206... gi\|208813350, gi... - gi\|208813350\|ref\|ZP_03254679.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC4045... gi\|208738411, gi... - gi\|208818288\|ref\|ZP_03258608.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC4042... gi\|209158646, gi... - gi\|209397246\|ref\|YP_002272672.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. EC411... gi\|217326841, gi... - gi\|217326841\|ref\|ZP_03442924.1\| RNA polymerase sigma-54 factor [Escherichia coli O157:H7 str. TW1458... gi\|218560272, gi... - gi\|218560272\|ref\|YP_002393185.1\| RNA polymerase factor sigma-54 [Escherichia coli S88], gi\|218367041... gi\|218429056, gi... - gi\|218691492\|ref\|YP_002399704.1\| RNA polymerase factor sigma-54 [Escherichia coli ED1a], gi\|21842905... gi\|117625494, gi... - gi\|117625494\|ref\|YP_858817.1\| RNA polymerase factor sigma-54 [Escherichia coli APEC O1], gi\|11551461... gi\|218696907, gi... - gi\|218696907\|ref\|YP_002404574.1\| RNA polymerase factor sigma-54 [Escherichia coli 55989], gi\|2183536... gi\|124528482, gi... - gi\|124528482\|ref\|ZP_01699771.1\| RNA polymerase, sigma 54 subunit, RpoN [Escherichia coli B], gi\|1245... gi\|110345035, gi... - gi\|110643443\|ref\|YP_671173.1\| RNA polymerase factor sigma-54 [Escherichia coli 536], gi\|110345035\|gb... gi\|91212627, gi\|... - gi\|91212627\|ref\|YP_542613.1\| RNA polymerase factor sigma-54 [Escherichia coli UTI89], gi\|91074201\|gb... gi\|13363554, gi\|... - gi\|15833335\|ref\|NP_312108.1\| RNA polymerase factor sigma-54 [Escherichia coli O157:H7 str. Sakai], g... gi\|187730690, gi... - gi\|75176106\|ref\|ZP_00696274.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|157080903, gi... - gi\|75188008\|ref\|ZP_00701275.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|157162686, gi... - gi\|75197151\|ref\|ZP_00707221.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|191168644, gi... - gi\|75228163\|ref\|ZP_00714828.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|75236217, gi\|... - gi\|75236217\|ref\|ZP_00720327.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|75234884, gi\|... - gi\|75234884\|ref\|ZP_00719175.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|188488050, gi... - gi\|75511895\|ref\|ZP_00734507.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|26249788, gi\|... - gi\|26249788\|ref\|NP_755828.1\| RNA polymerase factor sigma-54 [Escherichia coli CFT073], gi\|26110216\|g... gi\|25288499, gi\|... - pir\|\|D85984 RNA polymerase sigma(54 or 60) factor RpoN [imported] - Escherichia coli (strain O157:H7... gi\|15803742, gi\|... - gi\|15803742\|ref\|NP_289776.1\| RNA polymerase factor sigma-54 [Escherichia coli O157:H7 EDL933], gi\|12... gi\|13363554, gi\|... - gi\|15833335\|ref\|NP_312108.1\| DNA-directed RNA polymerase subunit N [Escherichia coli O157:H7], gi\|13... gi\|83585420, gi\|... - gi\|83585420\|ref\|ZP_00924066.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma...	696.0	[0..1]	[477..1]
gi\|81242664, gi\|... - gi\|82778516\|ref\|YP_404865.1\| RNA polymerase factor sigma-54 [Shigella dysenteriae Sd197], gi\|8124266...	695.0	[0..1]	[477..1]
gi\|24053676, gi\|... - gi\|24114491\|ref\|NP_709001.1\| RNA polymerase factor sigma-54 [Shigella flexneri 2a str. 301], gi\|2405... gi\|30064540, gi\|... - gi\|30064540\|ref\|NP_838711.1\| RNA polymerase factor sigma-54 [Shigella flexneri 2a str. 2457T], gi\|30...	695.0	[0..1]	[477..1]
gi\|209913936, gi... - gi\|209920677\|ref\|YP_002294761.1\| RNA polymerase factor sigma-54 [Escherichia coli SE11], gi\|20991393... gi\|75256578, gi\|... - gi\|75256578\|ref\|ZP_00728208.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|75209645, gi\|... - gi\|75209645\|ref\|ZP_00709857.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma...	694.0	[0..1]	[477..1]
gi\|110807068, gi... - gi\|110807068\|ref\|YP_690588.1\| RNA polymerase factor sigma-54 [Shigella flexneri 5 str. 8401], gi\|110...	694.0	[0..1]	[477..1]
gi\|74313739, gi\|... - gi\|74313739\|ref\|YP_312158.1\| RNA polymerase factor sigma-54 [Shigella sonnei Ss046], gi\|73857216\|gb\|...	692.0	[0..1]	[477..1]
RP54_SALTY - RNA polymerase sigma-54 factor OS=Salmonella typhimurium GN=rpoN PE=3 SV=1 gi\|56415249, gi\|... - gi\|56415249\|ref\|YP_152324.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica ser... gi\|197215084, gi... - gi\|197251381\|ref\|YP_002148245.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica... gi\|194712643, gi... - gi\|194737141\|ref\|YP_002116270.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica... gi\|194469694, gi... - gi\|194469694\|ref\|ZP_03075678.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica ... gi\|194442910, gi... - gi\|194442910\|ref\|YP_002042578.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica... gi\|199604741, gi... - gi\|200387643\|ref\|ZP_03214255.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica ... gi\|198242246, gi... - gi\|198242246\|ref\|YP_002217291.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica... gi\|197095656, gi... - gi\|197364179\|ref\|YP_002143816.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica... gi\|197264214, gi... - gi\|197264214\|ref\|ZP_03164288.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica ... lcl\|NC_016856.1_... - [gene=rpoN] [protein=RNA polymerase factor sigma-54] [protein_id=YP_005239500.1] [location=3498306..... gi\|205333902, gi... - gi\|205333902\|gb\|EDZ20666.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica sero... gi\|205327621, gi... - gi\|205327621\|gb\|EDZ14385.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica sero... gi\|205323169, gi... - gi\|205323169\|gb\|EDZ11008.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica sero... gi\|161616330, gi... - gi\|161616330\|ref\|YP_001590295.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica... gi\|205343505, gi... - gi\|205343505\|gb\|EDZ30269.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica sero... gi\|195633540, gi... - gi\|195633540\|gb\|EDX51954.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica sero... RP54_SALTY - RNA polymerase sigma-54 factor OS=Salmonella typhimurium GN=rpoN PE=3 SV=1 gi\|168262667, gi... - gi\|205348368\|gb\|EDZ34999.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica sero... gi\|168238022, gi... - gi\|197289145\|gb\|EDY28514.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica sero... RP54_SALTY - RNA polymerase sigma-54 factor OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=rp... gi\|238910114 - gi\|238910114\|ref\|ZP_04653951.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica ... gi\|213053145 - gi\|213053145\|ref\|ZP_03346023.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica ... gi\|207858568, gi... - gi\|207858568\|ref\|YP_002245219.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica... gi\|204931181, gi... - gi\|204931181\|ref\|ZP_03221975.1\| RNA polymerase sigma-54 factor [Salmonella enterica subsp. enterica ...	689.0	[0..1]	[477..1]
gi\|29143571, gi\|... - gi\|29143571\|ref\|NP_806913.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica ser... gi\|213648387 - gi\|213648387\|ref\|ZP_03378440.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica ... gi\|16762082 - gi\|16762082\|ref\|NP_457699.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica ser... gi\|214000955 - gi\|214000955\|ref\|ZP_03411690.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica ... gi\|16504385, gi\|... - gi\|25288500\|pir\|\|AG0905 RNA polymerase sigma-54 factor (sigma-N) [imported] - Salmonella enterica su...	689.0	[0..1]	[477..1]
gi\|224585117, gi... - gi\|224585117\|ref\|YP_002638916.1\| DNA-directed RNA polymerase subunit N [Salmonella enterica subsp. e... gi\|62181828, gi\|... - gi\|62181828\|ref\|YP_218245.1\| RNA polymerase factor sigma-54 [Salmonella enterica subsp. enterica ser...	688.0	[0..1]	[477..1]

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Predicted Domain #1

Region A:
Residues: [1-102]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKQGLQLRLS QQLAMTPQLQ QAIRLLQLST LELQQELQQA LESNPLLEQI DTHEEIDTRE  60
   61 TQDSETLDTA DALEQKEMPE ELPLDASWDT IYTAGTPSGT SG

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

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: [103-309]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DYIDDELPVY QGETTQTLQD YLMWQVELTP FSDTDRAIAT SIVDAVDETG YLTVPLEDIL  60
   61 ESIGDEEIDI DEVEAVLKRI QRFDPVGVAA KDLRDCLLIQ LSQFDKTTPW LEEARLIISD 120
  121 HLDLLANHDF RTLMRVTRLK EDVLKEAVNL IQSLDPRPGQ SIQTGEPEYV IPDVLVRKHN 180
  181 GHWTVELNSD SIPRLQINQH YASMCNN

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	119.920819
Match:	PF04963.4
Description:	No description for PF04963.4 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 #3

Region A:
Residues: [310-410]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ARNDGDSQFI RSNLQDAKWL IKSLESRNDT LLRVSRCIVE QQQAFFEQGE EYMKPMVLAD  60
   61 IAQAVEMHES TISRVTTQKY LHSPRGIFEL KYFFSSHVNT E

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	12.431798
Match:	PF04552.4
Description:	No description for PF04552.4 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: [411-477]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GGGEASSTAI RALVKKLIAA ENPAKPLSDS KLTSLLSEQG IMVARRTVAK YRESLSIPPS  60
   61 NQRKQLV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	22.0
Match:	2ahqA
Description:	Solution Structure of the C-terminal RpoN Domain of Sigma-54 from Aquifex aeolicus
Matching Structure (courtesy of the PDB):

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