YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|213648387
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. J185
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 gi|213648387.

Description	E-value	Query Range	Subject Range
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 ...	0.0	[1..477]	[1..477]
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...	0.0	[1..477]	[1..477]
gi\|82545560, gi\|... - gi\|82545560\|ref\|YP_409507.1\| RNA polymerase factor sigma-54 [Shigella boydii Sb227], gi\|81246971\|gb\|...	0.0	[1..477]	[1..477]
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...	0.0	[1..477]	[1..477]
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...	0.0	[1..477]	[1..477]
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...	0.0	[1..477]	[1..477]
gi\|81242664, gi\|... - gi\|82778516\|ref\|YP_404865.1\| RNA polymerase factor sigma-54 [Shigella dysenteriae Sd197], gi\|8124266...	0.0	[1..477]	[1..477]
gi\|110807068, gi... - gi\|110807068\|ref\|YP_690588.1\| RNA polymerase factor sigma-54 [Shigella flexneri 5 str. 8401], gi\|110...	0.0	[1..477]	[1..477]
EG10898 - RNA polymerase, sigma 54 (sigma N) factor / RNA polymerase subunit, sigma 54; needed for expression ... gi\|170082736, gi... - gi\|170082736\|ref\|YP_001732056.1\| RNA polymerase, sigma 54 (sigma N) factor [Escherichia coli str. K-... gi\|73671322\|gb\|A... - RpoN [Escherichia coli] RP54_ECOLI - RNA polymerase sigma-54 factor - Escherichia coli EG10898 - RNA polymerase, sigma 54 (sigma N) factor / RNA polymerase subunit, sigma 54; needed for expression ... gi\|226839991, gi... - gi\|254038367\|ref\|ZP_04872425.1\| sigma-N [Escherichia sp. 1_1_43], gi\|226839991\|gb\|EEH72012.1\| sigma-... gi\|89109965, gi\|... - gi\|89109965\|ref\|AP_003745.1\| RNA polymerase, sigma 54 (sigma N) factor [Escherichia coli str. K-12 s... gi\|238902304, gi... - gi\|238902304\|ref\|YP_002928100.1\| RNA polymerase, sigma 54 (sigma N) factor [Escherichia coli BW2952]...	0.0	[1..477]	[1..477]
gi\|74313739, gi\|... - gi\|74313739\|ref\|YP_312158.1\| RNA polymerase factor sigma-54 [Shigella sonnei Ss046], gi\|73857216\|gb\|...	0.0	[1..477]	[1..477]

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Predicted Domain #1

Region A:
Residues: [1-102]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKQGLQLRLS QQLAMTPQLQ QAIRLLQLST LELQQELQQA LENNPLLEQT DLHDEIDTQQ  60
   61 PQDDDPLDTA DALEQKEMPE ELPLDASWDE IYTAGTPSGP 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 QGETTQSLQD YLMWQVELTP FSDTDRAIAT SIVDAVDDTG YLTVSLDEIR  60
   61 ESMGDVEVDL DEVEAVLKRI QRFDPVGVAA KDLRDCLLIQ LSQFDKSTPW LEEARLIICD 120
  121 HLDLLANHDF RTLMRVTRLK EEVLKEAVNL IQSLDPRPGQ SIQTGEPEYV IPDVLVRKHN 180
  181 GRWTVELNSD SIPRLQINQH YAAMCNS

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	124.267606
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: [310-409]

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

[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: [410-477]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EGGGEASSTA IRALVKKLIA AENPAKPLSD SKLTSLLSEQ GIMVARRTVA KYRESLSIPP  60
   61 SNQRKQLV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	21.045757
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