YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|213852301
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. M223
Length:	784 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|213852301.

Description	E-value	Query Range	Subject Range
gi\|146644 - gi\|146644\|gb\|AAA24079.1\| ATP-dependent proteinase (lon) [Escherichia coli]	0.0	[1..777]	[1..777]
gi\|304908 - gi\|304908\|gb\|AAA16837.1\| ATP-dependent protease [Escherichia coli str. K-12 substr. W3110] gi\|304908 - gi\|304908\|gb\|AAA16837.1\| ATP-dependent protease	0.0	[1..784]	[1..784]
gi\|251783948, gi... - gi\|251783948\|ref\|YP_002998252.1\| hypothetical protein B21_00395 [Escherichia coli BL21], gi\|24237622... gi\|238860849, gi... - gi\|238899727\|ref\|YP_002925523.1\| DNA-binding ATP-dependent protease La [Escherichia coli BW2952], gi... gi\|215263592, gi... - gi\|215485520\|ref\|YP_002327951.1\| DNA-binding ATP-dependent protease La [Escherichia coli O127:H6 str... gi\|218553006, gi... - gi\|218553006\|ref\|YP_002385919.1\| DNA-binding ATP-dependent protease La [Escherichia coli IAI1], gi\|2... gi\|218693902, gi... - gi\|218693902\|ref\|YP_002401569.1\| DNA-binding ATP-dependent protease La [Escherichia coli 55989], gi\|... LON_ECOLI - ATP-dependent protease La (EC 3.4.21.53) - Escherichia coli gi\|218698649, gi... - gi\|218698649\|ref\|YP_002406278.1\| DNA-binding ATP-dependent protease La [Escherichia coli IAI39], gi\|... gi\|218703723, gi... - gi\|218703723\|ref\|YP_002411242.1\| DNA-binding ATP-dependent protease La [Escherichia coli UMN026], gi... LON_ECOL6 - Lon protease OS=Escherichia coli O6 GN=lon PE=2 SV=1 EG10542 - DNA-binding ATP-dependent protease La / DNA-binding, ATP-dependent protease LA; lon mutants form lon... gi\|73854491, gi\|... - gi\|74311014\|ref\|YP_309433.1\| DNA-binding ATP-dependent protease La [Shigella sonnei Ss046], gi\|73854... EG10542 - DNA-binding ATP-dependent protease La / DNA-binding, ATP-dependent protease LA; lon mutants form lon... gi\|85674579, gi\|... - gi\|89107309\|ref\|AP_001089.1\| DNA-binding ATP-dependent protease La [Escherichia coli str. K-12 subst... LON_ECOL6 - Lon protease OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=lon PE=3 SV=1 gi\|157065646, gi... - gi\|75194660\|ref\|ZP_00704730.1\| COG0466: ATP-dependent Lon protease, bacterial type [Escherichia coli... gi\|75209804 - gi\|75209804\|ref\|ZP_00710006.1\| COG0466: ATP-dependent Lon protease, bacterial type [Escherichia coli... gi\|194437366, gi... - gi\|83587105\|ref\|ZP_00925735.1\| COG0466: ATP-dependent Lon protease, bacterial type [Escherichia coli... gi\|75189508, gi\|... - gi\|75189508\|ref\|ZP_00702775.1\| COG0466: ATP-dependent Lon protease, bacterial type [Escherichia coli... gi\|170021188, gi... - gi\|170021188\|ref\|YP_001726142.1\| DNA-binding ATP-dependent protease La [Escherichia coli ATCC 8739],... gi\|75239064, gi\|... - gi\|75239064\|ref\|ZP_00723046.1\| COG0466: ATP-dependent Lon protease, bacterial type [Escherichia coli... gi\|110342292, gi... - gi\|110640700\|ref\|YP_668428.1\| DNA-binding ATP-dependent protease La [Escherichia coli 536], gi\|11034... gi\|169887860, gi... - gi\|170080025\|ref\|YP_001729345.1\| DNA-binding ATP-dependent protease La [Escherichia coli str. K-12 s... gi\|193064117, gi... - gi\|75257915\|ref\|ZP_00729393.1\| COG0466: ATP-dependent Lon protease, bacterial type [Escherichia coli... gi\|170519957, gi... - gi\|170682239\|ref\|YP_001742583.1\| ATP-dependent protease La [Escherichia coli SMS-3-5], gi\|170519957\|... gi\|75226958 - gi\|75226958\|ref\|ZP_00713833.1\| COG0466: ATP-dependent Lon protease, bacterial type [Escherichia coli... gi\|188494694, gi... - gi\|188494694\|ref\|ZP_03001964.1\| ATP-dependent protease La [Escherichia coli 53638], gi\|188489893\|gb\|... gi\|75238192 - gi\|75238192\|ref\|ZP_00722193.1\| COG0466: ATP-dependent Lon protease, bacterial type [Escherichia coli... gi\|209910915, gi... - gi\|209917656\|ref\|YP_002291740.1\| DNA-binding ATP-dependent protease La [Escherichia coli SE11], gi\|2... gi\|253972410, gi... - gi\|254160509\|ref\|YP_003043617.1\| DNA-binding ATP-dependent protease La [Escherichia coli B str. REL6... gi\|254287313, gi... - gi\|254287313\|ref\|YP_003053061.1\| DNA-binding ATP-dependent protease La [Escherichia coli BL21(DE3)],...	0.0	[1..784]	[1..784]
gi\|187427314, gi... - gi\|75177623\|ref\|ZP_00697704.1\| COG0466: ATP-dependent Lon protease, bacterial type [Shigella boydii ... gi\|82542927, gi\|... - gi\|82542927\|ref\|YP_406874.1\| DNA-binding ATP-dependent protease La [Shigella boydii Sb227], gi\|81244...	0.0	[1..784]	[1..784]
gi\|124498426, gi... - gi\|124531648\|ref\|ZP_01701836.1\| ATP-dependent protease La [Escherichia coli B], gi\|124498426\|gb\|EAY4... gi\|91209513, gi\|... - gi\|91209513\|ref\|YP_539499.1\| DNA-binding ATP-dependent protease La [Escherichia coli UTI89], gi\|9107... gi\|26246450, gi\|... - gi\|26246450\|ref\|NP_752489.1\| DNA-binding ATP-dependent protease La [Escherichia coli CFT073], gi\|261... gi\|227838636, gi... - gi\|227884550\|ref\|ZP_04002355.1\| DNA-binding ATP-dependent protease La [Escherichia coli 83972], gi\|2... gi\|209743834, gi... - gi\|209743840\|gb\|ACI70227.1\| endopeptidase La [Escherichia coli], gi\|209743834\|gb\|ACI70224.1\| endopep... gi\|237707566, gi... - gi\|237707566\|ref\|ZP_04538047.1\| DNA-binding ATP-dependent protease La [Escherichia sp. 3_2_53FAA], g...	0.0	[1..784]	[16..799]
gi\|207855930, gi... - gi\|207855930\|ref\|YP_002242581.1\| DNA-binding ATP-dependent protease La [Salmonella enterica subsp. e... gi\|224466815, gi... - gi\|224582288\|ref\|YP_002636086.1\| Lon protease [Salmonella enterica subsp. enterica serovar Paratyphi... gi\|16418957, gi\|... - gi\|16763831\|ref\|NP_459446.1\| DNA-binding ATP-dependent protease La [Salmonella typhimurium LT2], gi\|... gi\|204930547, gi... - gi\|204930547\|ref\|ZP_03221477.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serov... gi\|238911419 - gi\|238911419\|ref\|ZP_04655256.1\| DNA-binding ATP-dependent protease La [Salmonella enterica subsp. en... gi\|205351761, gi... - gi\|205351761\|ref\|YP_002225562.1\| DNA-binding ATP-dependent protease La [Salmonella enterica subsp. e... gi\|198244399, gi... - gi\|198244399\|ref\|YP_002214404.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica sero... gi\|199601867, gi... - gi\|200389422\|ref\|ZP_03216033.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serov... gi\|197212263, gi... - gi\|197248560\|ref\|YP_002145431.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica sero... gi\|197264938, gi... - gi\|197264938\|ref\|ZP_03165012.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serov... gi\|194456566, gi... - gi\|194470202\|ref\|ZP_03076186.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serov... gi\|194735362, gi... - gi\|194735362\|ref\|YP_002113481.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica sero... gi\|168818938, gi... - gi\|205343953\|gb\|EDZ30717.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serovar W... gi\|194450573, gi... - gi\|194450573\|ref\|YP_002044485.1\| DNA-binding ATP-dependent protease La [Salmonella enterica subsp. e... gi\|205349766, gi... - gi\|205349766\|gb\|EDZ36397.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serovar H... gi\|168465544, gi... - gi\|195631706\|gb\|EDX50226.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serovar N... gi\|197289469, gi... - gi\|197289469\|gb\|EDY28832.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serovar S... gi\|205340013, gi... - gi\|205340013\|gb\|EDZ26777.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serovar H... gi\|205330861, gi... - gi\|205330861\|gb\|EDZ17625.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serovar 4... gi\|168231439, gi... - gi\|205334095\|gb\|EDZ20859.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serovar K... gi\|161364719, gi... - gi\|161615355\|ref\|YP_001589320.1\| DNA-binding ATP-dependent protease La [Salmonella enterica subsp. e... gi\|62179062, gi\|... - gi\|62179062\|ref\|YP_215479.1\| DNA-binding ATP-dependent protease La [Salmonella enterica subsp. enter... gi\|205323385, gi... - gi\|205323385\|gb\|EDZ11224.1\| ATP-dependent protease La [Salmonella enterica subsp. enterica serovar S... lcl\|NC_016856.1_... - [gene=lon] [protein=DNA-binding ATP-dependent protease La] [protein_id=YP_005236147.1] [location=506...	0.0	[1..784]	[1..784]
gi\|189362422, gi... - gi\|189362422\|gb\|EDU80841.1\| ATP-dependent protease La [Escherichia coli O157:H7 str. EC4486], gi\|168... gi\|25289966 - pir\|\|E90690 endopeptidase La [imported] - Escherichia coli (strain O157:H7, substrain RIMD 0509952) gi\|195940566 - gi\|195940566\|ref\|ZP_03085948.1\| DNA-binding ATP-dependent protease La [Escherichia coli O157:H7 str.... gi\|13359950, gi\|... - gi\|15829747\|ref\|NP_308520.1\| DNA-binding ATP-dependent protease La [Escherichia coli O157:H7 str. Sa... gi\|254791623, gi... - gi\|254791623\|ref\|YP_003076460.1\| DNA-binding ATP-dependent protease La [Escherichia coli O157:H7 str... gi\|13359950, gi\|... - gi\|15829747\|ref\|NP_308520.1\| endopeptidase La [Escherichia coli O157:H7], gi\|13359950\|dbj\|BAB33916.1... gi\|168754544, gi... - gi\|189357958\|gb\|EDU76377.1\| ATP-dependent protease La [Escherichia coli O157:H7 str. EC4401], gi\|168... gi\|189369044, gi... - gi\|189369044\|gb\|EDU87460.1\| ATP-dependent protease La [Escherichia coli O157:H7 str. EC4501], gi\|168...	0.0	[1..784]	[1..784]
gi\|30040185, gi\|... - gi\|30061941\|ref\|NP_836112.1\| DNA-binding ATP-dependent protease La [Shigella flexneri 2a str. 2457T]... gi\|110614015, gi... - gi\|110804467\|ref\|YP_687987.1\| DNA-binding ATP-dependent protease La [Shigella flexneri 5 str. 8401],... gi\|56383210, gi\|... - gi\|56479659\|ref\|NP_706333.2\| DNA-binding ATP-dependent protease La [Shigella flexneri 2a str. 301], ...	0.0	[1..784]	[1..784]
gi\|117622699, gi... - gi\|117622699\|ref\|YP_851612.1\| DNA-binding ATP-dependent protease La [Escherichia coli APEC O1], gi\|1...	0.0	[1..784]	[16..799]
gi\|238723958, gi... - gi\|77974301\|ref\|ZP_00829842.1\| COG0466: ATP-dependent Lon protease, bacterial type [Yersinia frederi... gi\|122090301, gi... - gi\|123443340\|ref\|YP_001007314.1\| DNA-binding ATP-dependent protease La [Yersinia enterocolitica subs...	0.0	[1..784]	[1..784]

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Predicted Domain #1

Region A:
Residues: [1-116]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNPERSERIE IPVLPLRDVV VYPHMVIPLF VGREKSIRCL EAAMDHDKKI MLVAQKEAST  60
   61 DEPGVNDLFT VGTVASILQM LKLPDGTVKV LVEGLQRARI SALSDNGEHF SAKAEY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	31.522879
Match:	2aneA
Description:	Crystal structure of N-terminal domain of E.Coli Lon Protease
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	0.679730538301274	bayes_pls_golite062009
protein binding	0.3997153647519	bayes_pls_golite062009
catalytic activity	0.147263815852997	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [117-493]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LDSPAIDERE QEVLVRTAIS QFEGYIKLNK KIPPEVLTSL NSIDDPARLA DTIAAHMPLK  60
   61 LADKQSVLEM SDVNERLEYL MAMMESEIDL LQVEKRIRNR VKKQMEKSQR EYYLNEQMKA 120
  121 IQKELGEMDD APDENEALKR KIDAAKMPKE AKEKAEAELQ KLKMMSPMSA EATVVRGYID 180
  181 WMVQVPWNAR SKVKKDLRQA QEILDTDHYG LERVKDRILE YLAVQSRVNK IKGPILCLVG 240
  241 PPGVGKTSLG QSIAKATGRK YVRMALGGVR DEAEIRGHRR TYIGSMPGKL IQKMAKVGVK 300
  301 NPLFLLDEID KMSSDMRGDP ASALLEVLDP EQNVAFSDHY LEVDYDLSDV MFVATSNSMN 360
  361 IPAPLLDRME VIRLSGY

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	4.88
Match:	1ksfX
Description:	N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone; ClpA, an Hsp100 chaperone, AAA+ modules
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
hydrolase activity	2.01016895260654	bayes_pls_golite062009
binding	1.50490858850371	bayes_pls_golite062009
catalytic activity	0.942640875796745	bayes_pls_golite062009
protein binding	0.224801331525112	bayes_pls_golite062009
purine nucleotide binding	0.212617804904722	bayes_pls_golite062009
nucleotide binding	0.208306366193408	bayes_pls_golite062009
purine ribonucleotide binding	0.20666003262166	bayes_pls_golite062009
ribonucleotide binding	0.206647692922152	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [494-583]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TEDEKLNIAK RHLLPKQIER NALKKGELTV DDSAIIGIIR YYTREAGVRS LEREISKLCR  60
   61 KAVKQLLLDK SLKHIEINGD NLHDYLGVQR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.69897
Match:	1qzmA
Description:	alpha-domain of ATPase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
hydrolase activity	2.18454736627863	bayes_pls_golite062009
binding	1.56871478970164	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
purine nucleotide binding	0.428373955572763	bayes_pls_golite062009
purine ribonucleotide binding	0.424644011903671	bayes_pls_golite062009
ribonucleotide binding	0.424583288440993	bayes_pls_golite062009
nucleotide binding	0.422354428195324	bayes_pls_golite062009
protein binding	0.193768631623192	bayes_pls_golite062009
ATP binding	0.04834397972685	bayes_pls_golite062009
adenyl ribonucleotide binding	0.0149501427627318	bayes_pls_golite062009
adenyl nucleotide binding	0.00365326483311895	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [584-651]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FDYGRADSEN RVGQVTGLAW TEVGGDLLTI ETACVPGKGK LTYTGSLGEV MQESIQAALT  60
   61 VVRARAEK

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	8.251812
Match:	PF05362.4
Description:	No description for PF05362.4 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 #5

Region A:
Residues: [652-784]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LGINPDFYEK RDIHVHVPEG ATPKDGPSAG IAMCTALVSC LTGNPVRADV AMTGEITLRG  60
   61 QVLPIGGLKE KLLAAHRGGI KTVLIPFENK RDLEEIPDNV IADLDIHPVK RIEEVLTLAL 120
  121 QNEPSGMQVV TAK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.154902
Match:	1rr9A
Description:	Catalytic domain of E.coli Lon protease
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
hydrolase activity	1.18773479836745	bayes_pls_golite062009
catalytic activity	0.878454819018611	bayes_pls_golite062009
peptidase activity	0.677675533122378	bayes_pls_golite062009
structural constituent of ribosome	0.543314877411748	bayes_pls_golite062009
peptidase activity, acting on L-amino acid peptides	0.444922294492883	bayes_pls_golite062009
binding	0.423668529068616	bayes_pls_golite062009
structural molecule activity	0.278122898090466	bayes_pls_golite062009
ribonuclease activity	0.214389253755211	bayes_pls_golite062009
protein binding	0.214066724623027	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:

Predicted functions:

Predicted functions:

Predicted functions: