YRC Public Data Repository - Protein Structure Prediction

Protein:	APPB_ECOLI
Organism:	Escherichia coli
Length:	378 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 APPB_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|28806041, gi\|... - gi\|28897828\|ref\|NP_797433.1\| cytochrome d ubiquinol oxidase, subunit II [Vibrio parahaemolyticus RIM... gi\|28806041 - gi\|28806041\|dbj\|BAC59317.1\| cytochrome d ubiquinol oxidase, subunit II [Vibrio parahaemolyticus RIMD...	407.0	[0..1]	[378..1]
gi\|213999925 - gi\|213999925\|ref\|ZP_03410660.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subsp... gi\|213649146 - gi\|213649146\|ref\|ZP_03379199.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subsp... gi\|56128399, gi\|... - gi\|56414142\|ref\|YP_151217.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subsp. e... lcl\|NC_016856.1_... - [gene=cydB] [protein=cytochrome d terminal oxidase polypeptide subunit II] [protein_id=YP_005236462.... gi\|205322564, gi... - gi\|205322564\|gb\|EDZ10403.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica subsp. e... gi\|161364390, gi... - gi\|161615026\|ref\|YP_001588991.1\| hypothetical protein SPAB_02786 [Salmonella enterica subsp. enteric... gi\|29138178, gi\|... - gi\|29142547\|ref\|NP_805889.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subsp. e... gi\|205347173, gi... - gi\|205347173\|gb\|EDZ33804.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica subsp. e... gi\|16759680 - gi\|16759680\|ref\|NP_455297.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subsp. e... gi\|168240599, gi... - gi\|205340298\|gb\|EDZ27062.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica subsp. e... gi\|16501973, gi\|... - gi\|25285480\|pir\|\|AI0591 cytochrome d ubiquinol oxidase chain II [imported] - Salmonella enterica sub... gi\|168238891, gi... - gi\|197288371\|gb\|EDY27752.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica subsp. e... gi\|16764111, gi\|... - gi\|16764111\|ref\|NP_459726.1\| cytochrome d terminal oxidase polypeptide subunit II [Salmonella typhim... gi\|205328885, gi... - gi\|205328885\|gb\|EDZ15649.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica subsp. e... gi\|238911673 - gi\|238911673\|ref\|ZP_04655510.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subsp... gi\|205352005, gi... - gi\|205352005\|ref\|YP_002225806.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subs... gi\|204930081, gi... - gi\|204930081\|ref\|ZP_03221102.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica subs... gi\|200390926, gi... - gi\|200390926\|ref\|ZP_03217537.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica subs... gi\|198244832, gi... - gi\|198244832\|ref\|YP_002214711.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica sub... gi\|213425390 - gi\|213425390\|ref\|ZP_03358140.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subsp... gi\|213423948 - gi\|213423948\|ref\|ZP_03356928.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subsp... gi\|213051759 - gi\|213051759\|ref\|ZP_03344637.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subsp... gi\|206707988, gi... - gi\|207856185\|ref\|YP_002242836.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subs... gi\|194450450, gi... - gi\|194450450\|ref\|YP_002044775.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica sub... gi\|194443845, gi... - gi\|194443845\|ref\|YP_002039982.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica sub... gi\|168820124, gi... - gi\|205343253\|gb\|EDZ30017.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica subsp. e... gi\|168467696, gi... - gi\|195629191\|gb\|EDX48559.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica subsp. e... gi\|197363064, gi... - gi\|197363064\|ref\|YP_002142701.1\| cytochrome d ubiquinol oxidase subunit II [Salmonella enterica subs... gi\|197264628, gi... - gi\|197264628\|ref\|ZP_03164702.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica subs... gi\|197247810, gi... - gi\|197247810\|ref\|YP_002145702.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica sub... gi\|194709910, gi... - gi\|194734408\|ref\|YP_002113849.1\| cytochrome d ubiquinol oxidase, subunit II [Salmonella enterica sub...	405.0	[0..1]	[378..1]
gi\|62179315, gi\|... - gi\|62179315\|ref\|YP_215732.1\| cytochrome d terminal oxidase polypeptide subunit II [Salmonella enteri...	404.0	[0..1]	[378..1]
gi\|151937537, gi... - gi\|254229968\|ref\|ZP_04923370.1\| cytochrome D ubiquinol oxidase, subunit II [Vibrio sp. Ex25], gi\|194...	404.0	[0..1]	[378..1]
gi\|113969584, gi... - gi\|82495198\|ref\|ZP_00880775.1\| Cytochrome bd ubiquinol oxidase, subunit II [Shewanella sp. MR-4], gi... gi\|78686234, gi\|... - gi\|78686234\|ref\|ZP_00851004.1\| Cytochrome bd ubiquinol oxidase, subunit II [Shewanella sp. ANA-3], g... gi\|78689587, gi\|... - gi\|78689587\|ref\|ZP_00854247.1\| Cytochrome bd ubiquinol oxidase, subunit II [Shewanella sp. MR-7], gi...	404.0	[0..1]	[378..1]
gi\|157158603, gi... - gi\|75189755\|ref\|ZP_00703022.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Escherichia co...	403.0	[0..1]	[378..1]
gi\|91188504, gi\|... - gi\|91227611\|ref\|ZP_01261915.1\| cytochrome d ubiquinol oxidase, subunit II [Vibrio alginolyticus 12G0...	402.0	[0..1]	[378..1]
EG10174 - cytochrome d terminal oxidase, subunit II / Cytochrome d (bd-I) ubiquinol oxidase subunit 2; upregul... gi\|227838721, gi... - gi\|227884300\|ref\|ZP_04002105.1\| cytochrome d ubiquinol oxidase subunit II [Escherichia coli 83972], ... gi\|226898514, gi... - gi\|237707304\|ref\|ZP_04537785.1\| cytochrome d terminal oxidase polypeptide subunit II [Escherichia sp... gi\|238899998, gi... - gi\|238899998\|ref\|YP_002925794.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli BW2952]... gi\|242376495, gi... - gi\|251784222\|ref\|YP_002998526.1\| hypothetical protein B21_00682 [Escherichia coli BL21], gi\|24237649... gi\|254287591, gi... - gi\|254287591\|ref\|YP_003053339.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli BL21(DE... gi\|254160803, gi... - gi\|254160803\|ref\|YP_003043911.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli B str. ... gi\|254591291, gi... - gi\|254791891\|ref\|YP_003076728.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli O157:H7... CYDB_ECOLI - Cytochrome d ubiquinol oxidase subunit 2 (EC 1.10.3.-) (Cytochrome d ubiquinol oxidase subunit II) (... gi\|124501505, gi... - gi\|124526811\|ref\|ZP_01698693.1\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli B], gi\|... gi\|218704061, gi... - gi\|218704061\|ref\|YP_002411580.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli UMN026]... gi\|218699106, gi... - gi\|218699106\|ref\|YP_002406735.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli IAI39],... CYDB_ECOL6 - Cytochrome bd-I ubiquinol oxidase subunit 2 OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 /... CYDB_ECO57 - Cytochrome bd-I ubiquinol oxidase subunit 2 OS=Escherichia coli O157:H7 GN=cydB PE=3 SV=1 EG10174 - cytochrome d terminal oxidase, subunit II / Cytochrome d (bd-I) ubiquinol oxidase subunit 2; upregul... gi\|15800450, gi\|... - gi\|15800450\|ref\|NP_286462.1\| cytochrome d terminal oxidase polypeptide subunit II [Escherichia coli ... gi\|215263827, gi... - gi\|215485755\|ref\|YP_002328186.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli O127:H6... gi\|209911244, gi... - gi\|209917985\|ref\|YP_002292069.1\| cytochrome d ubiquinol oxidase subunit II [Escherichia coli SE11], ... gi\|73854735, gi\|... - gi\|74311258\|ref\|YP_309677.1\| cytochrome d terminal oxidase polypeptide subunit II [Shigella sonnei S... gi\|218549693, gi... - gi\|218549693\|ref\|YP_002383484.1\| cytochrome d terminal oxidase, subunit II [Escherichia fergusonii A... gi\|188494157, gi... - gi\|75511621\|ref\|ZP_00734272.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Escherichia co... gi\|217322792, gi... - gi\|217326571\|ref\|ZP_03442655.1\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli O157:H7... gi\|218364416, gi... - gi\|218557647\|ref\|YP_002390560.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli S88], g... gi\|218553261, gi... - gi\|218553261\|ref\|YP_002386174.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli IAI1], ... gi\|218350890, gi... - gi\|218694158\|ref\|YP_002401825.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli 55989],... gi\|218688525, gi... - gi\|218688525\|ref\|YP_002396737.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli ED1a], ... gi\|157160216, gi... - gi\|75194894\|ref\|ZP_00704964.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Escherichia co... gi\|1651328, gi\|8... - gi\|89107591\|ref\|AP_001371.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli str. K-12 s... gi\|75175933, gi\|... - gi\|75175933\|ref\|ZP_00696120.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Shigella boydi... gi\|91209767, gi\|... - gi\|91209767\|ref\|YP_539753.1\| cytochrome d terminal oxidase polypeptide subunit II [Escherichia coli ... gi\|194439246, gi... - gi\|83585335\|ref\|ZP_00923982.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Escherichia co... gi\|13360228, gi\|... - gi\|15830023\|ref\|NP_308796.1\| cytochrome d terminal oxidase polypeptide subunit II [Escherichia coli ... gi\|110342533, gi... - gi\|110640941\|ref\|YP_668669.1\| cytochrome D ubiquinol oxidase subunit II [Escherichia coli 536], gi\|1... gi\|192926844, gi... - gi\|75256444\|ref\|ZP_00728102.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Escherichia co... gi\|190905679, gi... - gi\|75237350\|ref\|ZP_00721392.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Escherichia co... gi\|191167219, gi... - gi\|75229634\|ref\|ZP_00716171.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Escherichia co... gi\|75209697, gi\|... - gi\|75209697\|ref\|ZP_00709905.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Escherichia co... CYDB_ECOL6 - Cytochrome d ubiquinol oxidase subunit 2 OS=Escherichia coli O6 GN=cydB PE=3 SV=1 gi\|189376477, gi... - gi\|189406108\|ref\|ZP_02826353.2\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli O157:H7... gi\|189373023, gi... - gi\|189404899\|ref\|ZP_02811906.2\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli O157:H7... gi\|195939085 - gi\|195939085\|ref\|ZP_03084467.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli O157:H7 ... gi\|194434018, gi... - gi\|194434018\|ref\|ZP_03066289.1\| cytochrome d ubiquinol oxidase, subunit II [Shigella dysenteriae 101... gi\|208815105, gi... - gi\|208815105\|ref\|ZP_03256284.1\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli O157:H7... gi\|208728662, gi... - gi\|208808861\|ref\|ZP_03251198.1\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli O157:H7... gi\|209159613, gi... - gi\|209398213\|ref\|YP_002269367.1\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli O157:H... gi\|208737190, gi... - gi\|208822997\|ref\|ZP_03263315.1\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli O157:H7... gi\|169888235, gi... - gi\|170080400\|ref\|YP_001729720.1\| cytochrome d terminal oxidase, subunit II [Escherichia coli str. K-... gi\|170020922, gi... - gi\|170020922\|ref\|YP_001725876.1\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli ATCC 8... gi\|187776421, gi... - gi\|187776421\|ref\|ZP_02992951.1\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli O157:H7... gi\|170518495, gi... - gi\|170680777\|ref\|YP_001742844.1\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli SMS-3-... gi\|189402926, gi... - gi\|189402926\|ref\|ZP_03006900.1\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli O157:H7... gi\|189002960, gi... - gi\|189010039\|ref\|ZP_02804235.2\| cytochrome d ubiquinol oxidase, subunit II [Escherichia coli O157:H7...	402.0	[0..1]	[378..1]
gi\|69949673, gi\|... - gi\|69949673\|ref\|ZP_00637670.1\| Cytochrome bd ubiquinol oxidase, subunit II [Shewanella frigidimarina...	402.0	[0..1]	[378..1]
gi\|15641845, gi\|... - gi\|9656371\|gb\|AAF94991.1\| cytochrome d ubiquinol oxidase, subunit II [Vibrio cholerae O1 biovar El T... gi\|11255084 - pir\|\|D82149 cytochrome d ubiquinol oxidase, chain II VC1843 [imported] - Vibrio cholerae (strain N16... gi\|153827562, gi... - gi\|153827562\|ref\|ZP_01980229.1\| cytochrome d ubiquinol oxidase, subunit II [Vibrio cholerae MZO-2], ... gi\|75830160, gi\|... - gi\|75830160\|ref\|ZP_00759443.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Vibrio cholera... gi\|146315243, gi... - gi\|75827168\|ref\|ZP_00756603.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Vibrio cholera... gi\|121727667, gi... - gi\|75814781\|ref\|ZP_00745332.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Vibrio cholera... gi\|227081972, gi... - gi\|227081972\|ref\|YP_002810523.1\| cytochrome d ubiquinol oxidase, subunit II [Vibrio cholerae M66-2],... gi\|121591340, gi... - gi\|121591340\|ref\|ZP_01678628.1\| cytochrome d ubiquinol oxidase, subunit II [Vibrio cholerae 2740-80]... gi\|229355565, gi... - gi\|229508060\|ref\|ZP_04397565.1\| cytochrome d ubiquinol oxidase subunit II [Vibrio cholerae BX 330286... gi\|124117254, gi... - gi\|153225630\|ref\|ZP_01954816.1\| cytochrome d ubiquinol oxidase, subunit II [Vibrio cholerae MAK 757]... gi\|229351666, gi... - gi\|229511701\|ref\|ZP_04401180.1\| cytochrome d ubiquinol oxidase subunit II [Vibrio cholerae B33], gi\|... gi\|229515223, gi... - gi\|229515223\|ref\|ZP_04404683.1\| cytochrome d ubiquinol oxidase subunit II [Vibrio cholerae TMA 21], ... gi\|229518840, gi... - gi\|229518840\|ref\|ZP_04408283.1\| cytochrome d ubiquinol oxidase subunit II [Vibrio cholerae RC9], gi\|... gi\|229342669, gi... - gi\|229520303\|ref\|ZP_04409729.1\| cytochrome d ubiquinol oxidase subunit II [Vibrio cholerae TM 11079-... gi\|229529134, gi... - gi\|229529134\|ref\|ZP_04418524.1\| cytochrome d ubiquinol oxidase subunit II [Vibrio cholerae 12129(1)]... gi\|229607621, gi... - gi\|229607621\|ref\|YP_002878269.1\| cytochrome d ubiquinol oxidase subunit II [Vibrio cholerae MJ-1236]...	402.0	[0..1]	[378..1]

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Predicted Domain #1

Region A:
Residues: [1-110]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MFDYETLRFI WWLLIGVILV VFMISDGFDM GIGCLLPLVA RNDDERRIVI NSVGAHWEGN  60
   61 QVWLILAGGA LFAAWPRVYA AAFSGFYVAM ILVLCSLFFR PLAFDYRGKI

[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: [111-261]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ADARWRKMWD AGLVIGSLVP PVVFGIAFGN LLLGVPFAFT PQLRVEYLGS FWQLLTPFPL  60
   61 LCGLLSLGMV ILQGGVWLQL KTVGVIHLRS QLATKRAALL VMLCFLLAGY WLWVGIDGFV 120
  121 LLAQDANGPS NPLMKLVAVL PGAWMNNFVE S

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [262-378]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PVLWIFPLLG FFCPLLTVMA IYRGRPGWGF LMASLMQFGV IFTAGITLFP FVMPSSVSPI  60
   61 SSLTLWDSTS SQLTLSIMLV IVLIFLPIVL LYTLWSYYKM WGRMTTETLR RNENELY

[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.

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