YRC Public Data Repository - Protein Structure Prediction

Protein:	CYDB_ECOLI
Organism:	Escherichia coli
Length:	379 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 CYDB_ECOLI.

Description	E-value	Query Range	Subject Range
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...	413.0	[0..1]	[379..1]
gi\|157158603, gi... - gi\|75189755\|ref\|ZP_00703022.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Escherichia co...	412.0	[0..1]	[379..1]
gi\|62179315, gi\|... - gi\|62179315\|ref\|YP_215732.1\| cytochrome d terminal oxidase polypeptide subunit II [Salmonella enteri...	412.0	[0..1]	[379..1]
gi\|82776011, gi\|... - gi\|82776011\|ref\|YP_402358.1\| cytochrome d terminal oxidase polypeptide subunit II [Shigella dysenter...	411.0	[0..1]	[379..1]
gi\|34420278 - gi\|34420278\|gb\|AAQ67423.1\| cytochrome d subunit B [Klebsiella oxytoca]	409.0	[0..1]	[379..1]
gi\|1926319 - gi\|1926319\|emb\|CAA71118.1\| subunit II of cytochrome bd [Klebsiella pneumoniae]	409.0	[0..1]	[379..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...	409.0	[0..1]	[379..1]
gi\|69949673, gi\|... - gi\|69949673\|ref\|ZP_00637670.1\| Cytochrome bd ubiquinol oxidase, subunit II [Shewanella frigidimarina...	409.0	[0..1]	[379..1]
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...	408.0	[0..1]	[379..1]
gi\|167057035, gi... - gi\|167424186\|ref\|ZP_02315939.1\| cytochrome d ubiquinol oxidase, subunit II [Yersinia pestis biovar M... gi\|166962393, gi... - gi\|167419652\|ref\|ZP_02311405.1\| cytochrome d ubiquinol oxidase, subunit II [Yersinia pestis biovar O... gi\|186697575, gi... - gi\|186894549\|ref\|YP_001871661.1\| cytochrome d ubiquinol oxidase, subunit II [Yersinia pseudotubercul... gi\|169751719, gi... - gi\|170025185\|ref\|YP_001721690.1\| cytochrome d ubiquinol oxidase, subunit II [Yersinia pseudotubercul... Q66D97\|Q66D97_YERPS - Cytochrome D ubiquinol oxidase subunit II - Yersinia pseudotuberculosis gi\|149366882, gi... - gi\|149366882\|ref\|ZP_01888916.1\| cytochrome D ubiquinol oxidase subunit II [Yersinia pestis CA88-4125... gi\|108813040, gi... - gi\|229903481\|ref\|ZP_04518594.1\| cytochrome D ubiquinol oxidase subunit II [Yersinia pestis Nepal516]... gi\|162351299, gi... - gi\|77636423\|ref\|ZP_00798497.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Yersinia pesti... gi\|152961444, gi... - gi\|77632111\|ref\|ZP_00794697.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Yersinia pseud... gi\|165924808, gi... - gi\|165924808\|ref\|ZP_02220640.1\| cytochrome d ubiquinol oxidase, subunit II [Yersinia pestis biovar O... gi\|166211787, gi... - gi\|166211787\|ref\|ZP_02237822.1\| cytochrome d ubiquinol oxidase, subunit II [Yersinia pestis biovar A... gi\|165913696, gi... - gi\|89105197\|ref\|ZP_01177721.1\| COG1294: Cytochrome bd-type quinol oxidase, subunit 2 [Yersinia pesti... gi\|166011570, gi... - gi\|166011570\|ref\|ZP_02232468.1\| cytochrome d ubiquinol oxidase, subunit II [Yersinia pestis biovar A... gi\|229841054, gi... - gi\|229841054\|ref\|ZP_04461213.1\| cytochrome D ubiquinol oxidase subunit II [Yersinia pestis biovar Or... gi\|229843158, gi... - gi\|229843158\|ref\|ZP_04463304.1\| cytochrome D ubiquinol oxidase subunit II [Yersinia pestis biovar Or... gi\|229703880, gi... - gi\|229893995\|ref\|ZP_04509181.1\| cytochrome D ubiquinol oxidase subunit II [Yersinia pestis Pestoides... gi\|22126938, gi\|... - gi\|22126938\|ref\|NP_670361.1\| cytochrome D ubiquinol oxidase subunit II [Yersinia pestis KIM], gi\|219... gi\|145599843, gi... - gi\|145599843\|ref\|YP_001163919.1\| cytochrome D ubiquinol oxidase subunit II [Yersinia pestis Pestoide... gi\|25285476 - pir\|\|AF0137 cytochrome D ubiquinol oxidase chain II (EC 1.10.3.-) [imported] - Yersinia pestis (stra... gi\|16121418, gi\|... - gi\|218928286\|ref\|YP_002346161.1\| cytochrome D ubiquinol oxidase subunit II [Yersinia pestis CO92], g... gi\|51588778, gi\|... - gi\|51595496\|ref\|YP_069687.1\| cytochrome D ubiquinol oxidase subunit II [Yersinia pseudotuberculosis ...	407.0	[0..1]	[379..1]

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Predicted Domain #1

Region A:
Residues: [1-111]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MIDYEVLRFI WWLLVGVLLI GFAVTDGFDM GVGMLTRFLG RNDTERRIMI NSIAPHWDGN  60
   61 QVWLITAGGA LFAAWPMVYA AAFSGFYVAM ILVLASLFFR PVGFDYRSKI E

[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: [112-320]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ETRWRNMWDW GIFIGSFVPP LVIGVAFGNL LQGVPFNVDE YLRLYYTGNF FQLLNPFGLL  60
   61 AGVVSVGMII TQGATYLQMR TVGELHLRTR ATAQVAALVT LVCFALAGVW VMYGIDGYVV 120
  121 KSTMDHYAAS NPLNKEVVRE AGAWLVNFNN TPILWAIPAL GVVLPLLTIL TARMDKAAWA 180
  181 FVFSSLTLAC IILTAGIAMF PFVMPSSTM

[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: [321-379]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNASLTMWDA TSSQLTLNVM TWVAVVLVPI ILLYTAWCYW KMFGRITKED IERNTHSLY

[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