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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1308 IGR1309 IGR1310 IGR1302 IGR1304 IGR1313 IGR1306 IGR1305 IGR1303 IGR1307 IGR1312 IGR1311 HD1780 groES, - HD1785 ybgE, - HD1779 tolA, - HD1774 ybgC, - HD1778 tolR, - HD1776 tolA, - HD1775 tolQ, - HD1777 cydB, - HD1781 tolB, - HD1773 cydA, - HD1782 groEL, - HD1784 HD1783 HD1780 groES, - HD1785 ybgE, - HD1779 tolA, - HD1774 ybgC, - HD1778 tolR, - HD1776 tolA, - HD1775 tolQ, - HD1777 cydB, - HD1781 tolB, - HD1773 cydA, - HD1782 groEL, - HD1784 HD1783 groES, - HD1785 ybgE, - HD1779 tolA, - HD1774 ybgC, - HD1778 tolR, - HD1776 tolA, - HD1775 tolQ, - HD1777 cydB, - HD1781 tolB, - HD1773 cydA, - HD1782 groEL, - HD1784 HD1780 HD1783
* Calculated from Protein Sequence

Gene ID: HD1781

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
cydB  

Definition:
cytochrome D ubiquinol oxidase, subunit II

Gene Start:
1491666

Gene Stop:
1490530

Gene Length:
1137

Molecular Weight*:
42201

pI*:
8.60

Net Charge*:
2.62

EC:
1.10.3.-  

Functional Class:
Energy metabolism; Electron transport  

Pathway: pathway table

Secondary Evidence:
Green GN, Fang H, Lin RJ, Newton G, Mather M, Georgiou CD, Gennis RB. The nucleotide sequence of the cyd locus encoding the two subunits of the cytochrome d terminal oxidase complex of Escherichia coli. J Biol Chem 1988 Sep 15;263(26):13138-43. Medline: 88330812.

Bebbington KJ, Williams HD.
A role for DNA supercoiling in the regulation of the cytochrome bd oxidase of Escherichia coli.
Microbiology. 2001 Mar;147(Pt 3):591-8.
PMID: 11238966

Cotter PA, Melville SB, Albrecht JA, Gunsalus RP.
Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation.
Mol Microbiol. 1997 Aug;25(3):605-15.
PMID: 9302022

Muller MM, Webster RE.
Characterization of the tol-pal and cyd region of Escherichia coli K-12: transcript analysis and identification of two new proteins encoded by the cyd operon.
J Bacteriol. 1997 Mar;179(6):2077-80.
PMID: 9068659

Comment:
0

Blast Summary:  PSI-Blast Search
Significant hits to cytochrome D enzymes with gapped BLAST; e.g. residues 1-378 are 68% similar to probable cytochrome oxidase subunit II protein (U32787) of Haemophilus influenzae, residues 1-378 are 56% similar to subunit II of cytochrome bd (Y10012) of Klebsiella pneumoniae, residues 1-378 are 54% similar to cytochrome D (D90713) of E. coli.

COGS Summary:  COGS Search
BeTs to 7 clades of COG1294
COG name: Cytochrome bd quinol oxidase and cytochrome oxidase complexes, subunit 2
Functional Class:  C
The phylogenetic pattern of COG1294 is -----q-cEbrh------inx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB003317 (Cytochrome bd ubiquinol oxidase, subunit II) with a combined E-value of 4.7e-149.
    IPB003317A    3-42
    IPB003317B    43-60
    IPB003317C    72-106
    IPB003317D    112-143
    IPB003317E    158-174
    IPB003317F    323-365
    IPB003317E    204-220


ProDom Summary:  Protein Domain Search
Residues 5-364 are 68% similar to a (OXIDASE SUBUNIT II CYTOCHROME) protein domain (PD005057) which is seen in CYOB_HAEIN.

Residues 223-378 are 60% similar to a (CYTOCHROME PROTEOME II SUBUNIT) protein domain (PD188435) which is seen in Q9CM65_PASMU.



Paralogs:  Local Blast Search


HD1781 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 5 to 366 (E-value = 1.7e-194) place HD1781 in the Cyto_ox_2 family which is described as Cytochrome oxidase subunit II (PF02322)

PDB Hit:
No significant hits to the NCBI PDB database.

Gene Protein Sequence:
MIDYEILRFIWWILIAVLLIGFAITDGFDMGVLTLLPIIGKSNVERRVMI
NTVAPHWDGNQVWLLTAGGAIFAAWPTVYAVSFSGFYLAMILVLAALFFR
PVGFEYRAKIDSPKWRNAWDWGLFVGGFVPSLIFGVAFGNLLQGVPFEFN
ELNQAQYTGSFFGLLNPFALLCGALSLTMLMTQGATWLQMKTTGDLRYRA
RSVAQLAAIIVLVIFILAGVWLYFKDGFIITSDLDHNAKSLLSNKTVAVE
NGAWFRNFFEMPVLWIVPMLAILGAMFTVIASKANRSGFAFFSSSIMLLG
VILTAVVSMFPFIMPSISHPEMSLTVWDSTASKYTLTVMLIVACIFVPMV
LAYTGWTYYKMFGRLDAKYLEDNKASAY$

Gene Nucleotide Sequence:  Sequence Viewer
ATGATCGATTATGAAATTCTCCGCTTTATCTGGTGGATATTAATTGCTGT
TTTATTAATCGGCTTTGCGATTACTGATGGCTTTGATATGGGCGTATTAA
CTTTGTTACCTATTATTGGTAAAAGCAATGTTGAACGCCGTGTAATGATA
AATACAGTTGCACCACATTGGGATGGTAACCAAGTTTGGTTATTAACTGC
AGGTGGTGCTATCTTTGCTGCTTGGCCAACCGTGTATGCGGTATCATTTT
CTGGTTTCTATTTAGCGATGATTCTAGTCCTTGCAGCATTATTTTTCCGC
CCGGTTGGTTTTGAGTATCGTGCAAAAATCGACAGTCCAAAATGGCGTAA
TGCGTGGGATTGGGGATTATTTGTTGGTGGTTTTGTTCCGTCATTAATCT
TTGGTGTAGCATTTGGTAATTTATTACAAGGTGTACCATTTGAATTTAAT
GAGCTTAACCAAGCACAATATACCGGTTCATTTTTTGGTTTATTAAATCC
ATTTGCATTGTTGTGTGGTGCATTAAGTCTAACGATGTTGATGACACAAG
GTGCTACTTGGTTGCAAATGAAAACTACAGGTGATTTACGTTACCGTGCA
CGTTCAGTAGCACAGTTGGCTGCTATTATTGTGCTAGTCATCTTTATTTT
AGCGGGCGTTTGGCTGTATTTTAAAGATGGTTTTATTATTACCAGTGATT
TAGATCACAATGCGAAATCGTTGTTAAGTAATAAAACAGTTGCTGTAGAA
AATGGAGCTTGGTTCAGAAACTTTTTTGAAATGCCGGTATTATGGATTGT
ACCAATGTTAGCTATTTTAGGTGCAATGTTTACTGTCATTGCTTCAAAAG
CTAATCGTTCTGGTTTTGCATTTTTCTCATCATCTATTATGTTATTAGGT
GTAATTTTAACTGCTGTAGTCTCCATGTTCCCATTCATTATGCCATCAAT
TTCTCATCCAGAAATGAGTCTGACAGTTTGGGATTCAACAGCAAGTAAAT
ACACGTTAACGGTAATGTTAATCGTTGCATGTATTTTTGTTCCAATGGTA
TTGGCTTATACAGGCTGGACATATTATAAAATGTTTGGTCGTTTAGATGC
TAAATATTTAGAAGATAATAAAGCAAGCGCATACTAA


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