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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR7 IGR6 IGR9 IGR8 IGR3 IGR10 IGR5 IGR1.1 IGR4 IGR2 IGR11 atpE, - HD0005 HD0003 atpC, - HD0011 atpF, - HD0006 atpH, - HD0007 gidB, - HD0002 atpA, - HD0004 atpG, - HD0009 atpD, - HD0010 atpA, - HD0008 gidA, - HD0001 atpE, - HD0005 HD0003 atpC, - HD0011 atpF, - HD0006 atpH, - HD0007 gidB, - HD0002 atpA, - HD0004 atpG, - HD0009 atpD, - HD0010 atpA, - HD0008 gidA, - HD0001 atpE, - HD0005 HD0003 atpC, - HD0011 atpF, - HD0006 atpH, - HD0007 gidB, - HD0002 atpA, - HD0004 atpG, - HD0009 atpD, - HD0010 atpA, - HD0008 gidA, - HD0001
* Calculated from Protein Sequence

Gene ID: HD0007

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
atpH  

Definition:
ATP synthase F1, subunit delta

Gene Start:
5330

Gene Stop:
5863

Gene Length:
534

Molecular Weight*:
19923

pI*:
4.70

Net Charge*:
-6.04

EC:
3.6.1.34  

Functional Class:
Energy metabolism; ATP-proton motive force interconversion  

Pathway: pathway table
Oxidative phosphorylation

Secondary Evidence:
Mabuchi,K., Kanazawa,H., Kayano,T. and Futai,M.
Nucleotide sequence of the gene coding for the delta subunit of proton translocating ATPase of Escherichia coli.
Biochemical and biophysical research communications. 102 (1), 172-179 (1981)
Medline: 82068433.

Nielsen,J., Hansen,F.G., Hoppe,J., Friedl,P. and von Meyenburg,K. The nucleotide sequence of the atp genes coding for the F0 subunits a, b, c and the F1 subunit delta of the membrane bound ATP synthase of Escherichia coli.
Mol. Gen. Genet. 184 (1), 33-39 (1981)
Medline: 82147764.

Cain,B.D. and Simoni,R.D.
Impaired proton conductivity resulting from mutations in the a subunit of F1F0 ATPase in Escherichia coli.
J. Biol. Chem. 261 (22), 10043-10050 (1986)
Medline: 86278048.

Cain,B.D. and Simoni,R.D.
Proton translocation by the F1F0ATPase of Escherichia coli. Mutagenic analysis of the a subunit.
J. Biol. Chem. 264 (6), 3292-3300 (1989)
Medline: 89123453.

Valiyaveetil,F.I. and Fillingame,R.H.
Transmembrane topography of subunit a in the Escherichia coli F1F0 ATP synthase.
J. Biol. Chem. 273 (26), 16241-16247 (1998)
Medline: 98298136.

Comment:
From GenBank (gi:114580): This protein seems to be part of the stalk that links F0 to F1. It either transmits conformational changes from F0 into F1 or is implicated in proton conduction. F-type ATPases have two components, CF(1), the catalytic core, and CF(0), the membrane proton channel. CF(1) has five subunits: ALPHA(3), BETA(3), GAMMA(1), DELTA(1), and EPSILON(1). CF(0) has three main subunits: A, B and C.

See also other chains of the F1 subunit: atpA (alpha chain), HD0008; atpB (beta chain), HD0010; atpG (gamma chain), HD0009; atpE (epsilon chain), HD0011.

In addition, see chains of the F0 subunit of this ATPase: atpF (B chain), HD0006; and atp6 (A chain), HD0004; and atpL (C chain), HD0005.

Check the start codon. Hits start at residue 10, a methionine.

Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to atpD proteins; e.g. residues 10-186 are 55% similar to ATPD_HAEIN; residues 10-184 are 54% similar to ATPD_VIBAL; and residues 10-184 are 53% similar to ATPD_ECOLI. Also significant similarities to other bacterial and eukaryotic ATPD sequences.



COGS Summary:  COGS Search
BeTs to 9 clades of COG0712
COG name: FoF1-type ATP synthase delta subunit
Functional Class: C
The phylogenetic pattern of COG0712 is ----yqvcebrh--gp----x
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB000711 (ATP synthase, delta (OSCP) subunit) with a combined E-value of 1.1e-10.
    IPB000711    143-171


ProDom Summary:  Protein Domain Search
Residues 1-79 are 56% similar to a (SYNTHASE DELTA ION CF1) protein domain (PD286977) which is seen in Q9KNH2_VIBCH.

Residues 80-171 are 54% similar to a (DELTA SYNTHASE CHAIN HYDROLASE) protein domain (PD001250) which is seen in Q9CKW3_PASMU.

Residues 1-92 are 40% similar to a (PROTEOME SYNTHASE ATP COMPLETE) protein domain (PD331865) which is seen in Q9HT17_PSEAE.



Paralogs:  Local Blast Search
HD0007 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 7 to 175 (E-value = 7.5e-50) place HD0007 in the OSCP family which is described as ATP synthase delta (OSCP) subunit (PF00213)

PDB Hit:
pdb|1ABV| N-Terminal Domain Of The Delta Subunit Of The F1f0... 140 1e-034

Gene Protein Sequence:
MSELSTVARPYAKAAFDFALEQGQLDKWQEMLQFSALVAENEQVVEYITS
SLASGQISEIFLQICDDQLDQYGQNFIRVMAENKRLAILPEVFNRFNALR
AEYEAIKKVIVVSATELSQAQEEKIAKAMEKRLGQKVRLTTEIDSTLLTG
IIIKYDDIVIDGSSRGQLNRLTQALSL$

Gene Nucleotide Sequence:  Sequence Viewer
ATGTCAGAATTAAGTACAGTAGCTCGCCCCTATGCTAAAGCAGCTTTTGA
TTTTGCTTTAGAGCAAGGTCAGTTGGATAAATGGCAAGAAATGTTACAGT
TTTCAGCATTAGTCGCTGAAAATGAACAAGTAGTAGAATATATTACTTCA
TCTCTTGCAAGCGGTCAGATTTCAGAAATTTTTCTTCAAATCTGTGATGA
CCAACTTGATCAATATGGGCAAAATTTTATTCGCGTAATGGCTGAAAATA
AACGTTTAGCTATTTTACCTGAAGTTTTTAACCGCTTTAACGCATTACGT
GCTGAGTATGAAGCGATTAAAAAGGTGATTGTCGTTTCAGCAACCGAATT
AAGTCAAGCACAAGAAGAAAAAATCGCCAAGGCGATGGAAAAACGCTTAG
GGCAAAAAGTTCGTTTAACAACCGAAATTGATAGCACATTACTTACTGGT
ATTATTATTAAATATGATGATATCGTTATCGATGGCTCAAGTCGCGGTCA
GTTAAATCGCTTAACTCAAGCGTTGAGCTTGTAA


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