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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1382 IGR1389 IGR1387 IGR1384 IGR1386 IGR1385 IGR1381 IGR1383 IGR1390 IGR1388 HD1893 qacE, - HD1891 HD1892 secE, - HD1886 nusG, - HD1885 dprA, - HD1888 glmS, - HD1894 def, - HD1889 rfaD, - HD1890 HD1887 HD1893 qacE, - HD1891 HD1892 secE, - HD1886 nusG, - HD1885 dprA, - HD1888 glmS, - HD1894 def, - HD1889 rfaD, - HD1890 HD1887 qacE, - HD1891 HD1892 secE, - HD1886 nusG, - HD1885 dprA, - HD1888 glmS, - HD1894 HD1893 def, - HD1889 rfaD, - HD1890 HD1887
* Calculated from Protein Sequence

Gene ID: HD1889

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
def  

Definition:
peptide deformylase (PDF) (Polypeptide deformylase)

Gene Start:
1588176

Gene Stop:
1588691

Gene Length:
516

Molecular Weight*:
19354

pI*:
5.20

Net Charge*:
-5.22

EC:
3.5.1.27  3.5.1.31  3.5.1.88  

Functional Class:
Translation; Protein modification and translation factors  

Pathway: pathway table
Glyoxylate and dicarboxylate metabolism
Methionine metabolism

Secondary Evidence:
Mazel,D., Pochet,S. and Marliere,P.
Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation.
EMBO J. 13(4): 914-923. 1994.
Medline: 94155856.

Meinnel,T. and Blanquet,S.
Enzymatic properties of Escherichia coli peptide deformylase.
J.Bacteriol. 177(7): 1883-1887.1995.
Medline: 95204359.

Meinnel,T., Guillon,J.M., Mechulam,Y. and Blanquet,S.
The Escherichia coli fmt gene, encoding methionyl-tRNA(fMet)
formyltransferase, escapes metabolic control
J. Bacteriol. 175 (4), 993-1000 (1993)
Medline: 93163064


Comment:


Blast Summary:  PSI-Blast Search
Several significant hits using gapped BLAST to peptide deformylase (PDF) from H. influenzae (1169264), E. coli (120450, 3660174), Neisseria meningitidis (7225325), among others. Also signficant hits to pepteide deformylase catalytic core from E. coli (2098360, 2981897), and to peptide deformylase chain A from E. coli (4699740).

HD1889 is similar to polypeptide deformylase from T. pallidum (TP0757), C. trachomatis (CT353), C. pneumoniae (CPn1067), M. genitalium (MG106), M. pneumoniae (MP0586), and U. urealyticum (UU465).

COGS Summary:  COGS Search
BeTs to 12 clades of COG0242
COG name: N-formylmethionyl-tRNA deformylase
Functional Class: J
The phylogenetic pattern of COG0242 is -----qvceBrhujgpolinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB000181 (Formylmethionine deformylase) with a combined E-value of 7.9e-57.
    IPB000181A    21-61
    IPB000181B    73-88
    IPB000181C    101-147
    IPB000181C    113-159


ProDom Summary:  Protein Domain Search
Residues 6-143 are 73% similar to a (DEFORMYLASE POLYPEPTIDE HYDROLASE) protein domain (PD003844) which is seen in DEF_HAEIN.



Paralogs:  Local Blast Search
HD1889 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 3 to 153 (E-value = 1.5e-82) place HD1889 in the Pep_deformylase family which is described as Polypeptide deformylase (PF01327)

PDB Hit:
pdb|1BS4|A Chain A, Peptide Deformylase As Zn2+ Containing Form... 194 6e-051
pdb|1DFF| Peptide Deformylase 194 6e-051
pdb|1DEF| Peptide Deformylase Catalytic Core (Residues 1 - 1... 178 5e-046

Gene Protein Sequence:
MSVLQVVLYPDDRLTKVCEPVTQVDDELNQFIDDMFDTMYQEGGIGLAAS
QVGVLKRVITIDIEGDKTNQVVLINPEILESCGETGIEEGCLSIPGYRAL
VPRKEKITVKALNRQGEEVIYHADDLFAICIQHEIDHLNGIVFVDHISNL
KRQRIKDKMQKLKKQLYRSKA$

Gene Nucleotide Sequence:  Sequence Viewer
ATGTCAGTTTTACAAGTAGTACTTTATCCAGATGACCGATTAACTAAAGT
ATGTGAACCGGTCACACAAGTTGATGATGAATTAAATCAATTCATTGATG
ATATGTTTGATACAATGTATCAAGAAGGCGGTATCGGGCTCGCAGCCTCA
CAAGTGGGCGTATTAAAGCGAGTTATTACCATTGATATAGAAGGTGATAA
AACTAATCAAGTAGTATTAATTAATCCAGAAATTTTAGAGTCGTGTGGCG
AAACGGGGATTGAAGAAGGTTGCTTGTCTATCCCAGGCTATCGAGCCTTA
GTCCCTCGTAAAGAAAAGATCACCGTCAAAGCACTAAATCGCCAAGGCGA
AGAAGTGATTTACCACGCAGATGATCTCTTTGCTATTTGTATTCAGCACG
AAATCGATCATCTAAATGGCATTGTCTTTGTTGATCATATTTCTAATTTA
AAGCGCCAACGCATAAAAGACAAAATGCAAAAATTGAAAAAACAACTCTA
TCGATCCAAAGCATAG


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