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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1236 IGR1244 IGR1238 IGR1239 IGR1245 IGR1241 IGR1240 IGR1237 IGR1235 IGR1242 IGR1243 HD1694 greA, - HD1699 HD1698 mod, - HD1693 mod, - HD1691 imp, - HD1704 purH, - HD1702 pbp4, - HD1701 HD1697 tpn, - HD1696 pbp4,dacB, - HD1700 purH, - HD1703 HD1694 greA, - HD1699 HD1698 mod, - HD1693 mod, - HD1691 imp, - HD1704 purH, - HD1702 pbp4, - HD1701 HD1697 tpn, - HD1696 pbp4,dacB, - HD1700 purH, - HD1703 Type: tandem, Name:  - 18 HD1694 greA, - HD1699 HD1698 mod, - HD1693 mod, - HD1691 imp, - HD1704 mod, - HD1692 mod, - HD1692 purH, - HD1702 pbp4, - HD1701 HD1697 tpn, - HD1696 pbp4,dacB, - HD1700 purH, - HD1703 tpn, - HD1695 tpn, - HD1695
* Calculated from Protein Sequence

Gene ID: HD1700

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
pbp4  dacB  

Definition:
penicillin-binding protein 4 precursor/D-ala-D-ala carboxypeptidase

Gene Start:
1415608

Gene Stop:
1416564

Gene Length:
957

Molecular Weight*:
34748

pI*:
10.00

Net Charge*:
11.91

EC:
3.4.16.4  

Functional Class:
Cell envelope; Murein sacculus and peptidoglycan  

Pathway: pathway table

Secondary Evidence:
McDonough MA, Anderson JW, Silvaggi NR, Pratt RF, Knox JR, Kelly JA.
Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins.
J Mol Biol. 2002 Sep 6;322(1):111-22.
PMID: 12215418

Comment:
0

Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to penicillin-binding protein; i.e. residues 8-313 are 59% similar to (U32812) D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase (dacB) of Haemophilus influenzae, residues 39-313 are 42% similar to (AE000399) D-alanyl-D-alanine carboxypeptidase, fraction B; penicillin-binding protein 4 to Escherichia coli, residues 42-316 are 25% similar to (Z99113) penicillin-binding protein of Bacillus subtilis.

COGS Summary:  COGS Search
BeTs to 3 clades of COG2027
COG name: D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4)
Functional Class:  M
The phylogenetic pattern of COG2027 is -------Cebrh---------
Number of proteins in this genome belonging to this COG is 2

Blocks Summary:  Blocks Search
***** PR00922 (D-Ala-D-Ala carboxypeptidase 3 (S13) family signature) with a combined E-value of 2.8e-17.
    PR00922A    67-86
    PR00922B    292-314


ProDom Summary:  Protein Domain Search
Residues 68-179 are 54% similar to a (CARBOXYPEPTIDASE PROTEOME COMPLETE) protein domain (PD011380) which is seen in PBP4_ECOLI.

Residues 39-118 are 62% similar to a (PROTEOME COMPLETE CARBOXYPEPTIDASE) protein domain (PD037943) which is seen in PBP4_HAEIN.

Residues 120-281 are 65% similar to a (CARBOXYPEPTIDASE DD- ENDOPEPTIDASE) protein domain (PD037945) which is seen in PBP4_HAEIN.



Paralogs:  Local Blast Search


HD1700 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 69 to 316 (E-value = 8.6e-30) place HD1700 in the Peptidase_S13 family which is described as D-Ala-D-Ala carboxypeptidase 3 (S13) family (PF02113)

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

Gene Protein Sequence:
MLLKSIHLSLKKTALIGFTLFYSAFATAAINTNAIVANLPAGSSASFIAK
NLDTKQIITQYQSDIFMLPASTQKVFTALAAKLALPNDFRFHTTLLTNGT
IQKGILQGDLIAKFTGDPLLTSGHLYQLISQLKKQGISKITGDLILDTSV
FASHNKATGWVWNDLAMCFNSPPAAINVDHNCFHIMLDANQNVGQFAKVN
VPAAYPVQVFSSAYIVDKAEAPYCQLDVVVNDNNRYHVKGCMARQTQPFG
LSFSVQDPVAYGANLIKANLTRLGIAFNGKVQESLNKQQGHLLAEHNSEP
LPTLLRKMMKKSDKSNCR$

Gene Nucleotide Sequence:  Sequence Viewer
ATGTTGTTAAAATCCATTCACTTATCTCTCAAAAAAACCGCGTTGATTGG
TTTCACGCTTTTTTACTCGGCTTTTGCCACTGCGGCCATTAATACCAATG
CAATTGTAGCTAATTTACCTGCGGGTTCTTCTGCCAGCTTTATTGCTAAA
AACCTAGATACTAAGCAGATCATTACACAATATCAAAGTGATATTTTTAT
GTTACCTGCTAGTACACAAAAGGTGTTTACTGCACTCGCAGCAAAACTTG
CTTTACCAAATGATTTCCGCTTTCACACAACACTGTTAACCAATGGCACA
ATTCAAAAAGGTATATTACAAGGTGATTTAATTGCTAAATTTACAGGCGA
TCCGCTCTTAACAAGTGGCCACCTTTATCAATTAATCAGCCAATTGAAGA
AACAAGGCATTAGCAAAATTACAGGTGATTTAATTTTAGACACTTCTGTT
TTTGCTAGCCATAATAAAGCAACCGGTTGGGTTTGGAATGATTTAGCCAT
GTGTTTTAATTCCCCACCAGCGGCTATCAATGTTGATCATAATTGTTTCC
ATATTATGCTAGATGCCAACCAAAATGTGGGGCAATTCGCGAAAGTCAAC
GTGCCTGCCGCTTATCCAGTGCAAGTGTTTAGTTCAGCGTATATTGTCGA
TAAAGCAGAAGCGCCTTATTGTCAATTAGATGTGGTGGTAAATGATAATA
ACCGCTACCACGTAAAAGGCTGTATGGCTCGCCAAACGCAACCTTTCGGT
TTAAGTTTTTCTGTGCAAGATCCTGTAGCATATGGTGCAAATCTAATCAA
AGCAAACTTAACTCGTTTAGGCATTGCGTTTAATGGCAAAGTTCAAGAAT
CACTCAATAAACAACAAGGGCATTTACTTGCAGAACATAATTCTGAACCA
TTACCAACCTTACTGAGAAAAATGATGAAAAAATCGGATAAATCAAATTG
CCGATAG


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