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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1488 IGR1483 IGR1479 IGR1489 IGR1484 IGR1482 IGR1486 IGR1480 IGR1485 IGR1481 IGR1487 HD2014 ybeD, - HD2015 HD2023 HD2011 HD2022 rlpA, - HD2017 lipB, - HD2013 lipA, - HD2012 pbp5,dacA, - HD2016 pbp2, - HD2020 purL, - HD2010 purL, - HD2009 HD2014 ybeD, - HD2015 HD2023 HD2011 HD2022 rlpA, - HD2017 lipB, - HD2013 lipA, - HD2012 pbp5,dacA, - HD2016 pbp2, - HD2020 purL, - HD2010 purL, - HD2009 ybeD, - HD2015 HD2011 HD2022 rlpA, - HD2017 lipB, - HD2013 lipA, - HD2012 pbp5,dacA, - HD2016 pbp2, - HD2020 rodA,mrdB, - HD2019 rodA,mrdB, - HD2019 HD2014 HD2023 purL, - HD2010 purL, - HD2009
* Calculated from Protein Sequence

Gene ID: HD2016

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
pbp5  dacA  

Definition:
D-Ala-D-Ala carboxypeptidase (penicillin-binding protein 5)

Gene Start:
1679137

Gene Stop:
1677956

Gene Length:
1182

Molecular Weight*:
43241

pI*:
9.30

Net Charge*:
4.42

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

Fusetti F, Dijkstra BW.
Purification and light-scattering analysis of penicillin-binding protein 4 from Escherichia coli.
Microb Drug Resist. 1996 Spring;2(1):73-6.
PMID: 9158725

Comment:
0

Blast Summary:  PSI-Blast Search
Many significant hits using gapped BLAST to penicillin-binding proteins from H. influenzae (1169208), E. coli (118224, 1778549, 2506804, 78755), Salmonella typhimurium (585694), among others.

HD2016 is similar to D-Ala-D-Ala carboxypeptidase penicillin binding proteins from T. pallidum (TP0800), C. pneumoniae (CPn0672),C. trachomatis (CT551). No similarities to U. urealyticum, M. genitalium, or M. pneumoniae.

COGS Summary:  COGS Search
BeTs to 7 clades of COG1686
COG name: D-alanyl-D-alanine carboxypeptidase
Functional Class: M
The phylogenetic pattern of COG1686 is --------EBRH----olinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** PR00725 (D-Ala-D-Ala carboxypeptidase 1 (S11) family signature) with a combined E-value of 2.4e-21.
    PR00725A    64-75
    PR00725B    120-137
    PR00725C    147-160


ProDom Summary:  Protein Domain Search
Residues 282-384 are 63% similar to a (CARBOXYPEPTIDASE D-ALANYL-D-ALANINE PRECURSOR) protein domain (PD013409) which is seen in Q9CJR5_PASMU.

Residues 34-92 are 79% similar to a (CARBOXYPEPTIDASE PENICILLIN-BINDING D-ALANYL-D-ALANINE) protein domain (PD003893) which is seen in Q9CJR5_PASMU.

Residues 123-280 are 78% similar to a (CARBOXYPEPTIDASE COMPLETE PROTEOME D-ALANYL-D-ALANINE) protein domain (PD003024) which is seen in Q9CJR5_PASMU.



Paralogs:  Local Blast Search
HD2016 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 27 to 263 (E-value = 2e-127) place HD2016 in the Peptidase_S11 family which is described as D-alanyl-D-alanine carboxypeptidase (PF00768)

PDB Hit:
pdb|1ES4|A Chain A, C98n Mutant Of Streptomyces K15 Dd-Transpep... 91 2e-019
pdb|1ES3|A Chain A, C98a Mutant Of Streptomyces K15 Dd-Transpep... 88 2e-018
pdb|1SKF| Crystal Structure Of The Streptomyces K15 Dd-Trans... 87 3e-018

Gene Protein Sequence:
MKKRLFTSISLVALAFSHSAVAVDASVEFGISAPQLNAQTYVLMDYNSGA
VLASLNPQQRQHPASLTKMMTSYVVGDAIKQGKVKNSDMVTVSENAWARK
FPGSSLMFLDLNTQVSVADLMRGLIIVSGNDAAVALAEHTSGSQQAFIDQ
MNKFGQQFGLKNTHFTTVHGLDEESQYSSALDMAIIGAHVIRDQPEEYKI
YSEKEFKYNIKKPQPNRNGLLWDKTMNVDGMKTGHTNQAGYNLVASATNS
NTRLISVVMGVPTYKGREVESKKLLQWGFANFETVKSLPAGQTVSEQGVY
YGESNKVQLGTLTDSFVTIPKGKTTDLKVRHELTPKHLEAPLTKGQVVGK
VIYQLDSKDIAVHDLQVLQEVKETGLLGKIWDWLALTVKSLFD$

Gene Nucleotide Sequence:  Sequence Viewer
ATGAAGAAAAGATTATTTACATCAATCAGCCTTGTTGCATTAGCTTTTTC
CCACTCAGCAGTAGCAGTAGATGCAAGTGTTGAATTTGGTATTTCAGCAC
CACAATTAAATGCGCAAACTTATGTGTTAATGGACTATAACTCTGGTGCG
GTATTAGCAAGTTTAAATCCTCAACAACGTCAACATCCTGCATCATTAAC
TAAAATGATGACGAGTTATGTTGTCGGTGATGCGATTAAACAAGGTAAAG
TAAAAAACAGTGATATGGTCACAGTAAGTGAAAATGCTTGGGCTCGAAAA
TTTCCGGGTTCATCATTAATGTTTTTAGACTTAAATACCCAAGTGTCTGT
AGCCGATTTAATGCGAGGCTTAATTATTGTTTCAGGTAATGACGCTGCGG
TTGCATTAGCGGAACATACTTCAGGTTCGCAACAAGCGTTTATTGATCAA
ATGAATAAATTTGGTCAACAGTTTGGTTTGAAAAATACGCATTTTACAAC
GGTACATGGTCTAGATGAAGAGAGTCAATATTCATCCGCTTTAGATATGG
CTATTATTGGTGCTCATGTTATTCGTGATCAGCCAGAAGAATATAAAATC
TACTCTGAAAAAGAATTTAAATATAATATTAAAAAACCGCAACCGAATCG
TAATGGCTTATTATGGGATAAAACGATGAATGTGGACGGTATGAAAACCG
GTCACACTAATCAAGCGGGCTATAATTTAGTTGCATCAGCTACTAATAGT
AATACGCGTTTGATTTCTGTCGTGATGGGCGTGCCAACTTATAAAGGTCG
TGAAGTTGAAAGTAAAAAGTTATTACAATGGGGCTTTGCTAATTTCGAGA
CGGTTAAATCATTGCCTGCGGGTCAAACTGTTTCAGAACAAGGCGTTTAC
TATGGTGAAAGTAATAAAGTTCAACTTGGTACGTTAACGGATAGTTTTGT
CACGATTCCTAAAGGCAAAACAACAGATTTGAAAGTTCGCCATGAGTTAA
CACCTAAACATTTAGAAGCGCCATTAACTAAAGGTCAAGTTGTGGGGAAA
GTGATTTATCAATTAGACAGTAAAGATATTGCGGTGCACGATTTGCAAGT
ATTACAAGAAGTGAAAGAAACGGGGCTTTTAGGCAAAATATGGGATTGGT
TAGCATTAACCGTAAAAAGTTTATTTGACTAG


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