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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR588 IGR587 IGR585 IGR589 IGR586 IGR591 IGR584 IGR590 adk, - HD0826 ftsQ, - HD0820 ddlB, - HD0821 lpxC,envA, - HD0816 murG, - HD0824 ftsZ, - HD0817 ftsA, - HD0818 HD0827 murC, - HD0823 recN, - HD0815 adk, - HD0826 ftsQ, - HD0820 ddlB, - HD0821 lpxC,envA, - HD0816 murG, - HD0824 ftsZ, - HD0817 ftsA, - HD0818 HD0827 murC, - HD0823 recN, - HD0815 adk, - HD0826 ftsQ, - HD0820 ddlB, - HD0821 lpxC,envA, - HD0816 murG, - HD0824 ftsZ, - HD0817 ftsA, - HD0818 HD0827 murC, - HD0823 recN, - HD0815
* Calculated from Protein Sequence

Gene ID: HD0821

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
ddlB  

Definition:
D-alanine-D-alanine ligase B

Gene Start:
653429

Gene Stop:
652518

Gene Length:
912

Molecular Weight*:
32991

pI*:
5.00

Net Charge*:
-8.11

EC:
6.3.2.4  

Functional Class:
Cell envelope; Murein sacculus and peptidoglycan  

Pathway: pathway table
D-Alanine metabolism
Glycerolipid metabolism
Peptideglycan biosynthesis

Secondary Evidence:
Fan,C., Park,I.S., Walsh,C.T. and Knox,J.R.
D-alanine:D-alanine ligase: phosphonate and phosphinate
intermediates with wild type and the Y216F mutant
Biochemistry 36 (9), 2531-2538 (1997)
MEDLINE: 97207065

Fan,C., Moews,P.C., Walsh,C.T. and Knox,J.R.
Vancomycin resistance: structure of D-alanine:D-alanine ligase at
2.3 A resolution
Science 266 (5184), 439-443 (1994)
MEDLINE: 95025939

al-Bar,O.A., O"Connor,C.D., Giles,I.G. and Akhtar,M.
D-alanine: D-alanine ligase of Escherichia coli. Expression,
purification and inhibitory studies on the cloned enzyme
Biochem. J. 282 (Pt 3), 747-752 (1992)
MEDLINE: 92207163

Robinson,A.C., Kenan,D.J., Sweeney,J. and Donachie,W.D.
Further evidence for overlapping transcriptional units in an
Escherichia coli cell envelope-cell division gene cluster: DNA
sequence and transcriptional organization of the ddl ftsQ region
J. Bacteriol. 167 (3), 809-817 (1986)
MEDLINE: 86304170


Comment:
0

Blast Summary:  PSI-Blast Search
Numerous significant hits using gapped BLAST to D-alanine-D-alanine ligase B from H. influenzae (1169257), E. coli (118407), Neisseria meningitidis (7225647), among others. HD0821 is 64% similar to residues 1-306 from DDL_HAEIN.

HD0821 is similar to MUR-NAC-L-alanine and D-alanine-D-alanine ligase (fusion protein) from T. pallidum (TP0670), C. trachomatis (CT762), and C. pneumoniae (CPn0905), and weakly similar to biotin carboxylase (CT124). No similarities to U. urealyticum, M. genitalium, or M. pneumoniae.


COGS Summary:  COGS Search
BeTs to 11 clades of COG1181
COG name: D-alanine-D-alanine ligase and related ATP-grasp enzymes
Functional Class:  M
The phylogenetic pattern of COG1181 is -----qvcEbrhuj--olinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB000291 (D-alanine--D-alanine ligase) with a combined E-value of 8.2e-75.
    IPB000291A    10-33
    IPB000291B    59-96
    IPB000291C    137-174
    IPB000291D    207-216
    IPB000291E    222-257
    IPB000291F    265-275


ProDom Summary:  Protein Domain Search
Residues 7-300 are 64% similar to a (LIGASE SYNTHETASE CARBOXYLASE COMPLETE) protein domain (PD000180) which is seen in DDL_HAEIN.



Paralogs:  Local Blast Search


HD0821 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 6 to 300 (E-value = 3.7e-127) place HD0821 in the Dala_Dala_ligas family which is described as D-ala D-ala ligase (PF01820)

PDB Hit:
pdb|1IOV| Complex Of D-Ala:d-Ala Ligase With Adp And A Phosph... 295 4e-081
pdb|1IOW| Complex Of Y216f D-Ala:d-Ala Ligase With Adp And A... 294 1e-080
pdb|1EHI|A Chain A, D-Alanine:d-Lactate Ligase (Lmddl2) Of Vanc... 122 4e-029

Gene Protein Sequence:
MNIKNEKIAVLYGGTSQEREVSLHSGAAVTEALKSLGYNVEGIDTKDIAI
EKLKEKGIQRVFNILHGGIGENGVLQGALEQMGIPYTGCGVMASAITLDK
FRTKLLWNAVGLPTADMVVVQRGQAIDINQIIAKLSLPVFVKPSSEGSSV
GVFKVKTKEELLPAITAALEFDTIVLVEEFLTGAEYSVPVLDGEVLPAVQ
IIPDGEFYDYHAKYLSDKTQYIVPALTNERQAEVAKIVKAAYDVVGCRGW
SRIDVMEDQNQNFRLVEVNTNPGMTSHSIFPKSAATMGISFEKLVERVLE
LSI$

Gene Nucleotide Sequence:  Sequence Viewer
ATGAATATTAAGAACGAAAAAATTGCGGTGTTATATGGCGGTACTTCACA
AGAACGTGAAGTGTCTCTACACTCAGGTGCAGCAGTCACAGAAGCATTAA
AAAGCCTAGGTTACAATGTAGAAGGTATTGATACAAAAGATATCGCTATT
GAGAAATTAAAAGAAAAAGGCATTCAGCGAGTCTTCAACATTCTACATGG
CGGAATAGGTGAAAATGGTGTATTGCAAGGTGCTTTAGAACAAATGGGGA
TTCCATACACTGGTTGTGGTGTAATGGCTTCAGCTATCACATTAGATAAA
TTCCGTACCAAATTATTATGGAATGCTGTCGGTTTACCCACAGCAGATAT
GGTAGTAGTGCAACGAGGACAAGCAATCGATATTAATCAAATTATTGCAA
AATTAAGTTTACCTGTTTTTGTCAAACCATCAAGTGAAGGTTCAAGTGTC
GGCGTTTTCAAAGTCAAAACAAAAGAAGAATTACTGCCCGCGATTACCGC
AGCACTGGAATTTGATACTATCGTATTAGTAGAGGAATTTTTGACCGGTG
CTGAATATTCAGTCCCTGTTTTAGATGGCGAAGTTTTACCTGCGGTGCAA
ATCATTCCTGATGGTGAATTTTACGATTATCACGCTAAATACCTTTCCGA
CAAAACCCAATATATTGTGCCCGCATTAACTAATGAACGGCAAGCAGAAG
TCGCCAAAATAGTCAAAGCCGCTTATGATGTTGTTGGTTGTCGTGGTTGG
AGTCGAATTGATGTTATGGAAGATCAAAACCAAAATTTTCGTTTAGTAGA
AGTCAACACTAATCCTGGAATGACTAGCCATAGCATTTTTCCTAAATCTG
CTGCTACAATGGGTATTTCATTTGAAAAACTAGTTGAACGAGTATTGGAG
TTAAGCATCTAA


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