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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR485 IGR479 IGR483 IGR484 IGR481 IGR480 IGR488 IGR486 IGR487 IGR482 yadR, - HD0684 HD0680 HD0682 rpS21,rpsU,rs21, - HD0689 neuA,siaB, - HD0685 lst, - HD0686 rmlA, - HD0688 menA, - HD0683 rmlB, - HD0687 dnaG, - HD0690 rpoD, - HD0691 yadR, - HD0684 HD0680 HD0682 rpS21,rpsU,rs21, - HD0689 neuA,siaB, - HD0685 lst, - HD0686 rmlA, - HD0688 menA, - HD0683 rmlB, - HD0687 dnaG, - HD0690 rpoD, - HD0691 yadR, - HD0684 HD0682 HD0681 HD0680 HD0681 rpS21,rpsU,rs21, - HD0689 neuA,siaB, - HD0685 lst, - HD0686 rmlA, - HD0688 menA, - HD0683 rmlB, - HD0687 dnaG, - HD0690 rpoD, - HD0691
* Calculated from Protein Sequence

Gene ID: HD0687

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
rmlB  

Definition:
dTDP-D-glucose 4,6-dehydratase

Gene Start:
542295

Gene Stop:
543350

Gene Length:
1056

Molecular Weight*:
39671

pI*:
6.80

Net Charge*:
-1.38

EC:
4.2.1.46  

Functional Class:
Purines, pyrimidines, nucleosides, and nucleotides; Sugar-nucleotide biosynthesis and conversions  

Pathway: pathway table
Nucleotide sugars metabolism

Primary Evidence:
Tullius,M.V., Munson,R.S. Jr., Wang,J. and Gibson,B.W.
Purification, cloning, and expression of a cytidine
5'-monophosphate N-acetylneuraminic acid synthetase from
Haemophilus ducreyi
J. Biol. Chem. 271 (26), 15373-15380 (1996)
MEDLINE: 96279048

Bozue,J.A., Tullius,M.V., Wang,J., Gibson,B.W. and Munson,R.S. Jr.
Haemophilus ducreyi produces a novel sialyltransferase.
Identification of the sialyltransferase gene and construction of
mutants deficient in the production of the sialic acid-containing
glycoform of the lipooligosaccharide
J. Biol. Chem. 274 (7), 4106-4114 (1999)
MEDLINE: 99134335


Secondary Evidence:
Marolda,C.L. and Valvano,M.A.
Genetic analysis of the dTDP-rhamnose biosynthesis region of the
Escherichia coli VW187 (O7:K1) rfb gene cluster: identification of
functional homologs of rfbB and rfbA in the rff cluster and correct location of the rffE gene
Journal of bacteriology. 177 (19), 5539-5546 (1995)
Medline: 96032389

Allard ST, Giraud MF, Whitfield C, Graninger M, Messner P, Naismith JH.
The crystal structure of dTDP-D-Glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium, the second
enzyme in the dTDP-l-rhamnose pathway.
J Mol Biol. 2001 Mar 16;307(1):283-95.
PMID: 11243820


Comment:


Blast Summary:  PSI-Blast Search
The sequence corresponds to the previously reported gi 4741795 in GenBank.

Many very strong hits in gapped BLAST to dTDP-D-glucose 4,6-dehydratase proteins; e.g., residues 8-345 are 65% similar to the sequence for dTDP-D-glucose 4,6-dehydratase in Actinobacillus
actinomycetemcomitans [7592815], residues 7-346 are 65% similar to RFFG_ECOLI [2506450], and residues 7-345 are 63% similar to the sequence for dTDP-D-glucose-4,6-dehydratase in Neisseria meningitidis [7225283].

COGS Summary:  COGS Search
BeTs to 7 clades of COG1088
COG name: dTDP-D-glucose 4,6-dehydratase
Functional Class: M
The phylogenetic pattern of COG1088 is a-tk---cEbrh---------
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB001509 (NAD dependent epimerase/dehydratase family) with a combined E-value of 2.6e-41.
    IPB001509A    8-29
    IPB001509B    80-114
    IPB001509C    192-198
    IPB001509D    228-235
    IPB001509E    325-335
    IPB001509E    309-319


ProDom Summary:  Protein Domain Search
Residues 8-339 are 95% similar to a (COMPLETE PROTEOME 4-EPIMERASE REDUCTASE UDP-GLUCOSE NAD) protein domain (PD000038) which is seen in Q9X4A2_HAEDU.



Paralogs:  Local Blast Search

HD0687 is paralogously related to HD0829 (4e-13).


Pfam Summary:  Pfam Search
Residues 8 to 339 (E-value = 8.1e-190) place HD0687 in the Epimerase family which is described as NAD dependent epimerase/dehydratase family (PF01370)

PDB Hit:
pdb|1BXK|B Chain B, Dtdp-Glucose 4,6-Dehydratase From E. Coli >... 474 7e-135
pdb|1KVT| Udp-Galactose 4-Epimerase Complexed With Udp-Phenol 68 2e-012
pdb|1A9Y| Udp-Galactose 4-Epimerase Mutant S124aY149F COMPLE... 67 4e-012

Gene Protein Sequence:
VSCNCMKLLITGGAGFIGSAVIRYIINHTDDEVINVDKLTYAGNLASLSS
VSQHKRYTFEQVDINDSGRIAEIFYHYQPDKVMHLAAESHVDRSIEGSAP
FIQTNIIGTYTLLETARSYWQSLDQQKKAQFLFHHISTDEVFGDLAHQPQ
RFTEQSAYMPSSPYSASKAASDHLVQAWYRTYGLPTVISHCSNNYGPYHF
PEKLIPLTILNALSGKPLPVYGDGLQVRDWLFVEDHARALYKVIKQGRVG
ESYNIGASNERTNIEVVQAICQLLDELVPVKPNGIKTYQALITHVADRPG
HDLRYAIDASKITQQLGWQPQESFATGLRKTVEWYLAHKNWWQMIQHPVC
E$

Gene Nucleotide Sequence:  Sequence Viewer
GTGAGTTGTAATTGTATGAAGCTTTTAATTACAGGTGGAGCAGGTTTTAT
TGGATCGGCAGTGATTCGCTATATTATTAATCATACTGATGATGAAGTGA
TTAATGTTGATAAATTGACCTATGCGGGCAATTTAGCTTCGCTGTCATCA
GTGAGTCAGCATAAACGCTATACTTTTGAACAGGTAGATATTAATGACAG
CGGACGGATTGCTGAAATTTTTTACCATTATCAGCCTGATAAAGTAATGC
ATTTAGCCGCTGAAAGCCACGTAGATCGATCCATTGAAGGATCTGCACCA
TTTATACAAACTAATATCATCGGCACTTATACATTATTAGAAACAGCAAG
ATCCTATTGGCAAAGTCTAGATCAGCAAAAAAAAGCACAATTTCTTTTTC
ACCACATTTCAACGGATGAGGTCTTTGGTGATTTAGCTCATCAGCCTCAA
CGGTTTACTGAGCAAAGTGCTTATATGCCGAGCAGTCCTTATTCTGCGTC
AAAAGCAGCGAGTGATCATCTAGTGCAAGCTTGGTATCGTACTTATGGCT
TACCAACAGTGATTAGCCATTGTTCAAATAACTATGGACCTTATCACTTT
CCGGAAAAATTAATTCCATTAACCATTTTAAACGCCTTATCTGGTAAGCC
ATTGCCTGTTTATGGCGATGGCTTGCAAGTTCGAGATTGGCTTTTTGTTG
AAGATCATGCTCGCGCATTGTATAAAGTGATCAAACAAGGTCGCGTAGGG
GAAAGCTATAATATTGGCGCCAGTAATGAAAGAACCAATATTGAAGTTGT
GCAAGCTATTTGCCAGTTATTAGATGAATTAGTGCCGGTTAAACCTAATG
GAATTAAAACATATCAAGCGTTAATTACACATGTAGCAGATCGTCCTGGC
CATGATTTACGCTATGCAATTGATGCAAGCAAAATAACGCAACAGCTTGG
TTGGCAACCGCAAGAAAGTTTTGCTACAGGATTACGGAAAACGGTAGAGT
GGTATCTAGCGCATAAAAACTGGTGGCAAATGATTCAGCACCCTGTTTGC
GAGTAA


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