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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1389 IGR1387 IGR1391 IGR1384 IGR1386 IGR1385 IGR1383 IGR1390 IGR1388 HD1893 qacE, - HD1891 secE, - HD1886 HD1892 dprA, - HD1888 glmS, - HD1894 hmwC, - HD1895 def, - HD1889 rfaD, - HD1890 HD1887 HD1893 qacE, - HD1891 secE, - HD1886 HD1892 dprA, - HD1888 glmS, - HD1894 hmwC, - HD1895 def, - HD1889 rfaD, - HD1890 HD1887 qacE, - HD1891 secE, - HD1886 HD1892 dprA, - HD1888 glmS, - HD1894 hmwC, - HD1895 HD1893 def, - HD1889 rfaD, - HD1890 HD1887
* Calculated from Protein Sequence

Gene ID: HD1890

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
rfaD  

Definition:
ADP-L-glycero-D-manno-heptose-6-epimerase

Gene Start:
1588823

Gene Stop:
1589764

Gene Length:
942

Molecular Weight*:
35307

pI*:
5.90

Net Charge*:
-5.25

EC:
5.1.3.20  

Functional Class:
Cell envelope; Surface polysaccharides, lipopolysaccharides and antigens  

Pathway: pathway table
Lipopolysaccharide biosynthesis

Secondary Evidence:
Pegues,J.C., Chen,L.S., Gordon,A.W., Ding,L. and Coleman,W.G. Jr.
Cloning, expression, and characterization of the Escherichia coli K-12 rfaD gene.
J. Bacteriol. 172(8): 4652-4660, 1990.
Medline: 90330578.

Ding,L., Seto,B.L., Ahmed,S.A. and Coleman,W.G. Jr.
Purification and properties of the Escherichia coli K-12 NAD-dependent nucleotide diphosphosugar epimerase, ADP-L-glycero-D-mannoheptose 6-epimerase.
J. Biol. Chem. 269(39): 24384-24390, 1994.
Medline: 95014184.

Comment:
For other "rfa" genes, see HD1182 (rfaE) and HD0653 (rfaF).

Blast Summary:  PSI-Blast Search
Many significant hits using gapped BLAST to ADP-L-glycero-D-manno-heptose-6-epimerase from H. influenzae (1172915, 1294775), E. coli (132480), Salmonella typhimurium (585815), among others.

HD1890 is similar to UDP-glucose 4-epimerase from M. genitalium (MG118) and M. pneumoniae (MP0576). No similarities to C. trachomatis, C. pneumoniae, U. urealyticum, or T. pallidum.

COGS Summary:  COGS Search
BeTs to 10 clades of COG0451
COG name: Nucleoside-diphosphate-sugar epimerases
Functional Class:  M,G
The phylogenetic pattern of COG0451 is AMTKYQVCEBRHUJ--o----
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 1.7e-14.
    IPB001509A    2-23
    IPB001509B    68-102
    IPB001509C    168-174
    IPB001509D    209-216


ProDom Summary:  Protein Domain Search
Residues 29-110 are 74% similar to a (BIOSYNTHESIS ADP-) protein domain (PD337268) which is seen in Q9XCA1_KLEPN.

Residues 2-305 are 78% similar to a (COMPLETE PROTEOME 4-EPIMERASE REDUCTASE UDP-GLUCOSE NAD) protein domain (PD000038) which is seen in RFAD_HAEIN.



Paralogs:  Local Blast Search


HD1890 is paralogously related to HD0829 (3e-09).


Pfam Summary:  Pfam Search
Residues 1 to 310 (E-value = 8.1e-06) place HD1890 in the 3Beta_HSD family which is described as 3-beta hydroxysteroid dehydrogenase/isomerase family (PF01073)
Residues 2 to 307 (E-value = 1.3e-12) place HD1890 in the Epimerase family which is described as NAD dependent epimerase/dehydratase family (PF01370)

PDB Hit:
pdb|1EQ2|A Chain A, The Crystal Structure Of Adp-L-Glycero-D-Ma... 480 1e-136

Gene Protein Sequence:
MIIVTGGFGMIGSNIINALNDIGRKDILVVDNLKNGEKFINLVDLNIADY
CDKDDFIASIIAGDDFGEIDAIFHQGACSSTTEWNGKYLMQNNYEYSKEL
LHFCVDRQIPFLYASSAATYGGRADNFIEERKFEGPLNAYGYSKFLFDEY
VRRLLPEANSAICGFKYFNVYGPREQHKGSMASVAFHLNNQMLKGENPKL
FAGSEHFLRDFVYVEDVAKVNIWAWKNNISGIYNLGTGKAESFQTVAQAV
IDFHGKGHIETIPFPDHLKSRYQTFTQADLTKLRAAGYQDNFKTVAEGTK
AYMSWLNRSLTTE$

Gene Nucleotide Sequence:  Sequence Viewer
ATGATTATCGTAACTGGCGGTTTTGGTATGATCGGCAGCAATATCATTAA
CGCGTTAAATGATATTGGCAGAAAAGATATTTTAGTGGTAGATAACCTAA
AAAATGGTGAAAAATTCATTAACTTAGTGGATTTAAATATCGCGGATTAT
TGCGATAAAGATGATTTTATTGCTTCGATTATTGCTGGTGATGATTTTGG
TGAGATTGACGCAATTTTTCACCAAGGTGCTTGTTCCTCAACAACCGAAT
GGAATGGCAAATATTTAATGCAAAATAATTATGAATATTCCAAAGAGTTA
TTACATTTTTGTGTAGATCGACAAATTCCATTTTTATATGCTTCTAGCGC
GGCCACTTATGGCGGTCGCGCTGATAATTTTATCGAAGAACGGAAATTTG
AAGGCCCATTAAATGCCTATGGCTATTCCAAATTCCTATTTGATGAATAT
GTTCGTCGCCTTTTACCTGAAGCAAATTCCGCCATTTGTGGCTTTAAATA
TTTCAATGTTTATGGTCCACGTGAACAACATAAAGGGTCGATGGCAAGCG
TGGCTTTCCATCTTAATAACCAAATGTTAAAAGGTGAAAATCCAAAATTA
TTTGCTGGTTCTGAGCATTTTTTACGTGATTTCGTGTATGTTGAAGATGT
GGCTAAAGTCAATATTTGGGCGTGGAAAAATAATATTTCAGGGATCTATA
ATCTCGGCACAGGTAAAGCAGAATCATTCCAAACTGTTGCTCAAGCGGTG
ATTGATTTTCACGGAAAAGGGCATATTGAGACCATTCCGTTCCCCGATCA
TTTAAAATCGCGTTATCAAACCTTTACCCAAGCGGACTTAACTAAATTAC
GCGCTGCTGGTTATCAAGATAATTTTAAAACGGTCGCAGAAGGCACTAAA
GCCTATATGAGCTGGTTAAATCGTTCACTGACCACCGAATAA


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