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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR1353 IGR1355 IGR1354 IGR1356 IGR1357 IGR1358 IGR1352 HD1833 wzxE, - HD1838 wecA,rfe, - HD1844 wecB,rffE, - HD1843 rffA, - HD1840 nagA, - HD1845 wecC, - HD1842 wecF, - HD1835 HD1833 wzxE, - HD1838 wecA,rfe, - HD1844 wecB,rffE, - HD1843 rffA, - HD1840 nagA, - HD1845 wecC, - HD1842 wecF, - HD1835 HD1833 wzxE, - HD1838 wecA,rfe, - HD1844 wecB,rffE, - HD1843 rffA, - HD1840 nagA, - HD1845 wecC, - HD1842 wecF, - HD1835 wzxE, - HD1837 rffC, - HD1841 wecF, - HD1836 wzxE, - HD1837 rffC, - HD1841 wecF, - HD1836
* Calculated from Protein Sequence

Gene ID: HD1840

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
rffA  

Definition:
lipopolysaccharide biosynthesis protein

Gene Start:
1547426

Gene Stop:
1546296

Gene Length:
1131

Molecular Weight*:
42496

pI*:
5.90

Net Charge*:
-6.01

EC:
 

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

Pathway: pathway table

Secondary Evidence:
Barr K, Rick PD.
Physical map location of the rffC and rffA genes of Escherichia coli.
J Bacteriol. 1993 Sep;175(17):5738-9. No abstract available.
PMID: 8366065

Meier-Dieter U, Barr K, Starman R, Hatch L, Rick PD.
Nucleotide sequence of the Escherichia coli rfe gene involved in the synthesis of enterobacterial common antigen. Molecular cloning
of the rfe-rff gene cluster.
J Biol Chem. 1992 Jan 15;267(2):746-53.
PMID: 1730666

Comment:
0

Blast Summary:  PSI-Blast Search
Residues 1-375 are 70% similar to 16762205 lipopolysaccharide biosynthesis protein [Salmonella enterica subsp. enterica serovar Typhi].

Also, numerous significant hits in gapped BLAST to lipopolysaccharide biosynthesis proteins; e.g., residues 1-375 are 70% similar to RFFA_ECOLI. Residues 1-375 are also 70% to a protein in Salmonella typhimurium LT2 that is 92% similar to E. coli lipopolysaccharide biosynthesis protein WECE.

COGS Summary:  COGS Search
BeTs to 10 clades of COG0399
COG name: Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis
Functional Class:  M
The phylogenetic pattern of COG0399 is -mT--qVCEBR-uj---L---
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB000653 (DegT/DnrJ/EryC1/StrS family) with a combined E-value of 1.2e-59.
    IPB000653A    59-107
    IPB000653B    133-170
    IPB000653C    175-189
    IPB000653D    230-264
    IPB000653E    303-315


ProDom Summary:  Protein Domain Search
Residues 40-155 are 83% similar to a (AMINOTRANSFERASE PHOSPHATE PYRIDOXAL COMPLETE PROTEOME) protein domain (PD000087) which is seen in RFFA_ECOLI.

Residues 227-375 are 61% similar to a (BIOSYNTHESIS LIPOPOLYSACCHARIDE FAMILY) protein domain (PD206395) which is seen in Q9L6R0_BBBBB.

Residues 164-226 are 82% similar to a (AMINOTRANSFERASE COMPLETE PROTEOME) protein domain (PD411876) which is seen in Q9L6R0_BBBBB.



Paralogs:  Local Blast Search

HD1840 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 7 to 372 (E-value = 1.1e-84) place HD1840 in the DegT_DnrJ_EryC1 family which is described as DegT/DnrJ/EryC1/StrS aminotransferase family (PF01041)

PDB Hit:
pdb|1B9I|A Chain A, Crystal Structure Of 3-Amino-5-Hydroxybenzo... 106 5e-024
pdb|1B9H|A Chain A, Crystal Structure Of 3-Amino-5-Hydroxybenzo... 106 5e-024

Gene Protein Sequence:
MIPFNKPPLVGNELAYIQQALQQDKLSGDGYYNQQAEQWLEKQFSTVKAL
LTPSCTAALEMAAILLDIQAGDEVIMPSYTFVSTANAFVLRGAKIVFVDI
RPDTMNIDEQKIEATITDRTKVIVPVHYAGVACEMDTIMALAAKYQLYVV
EDAAQAMIASYKNRPLGTIGHLGCYSFHETKNYSSAGEGGALLINDATLV
SRAEIIREKGTDRSQFFRGQVDKYTWRDIGSSYLMSELQAAYLYAQFTVA
EQINQTRLAMWQRYYQALLPFANSGRIALAQLPPECQHNAHLFYLKLTDS
ADRNALLTWLKQHDILAVFHYIPLHSSPAGKQFGRFVGEDQFTTQESERL
LRLPLFYNLHLTEQQRVIEVVTDYFQ$

Gene Nucleotide Sequence:  Sequence Viewer
ATGATTCCTTTTAATAAACCACCATTGGTGGGCAATGAATTAGCCTATAT
TCAACAGGCGTTACAGCAAGATAAATTATCAGGTGATGGTTATTATAACC
AGCAAGCGGAACAATGGTTAGAAAAGCAATTTTCGACAGTGAAAGCGTTA
TTAACACCATCTTGTACTGCCGCATTAGAAATGGCGGCGATTCTGTTAGA
TATTCAAGCTGGCGATGAAGTGATTATGCCTAGCTATACTTTTGTGTCGA
CTGCAAATGCATTTGTGTTGCGTGGCGCTAAAATTGTGTTTGTTGATATT
CGCCCGGATACTATGAATATTGATGAACAGAAAATTGAAGCGACAATTAC
GGATAGAACTAAAGTGATTGTTCCAGTGCATTACGCGGGCGTAGCTTGTG
AGATGGATACAATTATGGCATTAGCGGCTAAATATCAGCTATATGTGGTT
GAAGATGCTGCACAGGCAATGATAGCAAGCTATAAAAATCGCCCATTAGG
CACGATTGGACATTTGGGGTGTTATAGTTTTCACGAAACTAAAAATTATA
GTTCGGCAGGTGAAGGTGGAGCGCTGTTAATTAATGATGCGACATTAGTT
AGTCGCGCAGAAATTATTCGCGAGAAAGGCACTGATCGAAGTCAGTTTTT
TCGAGGACAAGTTGATAAATATACGTGGCGAGATATTGGATCAAGTTATC
TCATGTCGGAGTTACAAGCGGCTTATTTATATGCACAATTTACGGTGGCA
GAACAGATTAATCAAACACGTTTAGCAATGTGGCAACGTTATTATCAAGC
GTTATTGCCTTTTGCTAATAGCGGGCGGATAGCATTAGCCCAATTACCGC
CCGAATGCCAACATAATGCGCATTTATTTTATTTAAAATTAACAGATTCA
GCCGATCGGAACGCGTTATTAACTTGGCTTAAACAACACGATATTTTAGC
GGTGTTTCATTATATTCCATTGCATTCCAGCCCAGCAGGTAAACAATTTG
GGCGCTTTGTCGGTGAAGATCAATTTACAACACAAGAAAGTGAGCGCTTG
CTAAGGTTACCCTTGTTTTATAATTTGCATCTAACAGAGCAACAACGTGT
GATTGAGGTTGTGACGGATTATTTTCAGTAA


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