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Haemophilus ducreyi Search Results

Record: 1 of 1  
MiniMap IGR852 IGR848 IGR851 IGR849 IGR853 IGR850 IGR846 IGR847 greB, - HD1167 kpsF, - HD1168 pepB, - HD1169 ribE, - HD1165 ribC, - HD1162 ribD,ribG, - HD1161 ribA, - HD1163 glpC, - HD1160 glpA, - HD1157 greB, - HD1167 kpsF, - HD1168 pepB, - HD1169 ribE, - HD1165 ribC, - HD1162 ribD,ribG, - HD1161 ribA, - HD1163 glpC, - HD1160 glpA, - HD1157 greB, - HD1167 kpsF, - HD1168 pepB, - HD1169 HD1166 HD1166 ribE, - HD1165 ribC, - HD1162 ribD,ribG, - HD1161 ribA, - HD1163 glpC, - HD1160 glpA, - HD1157 glpB, - HD1158 glpB, - HD1158
* Calculated from Protein Sequence

Gene ID: HD1161

DNA Molecule Name:
1  

Genbank ID:
0

Gene Name:
ribD  ribG  

Definition:
riboflavin-specific deaminase (bifunctional enzyme)

Gene Start:
943331

Gene Stop:
944437

Gene Length:
1107

Molecular Weight*:
39808

pI*:
7.80

Net Charge*:
3.45

EC:
1.1.1.193  3.5.4.26  

Functional Class:
Biosynthesis of cofactors, prosthetic groups, and carriers; Riboflavin  

Pathway: pathway table
Riboflavin metabolism

Secondary Evidence:
Fuller,T.E. and Mulks,M.H.
Characterization of Actinobacillus pleuropneumoniae riboflavin
biosynthesis genes
J. Bacteriol. 177 (24), 7265-7270 (1995)
MEDLINE: 96099314

Mironov,V.N., Perumov,D.A., Kraev,A.S., Stepanov,A.I. and
Skriabin,K.G.
Unusual structure of the regulatory region of the riboflavin
biosynthesis operon in Bacillus subtilis
Mol. Biol. (Mosk.) 24 (1), 256-261 (1990)
MEDLINE: 90271920

Richter,G., Fischer,M., Krieger,C., Eberhardt,S., Luttgen,H.,
Gerstenschlager,I. and Bacher,A.
Biosynthesis of riboflavin: characterization of the bifunctional
deaminase-reductase of Escherichia coli and Bacillus subtilis
J. Bacteriol. 179 (6), 2022-2028 (1997)
MEDLINE: 97221604


Comment:
0

Blast Summary:  PSI-Blast Search
Many significant hits using gapped BLAST to riboflavin-specific deaminase from Actinobacillus pleuropneumoniae (1173516), Actinobacillus pleuropneumoniae (8039802), Bacillus subtilis (132565), among others. HD1161 is 73% similar to residues 13-374 from RIBD_ACTPL.

HD1161 is similar to riboflavin-specific deaminase from C. trachomatis (CT730) and C. pneumoniae (CPn0871). No similarities to U. urealyticum, T. pallidum, M. genitalium, or M. pneumoniae.

COGS Summary:  COGS Search
BeTs to 6 clades of COG0117
COG name: Pyrimidine deaminase, riboflavin biosynthesis
Functional Class:  H
The phylogenetic pattern of COG0117 is ----yqvcebrhuj----in-
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB002734 (RibD/ribG C-terminal domain) with a combined E-value of 1.2e-97.
    IPB002734A    23-33
    IPB002734B    50-84
    IPB002734C    108-119
    IPB002734D    151-160
    IPB002734E    166-207
    IPB002734F    213-222
    IPB002734G    289-321


ProDom Summary:  Protein Domain Search
Residues 289-358 are 71% similar to a (DEAMINASE REDUCTASE RIBOFLAVIN-SPECIFIC) protein domain (PD005260) which is seen in RIBD_ACTPL.

Residues 292-360 are 42% similar to a (REDUCTASE DEAMINASE RIBOFLAVIN) protein domain (PD203708) which is seen in RIB7_METTH.

Residues 50-96 are 85% similar to a (DEAMINASE COMPLETE PROTEOME REDUCTASE) protein domain (PD001793) which is seen in RIBD_ACTPL.

Residues 50-98 are 55% similar to a (REDUCTASE DEAMINASE RIBOFLAVIN) protein domain (PD411455) which is seen in RIBD_CHLMU.

Residues 7-47 are 78% similar to a (DEAMINASE REDUCTASE RIBOFLAVIN-SPECIFIC) protein domain (PD009434) which is seen in RIBD_ACTPL.

Residues 6-214 are 33% similar to a (RIBOFLAVIN-SPECIFIC PROTEOME COMPLETE) protein domain (PD134337) which is seen in Q9PM53_CAMJE.

Residues 6-48 are 62% similar to a (DEAMINASE RIBOFLAVIN-SPECIFIC REDUCTASE) protein domain (PD394213) which is seen in Q9KCL7_BACHD.

Residues 2-148 are 32% similar to a (DOMAIN OF UNKNO N) protein domain (PD305664) which is seen in Q9STY4_ARATH.

Residues 102-147 are 54% similar to a (DEAMINASE REDUCTASE RIBOFLAVIN-SPECIFIC) protein domain (PD235880) which is seen in RIBD_BACAM.

Residues 5-130 are 35% similar to a (RIBOFLAVIN HYDROLASE BIOSYNTHESIS) protein domain (PD037656) which is seen in P87241_SCHPO.

Residues 240-356 are 47% similar to a (REDUCTASE DEAMINASE PROTEOME COMPLETE) protein domain (PD086286) which is seen in Q9CGU9_LACLA.

Residues 233-288 are 58% similar to a (REDUCTASE DEAMINASE RIBOFLAVIN) protein domain (PD086287) which is seen in RIBD_ACTPL.

Residues 102-147 are 60% similar to a (DEAMINASE REDUCTASE RIBOFLAVIN-SPECIFIC) protein domain (PD378625) which is seen in RIBD_ACTPL.

Residues 148-232 are 84% similar to a (REDUCTASE DEAMINASE RIBOFLAVIN-SPECIFIC) protein domain (PD004302) which is seen in RIBD_ACTPL.



Paralogs:  Local Blast Search

HD1161 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 1 to 100 (E-value = 1.3e-44) place HD1161 in the dCMP_cyt_deam family which is described as Cytidine and deoxycytidylate deaminase zinc-binding region (PF00383)
Residues 147 to 356 (E-value = 2.1e-92) place HD1161 in the RibD_C family which is described as RibD C-terminal domain (PF01872)

PDB Hit:
No significant hits to the NCBI PDB database.

Gene Protein Sequence:
MTDVDYMARAIALAEQARGWTNPNPLVGCVIVKNDQIIAEGYHQKVGEWH
AERNAILNCQQDLTGATAYVTLEPCCHHGRTPPCTDLLIERGINKVFVGS
RDPNPLVTGKGIKQLQAAGIEVITDFMREACDQLNPIFFHYMQTTSPYVL
LKYAMTADGKIATATGESKWISGELARQNVQITRHQYSAIMVGVGTVLAD
NPMLNSRMPNAKQPIRVVCDSHLRTPLACQLVQTARQYPTIIATASTDST
KIAQLKAFGVQIIQCKVANKQVDLVDLLAKLGAMQIDSVLLEGGSTLNFS
ALKAGVVNRIHCYIAPKLLGGSTAKSPIGGAGILQLAEAVNLTLKSTQYI
GDDILLDYDVSSSQKLAS$

Gene Nucleotide Sequence:  Sequence Viewer
ATGACAGATGTTGACTATATGGCTCGTGCGATAGCACTGGCAGAACAAGC
ACGTGGTTGGACTAATCCTAATCCATTAGTGGGCTGTGTGATCGTTAAAA
ATGATCAAATCATCGCAGAAGGCTATCACCAAAAGGTAGGCGAATGGCAC
GCAGAGCGTAATGCTATTTTAAATTGTCAGCAAGATCTCACAGGGGCCAC
TGCTTACGTTACACTTGAGCCTTGTTGCCATCATGGGCGCACACCGCCTT
GTACTGATTTGCTTATTGAACGAGGAATTAACAAAGTGTTTGTGGGCTCT
CGTGATCCTAATCCACTGGTTACGGGGAAGGGGATTAAACAATTACAAGC
AGCGGGCATAGAAGTGATCACTGATTTTATGCGAGAAGCTTGCGATCAGC
TCAACCCCATTTTTTTTCATTATATGCAAACTACATCTCCTTATGTGTTG
CTTAAATATGCAATGACAGCAGATGGTAAAATTGCTACCGCTACAGGTGA
ATCCAAATGGATTAGCGGTGAATTAGCACGCCAAAATGTGCAAATCACAC
GTCATCAATATAGCGCCATTATGGTTGGAGTGGGCACCGTATTAGCGGAT
AATCCGATGTTAAATAGTCGAATGCCGAATGCTAAACAACCAATACGCGT
TGTGTGCGATAGCCACTTACGAACGCCTCTAGCGTGTCAATTAGTTCAAA
CAGCGCGCCAATATCCAACCATTATTGCAACCGCTTCAACTGATAGTACA
AAAATAGCGCAATTGAAAGCCTTTGGCGTGCAAATTATCCAATGTAAGGT
AGCCAACAAACAAGTTGATTTAGTTGATTTATTAGCCAAATTAGGTGCAA
TGCAAATTGACAGTGTCTTGCTTGAAGGGGGATCAACACTGAATTTTAGT
GCATTGAAAGCTGGCGTTGTTAACAGAATTCATTGTTATATTGCACCTAA
ATTATTAGGCGGAAGCACTGCCAAAAGTCCTATCGGTGGTGCAGGTATTT
TGCAACTAGCGGAAGCGGTTAATTTAACGCTTAAATCCACACAATACATA
GGCGACGATATCTTGTTAGATTATGACGTTTCATCATCGCAAAAATTAGC
AAGCTGA


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