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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR0069 IGR0072 IGR0071 IGR0074 IGR0070 IGR0073 IGR0075 NG0090 aroK, - NG0093 yafJ, - NG0091 NG0087 aroB, - NG0092 ribD, - NG0089 pglB, - NG0085 NG0088 NG0090 aroK, - NG0093 yafJ, - NG0091 NG0087 aroB, - NG0092 ribD, - NG0089 pglB, - NG0085 NG0088 NG0090 aroK, - NG0093 yafJ, - NG0091 NG0087 aroB, - NG0092 ribD, - NG0089 pglB, - NG0085 NG0088 NG0086 NG0086
* Calculated from Protein Sequence

Gene ID: NG0089

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
ribD  

Definition:
riboflavin biosynthesis protein RibD

Gene Start:
98365

Gene Stop:
97259

Gene Length:
1107

Molecular Weight*:
40046

pI*:
8.50

Net Charge*:
6.38

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:
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)
M:97221604


Comment:
Oklahoma ID: NGO.89c

For other riboflavin synthesis proteins, see NG0068, NG0257, NG0704, NG0755.

Blast Summary:  PSI-Blast Search
Several hits in gapped BLAST to riboflavin-specific deaminases, e.g. residues 10-342 are 52% similar to the riboflavin-specific deaminase/reductase PA4056 in Pseudomonas aeruginosa (gb|AAG07443).

Residues 1-369 are virtually identical to the riboflavin bifunctional biosynthesis protein ribD NMA0644 in N.meningitidis (AL162753).

COGS Summary:  COGS Search
BeTs to 8 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 6.8e-105.
    IPB002734A    26-36
    IPB002734B    53-87
    IPB002734C    111-122
    IPB002734D    154-163
    IPB002734E    169-210
    IPB002734F    217-226
    IPB002734G    294-326


ProDom Summary:  Protein Domain Search
Residues 53-100 are 79% similar to a (PROTEIN DEAMINASE HYDROLASE ZINC BIOSYNTHESIS) protein domain (PD001793) which is seen in O51825_SHIFL.

Residues 10-51 are 57% similar to a (RIBOFLAVIN DEAMINASE BIOSYNTHESIS PROTEIN RIBD) protein domain (PD009434) which is seen in RIBD_HAEIN.

Residues 8-233 are 29% similar to a (PROTEIN RIBOFLAVIN BIOSYNTHESIS RIBG) protein domain (PD134337) which is seen in O26035_HELPY.

Residues 52-99 are 54% similar to a (RIBOFLAVIN DEAMINASE BIOSYNTHESIS PROTEIN) protein domain (PD190048) which is seen in O84735_CHLTR.

Residues 101-235 are 51% similar to a (RIBOFLAVIN BIOSYNTHESIS REDUCTASE PROTEIN DEAMINASE RIBD) protein domain (PD004302) which is seen in RIBD_HAEIN.



Paralogs:  Local Blast Search


NG0089 is paralogously related to NG0941 (cytosine deaminase) (2e-06).


Pfam Summary:  Pfam Search
Residues 4 to 103 (E-value = 1.5e-35) place NG0089 in the dCMP_cyt_deam family which is described as Cytidine and deoxycytidylate deaminase zinc-binding region (PF00383)
Residues 150 to 360 (E-value = 1.5e-60) place NG0089 in the RibD_C family which is described as RibD C-terminal domain (PF01872)

Structural Feature(s):
Feature Type  Start  Stop
No predicted structural features.  
  

PDB Hit:
No hits to the PDB database.

Gene Protein Sequence:
MFSDTNISMMENALRLAALGRFSTSPNPRVGCVIAHGSQIVGQGFHVKAG
EPHAEVHALRQAGEMAKGATAFVTLEPCSHYGRTPPCAEALLRSGVTRVV
AAMRDPNPPVAGKGLVLLKAAGIKTECGLLENKARELNRGFLSRIERRRP
FVRLKCAVSLDGKTALSDGSSFWITGEEARADVQVLRAESCAVLTGIGTV
LADNPRLNVRAFPTLRQPARIVLDSRLRLPPNSHLVTDGQSPTYIATLER
DEDKLRPYREHAHIRILMPSETADGKIDLHHLMRLLADEGFGEIMVEAGS
ELTSAFLAENLADEIVLYRSPKILGGGKDLFSLPENRAALSAPPLWTPVS
SEILGHDIKTVFRKNGNAF

Gene Nucleotide Sequence:  Sequence Viewer
ATGTTTTCGGACACAAATATATCCATGATGGAAAACGCCCTCCGACTTGC
CGCTTTGGGGCGTTTTTCCACTTCACCCAACCCGCGCGTCGGCTGCGTTA
TCGCACACGGCAGCCAAATTGTCGGACAGGGCTTCCACGTCAAAGCGGGC
GAACCCCATGCCGAAGTCCACGCCCTGCGTCAGGCGGGGGAAATGGCAAA
AGGCGCGACCGCCTTTGTTACCCTCGAACCGTGCAGCCATTACGGACGCA
CACCGCCCTGCGCCGAAGCCCTGCTCCGTTCCGGCGTAACACGCGTCGTC
GCCGCCATGCGCGACCCCAACCCGCCGGTTGCAGGCAAAGGGCTTGTCCT
GCTCAAAGCAGCGGGCATCAAGACGGAATGCGGACTACTTGAAAACAAAG
CACGCGAACTCAACCGGGGATTTTTATCGCGCATCGAACGCCGCCGCCCC
TTTGTCCGCCTCAAATGCGCCGTTTCGCTGGACGGCAAAACCGCCCTTTC
AGACGGCAGCAGCTTTTGGATTACCGGCGAGGAAGCTCGTGCCGACGTAC
AGGTTTTGCGTGCCGAAAGCTGCGCGGTGCTGACCGGCATCGGCACGGTG
TTGGCAGACAATCCCCGGCTCAACGTCCGCGCTTTTCCAACTTTGCGCCA
ACCCGCACGCATCGTTTTAGACAGCCGCCTGCGCCTGCCCCCGAACAGCC
ATTTGGTTACCGACGGGCAATCTCCGACCTACATCGCCACCTTGGAACGC
GATGAAGACAAACTCCGCCCCTATCGGGAACACGCACACATCCGCATCCT
GATGCCGTCTGAAACGGCAGACGGCAAAATCGACCTGCACCATCTGATGC
GCCTCCTTGCCGACGAAGGTTTCGGCGAAATCATGGTCGAAGCAGGCTCC
GAACTCACATCCGCATTTTTGGCGGAAAATTTGGCGGACGAAATCGTGCT
GTACCGTTCGCCCAAAATCCTCGGCGGCGGCAAAGACCTGTTTTCCCTGC
CCGAAAACCGTGCCGCCCTTTCCGCACCGCCCTTGTGGACACCCGTTTCA
AGCGAAATCCTCGGACACGACATCAAAACCGTGTTCCGGAAAAACGGCAA
CGCCTTT


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