Jump to navigation
Jump to search
NCBI: 10-JUN-2013
⊟Summary[edit | edit source]
- organism: Staphylococcus aureus USA300_FPR3757
- locus tag: SAUSA300_1715 [new locus tag: SAUSA300_RS09370 ]
- pan locus tag?: SAUPAN004458000
- symbol: ribD
- pan gene symbol?: ribD
- synonym:
- product: riboflavin biosynthesis protein
⊟Genome View[edit | edit source]
⊟Gene[edit | edit source]
⊟General[edit | edit source]
- type: CDS
- locus tag: SAUSA300_1715 [new locus tag: SAUSA300_RS09370 ]
- symbol: ribD
- product: riboflavin biosynthesis protein
- replicon: chromosome
- strand: -
- coordinates: 1897228..1898232
- length: 1005
- essential: unknown other strains
⊟Accession numbers[edit | edit source]
- Gene ID: 3913191 NCBI
- RefSeq: YP_494408 NCBI
- BioCyc: GH3C-1706 BioCyc
- MicrobesOnline: 1293230 MicrobesOnline
⊟Phenotype[edit | edit source]
Share your knowledge and add information here. [edit]
⊟DNA sequence[edit | edit source]
- 1
61
121
181
241
301
361
421
481
541
601
661
721
781
841
901
961ATGGTACAAGGTCAAACAGGTGTTAATCCACCCGTTGGCGCTGTTGTAGTTAAAGAAGGT
AGGATTGTTGGTATTGGTGCACACTTGAGAAAAGGTGACAAGCATGCGGAGGTTCAAGCA
CTTGATATGGCACAACAAAATGCTGAAGGTGCGACGATTTATATTACGTTAGAGCCATGT
AGTCATTTTGGTTCAACACCACCCTGTGTTAACAAAATAATTGATTGTAAGATAGCAAAA
GTAGTATACGCAACAAAAGACAATTCGTTAGACACACATGGTGATGAGACGTTACGGGCT
CACGGTATTGAGGTTGAATGCGTTGATGATGAACGGGCATCACAATTATACCAAGACTTT
TTTAAAGCAAAAGCAAAGCAACTGCCACAAATTACAGTGAAAGTATCTGCAAGTTTAGAT
GGTAAACAAGCGAATGATAATGGACAAAGTCAATGGATTACTAACAAAGAGGTTAAACAA
GATGTCTATAAGTTAAGACATCGACACGACGCAGTGTTAACTGGAAGACGTACAGTTGAA
TTAGATGATCCACAATATACTACACGTATTCAAGATGGAAAAAACCCTATAAAAGTAATA
TTGTCTAAGTCTGGGAATATTCATTTTAATCAGCAAATTTATCAAGATGAATCAACACCA
ATTTGGATATATACTGAAAATCCAAATTTAACAACCAATCAAACACATATTGAAATTATT
TACTTGAAGTCTTGCGATTTAACAACAATTCTTCACAATTTATATAAAAGAGGAGTTGGA
ACTTTGCTAGTTGAGGCAGGTCCAACCACTACTTCAGAATTTCTCCAATCTAATTATATA
GATGAATTTATTCTCTATTATGCCCCGAAATTAATTGGCGGATCTGGAAATTATCAATTT
TATCAAACAAATGATGTGATTGAGATACCAGATGCGAACCAATTTGAAATTGTTCATTCC
GAGTTATTAAATCAAAATGTTAAATTAACTTTACGAAAGAAGTGA60
120
180
240
300
360
420
480
540
600
660
720
780
840
900
960
1005
⊟Protein[edit | edit source]
⊟General[edit | edit source]
- locus tag: SAUSA300_1715 [new locus tag: SAUSA300_RS09370 ]
- symbol: RibD
- description: riboflavin biosynthesis protein
- length: 334
- theoretical pI: 6.58415
- theoretical MW: 37439
- GRAVY: -0.460778
⊟Function[edit | edit source]
- reaction: EC 3.5.4.26? ExPASyDiaminohydroxyphosphoribosylaminopyrimidine deaminase 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H2O = 5-amino-6-(5-phosphoribosylamino)uracil + NH3EC 1.1.1.193? ExPASy5-amino-6-(5-phosphoribosylamino)uracil reductase 5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP+ = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH
- TIGRFAM: Biosynthesis of cofactors, prosthetic groups, and carriers Riboflavin, FMN, and FAD riboflavin biosynthesis protein RibD (TIGR00326; EC 1.1.1.193,3.5.4.26; HMM-score: 293.9)and 3 moreriboflavin-specific deaminase C-terminal domain (TIGR00227; EC 3.5.4.-; HMM-score: 150.8)diaminohydroxyphosphoribosylaminopyrimidine reductase (TIGR01508; EC 1.1.1.-; HMM-score: 96.7)ComE operon protein 2 (TIGR02571; HMM-score: 15.4)
- TheSEED :
- 5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193)
- Diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC 3.5.4.26)
- PFAM: DHFred (CL0387) RibD_C; RibD C-terminal domain (PF01872; HMM-score: 141.8)and 3 moreCDA (CL0109) dCMP_cyt_deam_1; Cytidine and deoxycytidylate deaminase zinc-binding region (PF00383; HMM-score: 60.7)MafB19-deam; MafB19-like deaminase (PF14437; HMM-score: 43.4)APOBEC_N; APOBEC-like N-terminal domain (PF08210; HMM-score: 13.7)
⊟Structure, modifications & cofactors[edit | edit source]
- domains:
- modifications:
- cofactors: Zn2+
- effectors:
⊟Localization[edit | edit source]
- PSORTb: Cytoplasmic
- Cytoplasmic Score: 7.5
- Cytoplasmic Membrane Score: 1.15
- Cellwall Score: 0.62
- Extracellular Score: 0.73
- Internal Helices: 0
- LocateP: Intracellular
- Prediction by SwissProt Classification: Cytoplasmic
- Pathway Prediction: No pathway
- Intracellular possibility: 1
- Signal peptide possibility: -1
- N-terminally Anchored Score: 1
- Predicted Cleavage Site: No CleavageSite
- SignalP: no predicted signal peptide
- SP(Sec/SPI): 0.018645
- TAT(Tat/SPI): 0.002
- LIPO(Sec/SPII): 0.002366
- predicted transmembrane helices (TMHMM): 0
⊟Accession numbers[edit | edit source]
⊟Protein sequence[edit | edit source]
- MVQGQTGVNPPVGAVVVKEGRIVGIGAHLRKGDKHAEVQALDMAQQNAEGATIYITLEPCSHFGSTPPCVNKIIDCKIAKVVYATKDNSLDTHGDETLRAHGIEVECVDDERASQLYQDFFKAKAKQLPQITVKVSASLDGKQANDNGQSQWITNKEVKQDVYKLRHRHDAVLTGRRTVELDDPQYTTRIQDGKNPIKVILSKSGNIHFNQQIYQDESTPIWIYTENPNLTTNQTHIEIIYLKSCDLTTILHNLYKRGVGTLLVEAGPTTTSEFLQSNYIDEFILYYAPKLIGGSGNYQFYQTNDVIEIPDANQFEIVHSELLNQNVKLTLRKK
⊟Experimental data[edit | edit source]
⊟Expression & Regulation[edit | edit source]
⊟Operon[edit | edit source]
- MicrobesOnline: ribH < ribBA < ribE < ribD
⊟Regulation[edit | edit source]
- regulator: FMN-box (transcription termination) regulon
FMN-box (RNA) important in Riboflavin biosynthesis; regulatory site identified based on RegPrecise data for N315 RegPrecise
⊟Transcription pattern[edit | edit source]
- S.aureus Expression Data Browser: data available for NCTC8325
⊟Protein synthesis (provided by Aureolib)[edit | edit source]
⊟Protein stability[edit | edit source]
- half-life: no data available
⊟Biological Material[edit | edit source]
⊟Mutants[edit | edit source]
⊟Expression vector[edit | edit source]
⊟lacZ fusion[edit | edit source]
⊟GFP fusion[edit | edit source]
⊟two-hybrid system[edit | edit source]
⊟FLAG-tag construct[edit | edit source]
⊟Antibody[edit | edit source]
⊟Other Information[edit | edit source]
You are kindly invited to share additional interesting facts.