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Conserved domains on  [gi|648655542|ref|WP_026347289|]
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MULTISPECIES: hypothetical protein [Stenotrophomonas]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DMB-PRT_CobT super family cl11435
Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called ...
111-177 6.12e-03

Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT/CobT, not to be confused with the CobT subunit of cobaltochelatase, which does not belong to this group) catalyzes the synthesis of alpha-ribazole-5'-phosphate, from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). This function is essential to the anaerobic biosynthesis pathway of cobalamin (vitamin B12), which is the largest and most complex cofactor in a number of enzyme-catalyzed reactions in bacteria, archaea and eukaryotes. Only eubacteria and archaebacteria can synthesize vitamin B12; multicellular organisms have lost this ability during evolution. DMB-PRT/CobT works sequentially with CobC (a phosphatase) to couple the lower ligand of cobalamin to a ribosyl moiety. DMB is the most common lower ligand of cobamides; other lower ligands include adenine, 5-methoxybenzimidazole or phenol. It has been suggested that earlier metabolic or enzymatic steps may control which lower ligand is available to DMB-PRT/CobT. In Salmonella enterica, for example, the lower ligand is DMB under aerobic conditions and adenine or 2-methyladenine under anaerobic conditions. Salmonella enterica DMB-PRT/CobT is a homodimer with two active sites, each active site is comprised of residues from both monomers. This group includes two distinct subfamilies, one archaeal-like, the other comprised of bacterial sequences.


The actual alignment was detected with superfamily member PRK04447:

Pssm-ID: 472180  Cd Length: 351  Bit Score: 36.33  E-value: 6.12e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 648655542 111 ADnVEILWLGtPPASIASLPALRPLAPSPAL--RAALpgvdDPAGLPVYVIDPnGFVIMRHAPGSDLGG 177
Cdd:PRK04447  53 AD-AELLLYG-KPLSLPPLPVTPTGCPTPALitRAVL----ELLGIPVLVVDA-GLYVKPKVPYIDLGG 114
 
Name Accession Description Interval E-value
PRK04447 PRK04447
hypothetical protein; Provisional
111-177 6.12e-03

hypothetical protein; Provisional


Pssm-ID: 235300  Cd Length: 351  Bit Score: 36.33  E-value: 6.12e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 648655542 111 ADnVEILWLGtPPASIASLPALRPLAPSPAL--RAALpgvdDPAGLPVYVIDPnGFVIMRHAPGSDLGG 177
Cdd:PRK04447  53 AD-AELLLYG-KPLSLPPLPVTPTGCPTPALitRAVL----ELLGIPVLVVDA-GLYVKPKVPYIDLGG 114
 
Name Accession Description Interval E-value
PRK04447 PRK04447
hypothetical protein; Provisional
111-177 6.12e-03

hypothetical protein; Provisional


Pssm-ID: 235300  Cd Length: 351  Bit Score: 36.33  E-value: 6.12e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 648655542 111 ADnVEILWLGtPPASIASLPALRPLAPSPAL--RAALpgvdDPAGLPVYVIDPnGFVIMRHAPGSDLGG 177
Cdd:PRK04447  53 AD-AELLLYG-KPLSLPPLPVTPTGCPTPALitRAVL----ELLGIPVLVVDA-GLYVKPKVPYIDLGG 114
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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