Clusters of Characterized Proteins

Clustering the characterized proteins for ramA (ATP-dependent reduction of co(II)balamin) in L-methionine biosynthesis

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Definition of ramA

• HMM PF14574
• Curated proteins matching ATP-dependent reduction of co(II)balamin
• Comment: As of April 2019, all characterized members of the RamA family or PF14574 are involved in the reactivation of co(II)balamin. This includes RamA (B8Y445), DvMF_1398, PGA1_c15200, and ELI_0370 (part of a O-demethylase). Many bacteria contain MetH and probably rely on a distant homolog of RamA for reactivation of B-12. PF14574 describes only the C-terminal putative ATPase domain of RamA, but no other functions are known, except for the reactivation of Co(II) corrinoid proteins (i.e. RamQ, P0DX10).

Fetched 6 sequences

Running BLASTp

Found similarities, at above 30% identity and 75% coverage, for 3 of these sequences

Found 1 clusters of similar sequences. Another 3 sequences are not clustered. Download as table or as draft rules or view by cluster

Acetobacterium dehalogenans

B8R2M5 [Co(II) methylated amine-specific corrinoid protein] reductase (EC 1.16.99.1) (from HMM only) from Acetobacterium dehalogenans
PFams: Raco_middle, RACo_C_ter
598 amino acids: PaperBLAST, CDD (Cluster 1)

Desulfovibrio vulgaris

DVU0908 ATP-dependent reduction of co(II)balamin from Desulfovibrio vulgaris Hildenborough JW710
PFams: Fer2, Raco_middle, RACo_C_ter
543 amino acids: PaperBLAST, CDD (Singleton 2)

DvMF_1398 ATP-dependent reduction of co(II)balamin (RamA-like) from Desulfovibrio vulgaris Miyazaki F
PFams: Raco_middle, RACo_C_ter
685 amino acids: PaperBLAST, CDD (Singleton 3)

Eubacterium limosum

RAMQ_EUBLI / P0DX10 Corrinoid activation enzyme RamQ (from HMM only) from Eubacterium limosum
PFams: Raco_middle, RACo_C_ter
593 amino acids: PaperBLAST, CDD (Cluster 1)

Methanosarcina barkeri

B8Y445 [Co(II) methylated amines-specific corrinoid protein] reductase (EC 1.16.99.1) from Methanosarcina barkeri
B8Y445 [Co(II) methylated amine-specific corrinoid protein] reductase (EC 1.16.99.1) (from HMM only) from Methanosarcina barkeri
PFams: Raco_middle, RACo_C_ter, Fer4, Fer4_21, Fer4_7, Fer4_9
540 amino acids: PaperBLAST, CDD (Singleton 1)

Phaeobacter inhibens

PGA1_c15200 ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) from Phaeobacter inhibens BS107
PFams: RACo_linker, Raco_middle, RACo_C_ter
698 amino acids: PaperBLAST, CDD (Cluster 1)