Protein Info for DvMF_0476 in Desulfovibrio vulgaris Miyazaki F

Updated annotation (from data): vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13)
Rationale: Important for fitness in most defined media and strongly cofit with the ATP-dependent co(II)balamin reductase (DvMF_1398). This lacks the usual reactivation domain for converting co(II)balamin to co(I)balamin; that activity is instead provided by DvMF_1398.
Original annotation: homocysteine S-methyltransferase (RefSeq)

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

• PF02574: S-methyl_trans
  • amino acids 14 to 288 (275 residues), 257 bits, E=6.3e-80
• PF00809: Pterin_bind
  • amino acids 327 to 549 (223 residues), 74.2 bits, E=2.7e-24
• PF02607: B12-binding_2
  • amino acids 613 to 683 (71 residues), 72.4 bits, E=5.7e-24
• PF02310: B12-binding
  • amino acids 698 to 808 (111 residues), 99 bits, E=3.5e-32

Best Hits

KEGG orthology group: K00548, 5-methyltetrahydrofolate--homocysteine methyltransferase [EC: 2.1.1.13] (inferred from 100% identity to dvm:DvMF_0476)

Predicted SEED Role

"5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)" in subsystem Methionine Biosynthesis (EC 2.1.1.13)

MetaCyc Pathways

• aspartate superpathway (20/25 steps found)
• superpathway of L-methionine biosynthesis (by sulfhydrylation) (9/12 steps found)
• superpathway of L-lysine, L-threonine and L-methionine biosynthesis I (13/18 steps found)
• superpathway of S-adenosyl-L-methionine biosynthesis (6/9 steps found)
• superpathway of L-methionine biosynthesis (transsulfuration) (6/9 steps found)
• superpathway of L-homoserine and L-methionine biosynthesis (5/8 steps found)
• L-methionine biosynthesis III (2/4 steps found)
• L-methionine salvage from L-homocysteine (1/3 steps found)
• folate transformations III (E. coli) (5/9 steps found)
• L-methionine biosynthesis I (2/5 steps found)
• folate transformations II (plants) (6/11 steps found)
• folate transformations I (7/13 steps found)
• superpathway of L-methionine salvage and degradation (5/16 steps found)

KEGG Metabolic Maps

• Methionine metabolism
• One carbon pool by folate

Isozymes

No predicted isozymes

Use Curated BLAST to search for 2.1.1.13

Sequence Analysis Tools

See B8DKK4 at UniProt or InterPro

Protein Sequence (818 amino acids)

>DvMF_0476 vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) (Desulfovibrio vulgaris Miyazaki F)
MPDFRQALRSGRRLVFDGGMGTMLQSRGLPPGVSPELFCLARPDVLVGIHADYLRAGADV
LTTNTFGGCIHKLGTGPGAPDVVEFNRAMARAAREAVLASGREAFVAGSVGPSGHFMRPL
GDLDPAELVAAFRAQIRGLVQGGVDLILAETQFDLAEARAIVLAARAECDLPVGVSMTFE
NGVSLTGTRPEVFVQSMLNMGVDLVGTNCSAGPEQMAEVADELLAISEVPVLVEPNAGLP
ELVDGKTVFRLGPDDFARHTARFAASGVRMLGGCCGTTPDHIAALRGALDNLSGGLVPDP
ARRDGIVLTTRAQAVHIGAGSPIRIIGERINPTGKKLLTAELQAGEFAQALRFADEQVEA
GAPLLDVNVGAPMVDEAVLLPALVERLVARHSLPLSLDSSNADAIAAALPFHPGSPLVNS
ISGEPGRMEHLGPLCRDHGAPFILLPLKGRKLPVTAAERIAIIEELLQQADSLRIPRRLV
MVDVLALAVSSKAEAARHCLDTIRWCAAQGLPTTIGLSNISFGLPARELLNSTFLAMAAG
AGLSSCIAHPGNARIREAVAASSVLLGLDANAESFIEGYSGWTPGGDATGATPAGVAGGT
GGGTGGVKAKAATLEEAVIRGDREGALALVERALSEGADPFSLVQEKLIPGITEVGRRYE
RREYFLPQLIRSAETMQHAFRKLQPLLEAQRGHEARPVIIMATVEGDIHDIGKNIVTLML
GNHGFDVVDLGKDVKAADIVEAAERHGARVIGLSALMTTTMVRMEDTVRLVRERGLPVKV
MVGGAVVTPAYAEAIGADGYSADAVEAVRVAKELLTVQ