Protein Info for AMB_RS13995 in Magnetospirillum magneticum AMB-1
Annotation: NADH-quinone oxidoreductase subunit D
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
Best Hits
Swiss-Prot: 100% identical to NUOD_MAGSA: NADH-quinone oxidoreductase subunit D (nuoD) from Magnetospirillum magneticum (strain AMB-1 / ATCC 700264)
KEGG orthology group: K00333, NADH dehydrogenase I subunit D [EC: 1.6.5.3] (inferred from 100% identity to mag:amb2784)MetaCyc: 66% identical to MbhL (Pyrococcus furiosus)
Ferredoxin hydrogenase. [EC: 1.12.7.2]
Predicted SEED Role
"NADH-ubiquinone oxidoreductase chain D (EC 1.6.5.3)" in subsystem Respiratory Complex I (EC 1.6.5.3)
MetaCyc Pathways
- superpathway of hydrogen production (2/2 steps found)
- hydrogen production III (1/1 steps found)
- hydrogen production VIII (1/1 steps found)
- aerobic respiration I (cytochrome c) (3/4 steps found)
- aerobic respiration III (alternative oxidase pathway) (2/3 steps found)
- NADH to cytochrome bd oxidase electron transfer I (1/2 steps found)
- NADH to cytochrome bo oxidase electron transfer I (1/2 steps found)
- hydrogen production VI (1/2 steps found)
- NAD(P)/NADPH interconversion (3/6 steps found)
- Fe(II) oxidation (2/6 steps found)
- superpathway of fermentation (Chlamydomonas reinhardtii) (4/9 steps found)
- L-glutamate degradation VII (to butanoate) (6/12 steps found)
- superpathway of photosynthetic hydrogen production (1/6 steps found)
KEGG Metabolic Maps
Isozymes
Compare fitness of predicted isozymes for: 1.6.5.3
Use Curated BLAST to search for 1.12.7.2 or 1.6.5.3
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Predict protein localization: PSORTb (Gram-negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the current SEED with FIGfam search
Find homologs in fast.genomics or the ENIGMA genome browser
See Q2W3I7 at UniProt or InterPro
Protein Sequence (392 amino acids)
>AMB_RS13995 NADH-quinone oxidoreductase subunit D (Magnetospirillum magneticum AMB-1) MAESQIQSYTINFGPQHPAAHGVLRLILEMSGEVVDRADPHVGLLHRGTEKLIEHKTYLQ ATPYFDRLDYVGTMNQEHAFVLATEKLLGIDIPIRAKFIRTLYDEIGRILNHLLNVTAFI FDVGGMTPLLYGFEEREKLMEFYERVCGARLHANYYRPGGVAADLPAGLLEDIAAWCETF PKVLDDIETLATDNRIFKQRVVDIGVVSPEQALDWGFTGPNLRASGIAWDLRKSQPYDVY DQMEFDIPVGKNGDGYDRYLVRVLEMRESVKIMKQCIAKMPGGPVRVEDNKITPPKRSEM KTSMESLIHHFKLFTEGFKVPAGEVYGAIEAPKGEFAVYLVSDGTGKPYRCKIRPPGYVH LQALDMMSKGHMLADVVANIGSIDIVFGEIDR