Annotation: NCBI__GCF_001431535.1:WP_057507948.1
Length: 894 amino acids
Source: GCF_001431535.1 in NCBI
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-methionine biosynthesis | metH | hi | methionine synthase; EC 2.1.1.13 (characterized) | 63% | 96%* | 1506.1 | Bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase; EC 2.1.1.10; EC 1.5.1.20 | 31% | 116.7 |
L-methionine biosynthesis | metH | med | metH: methionine synthase (EC 2.1.1.13) (TIGR02082) | 73% | 1221.9 | Bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase; EC 2.1.1.10; EC 1.5.1.20 | 31% | 116.7 | |
L-methionine biosynthesis | B12-reactivation-domain | hi | Met_synt_B12 (PF02965) | 100% | 420.3 | ||||
L-methionine biosynthesis | split_metH_1 | lo | Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized) | 30% | 94% | 104 | methionine synthase; EC 2.1.1.13 | 63% | 1123.2 |
View WP_057507948.1 at NCBI
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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MSTAPHTRLSGLEPLVITPDLLFINIGERTNVTGSAQFRKLVKEERYEEAVDVARQQVAS GAQILDVNMDEGLIDSEAAMTRYLNLIMSEPDIARIPVMVDSSKWSVIEAGLKCLQGKSV VNSISLKEGEDLFREHARKVLRYGAAAVVMAFDEAGQADTCARKVEICTRAYRILVDEIG FPPQDIIFDPNIFAVATGIEEHDNYAVDFIEATRIIKRTLPHCHVSGGVSNVSFSFRGNE TVRQAIHSVFLYHAIAAGMDMGIVNAGAMPIYDDLDAELRERVEDVILNRRADGTERLLE IAERYKGSKGAARVEDLAWREKPVTDRLAHALVHGLDAWVEQDTEEARQASTRPLDVIEG PLMNGMNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLLPYIEAEKLRSGDTARSNGKIIM ATVKGDVHDIGKNIVGVVLACNNFEVIDLGVMVPAQKILDAARAENADIIGLSGLITPSL EEMSHVAREMQRQGFELPLMIGGATTSRAHTALKIDPHYKAPTVWVKDASRAVGVAQSLI SHDLRAAFVAANEADYADIRLRHRNRGDAKRLVSLAHARGQRFDGGWADYVPPAPNQPGL HVFDDYPLAELVDYIDWTPFFQAWELAGKYPAILTDEIVGSQASELYRDARQMLDRIVKE RWLQARAVFGLWPANSVGDDVRVQHPDGEATLHFLRQQVDKPAERPDFCLADFIAPADSG RQDWIGAFAVTAGIGIDAHVARFEAAHDDYNAILLKALADRFAEALAERLHQRVRKEFWG HANDETLDNDALIAEKYSGIRPAPGYPACPEHSEKDTLFRLLDAQGNAGMQLTESFAMLP TAAVSGYYFSHPQSQYFVVGRVSREQVTDYAKRKGVDRVQAERWLASNLDYDPE
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory