Annotation: NCBI__GCF_000025725.1:WP_013010361.1
Length: 376 amino acids
Source: GCF_000025725.1 in NCBI
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-lysine biosynthesis | hcs | hi | homocitrate synthase (EC 2.3.3.14) (characterized) | 47% | 97% | 340.9 | 2-phosphonomethylmalate synthase; EC 2.3.3.19 | 37% | 273.5 |
L-lysine biosynthesis | hcs | hi | nifV: homocitrate synthase (EC 2.3.3.14) (TIGR02660) | 99% | 468.9 | 2-phosphonomethylmalate synthase; EC 2.3.3.19 | 37% | 273.5 | |
L-leucine biosynthesis | leuA | med | 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized) | 50% | 96% | 367.1 | homocitrate synthase (EC 2.3.3.14) | 47% | 340.9 |
L-isoleucine biosynthesis | cimA | lo | Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized) | 40% | 70% | 270.4 | homocitrate synthase (EC 2.3.3.14) | 47% | 340.9 |
View WP_013010361.1 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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MIIDDTTLRDGEQTPGVAFSRKEKLTIVKHLDAIGVQEIEAGIPVMGLAESRMFESIMEL GLDARIIAWNRALIGDVQASIAAGANSIEISLPMSDVQINTKLNKTRGWILDQVKSVLDF CANHDLYISVGGEDASRADFDFLAEYIRTIEAHGADRFRFCDTVGILDPFKTYELTAKIR EITSMDIEIHTHNDFGMATANALAAVRAGATHVNTTVIGLGERAGNAPLEEIIMASRHVY GMDDAFDTKTMRSLSEYVAQAAGRNLDPQRPVIGEFMFTHESGIHTDGVLKNPKNYEAFD PAELNMQRNLVFGNQSGLAVLKYILEQEGIVLESYQLTGLLHEAKKLARKNKAVLNKAQV IGLYSKVCNVVRDTTA
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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