Annotation: NCBI__GCF_000183405.1:WP_013450135.1
Length: 400 amino acids
Source: GCF_000183405.1 in NCBI
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-isoleucine biosynthesis | ilvA | hi | L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 (characterized) | 48% | 99% | 363.6 | serine racemase (EC 5.1.1.18) | 42% | 310.8 |
L-isoleucine biosynthesis | ilvA | med | ilvA: threonine ammonia-lyase (EC 4.3.1.19) (TIGR01127) | 99% | 481.5 | serine racemase (EC 5.1.1.18) | 42% | 310.8 | |
L-threonine biosynthesis | thrC | lo | threonine synthase (EC 4.2.3.1) (characterized) | 31% | 89% | 95.5 | L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 | 48% | 363.6 |
L-cysteine biosynthesis | cysK | lo | cysteine synthase (EC 2.5.1.47) (characterized) | 30% | 94% | 73.2 | L-threonine ammonia-lyase; L-serine ammonia-lyase; Threonine dehydratase; EC 4.3.1.19; EC 4.3.1.17 | 48% | 363.6 |
View WP_013450135.1 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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MGIGKIVEAYERIKPYIKYLPLYYSNNFSEPYKANIYFKMENLQRTGSFKLRGALNAILK NYDKCKNGVITASAGNHAQGVAFGCNLLSIPAVIVMPEITPLVKVENTKRYGAEVILYGK SYDDAYMKALSIAKNRNLFFVHPFNDEDVIDGQATIAYEILKEKEDIDTIVIPIGGGGLI SGISKFVKNVNSRINIIGVQAENAASMYNAVKKGNIVKLTNSNTIAEGIAVKEAGDITFE HCKKYVDDIILVSENEIAYAILQYIEKSKLVVEGAGAAPLATILSNKLSVEGKNVVLILS GGNIDVNLLTRVFYKGLASTGRFLELTVILKDIPGSLAAVTKDVADLGANVLDIRHFRYD VNLPVGSTKVIFHLETKGSSHIEEIVHTLTEKGYDISIYG
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