Annotation: NCBI__GCF_002117405.1:WP_085770037.1
Length: 598 amino acids
Source: GCF_002117405.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| L-methionine biosynthesis | metY | hi | O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized) | 51% | 98% | 443.4 | Sulfhydrylase FUB7; Fusaric acid biosynthesis protein 7; EC 2.5.1.- | 49% | 406.4 |
| L-methionine biosynthesis | metB | lo | O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized) | 35% | 99% | 246.5 | O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- | 51% | 443.4 |
| L-methionine biosynthesis | metZ | lo | O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized) | 35% | 99% | 246.5 | O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- | 51% | 443.4 |
| L-cysteine biosynthesis | CGL | lo | cystathionine gamma-lyase (EC 4.4.1.1) (characterized) | 39% | 99% | 243 | O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- | 51% | 443.4 |
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
Fitness BLAST: loading...
MTDDLSYSEDYLREILSTTRTIAQVGATKKWNRPAFFVMKYLQSKGYRVIPVNPAFAGEE ILGERVYPDLKSIPEPVDFVQIFRRSEFAGAAADEAVAIGAKVVWMQLGVRDDAAAERAK AAGLKVVMNRCPKIEYGRLAGELSWGGVNSGVISNRAPSPPTRAPLRKSAGTLKADFGFE TKAIHAGARPEAVTGARVTPIFQTSSYVFDDAEAAASLFNLHNFGHIYSRLSNPTVAVLE ERIAALEGGRAAVAAASGHAAQFLAFFTLLEPGDVFLASRNLYGGTLTQFGLSFKKLGWT CRFVDQSDPENFRRALTERCKAIFIESLANPGGIVGDLEAIAKIAQDAGIPLVVDNTLAT PFLCRPMEWGADIICHSTTKFLAGHGNSLGGVVVESGRFNWANGKFPALAGPEPAYHGLD FFENFGDFAFTTKARAVALRDFGPALAPMNAFLTLTGIETLPLRMERHVANALAVARFLE SQPKVAWVSYAGLDSSPYRAAAQKYLPRGAGAVFTFGLNGGYAAGIKLVESVRLFSHLAN VGDTRSLILHPASTTHRQLTDEQRLAAGAGPEVVRLSVGLETAQDLIDDLAQALSAAE
This GapMind analysis is from Apr 10 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