Annotation: NCBI__GCF_000375485.1:WP_018123824.1
Length: 759 amino acids
Source: GCF_000375485.1 in NCBI
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-cysteine biosynthesis | cysK | hi | cysteine synthase (EC 2.5.1.47) (characterized) | 51% | 98% | 288.5 | |||
L-cysteine biosynthesis | cysK | hi | cysteine synthase (EC 2.5.1.47) (TIGR01136) | 99% | 353 | ||||
L-cysteine biosynthesis | PSSH | hi | O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized) | 51% | 98% | 286.6 | Cysteine synthase B; CSase B; O-acetylserine (thiol)-lyase B; OAS-TL B; O-acetylserine sulfhydrylase B; EC 2.5.1.47 | 49% | 267.3 |
L-cysteine biosynthesis | Mt_cysM | med | [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase (EC 2.5.1.113); O-phosphoserine sulfhydrylase (EC 2.5.1.65) (characterized) | 43% | 94% | 218 | cysteine synthase (EC 2.5.1.47) | 51% | 288.5 |
L-cysteine biosynthesis | CBS | lo | Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized) | 41% | 64% | 204.9 | cysteine synthase (EC 2.5.1.47) | 51% | 288.5 |
View WP_018123824.1 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
Fitness BLAST: loading...
MENGILGLIGNTPLVELKRLNPNPRVRILAKLETANPGGSVKDRVAWAMIRRAEENGELQ PGKILIEATSGNTGIGLAMVAAVKGYPIRLIMPETASEERKMIMRAYGAEIELTPGHLAT DGAIELAYRMAREEPDKYVLLDQYNNPACVEAHYNGTGLEIWEQTGGEVTHAVATLGTTG TAMGMARRLHEMGGVFVAAVEPYEGHRIQGLKNMHESYPPGIYDKSELDAVLRVDDETAF DLCRRLAAEEGIFAGMSSGAALGGAIRLAEDMEQGTIVVLFPDGGERYLSTPLFAPRTRQ GVRLYDVARAGKELVRTEQGTGIYTMGPSLDNPAGLDSWRRVLVADVLFRHLTLRGVDVT PVAGLSDMDDRTLAAARARDASRADFASRTRQTILDTAKELGVSEAMLFPLTGPSEGTAL DLCRKMLGKGLAYEKLRSVYFDIFRDPRYGAFGLQDPEHLSAGKTVDLDAYVKDNPFDFT LLKRATLLDLKLGDVLETEWGNVRPSWFLQHAACATEVTGRTDIFIGSESHRFPHLENLR AIWSSAGREVQAWMVANRTGSGNLDGITQLVEILGSAHAARMWLLSAHYRKPLAATEENL RMWARNWQRVQDAAATLATMQDAPGTETDDRAEQMVFDLNAALREAMDDDLALHHFWPAL FTFAKSVNTLSAERKLSGKTAQMLLEALHSADQVLAIIDNDALPHPLSSLPEEVRGLVAD RQKARAEKNYTESDRIRDTLATKGFKVEDSNQGPRVYRI
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