Align Cysteine synthase; CSase; EC 2.5.1.47; O-acetylserine (thiol)-lyase; OAS-TL; O-acetylserine sulfhydrylase (uncharacterized)
to candidate WP_074874168.1 AFE_RS03420 threonine ammonia-lyase, biosynthetic
Query= curated2:Q9ZMW6 (305 letters) >NCBI__GCF_000021485.1:WP_074874168.1 Length = 521 Score = 61.2 bits (147), Expect = 5e-14 Identities = 55/179 (30%), Positives = 80/179 (44%), Gaps = 7/179 (3%) Query: 27 LKSAIYAKLEHLNPGGSVKDRLGQYLIKEAFRTRKITSTTTIIEPTAGNTGIALALVAIK 86 L+ + K E L P S K R I + K +I +AGN +A A K Sbjct: 47 LQREVLFKREDLQPVFSFKLRGAYNKIAQLSDAEKARG---VITASAGNHAQGVAYAAQK 103 Query: 87 HHLKTIFVVPKKFSTEKQQIMRALGALVINTPTSEGISGAIKKSKELAESIPDSYLPLQF 146 ++ + V+P K +RA GA VI + S A L ++P F Sbjct: 104 LGIRAVIVMPGTTPEIKVNAVRARGAEVILH--GDSYSDAQAHCDALIAESGLVFIP-PF 160 Query: 147 ENPDNPAAYYHTLAPEIVQELGTNLTSFVAGIGSGGTFAGMAKYLKERIPNIRLIGVEP 205 ++P A T+ EI+++ G L + +G GG AG+A YLK +P IR+IGVEP Sbjct: 161 DDP-LVIAGQGTIGAEILRQRGAGLEAIFVPVGGGGLIAGVAAYLKSIVPEIRIIGVEP 218 Lambda K H 0.317 0.137 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 314 Number of extensions: 16 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 305 Length of database: 521 Length adjustment: 31 Effective length of query: 274 Effective length of database: 490 Effective search space: 134260 Effective search space used: 134260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
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