Align Cysteine synthase; CSase; EC 2.5.1.47; O-acetylserine (thiol)-lyase; OAS-TL; O-acetylserine sulfhydrylase (uncharacterized)
to candidate WP_012506490.1 PAES_RS09705 pyridoxal-phosphate dependent enzyme
Query= curated2:P73410 (312 letters) >NCBI__GCF_000020625.1:WP_012506490.1 Length = 457 Score = 181 bits (460), Expect = 2e-50 Identities = 111/311 (35%), Positives = 179/311 (57%), Gaps = 13/311 (4%) Query: 3 IASNITELIGRTPLVRLNRIPLLEGCGAKIVVKLEGMNPAASVKDRIGINMINRAEQEGL 62 + NI + + P+V + R L +IV +LE +NP+ + + +I AE+EGL Sbjct: 2 LQQNIFSMNAQVPMVAIKR--LAAHIQPEIVARLEYLNPSGTHYWSVASVIIENAEKEGL 59 Query: 63 IEPGKTLLIEPTSGNTGIALAMVAAAKGYQLILTMPETMSQERRAMLKAYGAKLELTPGS 122 I PG TL ++ T G++GIALAM A AKGY+++L +P+ +S+E++ +LKA GA++ +TP Sbjct: 60 ISPGMTL-VDWTYGSSGIALAMAAIAKGYKVLLVVPDKISREKQQVLKAMGAEVVITPSD 118 Query: 123 EGMGG---CIRRAQELAESLPNAYMLQQFDNPANPQIHQQTTALEIWQDTDGAIDFLVAG 179 G C+ AQ L ++L +AY ++NP + +H +TT IW+ T G + L Sbjct: 119 ALPGAPRSCVNVAQNLVQNLKHAYFTNMYENPLSFSVHAETTGPMIWEQTGGEVTHLFVP 178 Query: 180 VGTGGTITGVASVLKEKKPSFQAIAVEPQNS---PVLSGGK---PGPHKIQGIGAGFIPE 233 V +G I+G+ LK K+ + + I VEP+ S +L K P +++ IG + + Sbjct: 179 VTSGAMISGIGQFLKSKRQNIRIIGVEPEGSIYRELLQHRKLSAPALFELEEIGGLWESK 238 Query: 234 VLDVNLIDEVIAVTDEEAIAYGRRLAREEGILSGISTGAALAAAIKVAKRPANKDKLIVM 293 D ++ID+++ V+D +A GR L R E I SG S+GAA+ AA++ A +D IV+ Sbjct: 239 YWDASVIDDIVQVSDFDAFNCGRELLRSEAIFSGGSSGAAMFAALR-AGAHLGRDARIVV 297 Query: 294 IQPSFGERYLS 304 + FG YLS Sbjct: 298 MMSDFGGYYLS 308 Lambda K H 0.316 0.135 0.377 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: 290 Number of extensions: 13 Number of successful extensions: 4 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: 312 Length of database: 457 Length adjustment: 30 Effective length of query: 282 Effective length of database: 427 Effective search space: 120414 Effective search space used: 120414 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 09 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