Align O-acetylhomoserine (thiol)-lyase; EC 2.5.1.49 (characterized)
to candidate WP_012466737.1 CLIM_RS09185 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= CharProtDB::CH_122447 (437 letters) >NCBI__GCF_000020465.1:WP_012466737.1 Length = 430 Score = 552 bits (1422), Expect = e-162 Identities = 268/424 (63%), Positives = 331/424 (78%), Gaps = 2/424 (0%) Query: 5 SPKRFETLQLHAGQEPDPATNSRAVPIYATTSYTFNDSAHGARLFGLKEFGNIYSRIMNP 64 +P RFETLQ+HAGQ+PDP T SRAVPIY TTSYTF+ +AHGA LF L+EFGNIY+R+MNP Sbjct: 6 TPYRFETLQVHAGQQPDPTTKSRAVPIYQTTSYTFDSAAHGADLFALREFGNIYTRLMNP 65 Query: 65 TVDVFEKRIAALEGGVAAVAASSGQAAQFMAISALAHAGDNIVSTSNLYGGTYNQFKVLF 124 T DVFE+R+AALEGG AA+A +SG +AQF+A+++L AGD IVS+S LYGGTYNQFKV F Sbjct: 66 TTDVFEQRVAALEGGKAALAVASGHSAQFIALTSLCQAGDTIVSSSYLYGGTYNQFKVAF 125 Query: 125 PRLGITTKFVQGDKAEDIAAAIDDRTKAVYVETIGNPRYNVPDFEVIAKVAHEKGIPLVV 184 RLGIT KFV G+ A+DDRTKA+Y+E+IGNP ++VPDFE IA VA E GIPLVV Sbjct: 126 GRLGITVKFVDGNDPSAFREAVDDRTKALYLESIGNPAFHVPDFEAIAAVAGEHGIPLVV 185 Query: 185 DNTFGAGGYFVRPIEHGADIVVHSATKWIGGHGTTIGGVVVDSGKFDWGKNAARFPQFTQ 244 DNTFG GY RP++HGA IVV SATKWIGGHGT++GGV+VD G FDWG +FP ++ Sbjct: 186 DNTFGCCGYLCRPLQHGASIVVESATKWIGGHGTSMGGVIVDGGTFDWGN--GKFPMLSE 243 Query: 245 PSEGYHGLNFWETFGPIAFAIRVRVEILRDLGSALNPFAAQQLILGLETLSLRAERHASN 304 PSEGYHGL F ETFG +AF I+ RVE LRD G ++PF + L+ GLETLSLR +RHA N Sbjct: 244 PSEGYHGLKFRETFGDLAFIIKARVEGLRDFGPVISPFNSFMLLQGLETLSLRVQRHADN 303 Query: 305 ALALANWLKKNDHVSWVSYVGLEEHSSHEVAKKYLKRGFGGVLSFGVKGEAAVGSQVVDN 364 L LA WL + V+WV+Y GLEEH +H A +YL GFG VL+FG+KG + +++ Sbjct: 304 TLELARWLAAHPSVAWVNYPGLEEHPTHRQALRYLTNGFGCVLTFGIKGGYEETVRFIES 363 Query: 365 FKLISNLANVGDSKTLAIHPWSTTHEQLTDQERIDSGVTEDAIRISVGTEHIDDIIADFE 424 +L S+LANVGD+KTL IHP STTH+QL+ +E+ +GV+ D +R+SVG EHIDDI ADFE Sbjct: 364 VRLASHLANVGDAKTLVIHPASTTHQQLSPEEQSAAGVSLDMVRVSVGIEHIDDIKADFE 423 Query: 425 QSFA 428 Q+FA Sbjct: 424 QAFA 427 Lambda K H 0.318 0.134 0.394 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: 573 Number of extensions: 23 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: 437 Length of database: 430 Length adjustment: 32 Effective length of query: 405 Effective length of database: 398 Effective search space: 161190 Effective search space used: 161190 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 (21.7 bits) S2: 51 (24.3 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