Align O-acetylhomoserine (thiol)-lyase; EC 2.5.1.49 (characterized)
to candidate NP_661504.1 CT0604 O-acetylhomoserine (thiol)-lyase
Query= CharProtDB::CH_122447 (437 letters) >NCBI__GCF_000006985.1:NP_661504.1 Length = 429 Score = 556 bits (1432), Expect = e-163 Identities = 267/427 (62%), Positives = 332/427 (77%), Gaps = 2/427 (0%) Query: 1 MSDPSPKRFETLQLHAGQEPDPATNSRAVPIYATTSYTFNDSAHGARLFGLKEFGNIYSR 60 MS+ + RFETLQ+HAGQEPDP T SRAVPIY TTSY F ++ HGA LF L++ GNIY+R Sbjct: 1 MSEDNTFRFETLQVHAGQEPDPVTGSRAVPIYQTTSYVFENAEHGADLFALRKAGNIYTR 60 Query: 61 IMNPTVDVFEKRIAALEGGVAAVAASSGQAAQFMAISALAHAGDNIVSTSNLYGGTYNQF 120 +MNPT DV EKR+AALEGG AA+ +SG +AQF+AI+ + AGDNIVS+S LYGGTYNQF Sbjct: 61 LMNPTTDVLEKRMAALEGGKAALGVASGHSAQFIAIATICQAGDNIVSSSYLYGGTYNQF 120 Query: 121 KVLFPRLGITTKFVQGDKAEDIAAAIDDRTKAVYVETIGNPRYNVPDFEVIAKVAHEKGI 180 KV F RLGI +FV G+ E AID+ TKA+Y+E+IGNP ++VPDF+ IAK+A E GI Sbjct: 121 KVAFKRLGIEVRFVDGNDQEAFRKAIDENTKALYMESIGNPAFHVPDFDAIAKIARENGI 180 Query: 181 PLVVDNTFGAGGYFVRPIEHGADIVVHSATKWIGGHGTTIGGVVVDSGKFDWGKNAARFP 240 PL+VDNTFG GY RPI+HGA IVV SATKWIGGHGT++GG++VD+G FDWG +FP Sbjct: 181 PLIVDNTFGCAGYLCRPIDHGASIVVESATKWIGGHGTSMGGIIVDAGTFDWGN--GKFP 238 Query: 241 QFTQPSEGYHGLNFWETFGPIAFAIRVRVEILRDLGSALNPFAAQQLILGLETLSLRAER 300 FT+PSEGYHGL F+E G +AF IR RVE LRD G A++PF + L+ GLETLSLR +R Sbjct: 239 LFTEPSEGYHGLKFYEAVGELAFIIRARVEGLRDFGPAISPFNSFMLLQGLETLSLRVQR 298 Query: 301 HASNALALANWLKKNDHVSWVSYVGLEEHSSHEVAKKYLKRGFGGVLSFGVKGEAAVGSQ 360 H N L LA WL+++D V+WV+Y GLE H +H +AKKYL GFG VL+FGVKG + Sbjct: 299 HLDNTLELARWLERHDAVAWVNYPGLESHPTHALAKKYLTHGFGCVLTFGVKGGYENAVK 358 Query: 361 VVDNFKLISNLANVGDSKTLAIHPWSTTHEQLTDQERIDSGVTEDAIRISVGTEHIDDII 420 +D+ KL S+LANVGD+KTL IHP STTH+QL+ +E++ +GVT D +R+SVG EHIDDI Sbjct: 359 FIDSVKLASHLANVGDAKTLVIHPASTTHQQLSAEEQVSAGVTADMVRVSVGIEHIDDIK 418 Query: 421 ADFEQSF 427 ADF Q+F Sbjct: 419 ADFSQAF 425 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: 555 Number of extensions: 21 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: 429 Length adjustment: 32 Effective length of query: 405 Effective length of database: 397 Effective search space: 160785 Effective search space used: 160785 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