Align O-acetylhomoserine (thiol)-lyase; EC 2.5.1.49 (characterized)
to candidate WP_041471291.1 CPHAMN1_RS04115 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= CharProtDB::CH_122447 (437 letters) >NCBI__GCF_000020545.1:WP_041471291.1 Length = 429 Score = 546 bits (1408), Expect = e-160 Identities = 265/425 (62%), Positives = 329/425 (77%), Gaps = 2/425 (0%) Query: 4 PSPKRFETLQLHAGQEPDPATNSRAVPIYATTSYTFNDSAHGARLFGLKEFGNIYSRIMN 63 P+ RFETLQ+HAGQEPD +TNSRAVPIY TTSY FN + HGA LF LKEFGNIY+R+MN Sbjct: 5 PTTYRFETLQVHAGQEPDSSTNSRAVPIYQTTSYVFNSAEHGANLFALKEFGNIYTRLMN 64 Query: 64 PTVDVFEKRIAALEGGVAAVAASSGQAAQFMAISALAHAGDNIVSTSNLYGGTYNQFKVL 123 PT DV EKR+AALEGG AA+ +SG AAQF+A++ + AGD+IVS+S LYGGTYNQFKV Sbjct: 65 PTTDVLEKRMAALEGGKAALVLASGHAAQFIALTNICQAGDSIVSSSFLYGGTYNQFKVS 124 Query: 124 FPRLGITTKFVQGDKAEDIAAAIDDRTKAVYVETIGNPRYNVPDFEVIAKVAHEKGIPLV 183 PRLGI+ +F + + + IDD TKA+Y+E+IGNP ++VPDFE IA VAH+K IPL+ Sbjct: 125 LPRLGISVRFAEDLSPDTFESLIDDTTKAIYLESIGNPAFHVPDFEAIAAVAHKKNIPLI 184 Query: 184 VDNTFGAGGYFVRPIEHGADIVVHSATKWIGGHGTTIGGVVVDSGKFDWGKNAARFPQFT 243 VDNTFG GY RPI+HGADIVV SATKWIGGHGT++GGV+VDSG FDW +FP FT Sbjct: 185 VDNTFGCAGYLCRPIDHGADIVVSSATKWIGGHGTSMGGVIVDSGTFDWSN--GKFPVFT 242 Query: 244 QPSEGYHGLNFWETFGPIAFAIRVRVEILRDLGSALNPFAAQQLILGLETLSLRAERHAS 303 +PS GYHGL F ++FG +AF IR RVE LRD G A++PF + L+ GLETLSLR +RHA Sbjct: 243 EPSPGYHGLKFHDSFGDLAFIIRARVEGLRDFGPAISPFNSFMLLQGLETLSLRVQRHAD 302 Query: 304 NALALANWLKKNDHVSWVSYVGLEEHSSHEVAKKYLKRGFGGVLSFGVKGEAAVGSQVVD 363 N +ALA WL+ + V+WV+Y GL +H +H A+KYL+ GFG VL+FGVK +D Sbjct: 303 NTMALALWLQDHPAVAWVNYPGLPDHPTHRNARKYLENGFGCVLTFGVKKGYEGAVSFID 362 Query: 364 NFKLISNLANVGDSKTLAIHPWSTTHEQLTDQERIDSGVTEDAIRISVGTEHIDDIIADF 423 N KL S+LANVGD+KTL IHP STTH+QL++ E+ +GV D +R+SVG EHIDDI+ DF Sbjct: 363 NVKLASHLANVGDAKTLVIHPASTTHQQLSEAEQDAAGVKSDMVRVSVGIEHIDDIMEDF 422 Query: 424 EQSFA 428 EQ+F+ Sbjct: 423 EQAFS 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: 592 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: 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