Align O-acetylhomoserine (thiol)-lyase; EC 2.5.1.49 (characterized)
to candidate WP_011320765.1 AVA_RS20675 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= CharProtDB::CH_122447 (437 letters) >NCBI__GCF_000204075.1:WP_011320765.1 Length = 434 Score = 597 bits (1538), Expect = e-175 Identities = 295/426 (69%), Positives = 341/426 (80%), Gaps = 8/426 (1%) Query: 8 RFETLQLHAGQEPDPATNSRAVPIYATTSYTFNDSAHGARLFGLKEFGNIYSRIMNPTVD 67 RFETLQ+HAGQEP TN+RAVPIY TTSY F+D+ HGARLF L+EFGNIY+RIMNPT D Sbjct: 6 RFETLQVHAGQEPALGTNARAVPIYQTTSYVFDDADHGARLFALQEFGNIYTRIMNPTTD 65 Query: 68 VFEKRIAALEGGVAAVAASSGQAAQFMAISALAHAGDNIVSTSNLYGGTYNQFKVLFPRL 127 VFEKRIAALEGGVAA+A SSGQAAQF+AIS +A AGDNIVSTS LYGGTYNQFKV PRL Sbjct: 66 VFEKRIAALEGGVAALATSSGQAAQFLAISTIAQAGDNIVSTSFLYGGTYNQFKVSIPRL 125 Query: 128 GITTKFVQGDKAEDIAAAIDDRTKAVYVETIGNPRYNVPDFEVIAKVAHEKGIPLVVDNT 187 GI KFV+GD E AIDDRTKA+YVETIGNP++N+PDF +A +AHE GIPL+VDNT Sbjct: 126 GINVKFVEGDDVETFRQAIDDRTKALYVETIGNPQFNIPDFAALAHIAHEHGIPLIVDNT 185 Query: 188 FGAGGYFVRPIEHGADIVVHSATKWIGGHGTTIGGVVVDSGKFDWGKNAARFPQFTQPSE 247 FGAGGY RPIEHGADIVV SATKWIGGHGT+IGGV+VDSGKF+WG +FP FT+PS Sbjct: 186 FGAGGYLARPIEHGADIVVESATKWIGGHGTSIGGVIVDSGKFNWGN--GKFPVFTEPSP 243 Query: 248 GYHGLNFWET------FGPIAFAIRVRVEILRDLGSALNPFAAQQLILGLETLSLRAERH 301 GYHGLNF E FG IAF IR RVE LRD G +L+PF A L+ GLETLSLR +RH Sbjct: 244 GYHGLNFQEVFGVGSPFGNIAFIIRARVEGLRDFGPSLSPFNAFLLLQGLETLSLRVDRH 303 Query: 302 ASNALALANWLKKNDHVSWVSYVGLEEHSSHEVAKKYLKRGFGGVLSFGVKGEAAVGSQV 361 SNAL LA WL++ V+WV+Y GL H HE AKKYL+ GFGGVL+FG+KG G Sbjct: 304 VSNALELAQWLEQQPQVAWVNYPGLPHHPYHERAKKYLRHGFGGVLNFGIKGGLEAGKTF 363 Query: 362 VDNFKLISNLANVGDSKTLAIHPWSTTHEQLTDQERIDSGVTEDAIRISVGTEHIDDIIA 421 +++ KL S+LANVGD+KTL IHP STTH+QL+D E++ +GVT D +R+SVG EHIDDI Sbjct: 364 INHVKLASHLANVGDAKTLVIHPASTTHQQLSDTEQLSAGVTPDLVRVSVGIEHIDDIKE 423 Query: 422 DFEQSF 427 DFEQ+F Sbjct: 424 DFEQAF 429 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: 637 Number of extensions: 16 Number of successful extensions: 3 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: 434 Length adjustment: 32 Effective length of query: 405 Effective length of database: 402 Effective search space: 162810 Effective search space used: 162810 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