Align O-acetylhomoserine (thiol)-lyase; EC 2.5.1.49 (characterized)
to candidate CA265_RS08180 CA265_RS08180 O-acetylhomoserine aminocarboxypropyltransferase
Query= CharProtDB::CH_122447 (437 letters) >FitnessBrowser__Pedo557:CA265_RS08180 Length = 443 Score = 528 bits (1361), Expect = e-154 Identities = 267/427 (62%), Positives = 326/427 (76%), Gaps = 8/427 (1%) Query: 8 RFETLQLHAGQEPDPATNSRAVPIYATTSYTFNDSAHGARLFGLKEFGNIYSRIMNPTVD 67 +FETLQLHAGQE DP T SRAVPIY TTSY F ++ HGA LF LKEFGNIY+RIMNPT D Sbjct: 6 KFETLQLHAGQEIDPTTGSRAVPIYQTTSYGFKNAEHGANLFALKEFGNIYTRIMNPTND 65 Query: 68 VFEKRIAALEGGVAAVAASSGQAAQFMAISALAHAGDNIVSTSNLYGGTYNQFKVLFPRL 127 VFEKRIAALEGGVAA+A +SGQAAQF+A++ + AGD+IVS+S++YGGTYNQFKV F RL Sbjct: 66 VFEKRIAALEGGVAALAVASGQAAQFIALNNILEAGDSIVSSSHIYGGTYNQFKVAFKRL 125 Query: 128 GITTKFVQGDKAEDIAAAIDDRTKAVYVETIGNPRYNVPDFEVIAKVAHEKGIPLVVDNT 187 GI F D E+ I D+TKA+++ETIGNP ++VPDFE IA +A + +PLVVDNT Sbjct: 126 GIHVDFANPDVPEEFENKITDKTKAIFLETIGNPAFSVPDFEKIAAIAKKYDLPLVVDNT 185 Query: 188 FGAGGYFVRPIEHGADIVVHSATKWIGGHGTTIGGVVVDSGKFDWGKNAARFPQFTQPSE 247 FGAGGY +P+EHGA+IVV SATKWIGGHGT+IGGV+VD G ++WG +FPQF++PSE Sbjct: 186 FGAGGYLFKPLEHGANIVVESATKWIGGHGTSIGGVIVDGGNYNWGN--GKFPQFSEPSE 243 Query: 248 GYHGLNFWET------FGPIAFAIRVRVEILRDLGSALNPFAAQQLILGLETLSLRAERH 301 GYHGL F + FG I F IR RVE LRDLG AL+PF + L+ GLETLSLR +RH Sbjct: 244 GYHGLVFSDVFGIGGPFGNIQFIIRARVEGLRDLGPALSPFNSFLLLQGLETLSLRVQRH 303 Query: 302 ASNALALANWLKKNDHVSWVSYVGLEEHSSHEVAKKYLKRGFGGVLSFGVKGEAAVGSQV 361 NAL LA WL+ + V V Y GL + +AKKYL GFG VLSF + G +QV Sbjct: 304 VDNALELATWLENHPLVKEVQYPGLASSKYNNLAKKYLSNGFGAVLSFELTGSKENATQV 363 Query: 362 VDNFKLISNLANVGDSKTLAIHPWSTTHEQLTDQERIDSGVTEDAIRISVGTEHIDDIIA 421 VDN KL+S+LANVGD+KTL I P +TTH+QL++ E++ +GV +A+R+SVG EHIDDI A Sbjct: 364 VDNLKLVSHLANVGDAKTLIIQPSATTHQQLSETEQLAAGVKPNALRVSVGIEHIDDIKA 423 Query: 422 DFEQSFA 428 DFEQ+FA Sbjct: 424 DFEQAFA 430 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: 593 Number of extensions: 19 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: 443 Length adjustment: 32 Effective length of query: 405 Effective length of database: 411 Effective search space: 166455 Effective search space used: 166455 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 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