Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate AZOBR_RS07765 AZOBR_RS07765 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__azobra:AZOBR_RS07765 Length = 429 Score = 375 bits (963), Expect = e-108 Identities = 199/431 (46%), Positives = 280/431 (64%), Gaps = 15/431 (3%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F+T +HAG D A +R PIY TTS+VF++ + LF L+ G++YSR NPT Sbjct: 9 FETRAIHAGAAP--DPATGARQTPIYQTTSFVFDDVDDAASLFNLQKVGFIYSRLTNPTV 66 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 +VLEER+A LEGGA A A SSG AAQ LA+ L GD IV++ LYGGT NQ SF R Sbjct: 67 SVLEERLANLEGGAGATATSSGHAAQLLALFPLMEPGDEIVASRKLYGGTLNQLGTSFPR 126 Query: 125 -FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVD 183 FG ++ FV+ D PE +TKA+++E++ NP V D E I IA + GIP++VD Sbjct: 127 AFGWKSVFVDTDQPENVRAAITAKTKAIFVESLANPGGVVTDLEAIAKIADEAGIPLIVD 186 Query: 184 NTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQP 243 NT A Y PI++GA +V HS TK++ G+GT++GG+++DSG F W KFP S+P Sbjct: 187 NTL-ATPYLINPIQWGATLVVHSTTKFLSGNGTSVGGVVIDSGSFDWGK-SGKFPALSEP 244 Query: 244 AEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENA 303 GYHG + E +G+LA+ +H LRDLGP P +FL L G+ETL LR +RH ++A Sbjct: 245 DAGYHGLKFQETFGHLAFTIHGHAVGLRDLGPSQAPLNAFLTLNGIETLPLRMQRHSDSA 304 Query: 304 LKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFK 363 LK+A++LE P V WVSY GL S ++ AKKYL G G VL+FGVK + Sbjct: 305 LKVAQFLESHPAVGWVSYAGLESSKYNALAKKYLPKGAGAVLTFGVKGGFD--------- 355 Query: 364 LSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEF 423 +G +VV+N++L S+LAN+GD+++L+I P TTH+QL+ + + +G D++R+S+G+E Sbjct: 356 -TGVKVVENVQLLSHLANIGDSRSLIIHPSSTTHRQLSPEGQAQAGAGPDVLRLSIGLES 414 Query: 424 IDDIIADFQQS 434 ++DIIAD ++ Sbjct: 415 VEDIIADLDRA 425 Lambda K H 0.317 0.136 0.402 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: 520 Number of extensions: 26 Number of successful extensions: 5 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: 444 Length of database: 429 Length adjustment: 32 Effective length of query: 412 Effective length of database: 397 Effective search space: 163564 Effective search space used: 163564 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 (21.6 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