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 CA265_RS08180 CA265_RS08180 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Pedo557:CA265_RS08180 Length = 443 Score = 516 bits (1329), Expect = e-151 Identities = 262/442 (59%), Positives = 333/442 (75%), Gaps = 20/442 (4%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F+T+QLHAGQE D SRAVPIY TTSY F+N++HG+ LF L+ G +Y+R NPT+ Sbjct: 7 FETLQLHAGQEI--DPTTGSRAVPIYQTTSYGFKNAEHGANLFALKEFGNIYTRIMNPTN 64 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 +V E+RIAALEGG AALAV+SGQAAQ +A+ + GD+IVS+S++YGGTYNQFK++FKR Sbjct: 65 DVFEKRIAALEGGVAALAVASGQAAQFIALNNILEAGDSIVSSSHIYGGTYNQFKVAFKR 124 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 GI F D PEEFE ++TKA++LETIGNP ++VPDFEKI AIA K+ +P+VVDN Sbjct: 125 LGIHVDFANPDVPEEFENKITDKTKAIFLETIGNPAFSVPDFEKIAAIAKKYDLPLVVDN 184 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 TFGAGGY +P+++GA+IV SATKWIGGHGT+IGG+IVD G + W + KFPQFS+P+ Sbjct: 185 TFGAGGYLFKPLEHGANIVVESATKWIGGHGTSIGGVIVDGGNYNWGN--GKFPQFSEPS 242 Query: 245 EGYHGTIYNEA------YGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAER 298 EGYHG ++++ +GN+ +I+ R E LRDLGP ++PF SFLLLQG+ETLSLR +R Sbjct: 243 EGYHGLVFSDVFGIGGPFGNIQFIIRARVEGLRDLGPALSPFNSFLLLQGLETLSLRVQR 302 Query: 299 HGENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKE 358 H +NAL+LA WLE P V V YPGLAS ++ AKKYLSNGFG VLSF E Sbjct: 303 HVDNALELATWLENHPLVKEVQYPGLASSKYNNLAKKYLSNGFGAVLSF----------E 352 Query: 359 TDPFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVS 418 K + QVVDNLKL S+LANVGDAKTL+I P TTH+QL++ E+LA+GV + +RVS Sbjct: 353 LTGSKENATQVVDNLKLVSHLANVGDAKTLIIQPSATTHQQLSETEQLAAGVKPNALRVS 412 Query: 419 VGIEFIDDIIADFQQSFETVFA 440 VGIE IDDI ADF+Q+F T+ A Sbjct: 413 VGIEHIDDIKADFEQAFATIKA 434 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: 694 Number of extensions: 30 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: 443 Length adjustment: 32 Effective length of query: 412 Effective length of database: 411 Effective search space: 169332 Effective search space used: 169332 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