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 WP_012466737.1 CLIM_RS09185 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000020465.1:WP_012466737.1 Length = 430 Score = 510 bits (1314), Expect = e-149 Identities = 248/437 (56%), Positives = 331/437 (75%), Gaps = 14/437 (3%) Query: 2 PSHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQN 61 P F+T+Q+HAGQ+ D +SRAVPIY TTSY F+++ HG+ LF L G +Y+R N Sbjct: 7 PYRFETLQVHAGQQP--DPTTKSRAVPIYQTTSYTFDSAAHGADLFALREFGNIYTRLMN 64 Query: 62 PTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKIS 121 PT++V E+R+AALEGG AALAV+SG +AQ +A+ L GD IVS+SYLYGGTYNQFK++ Sbjct: 65 PTTDVFEQRVAALEGGKAALAVASGHSAQFIALTSLCQAGDTIVSSSYLYGGTYNQFKVA 124 Query: 122 FKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVV 181 F R GI +FV+G++P F + D+RTKA+YLE+IGNP ++VPDFE I A+A +HGIP+V Sbjct: 125 FGRLGITVKFVDGNDPSAFREAVDDRTKALYLESIGNPAFHVPDFEAIAAVAGEHGIPLV 184 Query: 182 VDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFS 241 VDNTFG GY C+P+++GA IV SATKWIGGHGT++GG+IVD G F W + KFP S Sbjct: 185 VDNTFGCCGYLCRPLQHGASIVVESATKWIGGHGTSMGGVIVDGGTFDWGN--GKFPMLS 242 Query: 242 QPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGE 301 +P+EGYHG + E +G+LA+I+ R E LRD GP+++PF SF+LLQG+ETLSLR +RH + Sbjct: 243 EPSEGYHGLKFRETFGDLAFIIKARVEGLRDFGPVISPFNSFMLLQGLETLSLRVQRHAD 302 Query: 302 NALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDP 361 N L+LA+WL P V+WV+YPGL H H A +YL+NGFG VL+FG+K +ET Sbjct: 303 NTLELARWLAAHPSVAWVNYPGLEEHPTHRQALRYLTNGFGCVLTFGIK---GGYEETVR 359 Query: 362 FKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGI 421 F +++++LAS+LANVGDAKTLVI P TTH+QL+ +E+ A+GV+ D++RVSVGI Sbjct: 360 F-------IESVRLASHLANVGDAKTLVIHPASTTHQQLSPEEQSAAGVSLDMVRVSVGI 412 Query: 422 EFIDDIIADFQQSFETV 438 E IDDI ADF+Q+F T+ Sbjct: 413 EHIDDIKADFEQAFATL 429 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: 628 Number of extensions: 17 Number of successful extensions: 4 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: 430 Length adjustment: 32 Effective length of query: 412 Effective length of database: 398 Effective search space: 163976 Effective search space used: 163976 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 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