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_026606931.1 METAC_RS0110085 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000427445.1:WP_026606931.1 Length = 425 Score = 229 bits (584), Expect = 1e-64 Identities = 154/431 (35%), Positives = 225/431 (52%), Gaps = 18/431 (4%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F T LHAG E D++ A S VF++ + S V + ++ Sbjct: 9 FATKALHAGAER--DHSLCGGAPAHSDIWSMVFDSDANASPSLRPSRLCGVQMQAESRAV 66 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 +LEERIAALE G AA+A +SG+ A L G++I++ GG +Q F Sbjct: 67 ALLEERIAALEEGVAAVAFASGRGALLATFHLLMKPGEDIIAARAARGGAMDQLAHGFGD 126 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 FG+ ++ + + F RTKA+++E+ P + D E I ++A GIP++VDN Sbjct: 127 FGMRIKWADPMDLSTFTAAIGPRTKAIFVESTWGPGGAIVDLEAIGSVAKSVGIPLIVDN 186 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 T A Y +P ++GADIV HSA + G G GG+I+D G F W E++P S P Sbjct: 187 T-AATPYLVRPFEHGADIVVHSAAALLSGRGDQRGGLIIDGGGFNWLQ-DERYPMLSAPR 244 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 + GTI +GN ++ V R L G + P + L+L GVETL+LR +RH ENA Sbjct: 245 PEFDGTILANTFGNFSFAVAARALGLGHFGCELAPLDALLILAGVETLALRMQRHCENAR 304 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 +A+ L + P V WVSYPGL+ + A+KY NG G L+ G+ T + Sbjct: 305 TIAEHLARHPAVRWVSYPGLSGDRSNALAQKYCPNGAGAALTLGL---------TGGYP- 354 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLN-DKEKLASGVTKDLIRVSVGIEF 423 + A VV LKL S L+N GDA++ + P + ++ + D E S DL+R+S+GIE Sbjct: 355 AAAAVVSRLKLFSALSNFGDARSRALHPASSAERRPSYDGE---SDEPPDLVRLSIGIED 411 Query: 424 IDDIIADFQQS 434 +DIIAD Q+ Sbjct: 412 TNDIIADLDQA 422 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: 458 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: 425 Length adjustment: 32 Effective length of query: 412 Effective length of database: 393 Effective search space: 161916 Effective search space used: 161916 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