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_012332478.1 M446_RS12590 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000019365.1:WP_012332478.1 Length = 431 Score = 308 bits (790), Expect = 2e-88 Identities = 169/430 (39%), Positives = 253/430 (58%), Gaps = 14/430 (3%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F T +H G D A +RA PIY T +VFE+++ + +F + G+ YSR NPT Sbjct: 11 FATRAVHGGAAP--DPATGARAQPIYLTNGFVFESNEQAADIFAMRATGFSYSRGSNPTV 68 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 LE R+A+LEG AA+AV SGQAA L + L GD+ V+++ L+GG+ + R Sbjct: 69 AALERRVASLEGAKAAVAVGSGQAAMLLVLLTLLQAGDSYVASARLFGGSLGLMRRLETR 128 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 + + +F G PE+FE+ +RT+A+ E+I NP V D + A+A +HG+P++VDN Sbjct: 129 YALTPQFSRGLTPEDFERAITDRTRAIICESIVNPCGTVVDVAGVAAVARRHGLPLIVDN 188 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 T A +PI++GADIV HS +K++ G GT IGGI+ D+G+F W+ ++ ++P Sbjct: 189 TL-ASPALIRPIEHGADIVVHSTSKFLSGSGTVIGGIVCDAGRFDWR-ATGRYNLINEPW 246 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 Y G + +E + A+ R LRDLGP ++P +FL L G+ETL LR ERH NA Sbjct: 247 PDYDGLVVSERFPETAFATACRLFGLRDLGPGLSPMNAFLTLTGIETLPLRMERHCANAR 306 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 +A L+ P V+WVSYP L + A +Y+ G G + +F +K +P L Sbjct: 307 AVAARLKAHPKVAWVSYPSLPGQAGEAVANRYVPQGAGAIFTFALKG-------GEPAAL 359 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424 + + L L S+L N+G+ K+L I P TTH+QL EK A+ V + +R+S+G+E I Sbjct: 360 A---FISGLDLISHLVNIGEIKSLAIHPATTTHRQLRQDEKAAACVGPETVRLSIGLESI 416 Query: 425 DDIIADFQQS 434 +D+IAD +QS Sbjct: 417 EDLIADVEQS 426 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: 444 Number of extensions: 12 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: 431 Length adjustment: 32 Effective length of query: 412 Effective length of database: 399 Effective search space: 164388 Effective search space used: 164388 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