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 Dsui_2039 Dsui_2039 OAH/OAS sulfhydrylase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__PS:Dsui_2039 Length = 428 Score = 434 bits (1117), Expect = e-126 Identities = 224/430 (52%), Positives = 292/430 (67%), Gaps = 15/430 (3%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 FDT+ LHAGQ D A SRA PIY T +YVF++ +H + LF L+ G VYSR NPT Sbjct: 8 FDTLSLHAGQVP--DAATGSRATPIYQTAAYVFDSPEHAASLFNLQTFGNVYSRLSNPTV 65 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 VLEERIAALEGG AA+AV+SG AAQ +A+ L GD IV+ LYGGT+ Q ++F++ Sbjct: 66 AVLEERIAALEGGKAAVAVASGMAAQMVALLNLCEAGDEIVAARTLYGGTHTQLDVNFRK 125 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 GI FV+ D+PE F K RTK +Y ET+GNP NV D E + IA+ G+P+ VDN Sbjct: 126 LGINTIFVDSDDPENFAKAITPRTKVIYAETMGNPGLNVLDIEAVARIANAAGLPLFVDN 185 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 TF A Y C+P ++GA IV HSATK+IGGHGTT+GGIIV+SGKFPW + KF ++P+ Sbjct: 186 TF-ASPYLCRPFEWGAAIVVHSATKFIGGHGTTLGGIIVESGKFPWDN--GKFATMTEPS 242 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 GYHG + E +GN + R E LR GP ++PF +FLLLQGVETLSLR +RH NAL Sbjct: 243 PGYHGVKFYETFGNFGFTAKCRMEGLRTFGPALSPFNAFLLLQGVETLSLRMDRHCSNAL 302 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 +A+ LE P V WV+YPGL S +H+ A+KYL G G VL+FG+K A Sbjct: 303 AIARHLEAHPQVEWVNYPGLPSSKYHDLAQKYLPKGAGAVLTFGIKGGAAA--------- 353 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424 G + +D+++ S+LAN+GDAKTLVI P TTH+Q+ +++ A+GV DLIR+SVG+E + Sbjct: 354 -GQEFIDSVEFLSHLANIGDAKTLVIHPASTTHRQMTPEQQTAAGVPPDLIRLSVGLETL 412 Query: 425 DDIIADFQQS 434 DDI+ D Q+ Sbjct: 413 DDILWDIDQA 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: 543 Number of extensions: 16 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: 428 Length adjustment: 32 Effective length of query: 412 Effective length of database: 396 Effective search space: 163152 Effective search space used: 163152 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