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 Ac3H11_2928 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2928 Length = 436 Score = 345 bits (884), Expect = 2e-99 Identities = 186/435 (42%), Positives = 275/435 (63%), Gaps = 17/435 (3%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 FDT+ LHAG D A +RA PI+ TTS+VFE+S H + LF LE G+VYSR NPT+ Sbjct: 9 FDTLALHAGASP--DPATGARATPIHLTTSFVFESSDHAASLFNLERGGHVYSRISNPTN 66 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 VLE+R+AALEGG A+A +SGQAA LAI + G +IV+++ LYGG+ N + R Sbjct: 67 AVLEQRVAALEGGVGAIATASGQAALHLAIATIMGAGSHIVASTALYGGSQNLLHYTLSR 126 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 FGIE FV+ + + + TK + ET+GNP +V D + +IAH+ G+P++VD+ Sbjct: 127 FGIETTFVKPGDIDAWRAAVRPNTKLFFGETVGNPGLDVLDIPTVSSIAHEAGVPLLVDS 186 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPE---KFPQFS 241 T + +P ++GAD+V HSATK++ GHGT +GGI+VD G F W D P+ KF + + Sbjct: 187 TL-TSPWLIKPFEHGADLVYHSATKFLSGHGTVVGGIVVDGGSFDW-DGPKSAGKFAELT 244 Query: 242 QPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGE 301 QP +G+H ++ E A+++ R E LRD G M+P ++L+LQG+ETL LR +H Sbjct: 245 QPYDGFHNMVFTEESTVGAFLLRARREGLRDFGACMSPHTAWLILQGIETLPLRMAQHMR 304 Query: 302 NALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDP 361 N K+ ++L P+VS V +P L SH H A+K L G G V SF +K ++E Sbjct: 305 NTEKVVEFLAAQPFVSRVGHPMLESHPSHALAQKLLPRGAGSVFSFDLK----GNRE--- 357 Query: 362 FKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGI 421 G + ++ LK+ S+LANVGD ++LVI P TTH +++D+ +G+T+ IR+S+G+ Sbjct: 358 ---QGKKFIETLKVFSHLANVGDCRSLVIHPASTTHFRMSDEALAGAGITQGTIRLSIGL 414 Query: 422 EFIDDIIADFQQSFE 436 E DD+I D +++ + Sbjct: 415 EDADDLIDDLKRALK 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: 481 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: 436 Length adjustment: 32 Effective length of query: 412 Effective length of database: 404 Effective search space: 166448 Effective search space used: 166448 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