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_041098967.1 SUTH_RS09960 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000828635.1:WP_041098967.1 Length = 427 Score = 345 bits (884), Expect = 2e-99 Identities = 188/433 (43%), Positives = 270/433 (62%), Gaps = 14/433 (3%) Query: 1 MPSHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQ 60 M +FDT+ LHAGQ D + +RA PIY TTS+VF++S + LF +E G+VYSR Sbjct: 1 MTYNFDTLALHAGQVP--DERYGARATPIYLTTSFVFKDSDQAAALFNMERAGHVYSRIS 58 Query: 61 NPTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKI 120 NPT+ VLEERIAALEGG A+AV+SGQAA LAI L G +IV++ LYGG++N Sbjct: 59 NPTNAVLEERIAALEGGVGAIAVASGQAALHLAIATLMGAGSHIVASRSLYGGSHNLLDY 118 Query: 121 SFKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPV 180 + RFGI FV+ + + + T+ ++ ET+GNP +V + ++ A+AH+HG+P+ Sbjct: 119 TLPRFGITTTFVDPRDLDAWRAAIRPETRLLFGETLGNPGLDVLNIPEVAALAHEHGLPL 178 Query: 181 VVDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQF 240 +VD+TF + +P +GAD++ HSATK++GGHG IGG++VD G F W D KFP Sbjct: 179 MVDSTF-TTPWLMRPFDHGADLIFHSATKFLGGHGVAIGGLLVDGGTFDW-DKSGKFPTL 236 Query: 241 SQPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHG 300 ++P EG+HG ++E A+++ R E LRD G M+P +F LLQGVETL LR ERH Sbjct: 237 TEPYEGFHGMDFSEESTVAAFLLRARREGLRDFGACMSPMTAFQLLQGVETLPLRMERHI 296 Query: 301 ENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETD 360 N + L + V+ V YP L +H H A+K L G G V SF +K Sbjct: 297 ANTRQAVAHLVKHEAVAGVGYPELENHPDHALAQKLLPRGAGSVFSFTLKG--------- 347 Query: 361 PFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVG 420 + +G + ++ L++ S+LANVGDAK+LVI P TTH +++D +A+G+ IR+S+G Sbjct: 348 -GRAAGRKFIEALRVFSHLANVGDAKSLVIHPASTTHFRMSDAALVAAGIHPGTIRLSIG 406 Query: 421 IEFIDDIIADFQQ 433 +E D+I D + Sbjct: 407 LEDAGDLIEDLNR 419 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: 485 Number of extensions: 18 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: 427 Length adjustment: 32 Effective length of query: 412 Effective length of database: 395 Effective search space: 162740 Effective search space used: 162740 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