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 SMc01666 SMc01666 methionine gamma-lyase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Smeli:SMc01666 Length = 427 Score = 138 bits (347), Expect = 4e-37 Identities = 118/428 (27%), Positives = 189/428 (44%), Gaps = 72/428 (16%) Query: 28 PIYATTSYVFENSKHGSQLFGL-----EVP-----GYVYSRFQNPTSNVLEERIAALEGG 77 PI+ T+++VF +++ G F E P G VYSRF +P S ++E+R+A E Sbjct: 39 PIFLTSTFVFHSAEEGRDFFDFVSGRREPPAGVGAGLVYSRFNHPNSEIVEDRLAIFERA 98 Query: 78 AAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFGIEA-RFVEGDN 136 A SSG +A + GD+I+ + LYGGT +F G+ A F +G + Sbjct: 99 EAGALFSSGMSAIATTLLAFVRPGDSILHSQPLYGGTETLLAKTFLNLGVSAVGFADGTD 158 Query: 137 PEEFEKVFDE-----RTKAVYLETIGNPKYNVPDFEKIVAIAHK------HGIPVVVDNT 185 +E R + +ET NP ++ D + IA + H V DNT Sbjct: 159 EAAVNAAAEEAMSKGRVSVILIETPANPTNSLVDVALVRRIAERIGERQAHRPIVACDNT 218 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 G F PI++GAD+ +S TK++GGH I G ++ Sbjct: 219 L-LGPVFQHPIEHGADLSLYSLTKYVGGHSDLIAGAVL---------------------- 255 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 G+ A I V+ L +G ++P + +++ + +ETLS+R E+ +NA Sbjct: 256 -----------GSKALIRQVKA-LRGSIGTQLDPHSCWMIGRSLETLSVRMEKANDNARI 303 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLS---NGFGGVLSFGVKDLPNADKETDPF 362 +A++L P V + Y L H + + G G SF + A + F Sbjct: 304 VAEFLRDHPKVERIHY--LPFHDADTPVGRVFATQCTGAGSTFSFDI-----AGGQEAAF 356 Query: 363 KLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIE 422 + A + KLA +L G ++L P TH + + + GV + IR+S+GIE Sbjct: 357 RFLNALQI--FKLAVSL---GGTESLASHPAAMTHSGVPIEVRARIGVLESTIRLSIGIE 411 Query: 423 FIDDIIAD 430 DD++AD Sbjct: 412 HPDDLVAD 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: 396 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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