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 6937071 Sama_1242 methionine gamma-lyase (RefSeq)
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__SB2B:6937071 Length = 392 Score = 237 bits (604), Expect = 6e-67 Identities = 142/436 (32%), Positives = 228/436 (52%), Gaps = 48/436 (11%) Query: 3 SHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNP 62 S T+ +H G E A S P+Y + ++VF+N++ G F + GY+Y+R NP Sbjct: 5 SKLATLVVHGGHERDAMGALVS---PLYQSATFVFDNARQGGARFAGDEAGYIYTRLGNP 61 Query: 63 TSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISF 122 T+ LE ++A LEG A A +SG A + A+ GD++V++ +YG T+ Sbjct: 62 TTAELERKLAILEGAEEAAATASGMGAVSAALLANLSQGDHLVASRAVYGCTFALMTDLM 121 Query: 123 KRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVV 182 RFGIE V+ P E + T+A++ ET NP +V D + I AI +HG+ +V Sbjct: 122 ARFGIEVTLVDFKEPAAIEAAIRDNTRAIFCETPVNPHLDVFDLDAIAAIGKRHGLLTIV 181 Query: 183 DNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQ 242 DNTF +P+ +G D+V HSATK++ GHG I G++ Sbjct: 182 DNTF-MTPLLQRPLDHGIDMVIHSATKYLNGHGDVIAGMVA------------------- 221 Query: 243 PAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGEN 302 G+ I V+ ++++D+G +M+P ++L+L+G++TL +R +RH +N Sbjct: 222 --------------GSKEQIDKVKYQIIKDIGAVMSPHDAWLILRGMKTLDVRVQRHCDN 267 Query: 303 ALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPF 362 A K+A +LE P V V YP L SH H + GGV++F +K +D E Sbjct: 268 AEKIADFLEAHPRVGRVYYPALKSHQGHRFLGTQMRRA-GGVIAFELK----SDIE---- 318 Query: 363 KLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIE 422 VD+LK+ + ++GDA++L+ P TH + +L +G+T L+R+SVG+E Sbjct: 319 --GSINFVDSLKVFTIAVSLGDAESLIQHPASMTHSPYTPEARLEAGITDTLLRISVGLE 376 Query: 423 FIDDIIADFQQSFETV 438 +DD+IAD Q+ + Sbjct: 377 DVDDLIADLSQALAKI 392 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: 440 Number of extensions: 22 Number of successful extensions: 4 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: 392 Length adjustment: 32 Effective length of query: 412 Effective length of database: 360 Effective search space: 148320 Effective search space used: 148320 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: 50 (23.9 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