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 GFF1863 HP15_1820 methionine gamma-lyase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Marino:GFF1863 Length = 413 Score = 260 bits (664), Expect = 7e-74 Identities = 159/433 (36%), Positives = 233/433 (53%), Gaps = 49/433 (11%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 DT+ + AGQ G H I+ T+S+V+ ++ + FG E PG +YSRF NPT Sbjct: 22 DTLAVRAGQIRTGQLEHSDA---IFPTSSFVYGSAAQAAARFGGEEPGNIYSRFTNPTVQ 78 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 E RIAA+EGG A+A +SG +A L +GD+++ + ++G T F+ RF Sbjct: 79 AFEGRIAAMEGGERAVATASGMSAILSTCMALLKSGDHVICSRGVFGTTNVLFQKYMARF 138 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 G+E FV + EE++ T+ +++ET NP V D E + +A + VVDN Sbjct: 139 GVETTFVSLTDMEEWQASIRSETRMLFIETPSNPLCEVADMEILGQLARDNDALFVVDNC 198 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 F +P++ GADIV HSATK++ G G +GG++V S K Sbjct: 199 F-CTPVLQRPLEQGADIVIHSATKYLDGQGRCVGGVVVGSEK------------------ 239 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 + E YG LR GP M+PF +++ +G+ETL +R H +NAL+ Sbjct: 240 -----MMEEVYG-----------FLRSAGPTMSPFNAWVFQKGLETLPIRMRAHCDNALE 283 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 LA WLEQ P V V Y GL SH HE AKK GFGGVLSF +K A +E F Sbjct: 284 LALWLEQQPAVERVFYAGLQSHPQHELAKKQ-QTGFGGVLSFQLK---GAREEAWRF--- 336 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 +D ++ S AN+GD KT + P TTH +L+ ++K +G+T++LIR+SVGIE ++ Sbjct: 337 ----IDGTRMISITANLGDVKTTITHPATTTHGRLSPEDKARAGITENLIRISVGIEAVE 392 Query: 426 DIIADFQQSFETV 438 D+ D ++ F+ + Sbjct: 393 DLKTDLERGFQAL 405 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: 451 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: 413 Length adjustment: 32 Effective length of query: 412 Effective length of database: 381 Effective search space: 156972 Effective search space used: 156972 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