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 Echvi_2283 Echvi_2283 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Cola:Echvi_2283 Length = 391 Score = 239 bits (609), Expect = 1e-67 Identities = 143/434 (32%), Positives = 232/434 (53%), Gaps = 51/434 (11%) Query: 4 HFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPT 63 HF+T + H + PIY T+S+ F++++ Q+F E+PG +YSR+ NP Sbjct: 5 HFETEAVRIASSKSNQREH---SAPIYMTSSFTFDSAEEARQMFAEEIPGNIYSRYANPN 61 Query: 64 SNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFK 123 S+ L E++ A+EG +A +SG AA ++ L GD+I+++ L+G T+ F Sbjct: 62 SSDLIEKVCAVEGTEDGIATASGMAAMFGSMASLLEQGDHILASRSLFGSTHQLLTRVFP 121 Query: 124 RFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVD 183 ++GI + + + + E ++K+ TK +++ET NP V D E I A H + +VVD Sbjct: 122 KWGITSTYGDISDIENWDKLVKPNTKMLFIETPSNPGLEVIDLEWIGKFAKAHNLILVVD 181 Query: 184 NTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQP 243 N F A Y QP K+GADIV HSATK+I G G +GG+I+ K K QF Sbjct: 182 NCF-ATPYLQQPAKWGADIVAHSATKYIDGQGRVLGGLILG------KQELIKEVQF--- 231 Query: 244 AEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENA 303 R GP ++PF +++L + +ETL++R ERH NA Sbjct: 232 -------------------------FTRHTGPSISPFNAWILSRSMETLAIRMERHCANA 266 Query: 304 LKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVK-DLPNADKETDPF 362 L +A + + + + +V YP L SH H+ AKK + +G GG+++ +K + A + Sbjct: 267 LAVASYFQDNKELEFVKYPFLKSHPQHDLAKKQMKHG-GGIVTLTLKGGIERAQR----- 320 Query: 363 KLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIE 422 +D L++ + AN+GD ++++ P TTH +L ++E+ G+ LIR+S G+E Sbjct: 321 ------FIDELQMITVTANLGDTRSIITHPASTTHSKLTEEERQRVGILPGLIRLSAGLE 374 Query: 423 FIDDIIADFQQSFE 436 DDIIAD +++ E Sbjct: 375 HHDDIIADIERALE 388 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: 453 Number of extensions: 24 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: 391 Length adjustment: 31 Effective length of query: 413 Effective length of database: 360 Effective search space: 148680 Effective search space used: 148680 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