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_057508383.1 ABB28_RS09425 cystathionine gamma-synthase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_001431535.1:WP_057508383.1 Length = 392 Score = 212 bits (540), Expect = 1e-59 Identities = 140/431 (32%), Positives = 219/431 (50%), Gaps = 56/431 (12%) Query: 7 TVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSNV 66 T+ +H GQ D + + PIYAT++Y S G E G+ YSR NPT Sbjct: 17 TLAIHGGQSP--DPSTGAVMPPIYATSTYA--QSSPG------EHQGFEYSRTHNPTRFA 66 Query: 67 LEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQF-KISFKRF 125 E +A+LEGG+ A +SG AA T + L G ++V+ +YGGT+ F ++ + Sbjct: 67 YERCVASLEGGSRGFAFASGMAA-TSTVMELLDAGSHVVAMDDIYGGTFRLFERVRRRTA 125 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 G++ FV+ + FE TK V++ET NP + D + AIA +HG+ +VVDNT Sbjct: 126 GLDFSFVDLTDLAAFEAAITPATKMVWIETPTNPMLKIVDIAAVAAIAKQHGLIIVVDNT 185 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 F A +P++ GAD+V HSATK++ GH +GG++V Sbjct: 186 F-ASPMLQRPLELGADLVLHSATKYLNGHSDMVGGMVV---------------------- 222 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 G+ + L +G + PF SFL L+G++TL LR + H NAL Sbjct: 223 ----------VGDNTGLAEQMAFLQNSIGAVQGPFDSFLALRGLKTLPLRMKAHCANALA 272 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 LA+WLE P V V YPGL SH HE A + + NG+GG++S +K A K Sbjct: 273 LAQWLETQPSVEKVIYPGLTSHPQHELATRQM-NGYGGIVSIVLKGGFEAAK-------- 323 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 + + +L + ++G ++LV P TH + + + G+++ L+R+SVG+E + Sbjct: 324 --RFCERTELFTLAESLGGVESLVNHPAVMTHASIPVERRENLGISEGLVRLSVGVEELG 381 Query: 426 DIIADFQQSFE 436 D++ D +++ + Sbjct: 382 DLMVDLERALQ 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: 452 Number of extensions: 18 Number of successful extensions: 6 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 10 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