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_078427052.1 BK574_RS00635 methionine gamma-lyase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_002019605.1:WP_078427052.1 Length = 392 Score = 233 bits (594), Expect = 8e-66 Identities = 141/433 (32%), Positives = 230/433 (53%), Gaps = 47/433 (10%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T +H G E+ S P++ ++++ E+++ G + F + GY+YSR NPT Sbjct: 7 ETEVIHRGYESKSFQG--SLTPPLFQSSTFTMESAEQGERRFAGDEEGYIYSRLGNPTVT 64 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 +LEERIA LEGG A LA SSG AA + + L +GD+I+ + +YG TY ++ RF Sbjct: 65 ILEERIAELEGGEAGLAFSSGMAAVSATLFALVRSGDHILVSEGVYGCTYGLLELLKDRF 124 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 ++ + D E TK +Y+ET NP + D + I + + G VVVDNT Sbjct: 125 KVDYDLIAMDKEEHIRSYIRPETKVIYVETPINPTMKLVDLQLISKLGKETGAKVVVDNT 184 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 F A Y +PI GAD+V HSATK+I GHG + G++V S +F Sbjct: 185 F-ATPYLQRPILLGADVVVHSATKYISGHGDVVAGLMVGSEEF----------------- 226 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 I VR +D+G +++PF ++LL++G++TL +R +RH NA++ Sbjct: 227 ----------------INEVRMTTQKDIGGIISPFDAWLLIRGLKTLPVRMDRHCSNAIQ 270 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 +A ++ P + + +PG S S + +K + GG++SF L N KET Sbjct: 271 IANKMKNHPKIKEIIFPGDESFSQVDVIEKQMKQA-GGMISF----LVNGGKET------ 319 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 ++++ LKL ++GDA+TL+ P TH + ++++ G+ +L+R+SVG+E + Sbjct: 320 AQRLMNELKLIKIAVSLGDAETLIQHPATMTHSVVPEEKRAQMGIGPELLRLSVGLEAWE 379 Query: 426 DIIADFQQSFETV 438 DI D +Q+ E + Sbjct: 380 DIWVDIEQALEKI 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: 417 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 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