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_051378992.1 H566_RS0118805 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000482785.1:WP_051378992.1 Length = 403 Score = 257 bits (657), Expect = 4e-73 Identities = 153/425 (36%), Positives = 227/425 (53%), Gaps = 43/425 (10%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ + AG G H A ++ T+SYVF ++ + F +V G VYSRF NPT Sbjct: 15 ETLAVRAGTARSGFGEH---AEAMFLTSSYVFGSAAEAADRFSNKVEGNVYSRFTNPTVT 71 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 + E+R+AALEG AALA +SG +A G+ GD++V+++ L+G T F +F Sbjct: 72 MFEQRLAALEGAEAALATASGMSAILTCCMGVLKAGDHVVASTGLFGSTVQLFNNILSKF 131 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GI +V +P + TK Y+ET NP + D + ++A G +VVDN Sbjct: 132 GITTSYVSPADPAAWRAAVRPETKLFYVETPSNPMMELADIPALASVAKDAGALLVVDNC 191 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 F QP+K GAD+V HSATK+I G G +GG IV Sbjct: 192 FCTPA-LQQPLKLGADVVIHSATKYIDGQGRVLGGAIV---------------------- 228 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 G+ A+I LR GP ++PF +++LL+G+ETL++R ER ENAL Sbjct: 229 -----------GSKAFIKDQMLPFLRTAGPTLSPFNAWVLLKGLETLAIRMERQSENALA 277 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 +A+WLE P V V YPGL SH HE AK+ G G VLSF ++ + T+ ++ Sbjct: 278 VARWLEAQPQVKRVIYPGLESHPQHELAKRQQKTG-GAVLSFELRGETPEQQRTNAWR-- 334 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 V+DN +L S AN+GD +T + P TTH ++ + + A+G+T+ +IR++VG+E + Sbjct: 335 ---VIDNTRLVSITANLGDTRTTITHPATTTHGRVAPEVRAAAGITEGMIRLAVGLESPE 391 Query: 426 DIIAD 430 D+ D Sbjct: 392 DLCRD 396 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: 428 Number of extensions: 17 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: 403 Length adjustment: 32 Effective length of query: 412 Effective length of database: 371 Effective search space: 152852 Effective search space used: 152852 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