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_011384943.1 AMB_RS12895 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000009985.1:WP_011384943.1 Length = 430 Score = 377 bits (969), Expect = e-109 Identities = 199/434 (45%), Positives = 282/434 (64%), Gaps = 17/434 (3%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ LHAG D A S AVP+Y TTSY F +S+H + LF L+ G +Y+R NPT++ Sbjct: 9 ETIVLHAGYR--ADPATGSVAVPVYQTTSYQFRDSEHAANLFALKELGNIYTRLMNPTTD 66 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 VLE+R+AALEGG AALAV+SGQAA T AI LA GDN V+++ LYGGT+N F +FK+ Sbjct: 67 VLEQRLAALEGGVAALAVASGQAASTFAILNLAQAGDNFVTSTDLYGGTWNLFANTFKQL 126 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GIEARFV+ +PE F + D++T+A Y ET+ NPK V ++ +A++ G+P++VDNT Sbjct: 127 GIEARFVDPADPEAFVRATDDKTRAWYAETLPNPKLQVFPIAEVAKLANQVGVPLIVDNT 186 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 A +P+ GA IV +S TK+IGGHGT+IGG IVD G F W+ + ++FP ++P Sbjct: 187 --ASPVIAKPLSLGAHIVVYSCTKYIGGHGTSIGGAIVDGGTFDWEKHAKRFPLLNEPDP 244 Query: 246 GYHGTIYNEA---YGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGEN 302 YHG ++ +A G +AYI+ R LLRD+G ++PF +F +LQG+ETL LR H N Sbjct: 245 SYHGAVWTQAVKPLGPIAYIIRARVTLLRDIGAAISPFNAFQVLQGMETLPLRMREHCRN 304 Query: 303 ALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPF 362 A +A++L V+ V +P L + A L G+GG+L F +K A Sbjct: 305 ASAVAQFLAGHHKVAHVIHPSLQDGEYRRRADAALKGGYGGLLGFELKGGAEA------- 357 Query: 363 KLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIE 422 G + +D LKL ++AN+GDA++L I P TTH QL+ ++LASGVT +R+S+GIE Sbjct: 358 ---GRRFIDALKLLYHVANIGDARSLAIHPASTTHSQLSADDQLASGVTPGYVRLSIGIE 414 Query: 423 FIDDIIADFQQSFE 436 IDDI+AD +Q+ + Sbjct: 415 HIDDILADLKQALD 428 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: 494 Number of extensions: 15 Number of successful extensions: 4 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: 430 Length adjustment: 32 Effective length of query: 412 Effective length of database: 398 Effective search space: 163976 Effective search space used: 163976 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 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