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_007472892.1 CMTB2_RS00355 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase family protein
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000170735.1:WP_007472892.1 Length = 418 Score = 327 bits (838), Expect = 4e-94 Identities = 180/431 (41%), Positives = 265/431 (61%), Gaps = 17/431 (3%) Query: 7 TVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSNV 66 T+ LH G E + ++ VPIY +++Y ++++ H ++LF L+ G +Y+R NPT+ V Sbjct: 5 TLALHYGYEK---DKEKTMQVPIYMSSAYEYQDTDHAARLFNLQEEGNIYTRIGNPTTRV 61 Query: 67 LEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFG 126 E+RIAALE G ALA +SG +A +I L GDN++ ++ LYGG+ + K+FG Sbjct: 62 FEKRIAALENGIDALATASGMSAIFYSIANLVKNGDNVIISNKLYGGSITLSTQTLKQFG 121 Query: 127 IEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNTF 186 I+A++ + NPE E++ DE TKA+ E+I NP NV DFE I IA+K GI + DNT Sbjct: 122 IKAKYFDIKNPEMLEELIDENTKAILFESIANPALNVADFEIISEIANKRGIITICDNTI 181 Query: 187 GAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAEG 246 A Y +PI G DIV HSA+K++ G+GT IGG I++S K +++PQF++P + Sbjct: 182 -ATPYSLKPINLGIDIVVHSASKYLSGNGTVIGGCIIESKSAKEKLKGDRYPQFNKPDDS 240 Query: 247 YHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALKL 306 YHG IYNE + N +I R LLRD G +++PF S+LL+ G+ETL LR ERH NAL++ Sbjct: 241 YHGLIYNEKFDN-PFIARSRLALLRDYGAVISPFNSWLLILGLETLHLRIERHSYNALEI 299 Query: 307 AKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLSG 366 AK+L V VSYP L + ++ AKKYL G G+LSF + A Sbjct: 300 AKFLSSHKKVKKVSYPFLNNDENYNLAKKYLKYG-SGILSFELSSYEEA----------- 347 Query: 367 AQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFIDD 426 V LK+ + N+ D K++V P TTH+QLN +E +G+++ LIR+SVGIE ++D Sbjct: 348 KNFVKKLKIFKLVTNIADTKSIVTHPASTTHQQLNKEELKNAGISEGLIRLSVGIEDVED 407 Query: 427 IIADFQQSFET 437 +I D ++ + Sbjct: 408 LIKDLDEALNS 418 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: 539 Number of extensions: 27 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: 418 Length adjustment: 32 Effective length of query: 412 Effective length of database: 386 Effective search space: 159032 Effective search space used: 159032 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