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_092056756.1 BQ4888_RS09550 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_900111775.1:WP_092056756.1 Length = 429 Score = 436 bits (1121), Expect = e-127 Identities = 227/433 (52%), Positives = 296/433 (68%), Gaps = 15/433 (3%) Query: 2 PSHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQN 61 P T LHAGQ D A SRAVPIY T+SYVF +++H + LF L+ G +Y+R N Sbjct: 6 PQGIGTRALHAGQVP--DPATGSRAVPIYQTSSYVFNSTEHAANLFALKEMGNIYTRLMN 63 Query: 62 PTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKIS 121 PT++VLE+R+AAL+GG ALA+SSG +A LAI LA TGDNIVS+S LYGGT+N F+ + Sbjct: 64 PTTDVLEKRLAALDGGVGALALSSGSSAIFLAILNLARTGDNIVSSSSLYGGTHNLFRHT 123 Query: 122 FKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVV 181 R GI +FV+ E D TKAV+ E+IGNPK NV DF I IAHKHG+P + Sbjct: 124 LGRMGIAVKFVDTSRLESITAAIDGNTKAVFTESIGNPKNNVDDFAAIAKIAHKHGLPFI 183 Query: 182 VDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFS 241 VDNT F +PI++GADIV +S TK+IGGHGT++GG ++DSG F W +FP+F+ Sbjct: 184 VDNTVATAALF-RPIEHGADIVCYSLTKFIGGHGTSVGGAVIDSGNFDWAS--GRFPEFT 240 Query: 242 QPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGE 301 P YHG IY++A G LAYI+ +R LLRDLGP ++PF +F LQG+ETL +R RH + Sbjct: 241 SPDPSYHGLIYHQALGQLAYILKMRLTLLRDLGPCLSPFNAFQFLQGLETLHVRMPRHCD 300 Query: 302 NALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDP 361 NAL LA +LE P V+WV+YPGL +H H NA +YL G G ++ FG+K Sbjct: 301 NALALAHFLEGHPAVAWVNYPGLENHPDHANALRYLPKGQGAIIGFGIKG---------- 350 Query: 362 FKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGI 421 A+ +D +KLAS+LAN+GDAKTLVI P TTH+QL +E+ ++GV++D IRVSVGI Sbjct: 351 GAAGAARFIDGVKLASHLANIGDAKTLVIHPASTTHQQLTPEEQRSAGVSEDFIRVSVGI 410 Query: 422 EFIDDIIADFQQS 434 E IDDI+AD Q+ Sbjct: 411 EDIDDILADLDQA 423 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: 506 Number of extensions: 19 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: 429 Length adjustment: 32 Effective length of query: 412 Effective length of database: 397 Effective search space: 163564 Effective search space used: 163564 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