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_011307392.1 MBAR_RS12885 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000195895.1:WP_011307392.1 Length = 457 Score = 424 bits (1089), Expect = e-123 Identities = 217/432 (50%), Positives = 295/432 (68%), Gaps = 16/432 (3%) Query: 7 TVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSNV 66 T+ +HAG + D A +R+VPIY T +YVF++++ + LFGL G +Y+R NPT++V Sbjct: 42 TLAVHAGAKP--DPATGARSVPIYQTAAYVFKDAEEAADLFGLRKEGNIYTRLMNPTTDV 99 Query: 67 LEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFG 126 E+RIAALEGG ALAV+SG AA T A+ GD I+S LYGGTY F +F + G Sbjct: 100 FEKRIAALEGGIGALAVASGMAAITTALLTFTRPGDEIISGDKLYGGTYELFNYTFPKLG 159 Query: 127 IEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNTF 186 +FV+ PEEF+ E+TKA+Y+E+IGNP ++PDFEK+ IAH GIP VVDNT Sbjct: 160 RTVKFVDVGKPEEFKNAISEKTKAIYVESIGNPGLDIPDFEKLAEIAHGAGIPFVVDNT- 218 Query: 187 GAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAEG 246 +PI +G DIV +SATK+IGGHGT+IGG+IVDSG F WK PEKFP+ +P G Sbjct: 219 -VSPLILRPIDHGVDIVVYSATKFIGGHGTSIGGVIVDSGNFYWK--PEKFPEICEPDPG 275 Query: 247 YHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALKL 306 YHG Y EA+G A+I R + +RD G ++PF SFL G+ETL LR ++H +NAL++ Sbjct: 276 YHGLKYKEAFGKAAFIAKARVQFIRDTGACISPFNSFLFTLGLETLPLRMKKHCDNALEI 335 Query: 307 AKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLSG 366 AK+LE+ P VSWVSYPGL SH +E AKKYL +G+G ++ FG+K +E F Sbjct: 336 AKFLEKHPKVSWVSYPGLESHCSYELAKKYLKSGYGALIGFGIK---GGARECKKF---- 388 Query: 367 AQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFIDD 426 ++ L++ S+LAN+GDAK+LVI P TTH+QL+ +E+LA GVT+D IR+S+GIE D Sbjct: 389 ---IEGLEIFSHLANIGDAKSLVIHPASTTHEQLSKEEQLACGVTEDFIRLSIGIEDAKD 445 Query: 427 IIADFQQSFETV 438 +I+D +Q+ V Sbjct: 446 LISDIKQALSEV 457 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: 577 Number of extensions: 21 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: 457 Length adjustment: 33 Effective length of query: 411 Effective length of database: 424 Effective search space: 174264 Effective search space used: 174264 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 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