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_106716919.1 CU100_RS12820 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_003010935.1:WP_106716919.1 Length = 428 Score = 401 bits (1031), Expect = e-116 Identities = 204/430 (47%), Positives = 288/430 (66%), Gaps = 14/430 (3%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F+T+ +HAG + D +R PIY TT++VFE+S H + LFGL+ G +YSR NPT+ Sbjct: 8 FETLAVHAGAKP--DPVTGARVTPIYQTTAFVFEDSDHAASLFGLKAFGNIYSRITNPTN 65 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 VLEER+AALEGG AALAV+SG AAQ L L GDN VS++ LYGG+ NQF SFK Sbjct: 66 AVLEERVAALEGGTAALAVASGHAAQFLIFHALMQPGDNFVSSNKLYGGSINQFGQSFKS 125 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 F R+ +G +P F D+RT+A+++E+I NP V D I IAH+HG+P++VDN Sbjct: 126 FDWHVRWADGTDPAAFADQIDDRTRAIFVESIANPGGIVTDLSAIAEIAHRHGLPLIVDN 185 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 T A Y +P+ YGADI+ HSATK++GGHG ++GGIIVD G F W +P SQP Sbjct: 186 TL-ASPYLIRPVDYGADIIVHSATKFLGGHGNSMGGIIVDCGTFDWSK-SGNYPLLSQPR 243 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 Y+G + +E +GN A+ + R LRDLGP ++PF +F +L G+ETL LR +RH +NA+ Sbjct: 244 PEYNGIVLHETFGNFAFAIACRVLGLRDLGPALSPFNAFQILTGIETLPLRMQRHCDNAI 303 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 ++AKWL+Q+ VSWVSY GL + ++Y G G V +FG+K +A Sbjct: 304 EVAKWLKQNEKVSWVSYAGLDGDPYQTLQQRYSPKGAGSVFTFGLKGGYDA--------- 354 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424 G ++V++L+L S+LAN+GD ++L+I P TTH+QL+D++K+A+G D++R+S+GIE + Sbjct: 355 -GVKLVEHLQLFSHLANLGDTRSLIIHPASTTHRQLSDEQKIAAGAGPDVVRLSIGIESV 413 Query: 425 DDIIADFQQS 434 DIIAD Q+ Sbjct: 414 ADIIADLDQA 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: 551 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: 428 Length adjustment: 32 Effective length of query: 412 Effective length of database: 396 Effective search space: 163152 Effective search space used: 163152 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 Jul 26 2024. The underlying query database was built on Jul 25 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