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_041100571.1 SUTH_RS15735 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase family protein
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000828635.1:WP_041100571.1 Length = 435 Score = 411 bits (1056), Expect = e-119 Identities = 202/431 (46%), Positives = 295/431 (68%), Gaps = 7/431 (1%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ LHAG + D A +RA+PI+ TTS+VF++++H + LF L+ G VYSR NPT Sbjct: 9 ETLCLHAGAQP--DAATGARALPIHQTTSFVFDSAEHAASLFNLQTFGNVYSRIGNPTVA 66 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 EER+AALEGG AA+A ++G AAQ +A+ L GD IV+ LYGG+++Q +S ++ Sbjct: 67 AFEERMAALEGGRAAVAAATGLAAQMVALLTLCEAGDRIVAARSLYGGSFSQLDVSLRKL 126 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GIE FV+ D+PE F + TK ++ ET+ NP+ NV D + IAH HG+P+++DNT Sbjct: 127 GIETVFVDSDDPENFRAALSDNTKCLFAETVANPRLNVLDIAAVAEIAHGHGVPLIIDNT 186 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 C+P ++GADI+ HSATK++GGHGTT+GG++++SGKF W + KFP ++P+ Sbjct: 187 V-PSPCLCRPFEHGADIIVHSATKFLGGHGTTLGGVVIESGKFDWGN--GKFPGMTEPSA 243 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 GYHG + E +GN + + R E LR GP ++PF+++LL+QG+ETL LR +RH ENAL Sbjct: 244 GYHGVKFFETFGNFGFTMKARMETLRTFGPALSPFSAWLLMQGIETLPLRMKRHCENALA 303 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 +A+ LE+ P V+WV+YPGL + H A++YL G G +LSFGV K + + Sbjct: 304 VARHLEKHPRVAWVNYPGLPASPGHALAQRYLHGGAGAILSFGVDGGNPGAKGGG--QAA 361 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 G + +D L+ S+LAN+GDAKTLVI P TTH+QL++ ++ ASGVT D++R+SVG+E +D Sbjct: 362 GERFIDALQFCSHLANIGDAKTLVIHPASTTHRQLSEADQRASGVTPDMVRLSVGLETLD 421 Query: 426 DIIADFQQSFE 436 DI+ D Q+ E Sbjct: 422 DILWDIDQALE 432 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: 585 Number of extensions: 22 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: 435 Length adjustment: 32 Effective length of query: 412 Effective length of database: 403 Effective search space: 166036 Effective search space used: 166036 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