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 351451 BT1923 O-acetylhomoserine (thiol)-lyase (NCBI ptt file)
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Btheta:351451 Length = 426 Score = 356 bits (914), Expect = e-103 Identities = 182/411 (44%), Positives = 264/411 (64%), Gaps = 12/411 (2%) Query: 25 RAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSNVLEERIAALEGGAAALAVS 84 R +PIY +T++ ++ S+ ++LF LE GY Y+R QNPT++ + +IAALEGG AA+ S Sbjct: 24 RVLPIYQSTTFKYDTSEQMARLFDLEDSGYFYTRLQNPTNDAVAAKIAALEGGVAAMLTS 83 Query: 85 SGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRFGIEARFVEGD-NPEEFEKV 143 SGQAA AI + GD+ V +S +YGGT+N F ++ K+ GI+ FV D + EE Sbjct: 84 SGQAANFYAIFNICQAGDHFVCSSAIYGGTFNLFGVTMKKLGIDVTFVNPDASEEEISAA 143 Query: 144 FDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNTFGAGGYFCQPIKYGADIV 203 F TKA++ ETI NP V D EK IAH HG+P++VDNTF C+P ++GADI+ Sbjct: 144 FQPNTKALFGETISNPSLEVLDIEKFARIAHSHGVPLIVDNTFPTP-INCRPFEWGADII 202 Query: 204 THSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAEGYHGTIYNEAYGNLAYIV 263 HS TK++ GH T++GG IVDSG F W + +KFP P E YHG Y +A+G AYI Sbjct: 203 VHSTTKYMDGHATSVGGCIVDSGNFDWDAHADKFPGLCTPDESYHGLTYTKAFGKGAYIT 262 Query: 264 HVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALKLAKWLEQSPYVSWVSYPG 323 +L+RDLG + +P SFLL G+ETL LR +H NA K+A++L ++ V+WV+Y G Sbjct: 263 KATAQLMRDLGSIQSPQNSFLLNLGLETLHLRMPQHCRNAQKVAEYLSKNEKVAWVNYCG 322 Query: 324 LASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLSGAQVVDNLKLASNLANVG 383 L + ++ A+KY+ NG GV+SFG+K + + +D+L+ + + +V Sbjct: 323 LPDNKYYALAQKYMPNGSCGVISFGLKGGRDV----------SIKFMDSLEFIAIVTHVA 372 Query: 384 DAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFIDDIIADFQQS 434 DA++ V+ P TH+QL+D++ + +GV DLIR+SVGIE DDIIAD +Q+ Sbjct: 373 DARSCVLHPASHTHRQLSDEQLMEAGVRPDLIRLSVGIENADDIIADIEQA 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: 512 Number of extensions: 20 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: 426 Length adjustment: 32 Effective length of query: 412 Effective length of database: 394 Effective search space: 162328 Effective search space used: 162328 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