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 GFF750 PGA1_c07640 O-acetylhomoserine / O-acetylserine sulfhydrylase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Phaeo:GFF750 Length = 430 Score = 373 bits (958), Expect = e-108 Identities = 200/434 (46%), Positives = 277/434 (63%), Gaps = 15/434 (3%) Query: 2 PSH-FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQ 60 PS+ FDT+Q+HAG + D A +R PIY TT+YVF ++ H + LF L+ G++YSR Sbjct: 5 PSYGFDTLQIHAGAKP--DPATGARQTPIYQTTAYVFRDADHAAALFNLQEVGFIYSRLT 62 Query: 61 NPTSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKI 120 NPT VL+ERIA LEGG A+ SSG AAQ +A+ L G N+V+++ LYGGT QF Sbjct: 63 NPTVAVLQERIATLEGGVGAVCCSSGHAAQIMALFPLMGPGCNVVASTRLYGGTVTQFSQ 122 Query: 121 SFKRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPV 180 + KRFG A+FV+ DNPE D+ T+AV+ E++ NP V D I +A G+P+ Sbjct: 123 TIKRFGWSAKFVDFDNPEAVAAAIDDDTRAVFGESVANPGGYVTDIRSIADVADAAGVPL 182 Query: 181 VVDNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQF 240 ++DNT A Y C PI +GA +V HS TK++ G+GT GG+IVDSGKF W +KFP Sbjct: 183 IIDNT-SATPYLCSPIAHGATLVVHSTTKYLTGNGTVTGGVIVDSGKFDW-SANDKFPSL 240 Query: 241 SQPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHG 300 SQP YHG ++E +G LA+ H LRDLG MNP A+ L GVETLSLR ERH Sbjct: 241 SQPEPAYHGLKFHETFGGLAFTFHGIAIGLRDLGMTMNPQAAHYTLMGVETLSLRMERHC 300 Query: 301 ENALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETD 360 ENA +A WLEQ P V +V+Y GL S +H AK++ G GG+ +F VK +A Sbjct: 301 ENAKTVASWLEQDPRVDYVTYAGLPSSPYHARAKEHYPKGTGGLFTFAVKGGYDA----- 355 Query: 361 PFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVG 420 ++V++L++ S++AN+GD ++L+I TTH+QL +++ A+G +++RVS+G Sbjct: 356 -----CVKLVNSLEIFSHVANLGDTRSLIIHSASTTHRQLTPEQQEAAGAGANVVRVSIG 410 Query: 421 IEFIDDIIADFQQS 434 IE DD+IAD Q+ Sbjct: 411 IENADDLIADLDQA 424 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: 549 Number of extensions: 27 Number of successful extensions: 5 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: 430 Length adjustment: 32 Effective length of query: 412 Effective length of database: 398 Effective search space: 163976 Effective search space used: 163976 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