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 351915 BT2387 O-acetylhomoserine (thiol)-lyase (NCBI ptt file)
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__Btheta:351915 Length = 428 Score = 402 bits (1033), Expect = e-116 Identities = 206/435 (47%), Positives = 279/435 (64%), Gaps = 13/435 (2%) Query: 4 HFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPT 63 HF+T+Q+H GQE D A +RAVPIY TTSYVF NS H + FGL+ PG +Y R N T Sbjct: 7 HFETLQVHVGQEQ-ADPATDARAVPIYQTTSYVFHNSAHAAARFGLQDPGNIYGRLTNST 65 Query: 64 SNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFK 123 V EER+A LEGG A LAV+SG AA T A + + GD+IV+ +YGG+YN + Sbjct: 66 QGVFEERVAVLEGGVAGLAVASGAAAITYAFENITRAGDHIVAAKTIYGGSYNLLAHTLP 125 Query: 124 RFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVD 183 +G+ FV+ + FEK E TKAV++ET+GNP N+ D E + IAH+H IP+++D Sbjct: 126 NYGVTTTFVDPSDLSNFEKAIQENTKAVFIETLGNPNSNIIDIEAVSEIAHRHKIPLIID 185 Query: 184 NTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQP 243 NTFG Y +PI++GADIV HSATK+IGGHG+++GG+IVDSGKF W KFPQ ++P Sbjct: 186 NTFGT-PYLIRPIEHGADIVVHSATKFIGGHGSSLGGVIVDSGKFDWV-ASGKFPQLTEP 243 Query: 244 AEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENA 303 YHG + +A G AY+ +R LLRD G ++PF +F+LLQG+ETLSLR ERH ENA Sbjct: 244 DPSYHGVRFVDAAGPAAYVTRIRATLLRDTGATISPFNAFILLQGLETLSLRVERHVENA 303 Query: 304 LKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFK 363 LK+ +L P V V++P L+ H H ++Y NG G + +F VK +E F Sbjct: 304 LKVVNFLNNHPKVKKVNHPSLSDHPDHALYQRYFPNGAGSIFTFEVK---GGQEEAHRF- 359 Query: 364 LSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEF 423 +D+L++ S LANV D K+LVI P TTH QLN +E + +R+S+G E Sbjct: 360 ------IDSLEIFSLLANVADVKSLVIHPASTTHSQLNAQELAEQEIYPGTVRLSIGTEH 413 Query: 424 IDDIIADFQQSFETV 438 I+D+IAD +Q+ + Sbjct: 414 INDLIADLEQALAKI 428 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: 24 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: 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 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