Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate 351915 BT2387 O-acetylhomoserine (thiol)-lyase (NCBI ptt file)
Query= SwissProt::Q9WZY4 (430 letters) >FitnessBrowser__Btheta:351915 Length = 428 Score = 476 bits (1224), Expect = e-139 Identities = 239/428 (55%), Positives = 301/428 (70%), Gaps = 3/428 (0%) Query: 1 MDWKKYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTR 60 M+ K + T +H G E + AT +RAVPIYQTTSYVF +S HAA F L++PG IY R Sbjct: 1 MERKNLHFETLQVHVGQEQADPATDARAVPIYQTTSYVFHNSAHAAARFGLQDPGNIYGR 60 Query: 61 IGNPTVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLF 120 + N T V EER+A LE GV LAVASG AAITYA NI GD IV+ +YGG+YNL Sbjct: 61 LTNSTQGVFEERVAVLEGGVAGLAVASGAAAITYAFENITRAGDHIVAAKTIYGGSYNLL 120 Query: 121 RHTLYKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHG 180 HTL G+ FVD +D N E+AI E TKAV++ET+GNP + D EA++EIAHRH Sbjct: 121 AHTL-PNYGVTTTFVDPSDLSNFEKAIQENTKAVFIETLGNPNSNIIDIEAVSEIAHRHK 179 Query: 181 VPLIVDNTVA-PYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWT-NGKFPE 238 +PLI+DNT PY+ RP EHGADIVV+SATKFIGGHG+S+GG+IVDSGKFDW +GKFP+ Sbjct: 180 IPLIIDNTFGTPYLIRPIEHGADIVVHSATKFIGGHGSSLGGVIVDSGKFDWVASGKFPQ 239 Query: 239 LVEPDPSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKH 298 L EPDPSYHGV +V+ AAY+ + R LLRD G+ +SPFNAF+ + GLETLSLR+++H Sbjct: 240 LTEPDPSYHGVRFVDAAGPAAYVTRIRATLLRDTGATISPFNAFILLQGLETLSLRVERH 299 Query: 299 CENALKIVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKF 358 ENALK+V FL +HP V VN+P + +Y G G+I TF VKGG+E +F Sbjct: 300 VENALKVVNFLNNHPKVKKVNHPSLSDHPDHALYQRYFPNGAGSIFTFEVKGGQEEAHRF 359 Query: 359 IDSLTLISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIA 418 IDSL + S LAN+ D ++L IHPASTTH QL +E + + P +RLS+G E + D+IA Sbjct: 360 IDSLEIFSLLANVADVKSLVIHPASTTHSQLNAQELAEQEIYPGTVRLSIGTEHINDLIA 419 Query: 419 DLDQALRK 426 DL+QAL K Sbjct: 420 DLEQALAK 427 Lambda K H 0.317 0.136 0.398 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: 589 Number of extensions: 24 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: 430 Length of database: 428 Length adjustment: 32 Effective length of query: 398 Effective length of database: 396 Effective search space: 157608 Effective search space used: 157608 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