Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_012399806.1 BPHY_RS01925 acetyl-CoA C-acyltransferase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_000020045.1:WP_012399806.1 Length = 399 Score = 305 bits (782), Expect = 1e-87 Identities = 197/416 (47%), Positives = 238/416 (57%), Gaps = 32/416 (7%) Query: 7 LKDAYIVDAIRTPIGRYG-GALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQ 65 L+DAYIV A RTPIG+ G R D+L I++ + PDLD S I+D + GCA Sbjct: 5 LQDAYIVAASRTPIGKAPRGMFRNTRPDELLVHAIRSAVAQVPDLDTSLIEDAIIGCAIP 64 Query: 66 AGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVES 125 E +VARM LLAGLP V G T+NR C SG+ A+ AA IR GE+ +MIAGG ES Sbjct: 65 EAEQGLNVARMGALLAGLPSTVGGVTVNRFCASGVTALAMAADRIRVGESDVMIAGGCES 124 Query: 126 MSRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRE 185 MS P + K S IFD N + YG M TAE VA + +SRE Sbjct: 125 MSMVPMMGNKP----SLSPHIFDR-------NEDVGIAYG---MGLTAEKVAERWKVSRE 170 Query: 186 DQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLV---------VDTDEHPR-ET 235 QD F++ S ++ AAQ+ G A EI P I R D V DE PR +T Sbjct: 171 QQDHFSVESHRKAVAAQQAGEFADEIAPYAITERFPDLATGEVRVTMREVALDEGPRADT 230 Query: 236 SLEKLASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGV 295 S+E LA L T F GTVTAGN+S +DGA AL++ LKQ+NL P AR V+ A GV Sbjct: 231 SMEGLAKLRTVFANRGTVTAGNSSQTSDGAGALIVVSEKILKQFNLTPLARFVSFAVRGV 290 Query: 296 EPRIMGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNG 355 P IMG GP A L AGL+ D+D IELNEAFAAQ+LAV DLGL D VNP G Sbjct: 291 PPEIMGIGPKEAIPAALKAAGLKQDDIDWIELNEAFAAQSLAVINDLGL--DVSKVNPLG 348 Query: 356 GAIALGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411 GAIALGHPLG +GA T ++ L RR K +Y + TMC+G G G A IIER+ Sbjct: 349 GAIALGHPLGATGAIRAATVVHGLRRR-----KLKYGMVTMCVGTGMGAAGIIERV 399 Lambda K H 0.318 0.133 0.382 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: 442 Number of extensions: 19 Number of successful extensions: 6 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: 415 Length of database: 399 Length adjustment: 31 Effective length of query: 384 Effective length of database: 368 Effective search space: 141312 Effective search space used: 141312 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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