Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_053936560.1 WG78_RS04410 acetyl-CoA C-acyltransferase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_001294205.1:WP_053936560.1 Length = 401 Score = 302 bits (773), Expect = 1e-86 Identities = 191/418 (45%), Positives = 243/418 (58%), Gaps = 34/418 (8%) Query: 7 LKDAYIVDAIRTPIGRYG-GALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQ 65 +++AYIV A RTP+G+ G + VR DD+ A +K + P LD ++I+DV+ GCA Sbjct: 5 IQEAYIVAATRTPVGKAPRGMMKNVRPDDMLAHVLKGALAQVPGLDPARIEDVIVGCAMP 64 Query: 66 AGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVES 125 E +VAR+ LLLAGLP V G TINR C SG++AV AA IR GE +MIA G ES Sbjct: 65 EAEQGMNVARIGLLLAGLPETVGGVTINRFCSSGVNAVAMAADRIRVGEADVMIAAGTES 124 Query: 126 MSRAPFVMGKADSAFSRKAEIF--DTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGIS 183 MS P + K + EIF D +G F M TAE VA + +S Sbjct: 125 MSMVPMMGNKV----ALNPEIFAKDENLGIAF------------GMGLTAEKVAEQWKVS 168 Query: 184 REDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQD---------PLVVDTDEHPR- 233 REDQDAFA+ S +R AA + G+ A EITP+ R + + TDE PR Sbjct: 169 REDQDAFAVESHRRALAAIEGGKFADEITPLEATYRVPNLATGEVEYIKKTLTTDEGPRR 228 Query: 234 ETSLEKLASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATA 293 +TS+E LA L T F G+VTAGN+S ++DGA A++L LK+YNL P A+ V+ A Sbjct: 229 DTSMEGLAKLKTVFAAKGSVTAGNSSQMSDGAGAVILVSERILKEYNLTPLAKFVSFAVK 288 Query: 294 GVEPRIMGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNP 353 GV P IMG GP A L AGL D+ IELNEAFAAQ+LAV RDL L D +NP Sbjct: 289 GVPPSIMGIGPKEAIPAALRVAGLNQDDLAWIELNEAFAAQSLAVIRDLNL--DTSKINP 346 Query: 354 NGGAIALGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411 GGAIALGHPLG +GA T ++ + R AG +Y + TMCIG G G A II+ + Sbjct: 347 QGGAIALGHPLGATGAIRAATLVHGMRREGMAG---KYGMITMCIGTGMGAAGIIQSL 401 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: 447 Number of extensions: 27 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: 401 Length adjustment: 31 Effective length of query: 384 Effective length of database: 370 Effective search space: 142080 Effective search space used: 142080 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