Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_110205408.1 DNK54_RS02835 acetyl-CoA C-acetyltransferase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_003194585.1:WP_110205408.1 Length = 386 Score = 289 bits (739), Expect = 1e-82 Identities = 176/407 (43%), Positives = 242/407 (59%), Gaps = 23/407 (5%) Query: 7 LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66 + +AYIVDA+RTP+G+ GGAL+A+ + DLGA + AL +R +D + +DDV+ GC + Sbjct: 1 MAEAYIVDAVRTPVGKRGGALAAMHSADLGAHSLAALMQR-TGVDPAAVDDVIMGCCDTI 59 Query: 67 GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126 G DVAR + L+AGLP VPG TI+R CGS +V AA+ + +G L++AGG+++M Sbjct: 60 GSQAGDVARTAWLVAGLPDHVPGVTIDRQCGSSQQSVHFAAQGVMSGTQDLVVAGGLQNM 119 Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPE--TAENVAADFGISR 184 S P + + F + GW +YG + + +AE +A + +SR Sbjct: 120 SAIPISSAMLVAQQYGFSTPFAESPGW-------VARYGDVEVSQFNSAEMIAEKWDLSR 172 Query: 185 EDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLP 244 E+ + FAL S R A EGR AEI PV I D + DTD+ PR+TSLEK+A L Sbjct: 173 EEMERFALESHTRAKQAIAEGRFKAEIAPVEI-----DGTLFDTDQCPRDTSLEKMAGLD 227 Query: 245 TPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGP 304 P + G +TAG AS + DG+ ALL+A A+K + L PRAR+ ++ G +P M GP Sbjct: 228 -PLQPGGRITAGVASQICDGSAALLIASEQAVKDHGLTPRARIHHISVRGDDPIWMLTGP 286 Query: 305 APATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPL 364 AT+ L G+ + D+D+ E NEAFA+ LA ++ G P D VN NGG IALGHP+ Sbjct: 287 IRATQYALEKTGMSIDDIDLFECNEAFASVVLAWMKETGAPHD--KVNVNGGGIALGHPI 344 Query: 365 GMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411 G +GARL+TT LNELER RY L TMC G GQ IIER+ Sbjct: 345 GATGARLMTTLLNELER-----TGGRYGLQTMCEGGGQANVTIIERL 386 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: 428 Number of extensions: 19 Number of successful extensions: 7 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: 386 Length adjustment: 31 Effective length of query: 384 Effective length of database: 355 Effective search space: 136320 Effective search space used: 136320 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