Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_028312141.1 H566_RS0115455 acetyl-CoA C-acetyltransferase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_000482785.1:WP_028312141.1 Length = 392 Score = 322 bits (826), Expect = 9e-93 Identities = 189/406 (46%), Positives = 263/406 (64%), Gaps = 16/406 (3%) Query: 7 LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66 + D IV A RT +G++GG+L+ V A +LGA I+ L ++ + +I +V+ G A Sbjct: 1 MTDIVIVAAARTAVGKFGGSLAKVPAAELGATVIRGLLQK-TGVAGEQIGEVILGQVLTA 59 Query: 67 GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126 G ++ AR +++ +GLP VPG TIN++CGSG+ AV AA+AIR G++ ++IAGG E+M Sbjct: 60 G-CGQNPARQAVIGSGLPQAVPGMTINKVCGSGLKAVTLAAQAIRDGDSDIIIAGGQENM 118 Query: 127 SRAPFVMGKA-DSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRE 185 S +P V+ + D ++ DT I N L Y M TAENVA +GI+RE Sbjct: 119 SASPHVLPNSRDGMRMGDWKLVDTMI-----NDGLWDVYNRYHMGITAENVAKQYGITRE 173 Query: 186 DQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEH-PRETSLEKLASLP 244 QDA AL SQQ+ AAAQ G+ EI PV+IP+RK DP++ DTDE R+T+ E LA L Sbjct: 174 QQDALALASQQKAAAAQDAGKFKDEIVPVSIPQRKGDPILFDTDEFLNRKTNAEALAGLR 233 Query: 245 TPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGP 304 F + G+VTAGNASG+NDGA A++L A + NL R+ + A+AG++P IMG GP Sbjct: 234 PAFDKAGSVTAGNASGINDGAAAVMLMSAKKAAELNLPVLGRIASYASAGLDPAIMGMGP 293 Query: 305 APATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPL 364 PA++K LA AG AD+D++E+NEAFAAQA AV ++G D VN NGGAIA+GHP+ Sbjct: 294 VPASKKALARAGWSAADLDLLEINEAFAAQACAVHNEMGW--DLSKVNVNGGAIAIGHPI 351 Query: 365 GMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIER 410 G SG R++ T L+E++RR A+ + ++CIG G GIAL IER Sbjct: 352 GASGCRILVTLLHEMQRR-----DAKKGIASLCIGGGMGIALTIER 392 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: 424 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: 392 Length adjustment: 31 Effective length of query: 384 Effective length of database: 361 Effective search space: 138624 Effective search space used: 138624 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