Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate GFF3052 HP15_2996 acetyl-CoA acetyltransferase
Query= reanno::Marino:GFF2751 (415 letters) >FitnessBrowser__Marino:GFF3052 Length = 398 Score = 320 bits (819), Expect = 6e-92 Identities = 185/409 (45%), Positives = 257/409 (62%), Gaps = 22/409 (5%) Query: 7 LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66 ++D IV A RT IG +GG LS++ AD LG IKA+ E + +I++V+ G A Sbjct: 7 MRDVVIVAARRTAIGTFGGGLSSLSADQLGTAVIKAILEE-TGVAGDQINEVVLGQVLTA 65 Query: 67 GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126 G ++ AR S + AG+P VP TIN++CGSG+ AV A +AIR G+ ++MIAGG ESM Sbjct: 66 G-CGQNPARQSAINAGIPASVPAMTINKVCGSGLKAVHMAVQAIRCGDAEMMIAGGQESM 124 Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKK----QYGIDSMPETAENVAADFGI 182 S+AP V+ SR + W V+ ++K + M TAEN+ +GI Sbjct: 125 SQAPHVLPN-----SRNGQRMGN---WSMVDTMIKDGLWDAFNDYHMGITAENIVEKYGI 176 Query: 183 SREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRE-TSLEKLA 241 SR++QD FA SQQ+ AAA++ G +I PV+IP+RK DP+VVD DE PR+ + E L Sbjct: 177 SRDEQDEFAAASQQKAAAAREAGYFDGQIVPVSIPQRKGDPIVVDRDEGPRDGVTAEGLG 236 Query: 242 SLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMG 301 L F+++GTVTAGNAS +NDGA A+++ A+ ++ L P A + A A AGV+P IMG Sbjct: 237 KLRAAFKKDGTVTAGNASSLNDGAAAVMVCSAEKAEELGLTPIATIKAYANAGVDPTIMG 296 Query: 302 FGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALG 361 GP PA+++ L AG D+D++E NEAFAAQA++V RD+G D VN NGGAIALG Sbjct: 297 TGPIPASQRCLKLAGWSTEDLDLVEANEAFAAQAISVNRDMGW--DTGKVNVNGGAIALG 354 Query: 362 HPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIER 410 HP+G SG R++ + L+E+ RR L T+CIG G G+AL +ER Sbjct: 355 HPIGASGCRILVSLLHEMVRR-----DVHKGLATLCIGGGMGVALAVER 398 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: 413 Number of extensions: 18 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: 398 Length adjustment: 31 Effective length of query: 384 Effective length of database: 367 Effective search space: 140928 Effective search space used: 140928 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 17 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