Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate 3609950 Dshi_3331 acetyl-CoA acetyltransferase (RefSeq)
Query= SwissProt::Q0KBP1 (394 letters) >FitnessBrowser__Dino:3609950 Length = 394 Score = 460 bits (1184), Expect = e-134 Identities = 238/394 (60%), Positives = 288/394 (73%), Gaps = 2/394 (0%) Query: 1 MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60 + +++V++ G RTAIGTFGGSL AP LGA V + AL R+ V G +GHVVFG+VI T Sbjct: 3 LDQDIVILDGARTAIGTFGGSLAGTAPITLGATVAKAALERSGVEGAQIGHVVFGHVINT 62 Query: 61 EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120 EPRDMYL RVAA+ G+ PA+ VNRLCGSG QA+VS Q+++LGD + GGAESM Sbjct: 63 EPRDMYLSRVAAMEAGIPDTTPAMNVNRLCGSGAQALVSVIQSLMLGDAQFGLAGGAESM 122 Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180 SR+PY P ARWG +MGDA +DMMLGAL+ PF HMGVTAENVA E+ I RA QD A Sbjct: 123 SRSPYAMPVARWGQKMGDATAMDMMLGALNCPFGTGHMGVTAENVAAEHGIGRADQDAFA 182 Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240 LES RA+ A +AG+F QIVPV K ++ V F DEH + T + + LR VF K+ Sbjct: 183 LESQARAARAQEAGHFNSQIVPVPVKVKRDMVDFVRDEHPK-PTTAEALAGLRTVFQKD- 240 Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300 GTVTAGNASG+ND AAA+V+ + AE GLKP AR++ Y HAGV P+ MGIGPVPA + Sbjct: 241 GTVTAGNASGINDGAAALVLARASAAESAGLKPRARILGYAHAGVRPEVMGIGPVPAVQA 300 Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360 L + L VSD DVIE+NEAFAAQA AV K LGLDPAKVNPNG I+LGHP+GATGA+I Sbjct: 301 LLAKTDLSVSDFDVIESNEAFAAQALAVNKGLGLDPAKVNPNGGAIALGHPVGATGAIIA 360 Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394 +KAL+EL R+ G+ ALVTMCIGGGQGIA FE + Sbjct: 361 LKALYELERIGGKRALVTMCIGGGQGIALAFEAL 394 Lambda K H 0.318 0.134 0.381 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: 515 Number of extensions: 15 Number of successful extensions: 2 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: 394 Length of database: 394 Length adjustment: 31 Effective length of query: 363 Effective length of database: 363 Effective search space: 131769 Effective search space used: 131769 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