Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_041097722.1 SUTH_RS05575 beta-ketothiolase BktB
Query= SwissProt::Q0KBP1 (394 letters) >NCBI__GCF_000828635.1:WP_041097722.1 Length = 395 Score = 451 bits (1159), Expect = e-131 Identities = 229/392 (58%), Positives = 289/392 (73%), Gaps = 1/392 (0%) Query: 3 REVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEP 62 REVVV+S VR A+GTF GSL + PA+LG LVV+EA+AR+ V V GNVI TE Sbjct: 5 REVVVLSAVRAAVGTFMGSLSGMEPADLGGLVVKEAIARSGVDPKAVTFATVGNVIPTES 64 Query: 63 RDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSR 122 R Y+ R A + GG+T+ + VNRLCGS QA+VS+AQ ILLGD D AIGGG E MSR Sbjct: 65 RYPYVARNATIQGGMTMESVTFAVNRLCGSSQQAVVSSAQAILLGDADFAIGGGVEVMSR 124 Query: 123 APYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALE 182 YL+PA R GARMGD +VD M+ AL DPF HMG+TAEN+AK+++++R QDE A E Sbjct: 125 GAYLSPAMRSGARMGDTKMVDAMVAALTDPFGAGHMGITAENLAKKHNLTREMQDEFACE 184 Query: 183 SHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGT 242 S RRA+AA+ AGYFK+QIVP+ K RKGDV FDTDEH++ + T++ + K++P F K GT Sbjct: 185 SQRRAAAAVAAGYFKEQIVPITLKTRKGDVVFDTDEHIKANTTMESLAKMKPAFDKA-GT 243 Query: 243 VTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIAL 302 VTAGNASG+ND AA +V+ + A+A G KP+ARLVSYG GV + MG GP+P+T IAL Sbjct: 244 VTAGNASGINDGAAFLVLADAAKAAAGGHKPMARLVSYGIGGVSHEVMGEGPIPSTLIAL 303 Query: 303 ERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVK 362 +AGL+++D+ V+E+NEAFAAQ+ V K LGLDP K NPNG I++GHPIGA+GA+I K Sbjct: 304 AKAGLKIADIGVVESNEAFAAQSLTVAKVLGLDPKKTNPNGGAIAIGHPIGASGAVIITK 363 Query: 363 ALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394 AL+E RV +Y L TMCIGGGQGI I+E I Sbjct: 364 ALYEARRVGSKYCLATMCIGGGQGITTIWEMI 395 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: 471 Number of extensions: 13 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: 395 Length adjustment: 31 Effective length of query: 363 Effective length of database: 364 Effective search space: 132132 Effective search space used: 132132 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 Apr 09 2024. 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