Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_017600843.1 D471_RS0123265 acetyl-CoA C-acyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000341125.1:WP_017600843.1 Length = 411 Score = 410 bits (1055), Expect = e-119 Identities = 231/412 (56%), Positives = 290/412 (70%), Gaps = 17/412 (4%) Query: 4 EVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGE 63 +VY+ D VRTP GR+GG+LAAVR DDLAA V V R+ V +DEV LG ANQAGE Sbjct: 3 DVYLVDGVRTPQGRYGGALAAVRPDDLAATAVAEAVRRSG-VPGGSVDEVILGAANQAGE 61 Query: 64 DNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSR 123 DNRNVARMA LLAGL SVPG T+NRLCASG+ AV +A +AI +GEA++V+AGGVESM+R Sbjct: 62 DNRNVARMAALLAGLDPSVPGYTVNRLCASGLTAVASAAQAIRAGEADVVVAGGVESMTR 121 Query: 124 APYVMGKADSAFGRGQKIEDTTIGWRFINPLM---KAQYGVDAMP----------ETADN 170 AP+VM K + + + ++ DT++GWRF NP AQ DA P ETA+ Sbjct: 122 APWVMAKPGTPWAKPGEVADTSLGWRFTNPRFADHDAQAPADAAPNDLRYTLSMGETAEE 181 Query: 171 VADDYKVSRADQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGET-VVDADEHLRPD 229 VA ++R + DAFALRS Q A A AG F EIVPV + G+KG T V ADE RPD Sbjct: 182 VAALEGLTRQECDAFALRSHQRAVAAAEAGRFDREIVPVTVTGRKGATHEVTADEGPRPD 241 Query: 230 TTLEALAKLKPVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAG 289 T +LAKL+PV VTAGN+S ++DG+ AL+LASAEAV++HGL RA+V+ ASAG Sbjct: 242 TDEASLAKLRPVFRKGGIVTAGNSSSLSDGASALVLASAEAVQRHGLTPRARVVASASAG 301 Query: 290 VAPRVMGIGPVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPN 349 V P+VMG+GPVPA K+L R + + +ELNEAFAAQ L V R+LG+ D RVN + Sbjct: 302 VPPQVMGLGPVPATEKVLARAGWKLDEVGSVELNEAFAAQSLGVVRQLGL--DPERVNAD 359 Query: 350 GGAIALGHPLGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401 GGAIALGHPLG+SGAR+++T + ++E+ +RGL T+CVGVGQG AL VERV Sbjct: 360 GGAIALGHPLGSSGARILITLLGRMEREDTRRGLATLCVGVGQGAALLVERV 411 Lambda K H 0.317 0.134 0.379 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: 493 Number of extensions: 17 Number of successful extensions: 5 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: 401 Length of database: 411 Length adjustment: 31 Effective length of query: 370 Effective length of database: 380 Effective search space: 140600 Effective search space used: 140600 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 (21.6 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