Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_061532096.1 CAter10_RS02100 acetyl-CoA C-acyltransferase family protein
Query= SwissProt::Q0KBP1 (394 letters) >NCBI__GCF_001584165.1:WP_061532096.1 Length = 396 Score = 498 bits (1282), Expect = e-145 Identities = 252/393 (64%), Positives = 303/393 (77%) Query: 2 TREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTE 61 TREVV+V RTAIG++GG+LKD AP ELGA+ V+EA ARA V G ++FGNVI TE Sbjct: 4 TREVVIVGAARTAIGSYGGALKDFAPGELGAIAVKEAFARAGVDPLQAGQIIFGNVIHTE 63 Query: 62 PRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMS 121 RDMY+ RV +N G+ + ALT+NRLCGSGLQAI++AA I LG+TDVA+GGG ESMS Sbjct: 64 ARDMYVSRVVGLNAGMGKESTALTLNRLCGSGLQAIITAANAIQLGETDVAVGGGVESMS 123 Query: 122 RAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAAL 181 R+ Y AARWGARMGD +VDMM+GAL DPF HMG+TAENVA++Y ISR +QD AL Sbjct: 124 RSMYATQAARWGARMGDIKMVDMMVGALSDPFGAGHMGITAENVAEKYGISREEQDAFAL 183 Query: 182 ESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENG 241 ES RRA+AAI AG+FK QIVPV K RKG FDTDE+ + DAT++ + KL+P F KE G Sbjct: 184 ESQRRATAAIAAGHFKSQIVPVEIKTRKGVTLFDTDEYPKADATMESLAKLKPAFKKEGG 243 Query: 242 TVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIA 301 TVTAGNASG+ND AAA V+M A + GLKPLAR+VSYG AGVDP MG GP+PA ++A Sbjct: 244 TVTAGNASGINDGAAACVLMAADAAAQAGLKPLARVVSYGVAGVDPTIMGTGPIPAVQLA 303 Query: 302 LERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITV 361 L+RAGL +SD++VIE+NEAFAAQ+ V K LGLDPA N NG I+LGHP+GA+GA+I V Sbjct: 304 LKRAGLHLSDMEVIESNEAFAAQSLGVCKGLGLDPALTNVNGGAIALGHPLGASGAIIAV 363 Query: 362 KALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394 K L+EL R RY L+TMCIGGGQGIA I ERI Sbjct: 364 KCLYELIRTNKRYGLITMCIGGGQGIALIIERI 396 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: 509 Number of extensions: 14 Number of successful extensions: 1 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: 396 Length adjustment: 31 Effective length of query: 363 Effective length of database: 365 Effective search space: 132495 Effective search space used: 132495 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