Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_085121636.1 B9O00_RS06430 acetyl-CoA C-acyltransferase
Query= SwissProt::Q0KBP1 (394 letters) >NCBI__GCF_900177295.1:WP_085121636.1 Length = 393 Score = 463 bits (1192), Expect = e-135 Identities = 242/392 (61%), Positives = 294/392 (75%), Gaps = 2/392 (0%) Query: 4 EVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPR 63 EVV VS VR+AIGTFGG+L +P LGA VVREALARA V G+ VGHVVFGNVIQTEPR Sbjct: 3 EVVFVSAVRSAIGTFGGALAGESPCSLGAAVVREALARAGVEGEQVGHVVFGNVIQTEPR 62 Query: 64 DMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRA 123 D YL RVAA++GGV APA+T+NRLCGSG QAIVSAAQ+ILLGD +VA+ GGAE+MSRA Sbjct: 63 DAYLARVAALDGGVAKAAPAMTLNRLCGSGAQAIVSAAQSILLGDAEVAVAGGAEAMSRA 122 Query: 124 PYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALES 183 P+L R+G RMGD VD ++G L DPF MG+TAE VA ++ I R +QD ALES Sbjct: 123 PHLLTTGRFGQRMGDTAAVDALVGILTDPFGNGIMGLTAERVADKWGIGRERQDAFALES 182 Query: 184 HRRASAAIKAGYFKDQIVPV-VSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGT 242 RRA+ AI G F+ QI+P+ V +G + +F DEH + T +D+ L+P F ++ G+ Sbjct: 183 QRRAARAIGEGRFESQILPLEVGRGSRAR-SFAVDEHPKPQTTAEDLANLKPAFRRDGGS 241 Query: 243 VTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIAL 302 VTAGNASG+ND AAA+V+M AER G +PL RLV Y HAGV+P MGIGPVPA + L Sbjct: 242 VTAGNASGINDGAAALVLMSAEAAERGGHRPLGRLVGYAHAGVEPGEMGIGPVPAVRGLL 301 Query: 303 ERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVK 362 R GL V D D++E+NEAFAAQA AV+ LGLDP +VNPNG I+LGHP+GATGA++TVK Sbjct: 302 ARTGLAVEDFDLVESNEAFAAQALAVSDELGLDPERVNPNGGAIALGHPVGATGAILTVK 361 Query: 363 ALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394 AL+EL R GR ALVT+CIGGGQGIA ER+ Sbjct: 362 ALYELARSGGRRALVTLCIGGGQGIALALERL 393 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: 511 Number of extensions: 17 Number of successful extensions: 3 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: 393 Length adjustment: 31 Effective length of query: 363 Effective length of database: 362 Effective search space: 131406 Effective search space used: 131406 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