Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_011765903.1 AZO_RS10980 acetyl-CoA C-acyltransferase
Query= SwissProt::Q0KBP1 (394 letters) >NCBI__GCF_000061505.1:WP_011765903.1 Length = 393 Score = 439 bits (1130), Expect = e-128 Identities = 229/393 (58%), Positives = 286/393 (72%), Gaps = 2/393 (0%) Query: 2 TREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTE 61 +REVVV+S VR+A+G FGGSLKD+ PAELG +VV+EA++RA V V GN I TE Sbjct: 3 SREVVVLSAVRSAVGGFGGSLKDMEPAELGGVVVKEAISRAGVDPKQVTFATVGNCIPTE 62 Query: 62 PRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMS 121 R Y+ RVA + GG+++ + A VNRLCGS QAIV++AQ ILLGD D A+GGG E MS Sbjct: 63 SRYPYVARVATIQGGMSMESVAFAVNRLCGSAQQAIVNSAQAILLGDADYAVGGGVEVMS 122 Query: 122 RAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAAL 181 R YL PA R GARMGD +D M+ L DPF HMG+TAEN+A ++ ISR +QD AL Sbjct: 123 RGAYLMPALRNGARMGDTKAIDAMVAVLTDPFGVGHMGITAENLAAKWGISREEQDAFAL 182 Query: 182 ESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENG 241 ES RRA+ AI G FK QIVP+ + RKG V FDTDEH R T++ + K++P F K++G Sbjct: 183 ESQRRAAEAIADGRFKGQIVPITFETRKGPVVFDTDEHPR-ATTMEALAKMKPAF-KKDG 240 Query: 242 TVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIA 301 +VTAGNASG+NDAAA +V+ + A+A G KP+ARLVSY AGV MG GP+P++K+A Sbjct: 241 SVTAGNASGINDAAAFLVLADAAKASAAGHKPMARLVSYAIAGVPNDLMGEGPIPSSKLA 300 Query: 302 LERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITV 361 L+RAGL + +D+IE+NEAFAAQ+ V K L LDPAK NPNG I+LGHP+GATGA+I Sbjct: 301 LQRAGLTLDKIDLIESNEAFAAQSLTVAKGLELDPAKTNPNGGAIALGHPVGATGAVIIT 360 Query: 362 KALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394 K LHEL R GRY + TMCIGGGQGI I+ERI Sbjct: 361 KLLHELQRTGGRYGMATMCIGGGQGITTIWERI 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: 455 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: 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