Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_084198673.1 C0029_RS06075 acetyl-CoA C-acyltransferase family protein
Query= SwissProt::Q0KBP1 (394 letters) >NCBI__GCF_002869505.1:WP_084198673.1 Length = 395 Score = 501 bits (1290), Expect = e-146 Identities = 251/391 (64%), Positives = 305/391 (78%), Gaps = 1/391 (0%) Query: 3 REVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEP 62 REVVV+SGVR+AI FGGSLKDVAP E+ VV EA+ R+ + D+GHVV GNV ++ Sbjct: 4 REVVVLSGVRSAIADFGGSLKDVAPTEVAGQVVAEAVKRSGLEPTDIGHVVIGNVTHSDR 63 Query: 63 RDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSR 122 RDMY+ R AA+ GG+ I PALTVNRLCGSGLQ+++SAAQ ILLGD D A+ GGAESMSR Sbjct: 64 RDMYMSRTAALKGGLPIETPALTVNRLCGSGLQSVISAAQMILLGDCDAAVAGGAESMSR 123 Query: 123 APYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALE 182 PY P AR+GARMGD +VD M+GAL P HMG+TAEN+A +Y +SR +QDE A E Sbjct: 124 VPYWLPNARFGARMGDGQMVDAMMGALTCPMGDTHMGITAENLADKYSVSREEQDELAAE 183 Query: 183 SHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGT 242 SHRRA A + G F+ QI+P+ K RKG V FD DEHVR+DA +DM KLRP F K++G+ Sbjct: 184 SHRRAQQAQEEGRFESQILPIEIKTRKGTVVFDKDEHVRNDAKAEDMAKLRPAF-KKDGS 242 Query: 243 VTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIAL 302 VTAGNASGLND AAAVV+MER+EAE +GLKP+A++V Y A VDP MGIGP PA + + Sbjct: 243 VTAGNASGLNDGAAAVVLMERSEAEAKGLKPMAKMVGYAVAAVDPAIMGIGPAPAVRQLM 302 Query: 303 ERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVK 362 E+ G+ + D+D+ E NEAFAAQA +V K L LDPAKVNPNGSGISLGHPIGATG+++TVK Sbjct: 303 EKTGVAIEDVDIWECNEAFAAQALSVVKELDLDPAKVNPNGSGISLGHPIGATGSMLTVK 362 Query: 363 ALHELNRVQGRYALVTMCIGGGQGIAAIFER 393 A++EL R RYA+VTMCIGGGQGIAA+FER Sbjct: 363 AVYELERTGARYAVVTMCIGGGQGIAALFER 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: 485 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: 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 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