Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_012171399.1 AZC_RS14870 acetyl-CoA C-acyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_000010525.1:WP_012171399.1 Length = 395 Score = 317 bits (812), Expect = 4e-91 Identities = 174/394 (44%), Positives = 247/394 (62%), Gaps = 7/394 (1%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60 M +AVIVS ARTP+GKA++G+ + D+ A ++ L + +++++++GC PE Sbjct: 1 MVDAVIVSTARTPIGKAQRGAFNITKGADMAAHAIRHALAKGKVDPASVEEVVLGCGYPE 60 Query: 61 AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120 G N+AR+ +AG+P T TV+R+C+SGL++IA AA +I++ A+AGG ES+ Sbjct: 61 GATGGNVARHASLIAGIPVTASGATVSRFCASGLEAIAGAARRIVMDGVPVAVAGGVESI 120 Query: 121 SQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKAL 180 S V + N L P+ Y++M T + VA++YGVSRE QD FA+ S Q A+A Sbjct: 121 SLVQPVNRELFRNDWLMANRPDIYVTMIETGDTVARRYGVSREAQDQFALASQQRTARAQ 180 Query: 181 AEGKFKDEIVPV----EVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSV 236 A G F DEIVP+ E+T GE + + ++DEG R TT + L+ L+P Sbjct: 181 AGGLFDDEIVPMTVEKEITDKASGETRR---ESVTLAKDEGNRADTTLEGLAKLKPVRGD 237 Query: 237 DGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIP 296 D VTAGN+SQ SDGA+A +LM +A L FR +A G P+ MGIGPV A+P Sbjct: 238 DWYVTAGNASQLSDGASATVLMSSTEAARQNAPVLGIFRGYATAGCEPDEMGIGPVFAVP 297 Query: 297 RALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKL 356 R L+ GL++ DIGL+ELNEAFASQ++ LG+D E VNVNGGAI++GHP G +G +L Sbjct: 298 RLLERQGLKVSDIGLWELNEAFASQSLYCRDTLGLDPEIVNVNGGAISVGHPFGMSGARL 357 Query: 357 TLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390 + E +RR ++ VVTMCI GGMGAAG+ E+ Sbjct: 358 VGHAVLEGRRRGVRYAVVTMCIAGGMGAAGLIEI 391 Lambda K H 0.316 0.133 0.377 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: 421 Number of extensions: 14 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: 391 Length of database: 395 Length adjustment: 31 Effective length of query: 360 Effective length of database: 364 Effective search space: 131040 Effective search space used: 131040 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