Align Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate WP_025274382.1 HALAL_RS0112830 acetyl-CoA C-acyltransferase
Query= curated2:Q5HIU0 (393 letters) >NCBI__GCF_000527155.1:WP_025274382.1 Length = 426 Score = 176 bits (446), Expect = 1e-48 Identities = 133/431 (30%), Positives = 213/431 (49%), Gaps = 58/431 (13%) Query: 4 VVLAAAYRTPIGVFGGAFKDVPAYDLGATLIEHIIKETGLNPSEIDEVIIGNVLQAGQGQ 63 V + R P GG + D+ + ++ +I L+ ++DE G VL+ + Sbjct: 7 VAIVGGNRIPFAKEGGPYATKSNQDMLSAALDGLIDRFHLSGLKLDEFSAGAVLKHSRDF 66 Query: 64 NPARIAAMKGGLPETVPAFTVNKVCGSGLKSIQLAYQSIVTGENDIVLAGGMENMSQSPM 123 N AR + L PA+ V K C +G+++ I G+ D +AGG++ S +P+ Sbjct: 67 NLAREVVLGSRLDPATPAYDVQKACTTGMETAIGVSNKIALGQIDAGIAGGVDTTSDAPL 126 Query: 124 LVN-----------NSR---------FGFKMGHQSMVDSMVYDGLTDVFNQYHMGITAEN 163 +N NS+ G + H MV M + + MG A Sbjct: 127 GLNDRLRRLLLNARNSKSTGAKMKAVLGLRPSH--MVPDMPRNA--EPRTGLSMGEHAAQ 182 Query: 164 LAEQYGISREEQDTFAVNSQQKAVRAQQNGEFDSEIVPVSIPQRKGEPIVVTKDEGVREN 223 A+++GISR +QD FA S Q+ A + G FD + P +R D+ +R N Sbjct: 183 TAKEWGISRIDQDEFAATSHQRLAAAYEAGFFDDLLTPYENQRR---------DQILRPN 233 Query: 224 VSVEKLSRLRPAF-KKDGTVTAGNASGINDGAAMMLVMSEDKAKELNIEPLAVLDGFGSH 282 ++EKL++L P F +GT+TAGN++ ++DGAA +L+ S++ A+E ++ LA L S Sbjct: 234 SNMEKLTKLSPTFGGSEGTMTAGNSTPLSDGAATVLLSSDEWAREHDLPVLAHLVDVQSA 293 Query: 283 GVD----PSIMGIAPVGAVEKALKRSKKELSDIDVFELNEAFAAQSLA------------ 326 VD + APV AV + L+R++ L D D E++EAFA+Q LA Sbjct: 294 AVDFVDGDDGLLTAPVFAVPRLLERNELSLEDFDFIEIHEAFASQVLATLKAWENDEFCR 353 Query: 327 ----VDREL-KLPPEKVNVKGGAIALGHPIGASGARVLVT---LLHQLNDEVETGLTSLC 378 +D L + +++NV G ++A GHP A+GAR++ T LLHQ ++ + GL S+C Sbjct: 354 DRLNLDGALGSVARDRLNVNGSSLATGHPFAATGARIIATTAKLLHQTGEKGKLGLVSVC 413 Query: 379 IGGGQAIAAVV 389 GGQ AA++ Sbjct: 414 AAGGQGTAAII 424 Lambda K H 0.314 0.133 0.368 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: 419 Number of extensions: 27 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 393 Length of database: 426 Length adjustment: 31 Effective length of query: 362 Effective length of database: 395 Effective search space: 142990 Effective search space used: 142990 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: 42 (22.0 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