Align Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate WP_051305468.1 G494_RS22310 acetyl-CoA C-acyltransferase
Query= curated2:Q5HIU0 (393 letters) >NCBI__GCF_000429965.1:WP_051305468.1 Length = 443 Score = 234 bits (597), Expect = 4e-66 Identities = 156/427 (36%), Positives = 232/427 (54%), Gaps = 45/427 (10%) Query: 2 TRVVLAAAYRTPIGVFGGAFKDVPAYDLGATLIEHIIKETGLNPSEIDEVIIGNVLQAGQ 61 T V + RTP G A DL ++ P + EVIIG+V+ A Sbjct: 6 TAVYIVDGCRTPFLKATGRPGPFAAADLLVAAGRTLLGRQPFAPETLSEVIIGSVIPAPD 65 Query: 62 GQNPARIAAMKGGLPETVPAFTVNKVCGSGLKSIQLAYQSIVTGENDIVLAGGMENMSQS 121 N AR+ + + G VPA+TV + CGSG+++++ I G + +VL GG++ MS + Sbjct: 66 EVNIARVFSQRLGCGPRVPAWTVQRNCGSGMQALETGADRIRDGHSSLVLVGGVDAMSHA 125 Query: 122 PMLVN-----------NSRFGF---------KMGHQSMVDSMVYDGLTDVFNQYHMGITA 161 P+LVN +R G + GH +V ++ GLTD + +MG TA Sbjct: 126 PVLVNPKMVAWLSDFTRARGGLAKLRRLLELRPGHFRLVFGIL-QGLTDPVVRLNMGQTA 184 Query: 162 ENLAEQYGISREEQDTFAVNSQQKAVRAQQNGEFDSEIVPVSIPQRKGEPIVVTKDEGVR 221 E LAE + ISR E D +++ S Q+ RA G D E+VP+ P + V +D+G+R Sbjct: 185 EILAEMFAISRGEMDRYSLRSHQRLARAMDQGWLD-EVVPLYAPSGQ----VYEEDDGLR 239 Query: 222 ENVSVEKLSRLRPAFK-KDGTVTAGNASGINDGAAMMLVMSEDKAKELNIEPLAVLDGFG 280 + S+E+L+RLRP F + G ++AGN + I DGAA++L+ + +E L ++ Sbjct: 240 RDSSLERLARLRPVFDPRFGRISAGNGAQITDGAALLLLAGAEAVDRFQLEVLGSIEDTH 299 Query: 281 SHGVDPSIMGIAPVGAVEKALKRSKKELSDIDVFELNEAFAAQSLAVDR----------E 330 G+DP+ MG+ PV AV L+R+ L DID +ELNEAFAAQ LA + + Sbjct: 300 WAGLDPAQMGLGPVHAVAPLLERNDLGLEDIDYWELNEAFAAQVLACLKAFADPEYCASQ 359 Query: 331 LKLP-------PEKVNVKGGAIALGHPIGASGARVLVTLLHQL-NDEVETGLTSLCIGGG 382 LK P E++N+ GGAI+LGHP+GASGAR+++ LLH L + G+ +LCIGGG Sbjct: 360 LKRPIPWGNIDQERINIDGGAISLGHPVGASGARIVLHLLHVLRRQQARLGIATLCIGGG 419 Query: 383 QAIAAVV 389 Q A ++ Sbjct: 420 QGGAMLL 426 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: 453 Number of extensions: 22 Number of successful extensions: 6 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: 393 Length of database: 443 Length adjustment: 32 Effective length of query: 361 Effective length of database: 411 Effective search space: 148371 Effective search space used: 148371 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