Align Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate SMc00966 SMc00966 acetyl-COA acyltransferase
Query= curated2:Q5HIU0 (393 letters) >FitnessBrowser__Smeli:SMc00966 Length = 397 Score = 259 bits (662), Expect = 9e-74 Identities = 161/386 (41%), Positives = 222/386 (57%), Gaps = 14/386 (3%) Query: 5 VLAAAYRTPIGVFGGAFKDVPAYDLGATLIEHIIKETGLNPSEIDEVIIGNVLQAGQGQN 64 V+ AA RTP+G G+ V L A LIE II +TG++ +EID+V++GN A N Sbjct: 12 VVIAALRTPVGRVNGSLAAVEPARLAALLIERIIADTGIDRAEIDDVLVGNA--ANSAGN 69 Query: 65 PARIAAMKGGLPETVPAFTVNKVCGSGLKSIQLAYQSIVTGENDIVLAGGMENMSQSPML 124 AR+AA++ GLP +P TV++ CGSGL++I LA + I G LAGG E+ S++ + Sbjct: 70 LARLAALEAGLPVAIPGVTVDRQCGSGLEAIVLAARQIQAGAGRFYLAGGTESASRAHIR 129 Query: 125 VNNSRFGFKMGHQSMVDSMVYDGLTDVFNQYHMGITAENLAEQYGISREEQDTFAVNSQQ 184 + + M D + D MG+ AEN+A GISRE QD FA+ S + Sbjct: 130 LRPPLTRGEEPQPVKRARMAPDSIGDP----DMGVAAENVATACGISRERQDRFALESHR 185 Query: 185 KAVRAQQNGEFDSEIVPVSIPQRKGEPIVVTKDEGVRENVSVEKLSRLRPAFKKDGTVTA 244 +AV A+ G F EIVPV P+ + +DE R N S E LSRLRP F GTVTA Sbjct: 186 RAVAAEAEGRFSREIVPVPTPEGP-----IARDECPRANASAETLSRLRPVFVAGGTVTA 240 Query: 245 GNASGINDGAAMMLVMSEDKAKELNIEPLAVLDGFGSHGVDPSIMGIAPVGAVEKALKRS 304 GNA +NDGAAM+L+ + +A++L + GV+P ++G+ PV A+ K R+ Sbjct: 241 GNACPVNDGAAMVLMTNLAEARKLGTRFGLAFTDAATAGVEPKLLGLGPVPAMAKLRARN 300 Query: 305 KK-ELSDIDVFELNEAFAAQSLAVDRELKLPPEKVNVKGGAIALGHPIGASGARVLVTLL 363 +++ +D E NEAFA+Q L +L + PE+VN GGAIALGHP GASGA ++V L Sbjct: 301 PALDVARVDFIEFNEAFASQVLGSLDQLDIAPERVNRDGGAIALGHPYGASGAILVVRLF 360 Query: 364 HQL--NDEVETGLTSLCIGGGQAIAA 387 Q+ GL + IGGG IAA Sbjct: 361 SQMLAASSPAEGLAMMGIGGGMGIAA 386 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: 406 Number of extensions: 19 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: 397 Length adjustment: 31 Effective length of query: 362 Effective length of database: 366 Effective search space: 132492 Effective search space used: 132492 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 17 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