Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_034994514.1 DL88_RS08065 acetyl-CoA C-acyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411 (393 letters) >NCBI__GCF_000745425.1:WP_034994514.1 Length = 373 Score = 272 bits (695), Expect = 1e-77 Identities = 165/394 (41%), Positives = 223/394 (56%), Gaps = 32/394 (8%) Query: 5 EIYVVSAARTAIGTFG-GSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIPTET 63 E Y+V RT G+L + DLA + + A R + + +G P Sbjct: 3 EAYIVDYLRTPFAPANRGALAGIRPDDLAASVIAALAARMDFAIEEIEDVNLGCAFPEGE 62 Query: 64 RDAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMSR 123 + I+R AA+ AG+P+ VNR CGS +QAI AA + +G + + G ESMSR Sbjct: 63 QGLNIARCAALTAGLPQSIGGVTVNRWCGSSMQAIQMAAGAISMGAGEAFIAGGVESMSR 122 Query: 124 GPYL----MPAARW--GSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQ 177 P + +P W G R+ ++MG+TAEN+A R GI+RE Q Sbjct: 123 VPMMGFNPLPNPSWPEGRRLTF-----------------VNMGLTAENLAERYGISREEQ 165 Query: 178 DALAFEDQQRAAHAIANGYFSEQIATVEIQDRKGVKLFSVDEHPRATSLEQLAAMKPAFK 237 D + Q+++ A A+G + +IA V G PR T +LA +K FK Sbjct: 166 DDYSLASQKKSLAARADGRLAAEIAPVGAIVEDGC--------PRETDTTKLAGLKTVFK 217 Query: 238 KDGSVTAGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPAT 297 +GSVTAGN+S L DGA+A ++ S + ++ LKPLAR+VS+A +G EPE MG+GP+ A+ Sbjct: 218 AEGSVTAGNSSPLTDGASATLVCSEDFIKRRGLKPLARVVSFAISGCEPEIMGIGPVEAS 277 Query: 298 RLALKRAGLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAI 357 R ALKRAG+T DLDVIE N AFA Q A +ELD+DPA++N +G IALGHP+GATGA Sbjct: 278 RKALKRAGITATDLDVIEMNEAFAVQVLACCRELDIDPARLNRDGGAIALGHPLGATGAR 337 Query: 358 IATKAIHELHRTGGRYALVTMCIGGGQGIAAIFE 391 +A KA L R GRY L T CIGGGQGIA + E Sbjct: 338 LAGKAASLLKRDQGRYGLATQCIGGGQGIALVLE 371 Lambda K H 0.318 0.133 0.378 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: 372 Number of extensions: 21 Number of successful extensions: 3 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: 373 Length adjustment: 30 Effective length of query: 363 Effective length of database: 343 Effective search space: 124509 Effective search space used: 124509 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