Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_092484149.1 BM299_RS11340 acetyl-CoA C-acetyltransferase
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_900115975.1:WP_092484149.1 Length = 393 Score = 389 bits (999), Expect = e-113 Identities = 204/390 (52%), Positives = 268/390 (68%), Gaps = 1/390 (0%) Query: 1 MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60 M++ VI SA RT G G +LK++ A LG AI EAV++AGI V+ VI G VLQ G Sbjct: 1 MRQSVIVSAARTPFGKLGGALKNLKATQLGGIAIAEAVRRAGIDGATVDNVIFGQVLQGG 60 Query: 61 LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120 GQ P+RQA+ +AGLP E P+ TINKVC SGLR V++ QII+AGDADVI+AGGME+MS Sbjct: 61 CGQIPSRQAAREAGLPWETPSETINKVCASGLRAVTMGDQIIRAGDADVIVAGGMESMSN 120 Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFAL 180 APY ARWG RM N +F D M+ DGLW +F D HM I +A +NISREEQDE+AL Sbjct: 121 APYFVPGARWGLRMFNTQFTDLMVHDGLWCSFYDRHMAIHGGEVAVEYNISREEQDEWAL 180 Query: 181 ASQKKAEEAIKSGQFKDEIVPVVIKGRKGE-TVVDTDEHPRFGSTIEGLAKLKPAFKKDG 239 S + A AI G+ K+EI+PV I +KG+ VVDTDE PR +++E L KL P F + Sbjct: 181 RSHQLAISAIDGGRLKEEIIPVTIPRKKGDPVVVDTDEGPRRETSMEALRKLPPVFDPNN 240 Query: 240 TVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAA 299 TVTAGNA G+ND A LVIMS EKA ELG+KP+A ++ + S + + P + Sbjct: 241 TVTAGNAPGVNDGAGALVIMSNEKAGELGIKPMATVLGHASVSQEAKYIATVPGLSINKL 300 Query: 300 IEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILV 359 +++ G T+D++DL+E NEAFAA +L K ++ +KVNVNGGAIA GHPIGASGARIL+ Sbjct: 301 LKQKGMTIDQVDLLEVNEAFAAVALVSGKIAGWNPDKVNVNGGAIAFGHPIGASGARILM 360 Query: 360 TLVHAMQKRDAKKGLATLCIGGGQGTAILL 389 TL++ +++R G+A +C G QG A+++ Sbjct: 361 TLIYELRRRGGGIGVAAICSGAAQGDAVMV 390 Lambda K H 0.315 0.132 0.375 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: 455 Number of extensions: 16 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: 392 Length of database: 393 Length adjustment: 31 Effective length of query: 361 Effective length of database: 362 Effective search space: 130682 Effective search space used: 130682 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 Apr 09 2024. 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