Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_041096687.1 SUTH_RS01990 acetyl-CoA C-acyltransferase
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_000828635.1:WP_041096687.1 Length = 394 Score = 395 bits (1014), Expect = e-114 Identities = 203/389 (52%), Positives = 268/389 (68%) Query: 2 KEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAGL 61 +EVV+ + VRTAIG+Y SLKDV A LGA AI+E +K+A + P+ V +++GNV+QAG+ Sbjct: 4 REVVLCNPVRTAIGTYNGSLKDVAAPMLGAAAIRETLKRANLSPDKVEALVMGNVIQAGV 63 Query: 62 GQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSRA 121 NPARQA GLPVE+PA+T+N+VCGSG + V AA I +G D I GGMENM RA Sbjct: 64 KMNPARQAGIAGGLPVEVPALTVNRVCGSGAQGVVSAALEIWSGMIDCAIGGGMENMDRA 123 Query: 122 PYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFALA 181 PYL RWG RMG+ D M+ DGL DAF+D H G E++ + ISR +QD +AL Sbjct: 124 PYLMPQVRWGARMGDVTVYDAMLFDGLNDAFSDKHSGWHTEDLVTKNGISRADQDAWALR 183 Query: 182 SQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGTV 241 SQ+ A +G+F EIV V + GRKG T+ D DEH R +T E LAKLKPAF+K+GT+ Sbjct: 184 SQQNFSAAQAAGKFAAEIVAVEVPGRKGPTLFDKDEHNRPETTAESLAKLKPAFRKEGTI 243 Query: 242 TAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAAIE 301 TAGNA GLN AA +V+ A++ G+KP+AK+V+YG V+P G GP A + A+ Sbjct: 244 TAGNAPGLNTGAAAMVVAERNWAEKNGLKPMAKLVAYGIGAVEPGFFGLGPVPAVRQALA 303 Query: 302 KAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVTL 361 +AGW+V ++ +E NEAFAA +LA ++L F + VNV GGAIA GHPIGASGA + L Sbjct: 304 RAGWSVADVQRVEINEAFAAIALACQRELGFAPDIVNVEGGAIAHGHPIGASGAVLATRL 363 Query: 362 VHAMQKRDAKKGLATLCIGGGQGTAILLE 390 +H+MQ+ K+G+ TLCIGGGQG A+ +E Sbjct: 364 MHSMQRDGLKRGIVTLCIGGGQGIALAIE 392 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: 466 Number of extensions: 17 Number of successful extensions: 1 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: 394 Length adjustment: 31 Effective length of query: 361 Effective length of database: 363 Effective search space: 131043 Effective search space used: 131043 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