Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate BPHYT_RS21955 BPHYT_RS21955 acetyl-CoA acetyltransferase
Query= BRENDA::P45359 (392 letters) >FitnessBrowser__BFirm:BPHYT_RS21955 Length = 395 Score = 382 bits (982), Expect = e-111 Identities = 192/389 (49%), Positives = 266/389 (68%) Query: 2 KEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAGL 61 +EVVI + VRT IG++G +LK+VPA LGA A++E ++++ + ++ V++GNV+QAG Sbjct: 5 REVVICNPVRTPIGAFGGALKEVPATTLGAVAVRETLRRSRLDAAELASVVMGNVIQAGN 64 Query: 62 GQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSRA 121 N ARQAS G+PV +PA+T+N+VCGSG + ++ AAQ I G D +AGGMENM RA Sbjct: 65 KMNAARQASIGGGVPVAVPALTVNRVCGSGAQAIASAAQEILLGLGDAAVAGGMENMDRA 124 Query: 122 PYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFALA 181 PYL + RWGYRMGNA+ D ++ DGL DAF+ H G E++ +++I+RE QD +A Sbjct: 125 PYLLDGGRWGYRMGNAQIHDSLLRDGLNDAFSGEHSGWHTEDLVAQFDITRETQDRWAAR 184 Query: 182 SQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGTV 241 SQ++ EA G F E+V V I GRKG DE PR +T+E LAKL+PAF+ DGT+ Sbjct: 185 SQQRFSEAQARGDFDAELVGVEIAGRKGPQHFTRDEQPRPDTTVETLAKLRPAFRPDGTI 244 Query: 242 TAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAAIE 301 TAGNA GLN AA +++ A+ G+ PLA++VSYG A V+P + G GP A + A+ Sbjct: 245 TAGNAPGLNSGAAAMLVAERGFAEARGIAPLARLVSYGVAAVEPGMFGLGPVPAVQMALA 304 Query: 302 KAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVTL 361 +AGW + +++ E NEAFAA +AVA+ L +NV GGAIA GHPIGA+GA + L Sbjct: 305 RAGWQLHDVERFEINEAFAAVPIAVARKLGIADELINVRGGAIAHGHPIGATGAVLTTRL 364 Query: 362 VHAMQKRDAKKGLATLCIGGGQGTAILLE 390 +H+MQ+ K+G+ TLCIGGGQG A+ LE Sbjct: 365 LHSMQRDGIKRGIVTLCIGGGQGIALALE 393 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: 459 Number of extensions: 11 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: 395 Length adjustment: 31 Effective length of query: 361 Effective length of database: 364 Effective search space: 131404 Effective search space used: 131404 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 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