Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_084057804.1 B9A12_RS10300 acetyl-CoA C-acyltransferase
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_900176285.1:WP_084057804.1 Length = 398 Score = 260 bits (664), Expect = 5e-74 Identities = 160/398 (40%), Positives = 235/398 (59%), Gaps = 20/398 (5%) Query: 2 KEVVIASAVRTAIGSYGKS--LKDVPAVDLGATAIKEAVKK-AGIKPEDVNEVILGNVLQ 58 ++VV+ +RTA G G+ A D+ I+E +++ +KPE V E + G Q Sbjct: 4 RDVVVVDGIRTAFGKAGERGIFWMTRADDMVVKVIRELMRRNPQVKPEMVEENVWGATTQ 63 Query: 59 AG-LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMEN 117 G G R + AGLPV +++++C G+ V+ AA I G DV IAGG+E+ Sbjct: 64 EGDQGLTMGRTTAILAGLPVATAGYSVDRMCAGGMTAVACAASEIAVGACDVAIAGGVEH 123 Query: 118 MSRAPYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERW-NISREEQD 176 M P A N +F+ E + DA MG TAEN+ + + I++E D Sbjct: 124 MGHHPMGATADP------NPRFLTEKLVSQ--DALV---MGKTAENLHDMFPEITKEMAD 172 Query: 177 EFALASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFK 236 E++L QKK +A + G+ + IVP+ + + G V D DE PR +T+EGLA L+ F+ Sbjct: 173 EYSLLCQKKTAKAYQEGKIQKMIVPMTVYTKNGWKVADRDEQPRPETTMEGLANLRTPFR 232 Query: 237 KDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYAT 296 G VT GNASGLND A +++MS EKAKELG+KP ++V Y AGV P IMGYGP +T Sbjct: 233 VKGKVTPGNASGLNDGACGVLLMSEEKAKELGLKPKMRLVGYAFAGVKPEIMGYGPIPST 292 Query: 297 KAAIEKAGWTVDELDLIESNEAFAAQSLAVAKD--LKF-DMNKVNVNGGAIALGHPIGAS 353 K + + G ++LD++E NEAFA Q++A K+ +KF D ++N GGAIA GHP+ +S Sbjct: 293 KKVLARTGLKFEDLDVVELNEAFAVQAIAYMKEFGMKFPDDKRLNPYGGAIAFGHPLASS 352 Query: 354 GARILVTLVHAMQKR-DAKKGLATLCIGGGQGTAILLE 390 G R++V L+H ++ +A+ GLAT+C+G GQG +I+ E Sbjct: 353 GPRLVVHLMHYFEEHPEARYGLATMCVGLGQGGSIIWE 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: 431 Number of extensions: 23 Number of successful extensions: 5 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: 398 Length adjustment: 31 Effective length of query: 361 Effective length of database: 367 Effective search space: 132487 Effective search space used: 132487 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 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