Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate WP_011461057.1 DHAF_RS22625 acetyl-CoA C-acyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_000021925.1:WP_011461057.1 Length = 384 Score = 318 bits (815), Expect = 2e-91 Identities = 183/386 (47%), Positives = 238/386 (61%), Gaps = 8/386 (2%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDV-NLRPEQLGDICVGNVLQPG 95 + ++ +RTAI +AGRG PD+L + V+ VLK NL + D +G G Sbjct: 3 EAFIIEAKRTAIGKAGRGSLAHMRPDDLAAFVIQDVLKSAPNLNSADIDDCVIGCSFPEG 62 Query: 96 A-GAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMS 154 G MAR+ + +P V T+NR CSSGLQA++ A IR G +A G ESMS Sbjct: 63 EQGMNMARVIALRAGLPIDVSGLTINRFCSSGLQAISLAADRIRLGEAHAMLAGGAESMS 122 Query: 155 LADRGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQ 214 G G E + + MG+T+ENVA+++ I+RE+QD FA AS QKA AQ Sbjct: 123 AVPMGG-GKPAPNPYMMEHCPEVYLSMGLTAENVAKKYEITREQQDEFAAASHQKAHAAQ 181 Query: 215 SKGCFQAEIVPVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTAGN 274 G F+ EIVPV G K + ++DEGIR +T+E L KLKPAFK G TAGN Sbjct: 182 VGGRFEEEIVPVLIA----SGKKGEVWFSKDEGIRADSTVESLGKLKPAFKNGGCVTAGN 237 Query: 275 SSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKAGL 334 SSQ SDGAAA LL K +EL L L + R +AV GV ++MGIGP AIP L++ GL Sbjct: 238 SSQTSDGAAATLLMSEEKVKELDLKPLALWRGFAVAGVEAELMGIGPIKAIPKVLKQVGL 297 Query: 335 TVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITLLNEL 394 T+ +D+FE+NEAFASQ+ ++ L + P KVNP GGA+A GHPLGCTGA+ TLL+E+ Sbjct: 298 TLEQIDLFELNEAFASQSLAIIKTLGIDPAKVNPNGGAIAFGHPLGCTGAKLTATLLHEM 357 Query: 395 KRRGKRAYGVVSMCIGTGMGAAAVFE 420 KRRG + YG+V+MCIG GMGAA V+E Sbjct: 358 KRRGLK-YGMVTMCIGGGMGAAGVYE 382 Lambda K H 0.317 0.134 0.385 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: 425 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: 424 Length of database: 384 Length adjustment: 31 Effective length of query: 393 Effective length of database: 353 Effective search space: 138729 Effective search space used: 138729 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