Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_004300932.1 C665_RS04230 acetyl-CoA C-acyltransferase
Query= BRENDA::Q8VCH0 (424 letters) >NCBI__GCF_000310185.1:WP_004300932.1 Length = 399 Score = 296 bits (757), Expect = 1e-84 Identities = 176/392 (44%), Positives = 240/392 (61%), Gaps = 9/392 (2%) Query: 37 DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDV-KLKPEQLGDISVGNVL-QP 94 D +V RTP+ + + G F+ PD+LL+ VL V+ V L ++GD+ G + + Sbjct: 7 DAYIVAAVRTPVAKRN-GAFRAVRPDDLLARVLREVVAKVPNLDAREIGDVVTGCAMPEA 65 Query: 95 GAGAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154 G +ARI L+G+P++VP T+NR C+SGLQAVA+ A IR G D+ +A G ESM+ Sbjct: 66 EQGMNVARIGLLLAGLPDSVPGITINRFCASGLQAVADAASRIRLGEADVMIAAGTESMS 125 Query: 155 LSQR--GNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAAS 212 + GN +++ + + MG+T+E VA+++ VSR+ QDAFA+ S ++A + Sbjct: 126 AMPQIMGNKVSLNPEIFARAENLSIAYGMGLTAEKVAQQWKVSREDQDAFAVESHRRACA 185 Query: 213 AQSRGCFHAEIVPVTTTVLNDKGDKKT-IT---VSQDEGVRPSTTMQGLAKLKPAFKDGG 268 A + G F EI+P D IT V DEG RP L KLKP F G Sbjct: 186 AIAAGQFADEILPYAVKSYAPGVDGTVRITERLVEHDEGPRPDAAADRLGKLKPVFAARG 245 Query: 269 STTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAA 328 S TAGNSSQ+SDGAAAVLL + + + + S+AV GVPP+VMGIGP AIP A Sbjct: 246 SVTAGNSSQMSDGAAAVLLMSETALKRYDVTPIARFSSFAVAGVPPEVMGIGPVEAIPRA 305 Query: 329 LQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVV 388 L +AG+ + DI E+NEAFA+QA+ + +LG+ KVNPLGGAIALGHPLG TGA + Sbjct: 306 LARAGVALADIGWTELNEAFAAQALAVMRQLGMDPAKVNPLGGAIALGHPLGATGAIRTA 365 Query: 389 TLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 TL+ ++R YG++SMCIGTGMGAA VFE Sbjct: 366 TLMAAMQRDPGLRYGMISMCIGTGMGAAGVFE 397 Lambda K H 0.317 0.133 0.377 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: 442 Number of extensions: 19 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: 399 Length adjustment: 31 Effective length of query: 393 Effective length of database: 368 Effective search space: 144624 Effective search space used: 144624 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