Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_029133065.1 A3GO_RS0108690 acetyl-CoA C-acyltransferase
Query= BRENDA::Q8VCH0 (424 letters) >NCBI__GCF_000428045.1:WP_029133065.1 Length = 374 Score = 262 bits (669), Expect = 1e-74 Identities = 155/385 (40%), Positives = 224/385 (58%), Gaps = 16/385 (4%) Query: 37 DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDVKLKPEQLGDISVGNVLQPGA 96 ++V+ RTP ++++G PD+L +A + +++ + + + D+ +G G Sbjct: 3 NIVIAGYARTPFTQSNKGALVKVRPDDLAAAAVRGLVERAGVAVDDIEDLVLGCAFPEGE 62 Query: 97 -GAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTL 155 G MAR+ FLSG+P ++ TVNR C S +QA+ AG I G+ ++ + GVESMT Sbjct: 63 QGFNMARLVVFLSGLPVSIGGVTVNRFCGSSMQAIHQAAGAIALGAGEVYICAGVESMTR 122 Query: 156 SQRGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASAQS 215 + + L + MG T+EN+A ++ +SR +Q+AFA+AS QKAA+AQ+ Sbjct: 123 VPMAGFNPMPNPQLAAAMP-GAYVSMGETAENLARQYDISRAEQEAFAVASHQKAAAAQA 181 Query: 216 RGCFHAEIVPVTTTVLNDKGDKKTITVSQDEGVRPSTTMQGLAKLKPAFKDGGSTTAGNS 275 G AEIVPV+ V QD +RP TT + LA LK AF + GS TAG S Sbjct: 182 AGKLSAEIVPVSG-------------VEQDGCIRPETTAESLAGLKLAFDESGSVTAGTS 228 Query: 276 SQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAALQKAGLT 335 S ++DGA+AVL+ A GL IL +RS+A+ G P++MGIGP + AL++AGL+ Sbjct: 229 SPLTDGASAVLVCSEEYARSHGLDILARIRSFAISGCAPEIMGIGPVISSRKALKRAGLS 288 Query: 336 VNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVVTLLNELK 395 + DIDI E+NEAFASQ++ CV L + K N GGAIALGHPLG TGAR LK Sbjct: 289 MADIDIIELNEAFASQSLACVRDLEVDLAKTNLDGGAIALGHPLGATGARITGKAAALLK 348 Query: 396 RRGRRAYGVVSMCIGTGMGAAAVFE 420 R ++ + + + CIG G G A + E Sbjct: 349 REDKQ-FALATQCIGGGQGIATILE 372 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: 410 Number of extensions: 21 Number of successful extensions: 6 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: 374 Length adjustment: 31 Effective length of query: 393 Effective length of database: 343 Effective search space: 134799 Effective search space used: 134799 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