Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_043532471.1 JH15_RS16990 acetyl-CoA C-acyltransferase FadA
Query= SwissProt::Q0KBP1 (394 letters) >NCBI__GCF_000759345.1:WP_043532471.1 Length = 392 Score = 255 bits (652), Expect = 1e-72 Identities = 162/398 (40%), Positives = 227/398 (57%), Gaps = 18/398 (4%) Query: 3 REVVVVSGVRTAIGTF-GGSLKDVAPAELGALVVREALAR-AQVSGDDVGHVVFGNVIQT 60 R++VVV GVRTA+ G+ ++V L A V++ R A + ++V V++G V QT Sbjct: 6 RDIVVVDGVRTAMAKAKNGAFRNVRAENLSASVMQALFDRNAGLDPNEVDDVIWGCVNQT 65 Query: 61 EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120 + M + R AA+ G+ + PA TVNRLCGS + A+ AA I G D I GG E M Sbjct: 66 LEQSMNIARNAAIMTGIPRSVPAQTVNRLCGSSMTALHIAAANIKAGMGDFYIIGGVEHM 125 Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180 P A A MM MG+TAE ++K + ++R QD+ Sbjct: 126 EHVPMAHGVDVNPAASKYAAKAAMM------------MGLTAELLSKMHGVTREDQDKFG 173 Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKG-DVTFDTDEHVRHDATIDDMTKLRPVFVKE 239 + SH+RA AA + GYF ++IV + +G DE VR DA++++M KL+PVF Sbjct: 174 VRSHQRAYAANQQGYFDNEIVGIEGHDTQGFKRLIKHDEVVRIDASLEEMAKLKPVFDPR 233 Query: 240 NGTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATK 299 +GTV+AG +S L+ A+A+ +M A+ GL+P+AR++S G AG D MG GPVPA+K Sbjct: 234 SGTVSAGTSSALSVGASAMAVMSYERAQALGLQPIARVLSTGVAGCDASIMGYGPVPASK 293 Query: 300 IALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPA---KVNPNGSGISLGHPIGATG 356 AL+ AGL D+ +E NEAFAAQA V K LG A KVN NG I+LGHP+G +G Sbjct: 294 KALKAAGLSSKDIQTVELNEAFAAQAIPVLKDLGFYDAMDEKVNLNGGAIALGHPLGCSG 353 Query: 357 ALITVKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394 + I L+ + + L TMCIG GQG+A +FER+ Sbjct: 354 SRICTTLLNVMQQQDTTLGLATMCIGMGQGVATVFERL 391 Lambda K H 0.318 0.134 0.381 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: 388 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: 394 Length of database: 392 Length adjustment: 31 Effective length of query: 363 Effective length of database: 361 Effective search space: 131043 Effective search space used: 131043 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