Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_011383284.1 AMB_RS04295 acetyl-CoA C-acetyltransferase
Query= SwissProt::P50174 (393 letters) >NCBI__GCF_000009985.1:WP_011383284.1 Length = 390 Score = 513 bits (1321), Expect = e-150 Identities = 260/387 (67%), Positives = 301/387 (77%) Query: 6 IVIASAARTAVGSFNGAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLPAGEGQ 65 IVIA+A RT VGSFNG+ A +LG I+ L+RAGVEA VDEV+LG +L AG GQ Sbjct: 4 IVIAAATRTPVGSFNGSLAGLQAAQLGEIVIREALKRAGVEAEAVDEVLLGHILTAGCGQ 63 Query: 66 NPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAPH 125 N ARQAA+KAG+P TA +NQLCGSGLRAVALG Q I GDA +IVAGG ESMS A H Sbjct: 64 NTARQAAIKAGVPNTATAMAINQLCGSGLRAVALGFQAIKLGDANIIVAGGQESMSNAQH 123 Query: 126 CAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEFALASQN 185 ++RGGVKMGD ++DTMIKDGLTDAF HMGITAEN+A K+Q+TREEQD FAL SQN Sbjct: 124 AIYMRGGVKMGDASLVDTMIKDGLTDAFSPIHMGITAENLAEKFQITREEQDAFALGSQN 183 Query: 186 KAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKEGTVTAG 245 KAEAA KAGRF D+IVP + ++ + D DE+IR G TLD IAK +PAF K+GTVTA Sbjct: 184 KAEAASKAGRFKDQIVPVTITVKREEKLFDTDEFIRMGCTLDQIAKPKPAFKKDGTVTAA 243 Query: 246 NASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALEKAG 305 NASG+NDG AA +LMT EA +RGI+PLARI WATAG DP MG GP+PA++K L K G Sbjct: 244 NASGINDGGAALVLMTAKEADKRGIKPLARIAGWATAGTDPNTMGYGPVPATQKLLAKLG 303 Query: 306 WSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLFE 365 W D++L+EANEAFAAQA AVNK +GWD S VNVNGGAIAIGHPIGASGAR+L LL+E Sbjct: 304 WKHEDLDLIEANEAFAAQAIAVNKGMGWDTSKVNVNGGAIAIGHPIGASGARILVDLLYE 363 Query: 366 MKRRGVSKGLATLCIGGGMGVAMCVER 392 M RR KGLATLCIGGGMG+A+CVER Sbjct: 364 MGRRDAKKGLATLCIGGGMGIALCVER 390 Lambda K H 0.317 0.132 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: 441 Number of extensions: 18 Number of successful extensions: 1 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: 393 Length of database: 390 Length adjustment: 31 Effective length of query: 362 Effective length of database: 359 Effective search space: 129958 Effective search space used: 129958 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 17 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