Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate YP_425366.1 Rru_A0274 acetyl-CoA acetyltransferase
Query= SwissProt::P50174 (393 letters) >NCBI__GCF_000013085.1:YP_425366.1 Length = 390 Score = 566 bits (1458), Expect = e-166 Identities = 276/387 (71%), Positives = 324/387 (83%) Query: 6 IVIASAARTAVGSFNGAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLPAGEGQ 65 IVIA A RT VG+FNG AH LG I+ VL RA VEAGEVDEV+LGQ+L AG+GQ Sbjct: 4 IVIAGATRTPVGTFNGGLSGLPAHALGEIVIREVLRRAKVEAGEVDEVVLGQILTAGQGQ 63 Query: 66 NPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAPH 125 NPARQAA+ AG+P EKTA+G+NQLCGSGLR VALG Q I GDA ++VAGG ESMSMAPH Sbjct: 64 NPARQAAVNAGIPVEKTAYGINQLCGSGLRTVALGFQAITLGDADIVVAGGQESMSMAPH 123 Query: 126 CAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEFALASQN 185 +LR G+KMG +++DTM+KDGL DAF+GYHMG TAEN+A KWQ++RE+QD F+ SQN Sbjct: 124 ATYLRSGIKMGTTELVDTMLKDGLWDAFHGYHMGTTAENIAGKWQISREDQDLFSAGSQN 183 Query: 186 KAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKEGTVTAG 245 KAEAA AGRF DEIVP VK RKGD+ +D DE+ + G T +S+AKLRPAF K+GTVTAG Sbjct: 184 KAEAAIAAGRFKDEIVPVTVKGRKGDIVIDTDEHPKAGVTPESLAKLRPAFSKDGTVTAG 243 Query: 246 NASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALEKAG 305 NASG+NDGAAA +LM+EA AA+RG+ PLARIVSWATAGVDP IMGTGPIPA+RKALEKAG Sbjct: 244 NASGINDGAAALVLMSEANAAKRGVAPLARIVSWATAGVDPAIMGTGPIPATRKALEKAG 303 Query: 306 WSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLFE 365 WS+ D++L+EANEAFAAQA AVNKDLGWDP+ +NVNGGAIA+GHP+GASGAR+L TLL E Sbjct: 304 WSIDDLDLIEANEAFAAQALAVNKDLGWDPAKINVNGGAIALGHPVGASGARILVTLLHE 363 Query: 366 MKRRGVSKGLATLCIGGGMGVAMCVER 392 M +R KGLATLCIGGGMG+A+CVER Sbjct: 364 MIKRDAKKGLATLCIGGGMGIALCVER 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: 513 Number of extensions: 19 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 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