Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA acetyltransferase
Query= SwissProt::P50174 (393 letters) >FitnessBrowser__azobra:AZOBR_RS30610 Length = 391 Score = 564 bits (1454), Expect = e-165 Identities = 282/387 (72%), Positives = 320/387 (82%) Query: 6 IVIASAARTAVGSFNGAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLPAGEGQ 65 +VIASAART +GSFNGA + AH LG AI+ L RA +A EV EVILGQ+L AG+GQ Sbjct: 4 VVIASAARTPIGSFNGALSSVPAHYLGEIAIREALSRAKTDAAEVTEVILGQILTAGQGQ 63 Query: 66 NPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAPH 125 NPARQAA+ AG+P TA+G+NQLCGSGLR+VALG Q I GDA+V+V GG ESMS APH Sbjct: 64 NPARQAAVNAGIPASATAFGINQLCGSGLRSVALGYQAIRNGDAEVMVVGGQESMSQAPH 123 Query: 126 CAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEFALASQN 185 HLR GVKMG +M+DTM+KDGL DAF GYHMG TAENVA+KWQLTREEQD FA ASQ Sbjct: 124 VMHLRNGVKMGAAEMLDTMLKDGLMDAFKGYHMGTTAENVAQKWQLTREEQDVFAAASQQ 183 Query: 186 KAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKEGTVTAG 245 KAEAAQK+GRF DEI+P +K RKGD+ V DEY +HG T +S+AKLRPAF KEGTVTAG Sbjct: 184 KAEAAQKSGRFKDEIIPVTIKGRKGDIIVADDEYPKHGTTAESLAKLRPAFSKEGTVTAG 243 Query: 246 NASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALEKAG 305 NASG+NDGAAA +LMT AARRG+ PLARIVSWATAGVDP IMGTGPIPASR ALEKAG Sbjct: 244 NASGINDGAAALVLMTAENAARRGLTPLARIVSWATAGVDPAIMGTGPIPASRLALEKAG 303 Query: 306 WSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLFE 365 W D++L+EANEAFAAQA AVNKDLGWD S VNVNGGAIA+GHP+GASGARVL TLL+E Sbjct: 304 WKHDDLDLIEANEAFAAQALAVNKDLGWDTSKVNVNGGAIALGHPVGASGARVLTTLLYE 363 Query: 366 MKRRGVSKGLATLCIGGGMGVAMCVER 392 M++R KGLATLCIGGGMG+A+ VER Sbjct: 364 MQKRDAKKGLATLCIGGGMGIALTVER 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: 451 Number of extensions: 15 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: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 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