Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA acetyltransferase
Query= SwissProt::P50174 (393 letters) >FitnessBrowser__azobra:AZOBR_RS20220 Length = 382 Score = 280 bits (715), Expect = 6e-80 Identities = 168/392 (42%), Positives = 241/392 (61%), Gaps = 18/392 (4%) Query: 2 SNPSIVIASAARTAVGSFN-GAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLP 60 +NP +VIA AR+ N G +L A + A++ER GV ++++V++G P Sbjct: 5 ANP-VVIAGYARSPFAFANKGELAKVRPDDLLAHVVAALVERTGVNPQDIEDVVVGCAFP 63 Query: 61 AGE-GQNPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMES 119 GE G N AR + A LP A +N+ CGS ++A+ I G +V + GG+ES Sbjct: 64 EGEQGMNIARTVSFLAKLPLTAGATTINRYCGSSMQAIHQAAGAIQMGAGEVFLCGGIES 123 Query: 120 MSMAPHCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEF 179 MS P MG + +KD +A+ MG+TAENVAR+++++R +Q+ Sbjct: 124 MSRVP---------MMGYNPLPHPGLKDHYPEAYCS--MGVTAENVARRYEISRADQEAM 172 Query: 180 ALASQNKAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKE 239 A S KA AAQ+AGR A+EIV ++T G V++D IR G + ++++ L+PAF + Sbjct: 173 AAESHAKAAAAQQAGRLAEEIV--AIQTAAG--LVERDGCIRPGTSGETLSGLKPAFLAD 228 Query: 240 GTVTAGNASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRK 299 G+VTAG +S L DGA+A L+ TEA A G+ LARI S A AG P++MG GP+PA++K Sbjct: 229 GSVTAGTSSPLTDGASAVLVTTEAYAKANGLPILARIRSVAVAGCAPEVMGLGPVPAAQK 288 Query: 300 ALEKAGWSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVL 359 AL +AG S+ DI+++E NEAFAAQA A +DL DP+ VN++GGAIA+GHP+GA+GAR+ Sbjct: 289 ALARAGLSIRDIDVIELNEAFAAQAIACMRDLDIDPAKVNLDGGAIALGHPLGATGARIT 348 Query: 360 NTLLFEMKRRGVSKGLATLCIGGGMGVAMCVE 391 +KR G LAT CIGGG G+A +E Sbjct: 349 GKAAALLKREGKQFALATQCIGGGQGIATVLE 380 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: 362 Number of extensions: 22 Number of successful extensions: 4 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: 382 Length adjustment: 30 Effective length of query: 363 Effective length of database: 352 Effective search space: 127776 Effective search space used: 127776 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