Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_012709751.1 NGR_RS27475 acetyl-CoA C-acetyltransferase
Query= SwissProt::P50174 (393 letters) >NCBI__GCF_000018545.1:WP_012709751.1 Length = 393 Score = 743 bits (1919), Expect = 0.0 Identities = 373/393 (94%), Positives = 382/393 (97%) Query: 1 MSNPSIVIASAARTAVGSFNGAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLP 60 MSNPSIVIASAARTAVGSFNGAFGNT AHELGA IKAVLERAGV+A EVDEVILGQVLP Sbjct: 1 MSNPSIVIASAARTAVGSFNGAFGNTPAHELGATVIKAVLERAGVDAAEVDEVILGQVLP 60 Query: 61 AGEGQNPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESM 120 AGEGQNPARQAA+KAG+PQEKTAWGMNQLCGSGLRAVALGMQQIATGDA +IVAGGMESM Sbjct: 61 AGEGQNPARQAAIKAGVPQEKTAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESM 120 Query: 121 SMAPHCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEFA 180 SMAPHCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMG TAENVARKWQLTREEQDEFA Sbjct: 121 SMAPHCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGTTAENVARKWQLTREEQDEFA 180 Query: 181 LASQNKAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKEG 240 L SQNKAEAAQKAGRFADEIVPF+VKTRKGDV VDQDEYIRHGATL+SIAKLRPAFDKEG Sbjct: 181 LRSQNKAEAAQKAGRFADEIVPFIVKTRKGDVTVDQDEYIRHGATLESIAKLRPAFDKEG 240 Query: 241 TVTAGNASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRKA 300 TVTAGNASGLNDGAAA LLMTEAEAA+RGIQPLARIVSWATAGVDPQIMGTGPIPASRKA Sbjct: 241 TVTAGNASGLNDGAAATLLMTEAEAAKRGIQPLARIVSWATAGVDPQIMGTGPIPASRKA 300 Query: 301 LEKAGWSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLN 360 LEKAGW + D+ELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLN Sbjct: 301 LEKAGWPIGDVELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLN 360 Query: 361 TLLFEMKRRGVSKGLATLCIGGGMGVAMCVERL 393 TLLFEMKRRGVSKGLATLCIGGGMGVAMCVERL Sbjct: 361 TLLFEMKRRGVSKGLATLCIGGGMGVAMCVERL 393 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: 610 Number of extensions: 16 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: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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 Apr 09 2024. 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