Align acetyl-CoA:acetoacetyl-CoA transferase subunit &alpha (characterized)
to candidate WP_026606496.1 METAC_RS0107110 acetyl-CoA--acetoacetyl-CoA transferase subunit alpha
Query= ecocyc::ATOD-MONOMER (220 letters) >NCBI__GCF_000427445.1:WP_026606496.1 Length = 217 Score = 238 bits (606), Expect = 9e-68 Identities = 114/211 (54%), Positives = 152/211 (72%) Query: 4 KLMTLQDATGFFRDGMTIMVGGFMGIGTPSRLVEALLESGVRDLTLIANDTAFVDTGIGP 63 + ++ DA DG ++M GGFMG+GTP R+++AL+ G R LT+I NDTA G+G Sbjct: 3 RAISAADAAALIPDGASLMFGGFMGVGTPCRIIDALVARGARGLTVIGNDTARPGVGVGK 62 Query: 64 LIVNGRVRKVIASHIGTNPETGRRMISGEMDVVLVPQGTLIEQIRCGGAGLGGFLTPTGV 123 LI G V + SHIGTNP T ++MI GE+++ L+PQGTL E+IR GGAGLGG LTPTGV Sbjct: 63 LIDAGCVARARVSHIGTNPLTQKKMIEGEIEIELIPQGTLAERIRAGGAGLGGVLTPTGV 122 Query: 124 GTVVEEGKQTLTLDGKTWLLERPLRADLALIRAHRCDTLGNLTYQLSARNFNPLIALAAD 183 GTVVE+GK+ + +DG+ +LLE P+RAD ALI AH D NLTY+L+A NFNP+IA AAD Sbjct: 123 GTVVEKGKRLIEVDGREFLLELPIRADFALIHAHEADYNCNLTYRLTATNFNPVIAFAAD 182 Query: 184 ITLVEPDELVETGELQPDHIVTPGAVIDHII 214 + EPDE+V G + PD + TPG ++ H++ Sbjct: 183 CVIAEPDEIVPVGVIPPDAVRTPGILVHHLV 213 Lambda K H 0.320 0.140 0.403 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: 214 Number of extensions: 10 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: 220 Length of database: 217 Length adjustment: 22 Effective length of query: 198 Effective length of database: 195 Effective search space: 38610 Effective search space used: 38610 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 45 (21.9 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