Align acetyl-CoA:acetoacetyl-CoA transferase subunit &alpha (characterized)
to candidate WP_034991730.1 DL88_RS03590 acetyl-CoA--acetoacetyl-CoA transferase subunit alpha
Query= ecocyc::ATOD-MONOMER (220 letters) >NCBI__GCF_000745425.1:WP_034991730.1 Length = 224 Score = 213 bits (542), Expect = 2e-60 Identities = 110/215 (51%), Positives = 147/215 (68%) Query: 6 MTLQDATGFFRDGMTIMVGGFMGIGTPSRLVEALLESGVRDLTLIANDTAFVDTGIGPLI 65 +T +A DG ++M+GGFMG GTP L+EAL+ +G ++LT+I+ND V+ GIG LI Sbjct: 5 ITPAEAVAQIPDGASLMIGGFMGCGTPYTLIEALVTAGKKNLTIISNDNDRVNQGIGRLI 64 Query: 66 VNGRVRKVIASHIGTNPETGRRMISGEMDVVLVPQGTLIEQIRCGGAGLGGFLTPTGVGT 125 G V VI SHIG NPET + MI G + V LVPQGTL EQIR G GLGG LT TG+GT Sbjct: 65 REGCVSHVITSHIGLNPETQKGMIDGTIKVDLVPQGTLAEQIRAAGYGLGGVLTKTGLGT 124 Query: 126 VVEEGKQTLTLDGKTWLLERPLRADLALIRAHRCDTLGNLTYQLSARNFNPLIALAADIT 185 V + +T+ L+G+ W+ PL+AD ALI A + D GNLTYQL+A+NFNPL+ALAAD Sbjct: 125 VAAKAGETVHLNGEDWIYMPPLKADFALIHAAQADYTGNLTYQLTAQNFNPLMALAADQV 184 Query: 186 LVEPDELVETGELQPDHIVTPGAVIDHIIVSQESK 220 + E E + G + PD + TPG V+D ++ +Q ++ Sbjct: 185 ICEALEFMPVGTISPDLVRTPGVVVDILVPAQGNR 219 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: 205 Number of extensions: 9 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: 224 Length adjustment: 22 Effective length of query: 198 Effective length of database: 202 Effective search space: 39996 Effective search space used: 39996 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