Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit B (characterized)
to candidate WP_036261524.1 DL86_RS11550 acetate CoA-transferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2112 (221 letters) >NCBI__GCF_000746085.1:WP_036261524.1 Length = 224 Score = 218 bits (556), Expect = 6e-62 Identities = 111/216 (51%), Positives = 150/216 (69%), Gaps = 1/216 (0%) Query: 4 SREQMAQRVAREMQDGYYVNLGIGIPTLVANYIPEGMEVMLQSENGLLGMGAFPTEAEVD 63 ++E +A+RVA E++D VNLGIG+PTLVA Y+P G+ V QSENG++G GA P E D Sbjct: 3 AKELIARRVALELRDRTLVNLGIGLPTLVARYVPPGISVAFQSENGIIGFGAPPPEGMED 62 Query: 64 ADMINAGKQTVTARIGASIFSSAESFAMIRGGHIDLTVLGAFEVDVEGNIASWMIPGKLV 123 ++ +AG ++A GA+ F S SFA+IRGGH+D+TVLG +VD G +A+WM+PGKLV Sbjct: 63 PNLTDAGGGFISALPGAASFDSGTSFALIRGGHLDMTVLGGLQVDGSGRLANWMVPGKLV 122 Query: 124 KGMGGAMDLVAGAENIIVTMTHASKDGESKLLPRCSLPLTGAGCIKRVLTDLAYLEIQDG 183 GMGGAMDLV GA+ +IV M H +K G+ K++ +LP T + V+TDLA +E Sbjct: 123 PGMGGAMDLVVGAKRVIVAMQHVAK-GQPKIVASLALPATATRRVSLVVTDLAVIEPTSE 181 Query: 184 AFILKERAPGVSVEEIVAKTAGKLIVPDHVPEMQFA 219 +L+ERAPGVSV+EIVA T L++ VPEM A Sbjct: 182 GLLLRERAPGVSVDEIVANTGAALLIIGDVPEMPIA 217 Lambda K H 0.318 0.135 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: 201 Number of extensions: 9 Number of successful extensions: 2 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: 221 Length of database: 224 Length adjustment: 22 Effective length of query: 199 Effective length of database: 202 Effective search space: 40198 Effective search space used: 40198 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 (21.7 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