Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit B (characterized)
to candidate WP_078427039.1 BK574_RS00555 acyl CoA:acetate/3-ketoacid CoA transferase subunit beta
Query= reanno::pseudo6_N2E2:Pf6N2E2_2112 (221 letters) >NCBI__GCF_002019605.1:WP_078427039.1 Length = 220 Score = 193 bits (490), Expect = 2e-54 Identities = 93/213 (43%), Positives = 136/213 (63%) Query: 5 REQMAQRVAREMQDGYYVNLGIGIPTLVANYIPEGMEVMLQSENGLLGMGAFPTEAEVDA 64 R +M +R A+E++ VNLGIGIPTLVA++IPE VM +ENG+LG G P D Sbjct: 8 RIRMVKRAAKEIRPLMCVNLGIGIPTLVADFIPEEWNVMFHAENGILGAGRKPASGSEDE 67 Query: 65 DMINAGKQTVTARIGASIFSSAESFAMIRGGHIDLTVLGAFEVDVEGNIASWMIPGKLVK 124 ++ NAG +T G S F SA +FA++R +D+T+LG EV +G++A+W++PGK V Sbjct: 68 NLCNAGGYPITLSKGGSYFDSATAFAIVRKQLLDMTILGGLEVSEQGDLANWIVPGKRVP 127 Query: 125 GMGGAMDLVAGAENIIVTMTHASKDGESKLLPRCSLPLTGAGCIKRVLTDLAYLEIQDGA 184 GMGGAMDL + ++V M+H K G+SK++ +C LPLT C+ ++T+ A +E+ + Sbjct: 128 GMGGAMDLAVNGKKLVVMMSHTDKQGKSKIVKKCGLPLTATQCVNLIITERAVIEVGEAG 187 Query: 185 FILKERAPGVSVEEIVAKTAGKLIVPDHVPEMQ 217 ILKE SVE+IVA T L +P + + Q Sbjct: 188 LILKETMDRYSVEDIVANTGCTLTIPPDIEKFQ 220 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: 175 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: 221 Length of database: 220 Length adjustment: 22 Effective length of query: 199 Effective length of database: 198 Effective search space: 39402 Effective search space used: 39402 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