Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate WP_062736905.1 AYX06_RS05775 3-oxoacid CoA-transferase subunit B
Query= BRENDA::P0A102 (213 letters) >NCBI__GCF_001580365.1:WP_062736905.1 Length = 215 Score = 234 bits (597), Expect = 9e-67 Identities = 124/212 (58%), Positives = 152/212 (71%), Gaps = 2/212 (0%) Query: 1 MTITKKLSRTEMAQRVAADIQEGAYVNLGIGAPTLVANYL-GDKEVFLHSENGLLGMGPS 59 MT L E+A+ VA DI G+YVNLGIG PTLVA++L + +V LH+ENG+LGMGP+ Sbjct: 1 MTSATPLRPEELARVVARDIPAGSYVNLGIGQPTLVADHLTAEDDVTLHTENGMLGMGPA 60 Query: 60 PAPGEEDDDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANW 119 + D DLINAGK V G ++FHHADSF+MMRGGHLD VLGAFQV V G+LANW Sbjct: 61 AQGEDVDPDLINAGKIPVLETPGCSYFHHADSFAMMRGGHLDCCVLGAFQVDVHGNLANW 120 Query: 120 HTGAEGSIPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDL 179 HTG +IPAVGGAMDLATGA+Q FVMM ++ G++KLV CT PLTG+ CVSRIYTD Sbjct: 121 HTGKPDAIPAVGGAMDLATGAKQTFVMMSLQSRGGQAKLVERCTMPLTGVGCVSRIYTDQ 180 Query: 180 AVLEVTPEGLKVVEICADIDFDELQKLSGVPL 211 AV V +G+ V E F+EL+++ VPL Sbjct: 181 AVFLVEEDGVSVRETFG-TSFEELRRIVDVPL 211 Lambda K H 0.318 0.137 0.399 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: 188 Number of extensions: 7 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: 213 Length of database: 215 Length adjustment: 22 Effective length of query: 191 Effective length of database: 193 Effective search space: 36863 Effective search space used: 36863 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