Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate WP_036261633.1 DL86_RS11555 3-oxoacid CoA-transferase subunit A
Query= CharProtDB::CH_021928 (231 letters) >NCBI__GCF_000746085.1:WP_036261633.1 Length = 217 Score = 177 bits (449), Expect = 1e-49 Identities = 92/210 (43%), Positives = 134/210 (63%), Gaps = 2/210 (0%) Query: 8 SIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEIGLAALLM 67 S A A I DG+++M GGF G P+ +ID L+A GAR LTII N+ +G+ L+ Sbjct: 6 SAADAAALIPDGASVMFGGFMGVGSPNRIIDALVARGARGLTIIGNDTAFPGVGVGKLID 65 Query: 68 AGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAFFSPTGYG 127 AG V + S + V + AG+I ++++PQG LAERI A G+G+G +PTG G Sbjct: 66 AGCVAEARVS--HIGTNPVTQKKMIAGEISVDLIPQGTLAERIRAGGNGLGGILTPTGVG 123 Query: 128 TLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPIMAMAAKT 187 T++ +GK E+DGR ++LE+P+ ADFAL++AH+ D NLTYR A NF P+MA AA Sbjct: 124 TVVEKGKRVIEVDGRDFLLELPIRADFALLRAHESDYNCNLTYRLTATNFNPLMAFAAVC 183 Query: 188 AIAQVDQVVELGELDPEHIITPGIFVQRVV 217 IA+ D++V +G + P+ + TPGI V ++ Sbjct: 184 VIAEPDEIVPVGVIPPDAVRTPGILVHHLI 213 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: 138 Number of extensions: 5 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: 231 Length of database: 217 Length adjustment: 22 Effective length of query: 209 Effective length of database: 195 Effective search space: 40755 Effective search space used: 40755 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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