Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate 5210131 Shew_2575 3-oxoacid CoA-transferase, A subunit (RefSeq)
Query= CharProtDB::CH_021928 (231 letters) >FitnessBrowser__PV4:5210131 Length = 233 Score = 217 bits (552), Expect = 2e-61 Identities = 108/216 (50%), Positives = 148/216 (68%), Gaps = 2/216 (0%) Query: 2 INKTYESIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEIG 61 +NK S A+EG+TD T+MVGGFG G+P LI ++ +GA+ LT ISNNAG + G Sbjct: 4 LNKLVTSYEEALEGLTDNMTVMVGGFGLCGIPEGLIAQMVKSGAKGLTAISNNAGVDDFG 63 Query: 62 LAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAFF 121 L LL + + ++ S+ ++ F++ +G++ + + PQG LAE+I A G+GI AFF Sbjct: 64 LGLLLKSRQISTMIASYV--GENATFEQQMLSGELNVILTPQGTLAEKIRAGGAGIPAFF 121 Query: 122 SPTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPIM 181 + TGYGT +AEGKETREIDGR YVLE L ADFAL++A K D GNL +RK A NF P+M Sbjct: 122 TATGYGTPVAEGKETREIDGRHYVLEPALTADFALVRAWKADTMGNLVFRKTAANFNPMM 181 Query: 182 AMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVV 217 A A K + + + +VE GELDP+HI TPGI+V R++ Sbjct: 182 ATAGKITVVEAEHIVEPGELDPDHIHTPGIYVDRLI 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: 154 Number of extensions: 6 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: 233 Length adjustment: 23 Effective length of query: 208 Effective length of database: 210 Effective search space: 43680 Effective search space used: 43680 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 Sep 17 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