Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate RR42_RS22970 RR42_RS22970 3-oxoadipate CoA-transferase
Query= CharProtDB::CH_021928 (231 letters) >FitnessBrowser__Cup4G11:RR42_RS22970 Length = 230 Score = 249 bits (635), Expect = 4e-71 Identities = 120/220 (54%), Positives = 162/220 (73%) Query: 1 MINKTYESIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEI 60 M+NK S A A+ + DG+T+MVGGFG+AG+P LI ++A GARDLT+ISNNAG Sbjct: 1 MVNKRVASCAEAIADLRDGATVMVGGFGSAGLPDGLIAAVLAHGARDLTVISNNAGYDGE 60 Query: 61 GLAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAF 120 G+A+L+ AG +RK+VCS+P + + F + YR G++ELE+V QG L ERI AG+G+G F Sbjct: 61 GVASLIEAGRMRKLVCSYPLTAGATAFRDAYRRGEVELELVAQGTLVERIRCAGAGLGGF 120 Query: 121 FSPTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPI 180 + P GT+LA+GK+TREI+G ++VLE+PLHADFALI+ DR GNL Y A RNF PI Sbjct: 121 YCPITAGTILAQGKDTREINGVLHVLELPLHADFALIRGRHADRLGNLDYHLAGRNFNPI 180 Query: 181 MAMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVVAVS 220 MA AA+ +A+V+ +VE G ++PE I+TPGIFV RVV + Sbjct: 181 MATAARVVVAEVEAMVEAGAMNPEQIVTPGIFVHRVVTAN 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: 159 Number of extensions: 6 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: 231 Length of database: 230 Length adjustment: 23 Effective length of query: 208 Effective length of database: 207 Effective search space: 43056 Effective search space used: 43056 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