Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate WP_057508467.1 ABB28_RS09895 3-oxoacid CoA-transferase subunit A
Query= CharProtDB::CH_021928 (231 letters) >NCBI__GCF_001431535.1:WP_057508467.1 Length = 230 Score = 325 bits (834), Expect = 3e-94 Identities = 163/224 (72%), Positives = 187/224 (83%) Query: 1 MINKTYESIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEI 60 MI+KT A+AV I DG+T+M+GGFGTAGMP LID LI GAR+LTII+NNAGNG+ Sbjct: 1 MIDKTVADAAAAVADIHDGATVMIGGFGTAGMPDALIDALIEQGARELTIINNNAGNGDS 60 Query: 61 GLAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAF 120 GLAAL+ VR++VCSFPRQSDS FD Y+AG+IELE+VPQGNLA RI AAGSG+GA Sbjct: 61 GLAALIRHKRVRRMVCSFPRQSDSQHFDTAYKAGEIELELVPQGNLAARIHAAGSGLGAI 120 Query: 121 FSPTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPI 180 F+PTG+GT LAEGKETREIDGR YVLE+PLHADFALIKA +GDRWGNL YRK ARNFGP+ Sbjct: 121 FTPTGFGTQLAEGKETREIDGRHYVLELPLHADFALIKADRGDRWGNLVYRKTARNFGPL 180 Query: 181 MAMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVVAVSGAAA 224 MAMAA+ AI QV +VV LGELDPE ++TPGIFVQRVVAV A A Sbjct: 181 MAMAARCAIVQVREVVALGELDPEAVVTPGIFVQRVVAVDSAQA 224 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: 194 Number of extensions: 4 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 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