Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate WP_066601425.1 V473_RS05790 3-oxoacid CoA-transferase subunit A
Query= CharProtDB::CH_021928 (231 letters) >NCBI__GCF_001046645.1:WP_066601425.1 Length = 228 Score = 313 bits (803), Expect = 1e-90 Identities = 157/228 (68%), Positives = 185/228 (81%) Query: 1 MINKTYESIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEI 60 MI+K S+ AV + DG++IM+ GFG AG P EL++ +IA GA DLTIISNNAG GE Sbjct: 1 MIDKISPSLRQAVADLHDGASIMISGFGDAGAPHELMEAVIAHGASDLTIISNNAGAGES 60 Query: 61 GLAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAF 120 G+AAL+ A VRKV+CSFPRQ+ S+ FD YRAG++ELE+VPQGNLA RI AAGSG+GA Sbjct: 61 GIAALIKANRVRKVICSFPRQAASHHFDARYRAGEVELELVPQGNLAARIQAAGSGLGAI 120 Query: 121 FSPTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPI 180 F+PTGYGTLLA+GKETREIDGR YVLE P+HADFALIKA GDRWGNL YRK ARNFGPI Sbjct: 121 FTPTGYGTLLAQGKETREIDGRNYVLEYPIHADFALIKARAGDRWGNLVYRKVARNFGPI 180 Query: 181 MAMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVVAVSGAAASSIA 228 MAMAAKT IAQV +VVELG LDPE ++TPGIFV RVV V+ + ++ A Sbjct: 181 MAMAAKTTIAQVAEVVELGALDPETVVTPGIFVNRVVQVAPLSVAAAA 228 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: 178 Number of extensions: 3 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: 228 Length adjustment: 23 Effective length of query: 208 Effective length of database: 205 Effective search space: 42640 Effective search space used: 42640 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 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