Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate WP_085123231.1 B9O00_RS13580 CoA transferase subunit B
Query= BRENDA::P0A102 (213 letters) >NCBI__GCF_900177295.1:WP_085123231.1 Length = 235 Score = 241 bits (614), Expect = 1e-68 Identities = 115/206 (55%), Positives = 147/206 (71%), Gaps = 1/206 (0%) Query: 7 LSRTEMAQRVAADIQEGAYVNLGIGAPTLVANYL-GDKEVFLHSENGLLGMGPSPAPGEE 65 LSR +MA R A DI +GAYVNLGIG P LVA+Y+ +EV H+ENG+LG GP+P PG+E Sbjct: 9 LSRAQMAWRAAQDIPDGAYVNLGIGIPELVADYVPAGREVVYHTENGILGFGPAPEPGQE 68 Query: 66 DDDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAEG 125 D DLINAGK+ VTLL G AFFHHADSF+M+RGGH+D +LGA QV+ GD+ANW TGA G Sbjct: 69 DPDLINAGKKPVTLLPGAAFFHHADSFAMIRGGHIDYCILGAMQVAANGDIANWSTGAAG 128 Query: 126 SIPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEVT 185 +IPAVGGAMDL G R V V+ +H T+ GE KL+ C+YPLT V R++T V +VT Sbjct: 129 AIPAVGGAMDLVAGVRNVLVITEHTTREGEPKLMERCSYPLTAPGVVKRVFTTFGVFDVT 188 Query: 186 PEGLKVVEICADIDFDELQKLSGVPL 211 G + EI + ++++ + PL Sbjct: 189 ASGFLLQEIAPGVPVEQVRAATAAPL 214 Lambda K H 0.318 0.137 0.399 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: 186 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: 213 Length of database: 235 Length adjustment: 22 Effective length of query: 191 Effective length of database: 213 Effective search space: 40683 Effective search space used: 40683 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