Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate RR42_RS10010 RR42_RS10010 3-oxoadipate CoA-transferase
Query= BRENDA::P0A102 (213 letters) >FitnessBrowser__Cup4G11:RR42_RS10010 Length = 220 Score = 266 bits (679), Expect = 3e-76 Identities = 132/207 (63%), Positives = 160/207 (77%), Gaps = 1/207 (0%) Query: 6 KLSRTEMAQRVAADIQEGAYVNLGIGAPTLVANYLG-DKEVFLHSENGLLGMGPSPAPGE 64 +++R +A RVA DI GAYVNLGIG PTLVAN+L +EV LHSENG+LG + PG+ Sbjct: 3 QVARNLLAARVARDIPNGAYVNLGIGLPTLVANHLPRHREVILHSENGVLGQWSAAEPGQ 62 Query: 65 EDDDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAE 124 ED +LINAGK+ + L G AFFHHAD+F MMRGGHLDI VLGAFQVS +GDLANWHTGA Sbjct: 63 EDWELINAGKEAIRLERGAAFFHHADAFGMMRGGHLDICVLGAFQVSERGDLANWHTGAP 122 Query: 125 GSIPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEV 184 +IPAVGGAMDLA GA+QVFVMMDHLTK G SKL +C+YPLTG+ACVSR+YT+L + Sbjct: 123 DAIPAVGGAMDLAIGAKQVFVMMDHLTKDGTSKLRRQCSYPLTGMACVSRVYTELGTFAI 182 Query: 185 TPEGLKVVEICADIDFDELQKLSGVPL 211 P+G+ V+EI D+ LQ ++ V L Sbjct: 183 GPQGVSVIEIVGDMSSQALQSVTDVAL 209 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: 205 Number of extensions: 4 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: 220 Length adjustment: 22 Effective length of query: 191 Effective length of database: 198 Effective search space: 37818 Effective search space used: 37818 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: 45 (21.9 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