Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate N515DRAFT_1736 N515DRAFT_1736 3-oxoacid CoA-transferase
Query= BRENDA::P0A102 (213 letters) >FitnessBrowser__Dyella79:N515DRAFT_1736 Length = 451 Score = 187 bits (476), Expect = 2e-52 Identities = 98/202 (48%), Positives = 134/202 (66%), Gaps = 3/202 (1%) Query: 9 RTEMAQRVAADIQEGAYVNLGIGAPTLVANYL-GDKEVFLHSENGLLGMGPSPAPGEEDD 67 RT MAQR A ++++G YVNLGIG PTLVAN++ +V L SENGLLG+GP P D Sbjct: 241 RTAMAQRAAKELRDGFYVNLGIGIPTLVANFIPAGIDVTLQSENGLLGIGPFPDDAHVDP 300 Query: 68 DLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAEGSI 127 DLINAGKQ +T L G +FF A+SF+M+RGGH+D+++LG +VS GDLANW + + Sbjct: 301 DLINAGKQTITTLPGSSFFSSAESFAMIRGGHIDLSILGGLEVSCTGDLANWMVPGK-MV 359 Query: 128 PAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEVTP- 186 GGAMDL +G ++V V+M+H K G K+ +C PLTG V I TDL V EV Sbjct: 360 KGPGGAMDLVSGVKRVVVLMEHTAKDGSPKIKNQCDLPLTGQQVVDLIITDLCVFEVEKG 419 Query: 187 EGLKVVEICADIDFDELQKLSG 208 +GL ++E+ + +E++ +G Sbjct: 420 KGLTLIELQEGVTVEEVKAKTG 441 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: 301 Number of extensions: 12 Number of successful extensions: 3 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: 451 Length adjustment: 27 Effective length of query: 186 Effective length of database: 424 Effective search space: 78864 Effective search space used: 78864 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: 48 (23.1 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