Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate CA265_RS06310 CA265_RS06310 succinyl-CoA--3-ketoacid-CoA transferase
Query= BRENDA::P0A102 (213 letters) >FitnessBrowser__Pedo557:CA265_RS06310 Length = 219 Score = 204 bits (520), Expect = 8e-58 Identities = 105/207 (50%), Positives = 141/207 (68%), Gaps = 3/207 (1%) Query: 8 SRTEMAQRVAADIQEGAYVNLGIGAPTLVANYLGDK-EVFLHSENGLLGMGPSPAPGEED 66 S+ E+AQR+A +I++G YVNLGIG PTLVANY+ V L SENGLLGMGP P GEED Sbjct: 3 SKEEIAQRIAKEIKDGYYVNLGIGIPTLVANYIPKGINVVLQSENGLLGMGPFPFEGEED 62 Query: 67 DDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAEGS 126 DLINAGKQ +T L G + F A SF M+R +D+ +LGA +VS GD+ANW + Sbjct: 63 ADLINAGKQTITTLPGSSIFDSAMSFGMIRAQKVDLTILGAMEVSENGDIANWKIPGK-M 121 Query: 127 IPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEVTP 186 + +GGAMDL A+ + V M H+ K GESKL+P+CT PLTG+ C+ +I T+LAVL++ P Sbjct: 122 VKGMGGAMDLVASAKNIIVAMQHINKAGESKLLPKCTLPLTGVKCIKKIVTELAVLDILP 181 Query: 187 E-GLKVVEICADIDFDELQKLSGVPLI 212 E G K++E + + +Q+ + LI Sbjct: 182 EGGFKLLERAPGVSIEFIQQSTAGRLI 208 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: 182 Number of extensions: 9 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: 219 Length adjustment: 22 Effective length of query: 191 Effective length of database: 197 Effective search space: 37627 Effective search space used: 37627 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