Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate GFF1045 Psest_1078 3-oxoacid CoA-transferase, A subunit
Query= CharProtDB::CH_021928 (231 letters) >FitnessBrowser__psRCH2:GFF1045 Length = 231 Score = 215 bits (548), Expect = 5e-61 Identities = 111/217 (51%), Positives = 148/217 (68%), Gaps = 3/217 (1%) Query: 2 INKTYESIASAVEGIT-DGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEI 60 +NK Y S A A+EG+ DG TI VGGFG G+P +LI L +G +DLT ISNNAG Sbjct: 1 MNKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGF 60 Query: 61 GLAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAF 120 GL LL + K+V S+ ++ F+ Y AG++ LE PQG LAE++ A G+GI AF Sbjct: 61 GLGLLLETRQISKMVSSYVGENKE--FERQYLAGELALEFTPQGTLAEKLRAGGAGIPAF 118 Query: 121 FSPTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPI 180 ++ TGYGTL+AEGKETR+ +G YV+E L AD AL+KA K D+ GNL +RK ARNF P+ Sbjct: 119 YTKTGYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPL 178 Query: 181 MAMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVV 217 AMA + + +V+++VE GELDP+ I PGI+V R+V Sbjct: 179 AAMAGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIV 215 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: 145 Number of extensions: 7 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: 231 Length of database: 231 Length adjustment: 23 Effective length of query: 208 Effective length of database: 208 Effective search space: 43264 Effective search space used: 43264 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 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