Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A (characterized)
to candidate 6936329 Sama_0518 3-oxoacid CoA-transferase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2111 (232 letters) >FitnessBrowser__SB2B:6936329 Length = 253 Score = 357 bits (915), Expect = e-103 Identities = 174/231 (75%), Positives = 204/231 (88%) Query: 1 MAGFDKRVSSYEEALEGLKDGMTVIAGGFGLCGIPENLIAEIKRKGIRDLTVVSNNCGVD 60 +AG +K V+SY +AL GL+DGMTVIAGGFGLCGIPENLI EIKRKG R+LTVVSNNCG Sbjct: 17 VAGLNKVVTSYAQALAGLEDGMTVIAGGFGLCGIPENLIKEIKRKGTRNLTVVSNNCGTT 76 Query: 61 GFGLGVLLEDRQIRKVVASYVGENALFEQQLLSGEIEVVLTPQGTLAEKMRAGGAGIPAF 120 +GLG+LL D+QI+K+VASYVGEN FE Q++SGE+EV LTPQGTLAEKMRA GAGIPAF Sbjct: 77 EYGLGILLLDKQIKKMVASYVGENTNFEAQMMSGELEVELTPQGTLAEKMRAAGAGIPAF 136 Query: 121 FTATGVGTPVAEGKEVREFHGRQYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPL 180 +TATG GT VA GKEV+EF+GRQY++EESI GDFA+VK WKAD +GN+++R TA+NFNPL Sbjct: 137 YTATGFGTEVAVGKEVKEFNGRQYILEESIKGDFALVKAWKADTYGNLVFRKTARNFNPL 196 Query: 181 AATAGKITVVEVEEIVEPGELDPTQIHTPGIYVDRVICGTFEKRIEQRTVR 231 AA AGKITVVEVE+IV PGELDP +IHTPGIYVDR+I G+FEKRIEQ T+R Sbjct: 197 AAMAGKITVVEVEQIVAPGELDPDEIHTPGIYVDRLIQGSFEKRIEQLTIR 247 Lambda K H 0.319 0.139 0.403 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: 263 Number of extensions: 8 Number of successful extensions: 1 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: 232 Length of database: 253 Length adjustment: 23 Effective length of query: 209 Effective length of database: 230 Effective search space: 48070 Effective search space used: 48070 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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