Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A (characterized)
to candidate RR42_RS22970 RR42_RS22970 3-oxoadipate CoA-transferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2111 (232 letters) >FitnessBrowser__Cup4G11:RR42_RS22970 Length = 230 Score = 192 bits (488), Expect = 5e-54 Identities = 99/216 (45%), Positives = 140/216 (64%), Gaps = 4/216 (1%) Query: 5 DKRVSSYEEALEGLKDGMTVIAGGFGLCGIPENLIAEIKRKGIRDLTVVSNNCGVDGFGL 64 +KRV+S EA+ L+DG TV+ GGFG G+P+ LIA + G RDLTV+SNN G DG G+ Sbjct: 3 NKRVASCAEAIADLRDGATVMVGGFGSAGLPDGLIAAVLAHGARDLTVISNNAGYDGEGV 62 Query: 65 GVLLEDRQIRKVVASY---VGENALFEQQLLSGEIEVVLTPQGTLAEKMRAGGAGIPAFF 121 L+E ++RK+V SY G A F GE+E+ L QGTL E++R GAG+ F+ Sbjct: 63 ASLIEAGRMRKLVCSYPLTAGATA-FRDAYRRGEVELELVAQGTLVERIRCAGAGLGGFY 121 Query: 122 TATGVGTPVAEGKEVREFHGRQYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPLA 181 GT +A+GK+ RE +G +++E + DFA+++G AD GN+ Y +NFNP+ Sbjct: 122 CPITAGTILAQGKDTREINGVLHVLELPLHADFALIRGRHADRLGNLDYHLAGRNFNPIM 181 Query: 182 ATAGKITVVEVEEIVEPGELDPTQIHTPGIYVDRVI 217 ATA ++ V EVE +VE G ++P QI TPGI+V RV+ Sbjct: 182 ATAARVVVAEVEAMVEAGAMNPEQIVTPGIFVHRVV 217 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: 159 Number of extensions: 7 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: 232 Length of database: 230 Length adjustment: 23 Effective length of query: 209 Effective length of database: 207 Effective search space: 43263 Effective search space used: 43263 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