Align Tricarboxylic transport TctC (characterized, see rationale)
to candidate GFF2717 HP15_2661 tricarboxylic transport TctC
Query= uniprot:E4PJR1 (328 letters) >FitnessBrowser__Marino:GFF2717 Length = 328 Score = 654 bits (1687), Expect = 0.0 Identities = 328/328 (100%), Positives = 328/328 (100%) Query: 1 MTTMIIKRTLSFVAAAAVSMSAMAWQPSGKVECLAPADPGGGWDFTCRSVGNVLQDLGLV 60 MTTMIIKRTLSFVAAAAVSMSAMAWQPSGKVECLAPADPGGGWDFTCRSVGNVLQDLGLV Sbjct: 1 MTTMIIKRTLSFVAAAAVSMSAMAWQPSGKVECLAPADPGGGWDFTCRSVGNVLQDLGLV 60 Query: 61 DGSVQTVNMAGAGGGVAYAHTVSKRAEDNKLLVAASTATTTRLAQKQFPGMNADMVTWVG 120 DGSVQTVNMAGAGGGVAYAHTVSKRAEDNKLLVAASTATTTRLAQKQFPGMNADMVTWVG Sbjct: 61 DGSVQTVNMAGAGGGVAYAHTVSKRAEDNKLLVAASTATTTRLAQKQFPGMNADMVTWVG 120 Query: 121 ALGADYGIIAVGKNSEYQNLSELMAAVKANPKSVKFAGGSARGGWDHLKVLIAAKAAGAD 180 ALGADYGIIAVGKNSEYQNLSELMAAVKANPKSVKFAGGSARGGWDHLKVLIAAKAAGAD Sbjct: 121 ALGADYGIIAVGKNSEYQNLSELMAAVKANPKSVKFAGGSARGGWDHLKVLIAAKAAGAD 180 Query: 181 KLPSIPYLSYNNGGEAMSQVVGGQVDAFTGDISEATGFLESGDLRVVAVLAEERLPGKFS 240 KLPSIPYLSYNNGGEAMSQVVGGQVDAFTGDISEATGFLESGDLRVVAVLAEERLPGKFS Sbjct: 181 KLPSIPYLSYNNGGEAMSQVVGGQVDAFTGDISEATGFLESGDLRVVAVLAEERLPGKFS 240 Query: 241 DLPTAKEQGIDAVGPNWRGFYMPKGASEEAKSYWVEAVDTLYASEEWKKVMKSNGLIPFH 300 DLPTAKEQGIDAVGPNWRGFYMPKGASEEAKSYWVEAVDTLYASEEWKKVMKSNGLIPFH Sbjct: 241 DLPTAKEQGIDAVGPNWRGFYMPKGASEEAKSYWVEAVDTLYASEEWKKVMKSNGLIPFH 300 Query: 301 PPASQFDEFVRNQVQDIENLSREIGLLK 328 PPASQFDEFVRNQVQDIENLSREIGLLK Sbjct: 301 PPASQFDEFVRNQVQDIENLSREIGLLK 328 Lambda K H 0.315 0.131 0.384 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: 511 Number of extensions: 5 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: 328 Length of database: 328 Length adjustment: 28 Effective length of query: 300 Effective length of database: 300 Effective search space: 90000 Effective search space used: 90000 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: 42 (22.0 bits) S2: 49 (23.5 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