Align TreV, component of Trehalose porter (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_002115805.1:WP_085638943.1 Length = 350 Score = 243 bits (619), Expect = 7e-69 Identities = 134/300 (44%), Positives = 187/300 (62%), Gaps = 21/300 (7%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 V L ++K+YG+ VI+G+ ++ GEF V +GPSG GKSTLL+++AG+E+ +G I Sbjct: 4 VTLESVIKRYGQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGTIRIG 63 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 G D+T P R V+MVFQ YALYP+M+V +N+ F LKM G ++I E+V +A+++L + Sbjct: 64 GRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASRILKL 123 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 + L +K +SGGQ+QRVA+ RAIVR P FL DEPLSNLDA +R R E+ R+ KE+ Sbjct: 124 DDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLHKEI 183 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242 T IYVTHDQ EA++LAD+I +L G+ EQV P LY P ++VA F+G MNF+ Sbjct: 184 GATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSMNFIR 243 Query: 243 GELM---------------KEKAQE-----IGFRPEWVEVGKGNLSCMVESVEASGESRY 282 G + AQE IG RPE +E+ G+ S V+ E+ G Y Sbjct: 244 GRVQGGEVVSDGLVHSVSKTASAQEGQEVLIGLRPEHLELRPGS-SHRVDLTESLGGVSY 302 Lambda K H 0.318 0.137 0.385 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: 287 Number of extensions: 12 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: 324 Length of database: 350 Length adjustment: 28 Effective length of query: 296 Effective length of database: 322 Effective search space: 95312 Effective search space used: 95312 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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