Align TreV, component of Trehalose porter (characterized)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 238 bits (606), Expect = 2e-67 Identities = 120/241 (49%), Positives = 172/241 (71%), Gaps = 1/241 (0%) Query: 3 VELIDIVKKYGKNI-VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIA 61 + L ++ K Y N+ V++GI +I GEF VI+GPSG GKSTLL+++AG+E + G++ Sbjct: 4 LSLRNVQKTYAGNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGGEVHI 63 Query: 62 DGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLG 121 + P +R++AMVFQNYALYP+MSV DN+A+ LK+RGM K EI +RV+ AA +L Sbjct: 64 GDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAAGILE 123 Query: 122 ISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKE 181 ++ +L++K +SGGQ+QRVA+ RAIVR P+ FL DEPLSNLDA++R R ELK + + Sbjct: 124 LAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKELHRR 183 Query: 182 LKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFL 241 L+ T +YVTHDQ EA++LADR+ +L+ G EQ+ P +Y P + +VA F+G PMN + Sbjct: 184 LRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPPMNLV 243 Query: 242 P 242 P Sbjct: 244 P 244 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: 279 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: 324 Length of database: 367 Length adjustment: 29 Effective length of query: 295 Effective length of database: 338 Effective search space: 99710 Effective search space used: 99710 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 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