Align TreV, component of Trehalose porter (characterized)
to candidate SM_b20235 SM_b20235 sugar ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Smeli:SM_b20235 Length = 363 Score = 253 bits (645), Expect = 7e-72 Identities = 127/315 (40%), Positives = 202/315 (64%), Gaps = 18/315 (5%) Query: 2 TVELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIA 61 +VE+ ++VK++G V++G++ +I GEF ++GPSG GKSTLL+++AG+E++ G ++ Sbjct: 3 SVEIRNVVKRFGALEVVHGVSAEIADGEFVALVGPSGCGKSTLLRMIAGLEEISDGAVVI 62 Query: 62 DGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLG 121 G + + P+ RN++MVFQNYALYP+M+V +N+AF L++ + K+E +V +AA +LG Sbjct: 63 GGDIVNEVAPKDRNISMVFQNYALYPHMTVAENMAFALRLARLPKDEQKRKVGEAATMLG 122 Query: 122 ISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKE 181 + +LD+ Q+SGGQ+QRVA+ RAIVR P FL DEPLSNLDA++R R E+K + + Sbjct: 123 LGGLLDRYPGQLSGGQRQRVAMGRAIVRRPEVFLFDEPLSNLDAKLRVQMRAEIKGLHQR 182 Query: 182 LKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFL 241 L+ T IYVTHDQ EA+++ADRI ++ G EQ+ P +++YP+ +VA F+G MNF+ Sbjct: 183 LRTTSIYVTHDQIEAMTMADRIVVMRDGNVEQIGTPLEIFDYPRNLFVASFIGSPSMNFI 242 Query: 242 PGEL-----------------MKEKAQEI-GFRPEWVEVGKGNLSCMVESVEASGESRYL 283 GE+ + K + G RP +++G S V VE +G+ +L Sbjct: 243 EGEVVGGTFRAPGGIIIPAPDLAHKGPTVAGIRPNKLQIGATGPSAKVLIVEPTGDETHL 302 Query: 284 ICNFKNNNITILSQE 298 + + +L +E Sbjct: 303 LVELGGAQLAMLLRE 317 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: 305 Number of extensions: 11 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: 324 Length of database: 363 Length adjustment: 29 Effective length of query: 295 Effective length of database: 334 Effective search space: 98530 Effective search space used: 98530 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