Align TreV, component of Trehalose porter (characterized)
to candidate BWI76_RS17830 BWI76_RS17830 ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Koxy:BWI76_RS17830 Length = 364 Score = 234 bits (598), Expect = 2e-66 Identities = 116/245 (47%), Positives = 170/245 (69%) Query: 2 TVELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIA 61 +V L + K YG VI ++ I GEF V++GPSG GKSTLL+++AG+E++ G++ Sbjct: 3 SVVLNSVRKSYGDAHVIKDVSLTIPDGEFCVLVGPSGCGKSTLLRMIAGLEEISGGEVHI 62 Query: 62 DGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLG 121 + ++T+ P+ R++AMVFQ+YALYP M+VR+N+ F LKM + K EI ++V +AA LLG Sbjct: 63 NERNVTEVEPKLRDIAMVFQSYALYPQMTVRENMGFALKMAKLPKAEINQKVNEAAALLG 122 Query: 122 ISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKE 181 + +L++ +SGGQ+QRVA+ RAIVR P FL DEPLSNLDA++RT RGE++ + + Sbjct: 123 LEPLLERLPKDLSGGQRQRVAMGRAIVRKPQVFLFDEPLSNLDAKLRTQVRGEIRELHRR 182 Query: 182 LKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFL 241 LK T +YVTHDQ EA+++ I +L G+ EQ P LY+ P +VA F+G +N L Sbjct: 183 LKTTSVYVTHDQIEAMTMGQMIVVLRDGRIEQAGTPLELYDRPANLFVAGFIGSPEINQL 242 Query: 242 PGELM 246 PGE++ Sbjct: 243 PGEVV 247 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: 294 Number of extensions: 11 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: 364 Length adjustment: 29 Effective length of query: 295 Effective length of database: 335 Effective search space: 98825 Effective search space used: 98825 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