Align TreV, component of Trehalose porter (characterized)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Dino:3607124 Length = 338 Score = 246 bits (629), Expect = 4e-70 Identities = 131/295 (44%), Positives = 190/295 (64%), Gaps = 9/295 (3%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 +++ I K YG + I IE GEF V +GPSG GKSTLL+ LAG+E + G+I Sbjct: 4 IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 G D+T P R++AMVFQ+YALYP+M+VR+N+ F +K+ G + + ER+ +AA++L + Sbjct: 64 GRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQL 123 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 + LD+K Q+SGGQ+QRVA+ RAIV+NPS FL DEPLSNLDA++R R EL+ + K+L Sbjct: 124 EDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQL 183 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242 T IYVTHDQ EA+++AD+I +L++G+ EQV P LY P +++VA+F+G MN Sbjct: 184 GATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFS 243 Query: 243 GEL------MKEKAQEIGFRPEWVEV---GKGNLSCMVESVEASGESRYLICNFK 288 ++ + A +G RPE +E+ G G+++ V E G L K Sbjct: 244 SDVGLQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLGLK 298 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: 266 Number of extensions: 9 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: 338 Length adjustment: 28 Effective length of query: 296 Effective length of database: 310 Effective search space: 91760 Effective search space used: 91760 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