Align TreV, component of Trehalose porter (characterized)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Phaeo:GFF1645 Length = 355 Score = 244 bits (624), Expect = 2e-69 Identities = 137/298 (45%), Positives = 186/298 (62%), Gaps = 22/298 (7%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 +EL D+ K+YG V+ I I+ GEF V++GPSG GKSTLL+++AG+E + G D Sbjct: 4 IELRDVAKRYGAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDFEID 63 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 G + D P R++AMVFQ+YALYP+M V N+ F +++R EE RV +AA+ LG+ Sbjct: 64 GQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAETLGL 123 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 S ++D+ +SGGQ+QRVA+ RAI+R+P FL DEPLSNLDA +R R E+ R+ K+L Sbjct: 124 SSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLHKQL 183 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242 T IYVTHDQ EAL+LADRI +L+ G +QV P LYE P K+VAQF+G MN LP Sbjct: 184 GATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMNILP 243 Query: 243 ------------GELM-------KEKAQEIGFRPEW---VEVGKGNLSCMVESVEASG 278 G ++ A E+G RPE VE G+G+L + + VE G Sbjct: 244 VSGAASGVMATNGMMLTLDHMHDTAAAVELGIRPEHLDVVEPGEGHLIAVADVVERLG 301 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: 269 Number of extensions: 10 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: 355 Length adjustment: 28 Effective length of query: 296 Effective length of database: 327 Effective search space: 96792 Effective search space used: 96792 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