Align TreV, component of Trehalose porter (characterized)
to candidate 3607949 Dshi_1357 ABC transporter related (RefSeq)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Dino:3607949 Length = 349 Score = 243 bits (621), Expect = 4e-69 Identities = 136/301 (45%), Positives = 185/301 (61%), Gaps = 19/301 (6%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 + L + K +G VI G+ +I GEF V +GPSG GKSTLL+++ G+E +G ++ D Sbjct: 4 ITLSKVEKWFGDVQVIKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRGAMLID 63 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 G D+TD PP KR + MVFQ+YALYP+MSVR+N+ F LK G EI E+VE AA +L + Sbjct: 64 GVDVTDHPPAKRGLTMVFQSYALYPHMSVRENMGFSLKTAGAPAAEIAEKVEAAAAVLKL 123 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 LD++ +SGGQ+QRVA+ R+IVR P+ FL DEPLSNLDA +R R E+ ++ + L Sbjct: 124 EPYLDRRPKDLSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAKLHQSL 183 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242 T IYVTHDQ EA++LADRI +L GK QV P+ LYE P +VAQF+G MN +P Sbjct: 184 DTTMIYVTHDQVEAMTLADRIVVLEFGKIAQVGTPRELYETPANLFVAQFIGSPKMNVMP 243 Query: 243 ---------------GELMKEK-AQEIGFRPEWVEVG-KGNLSC--MVESVEASGESRYL 283 G ++ A ++G RPE + G G +C V+ VE G L Sbjct: 244 CTTDAGRYRLSAGRGGVFSGDRPAVQLGIRPEHITPGAPGTGACDGRVDVVEYLGADTLL 303 Query: 284 I 284 + Sbjct: 304 V 304 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: 260 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: 349 Length adjustment: 28 Effective length of query: 296 Effective length of database: 321 Effective search space: 95016 Effective search space used: 95016 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