Align TreV, component of Trehalose porter (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 221 bits (564), Expect = 2e-62 Identities = 115/310 (37%), Positives = 186/310 (60%), Gaps = 17/310 (5%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 ++L+++ + +G ++ ++ ++E G V+LGPSG GKST L+++AG+E + G+I+ Sbjct: 4 IQLLNVSRHWGDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRIMIG 63 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 D+T PP +R +AMVFQ+YAL+P+++VR+NI F L +R + + E +R+ +A +LG+ Sbjct: 64 ERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVDILGL 123 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 S +L +K ++SGGQQQRVAL RA+V + L+DEPLSNLDA++R R E++ +Q+ L Sbjct: 124 SALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRALQQTL 183 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFL- 241 T +YVTHDQ EA+S+ADRI ++ G+ Q + P LY P T + F+G PMN + Sbjct: 184 GMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPMNLVR 243 Query: 242 ----------------PGELMKEKAQEIGFRPEWVEVGKGNLSCMVESVEASGESRYLIC 285 ++ +G RPE + + +VESVE G L C Sbjct: 244 LDDARGSVCVAGSRSGTVSVVDSADYVLGIRPEHIRIVPEGWRAVVESVEYLGSGSVLGC 303 Query: 286 NFKNNNITIL 295 ++++ Sbjct: 304 RVGGEELSVV 313 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: 224 Number of extensions: 3 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: 350 Length adjustment: 28 Effective length of query: 296 Effective length of database: 322 Effective search space: 95312 Effective search space used: 95312 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