Align TreV, component of Trehalose porter (characterized)
to candidate WP_106710281.1 CU102_RS06970 ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_003010955.1:WP_106710281.1 Length = 333 Score = 260 bits (665), Expect = 3e-74 Identities = 145/337 (43%), Positives = 208/337 (61%), Gaps = 22/337 (6%) Query: 2 TVELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIA 61 ++++ +I K +G V+ GI +++ GEF + +GPSG GKSTLL+++AG+E G I+ Sbjct: 3 SLKIENIRKSFGHVDVLKGIDLEVKDGEFVIFVGPSGCGKSTLLRVIAGLEDATSGDILI 62 Query: 62 DGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLG 121 DG + + PP KR +AMVFQ YALYP++SVRDN+ LK G +EI ER A+ +L Sbjct: 63 DGKKVNNTPPAKRGIAMVFQTYALYPHLSVRDNMGLGLKQAGKPADEIKERTGIASSMLS 122 Query: 122 ISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKE 181 + E L+++ ++SGGQ+QRVA+ RAIVR P FL DEPLSNLDA +R R E+ R+ ++ Sbjct: 123 LDEYLERRPAELSGGQRQRVAIGRAIVREPQLFLFDEPLSNLDAALRVNTRLEIARLHRQ 182 Query: 182 LKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFL 241 LK T IYVTHDQ EA++LAD+I +L+KGK EQV P LY P+T +VA F+G MN + Sbjct: 183 LKATMIYVTHDQVEAMTLADKIVVLNKGKIEQVGSPMELYNAPQTIFVAGFIGSPQMNLI 242 Query: 242 -PGELMKEKAQEIGFRPEWVEVGK--GNLSCMVESVEASGESR--YLICNFKNNNITILS 296 +L + A+ IG RPE ++V K G V VE G YL +F + + Sbjct: 243 DAAKLGQSGAKTIGIRPEHIQVSKTSGEWKGSVIHVEHLGADTIIYLQTDFGPLTVRLFG 302 Query: 297 QEFYDV----------GQEVRFEIIKYRKYNDGRLVQ 323 + YDV G+ RF+ NDG++++ Sbjct: 303 EHNYDVDGVLYATPDAGRTYRFD-------NDGQVIK 332 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: 263 Number of extensions: 13 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: 333 Length adjustment: 28 Effective length of query: 296 Effective length of database: 305 Effective search space: 90280 Effective search space used: 90280 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 24 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