Align TreV, component of Trehalose porter (characterized)
to candidate GFF5028 PS417_25760 spermidine/putrescine ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__WCS417:GFF5028 Length = 370 Score = 224 bits (571), Expect = 3e-63 Identities = 126/316 (39%), Positives = 184/316 (58%), Gaps = 20/316 (6%) Query: 8 IVKKY-GKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADI 66 + K Y G+N+++ + +I GEF +LGPSG GK+T L +LAG E G+I G I Sbjct: 16 VQKSYDGENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQLAGRSI 75 Query: 67 TDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEIL 126 + PP KR++ MVFQNYAL+P+M+V +N+AFPL +R + K +I ERV++ ++ + Sbjct: 76 NNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLSVRALSKTDISERVKRVLSMVQLDAFA 135 Query: 127 DKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTF 186 + Q+SGGQQQRVALARA+V P L+DEPL LD ++R + E+K + + L T Sbjct: 136 QRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQRLGVTV 195 Query: 187 IYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLPGELM 246 +YVTHDQ EAL+++DR+A+ H+G+ +Q++ P+TLYE PK +VA F+GE N L G L Sbjct: 196 VYVTHDQGEALTMSDRVAVFHQGEIQQIAAPRTLYEEPKNTFVANFIGE--NNRLNGRLH 253 Query: 247 KEKAQEI------GFRPEWVEVGKG------NLSCMVESVEASGESRYLICNFKNNNITI 294 + G + E + V G LS E V +G S + F Sbjct: 254 SHSGERCVVELARGEKVEALAVNVGQVGGPVTLSVRPERVSLNGSSESCVNRFSGR---- 309 Query: 295 LSQEFYDVGQEVRFEI 310 EF +G VR + Sbjct: 310 -VAEFIYLGDHVRVRL 324 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: 304 Number of extensions: 14 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: 370 Length adjustment: 29 Effective length of query: 295 Effective length of database: 341 Effective search space: 100595 Effective search space used: 100595 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