Align TreV, component of Trehalose porter (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 196 bits (499), Expect = 5e-55 Identities = 108/249 (43%), Positives = 160/249 (64%), Gaps = 11/249 (4%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 +EL D++++YG + V++GI IE G +LGPSG GK+TLL+ +AG E + G I D Sbjct: 4 LELADVMQRYGAHTVVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSIALD 63 Query: 63 GADITDKP-----PEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAA 117 G ++ +P PE+R + MVFQ+YAL+P+++V DNIAF LK +G ++++ RV Sbjct: 64 G-ELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKGGERQQ---RVAAML 119 Query: 118 KLLGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKR 177 L+G++ +K ++SGGQQQRVALARA+ P LLDEP SNLD +R E++ Sbjct: 120 DLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLEVRE 179 Query: 178 IQKELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFP 237 I K+ T I VTHDQ EA ++AD I ++H+G+ +Q P LY P ++VA FVG+ Sbjct: 180 ILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVGQGV 239 Query: 238 MNFLPGELM 246 F+PG ++ Sbjct: 240 --FVPGTVL 246 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: 282 Number of extensions: 13 Number of successful extensions: 3 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: 356 Length adjustment: 28 Effective length of query: 296 Effective length of database: 328 Effective search space: 97088 Effective search space used: 97088 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