Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 202 bits (515), Expect = 8e-57 Identities = 128/351 (36%), Positives = 192/351 (54%), Gaps = 28/351 (7%) Query: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 MA+L+L + + +G H + GI I+ G +GPSGCGK+TLLR IAG E I GS+ Sbjct: 1 MAHLELADVMQRYGAHTVVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSI 60 Query: 61 MLDGRDITDQPSSK-----RDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQ 115 LDG ++ +P K R + MVFQ YAL+PH++V +N++F LK ++Q ++V Sbjct: 61 ALDG-ELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKGGERQ---QRVA 116 Query: 116 NAARILNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVE 175 ++ L ++ P ELSGGQ+QRVA+ RA+ AP++ L DEP SNLD LR + +E Sbjct: 117 AMLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLE 176 Query: 176 IAKLHRDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIG 235 + ++ + G T I VTHDQ EA +AD + V+ +G I+Q TP LY +PAN+FVA F+G Sbjct: 177 VREILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVG 236 Query: 236 TPQMNVVPVDKLP--------------QPVQQQAPAAPAGAAVGA-IGLRPENITVRTTG 280 Q VP L PV+ A G G I LRP+++ Sbjct: 237 --QGVFVPGTVLAGNRVQMELGILESGVPVECSAGCGVCGKGCGVDILLRPDDVV--HDD 292 Query: 281 ATPVGGQVDLIEALGAETLIYVTTPGGAQFVSRQNDRTDLRVGDAVSLDID 331 +P+ V+ GA+ L + GA+ +S + +G+ + + +D Sbjct: 293 KSPLQAAVEHKAFRGADILYTLRLESGARVLSLVPSHHNHALGEKIGIRLD 343 Lambda K H 0.320 0.137 0.388 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: 288 Number of extensions: 16 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: 350 Length of database: 356 Length adjustment: 29 Effective length of query: 321 Effective length of database: 327 Effective search space: 104967 Effective search space used: 104967 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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