Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 195 bits (495), Expect = 2e-54 Identities = 132/364 (36%), Positives = 188/364 (51%), Gaps = 23/364 (6%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + + + Y G V+ + HI G LLGPSGCGK+T+LR IAG EDI+ G+ Sbjct: 1 MAHLELADVMQRY-GAHTVVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGS 59 Query: 61 LRIGGTVVN----DLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVR 116 + + G +V+ L +R + MVFQ+YAL+PH++V DNIAFGL K E +RV Sbjct: 60 IALDGELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGL---KTKGGERQQRVA 116 Query: 117 EVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGD 176 + L+ L E+ P +SGGQQQR A+ARA+ P + L DEP SNLD LR +L + Sbjct: 117 AMLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLE 176 Query: 177 IKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIG 236 ++ + ++ TT + VTHDQ EA +AD + +M +GRI Q +P LY P N F A F+G Sbjct: 177 VREILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVG 236 Query: 237 ----TPAMNFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAG 292 P VQ + G L + A G V + +RPD V + Sbjct: 237 QGVFVPGTVLAGNRVQMELGILESGVPVECSAGCGV----CGKGCGVDILLRPDDV-VHD 291 Query: 293 EREPAASLTCPVSVELVEILGADALLTTRC-GDQTLTALVPADRLPQPGATLTLALDQHE 351 ++ P + +VE GAD L T R + +LVP+ G + + LD Sbjct: 292 DKSPLQA-----AVEHKAFRGADILYTLRLESGARVLSLVPSHHNHALGEKIGIRLDVDH 346 Query: 352 LHVF 355 + F Sbjct: 347 VVAF 350 Lambda K H 0.321 0.137 0.403 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: 366 Number of extensions: 15 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: 406 Length of database: 356 Length adjustment: 30 Effective length of query: 376 Effective length of database: 326 Effective search space: 122576 Effective search space used: 122576 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: 50 (23.9 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