Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 205 bits (521), Expect = 2e-57 Identities = 132/362 (36%), Positives = 187/362 (51%), Gaps = 15/362 (4%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M L L D+ + YGA V+ GI I+ G +GPSGCGK+TLLR IAG E+I G + Sbjct: 1 MAHLELADVMQRYGAHTVVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAGSI 60 Query: 61 FIDGERVN----DVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRG 116 +DGE V+ + P +R I MVFQ YAL+PH+TV DN+AFG++ +++ RV Sbjct: 61 ALDGELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKGGERQQ---RVAA 117 Query: 117 AADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEI 176 D++ L ++ P LSGGQ+QRVA+ RA+ P++ L DEP SNLD LR +E+ Sbjct: 118 MLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSLEV 177 Query: 177 AKLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIG 236 ++ ++ + TT I VTHDQ EA +AD I V+ G I+Q P LY +PAN FVA F+G Sbjct: 178 REILKK-AGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFVG 236 Query: 237 SPAMNVIPATITATG--QQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEAD 294 +P T+ A Q L G V G +RP+D V D Sbjct: 237 QGVF--VPGTVLAGNRVQMELGILESGVPVECSAGCGVCGKGCGVDILLRPDD--VVHDD 292 Query: 295 DFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFD 354 + V +A +LY L +++ +P G+K+ D + F Sbjct: 293 KSPLQAAVE-HKAFRGADILYTLRLESGARVLSLVPSHHNHALGEKIGIRLDVDHVVAFK 351 Query: 355 TN 356 N Sbjct: 352 QN 353 Lambda K H 0.320 0.137 0.387 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: 327 Number of extensions: 20 Number of successful extensions: 4 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: 362 Length of database: 356 Length adjustment: 29 Effective length of query: 333 Effective length of database: 327 Effective search space: 108891 Effective search space used: 108891 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