Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 197 bits (500), Expect = 5e-55 Identities = 138/387 (35%), Positives = 198/387 (51%), Gaps = 41/387 (10%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + L + + Y T V I+ +GPSGCGKTT LR IAG EDI G Sbjct: 1 MAHLELADVMQRYGAHT--VVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAG 58 Query: 61 NLYIGDRRVN----DVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRV 116 ++ + V+ + P+ R I MVFQ+YAL+PH+TV N+AFGLK + R Sbjct: 59 SIALDGELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKG------GERQ 112 Query: 117 QEAAKILDIAHLL---DRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQ 173 Q A +LD+ L ++ P LSGGQ+QRVAL RA+ P++ L+DEP SNLD LR + Sbjct: 113 QRVAAMLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRER 172 Query: 174 MRAEIRKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVA 233 + E+R++ ++ TT I VTHDQ EA M D I VM +G IQQ DTP +Y QP N FVA Sbjct: 173 LSLEVREILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVA 232 Query: 234 GFIGSPAMNFIRGEIVQDGDAFYFRAPSISLRLP-EGRYGVLKASGAIGKPVVLGVRPED 292 F+G F+ G ++ G+ + +P E G G ++L RP+D Sbjct: 233 DFVGQGV--FVPGTVLA-GNRVQMELGILESGVPVECSAGCGVCGKGCGVDILL--RPDD 287 Query: 293 -LHDEEVFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYH-VGSSVK 350 +HD++ S LQ VE G+++ + V + P H H +G + Sbjct: 288 VVHDDK--------SPLQAAVEHKAFRGADILYTLRLESGARVLSLVPSHHNHALGEKIG 339 Query: 351 LAIDLNKIHIFDAETEESIGFAAGPAG 377 + +D++ + + F PAG Sbjct: 340 IRLDVDHV----------VAFKQNPAG 356 Lambda K H 0.321 0.138 0.395 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: 339 Number of extensions: 18 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: 384 Length of database: 356 Length adjustment: 30 Effective length of query: 354 Effective length of database: 326 Effective search space: 115404 Effective search space used: 115404 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