Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__psRCH2:GFF857 Length = 371 Score = 332 bits (851), Expect = 1e-95 Identities = 186/363 (51%), Positives = 239/363 (65%), Gaps = 15/363 (4%) Query: 1 MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60 MA + L + K+Y + +I+LDI+ GE +VFVGPSGCGKSTLLR+IAGLE IT G L Sbjct: 1 MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60 Query: 61 EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120 ID VND+PP R + MVFQSYALYPHMTV ENM+F LK+A + EI VEA AE Sbjct: 61 LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120 Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180 LQL + L+R PK LSGGQRQRVAIGR++VR+PKV+LFDEPLSNLDA LRV R+EIA+L Sbjct: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180 Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240 + + STM+YVTHDQVEAMTLA +IVVL G IAQVG PL LY P+N FVA F+GSP+M Sbjct: 181 QRI-RSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQM 239 Query: 241 NLLPGKIIGTGAQT-TVEMTDGGRAVSDYPSDDSLMGAAVN------VGVRPEDMVEAAP 293 N + + I +T T+E+ G YP + G+AV+ +G+RPE V Sbjct: 240 NFVEVRAISASPETVTIELPSG------YPLTLPVDGSAVSPGDPLTLGIRPEHFV-MPD 292 Query: 294 GGDYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHV 353 D+ F G++ + E LG+ LLY +D + G + +G+ + K H+ Sbjct: 293 EADFTFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHL 352 Query: 354 FKD 356 F++ Sbjct: 353 FRE 355 Lambda K H 0.316 0.135 0.379 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: 425 Number of extensions: 25 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: 373 Length of database: 371 Length adjustment: 30 Effective length of query: 343 Effective length of database: 341 Effective search space: 116963 Effective search space used: 116963 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 (21.6 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