Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 272 bits (696), Expect = 1e-77 Identities = 155/324 (47%), Positives = 207/324 (63%), Gaps = 9/324 (2%) Query: 1 MADLKLTGVEKAYGDVKV--LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGG 58 MA L+L V+K+YG+ ++ L +I L I GE ++ VGPSGCGKSTL+ IAGLE ITGG Sbjct: 1 MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60 Query: 59 TLEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAA 118 + +DG ++ P R IAMVFQSYALYP M+VR+N++F LK+ K A+I+ V A Sbjct: 61 EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120 Query: 119 EKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQ 178 + LQ+ L+R P LSGGQ+QRVA+GR++ R PK+YLFDEPLSNLDA LRV R EI Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180 Query: 179 LKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSP 238 + + + ++T VYVTHDQ+EAMTL ++ V+ G I Q G+P E+Y P N FVA FIGSP Sbjct: 181 MHQRL-KTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSP 239 Query: 239 KMNLLPGKI-IGTGAQTTVEMTDGGRAVSDYP--SDDSLMGAAVNVGVRPEDMVEAAPGG 295 MN +P +I G V ++ G P SDD L + +G+RPE + AP G Sbjct: 240 PMNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPE-QIGLAPAG 298 Query: 296 --DYVFEGKVAITEALGEVTLLYF 317 D+ + + E G TL+ F Sbjct: 299 SADFSLAVDIEVVEPTGPDTLVVF 322 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: 381 Number of extensions: 17 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: 373 Length of database: 390 Length adjustment: 30 Effective length of query: 343 Effective length of database: 360 Effective search space: 123480 Effective search space used: 123480 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: 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