Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 298 bits (763), Expect = 2e-85 Identities = 169/358 (47%), Positives = 225/358 (62%), Gaps = 8/358 (2%) Query: 1 MADLKLTGVEKAYGDVKV-LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59 MA ++L + K Y + V ++ + +I GEL+V VGPSGCGK+TLLRMIAGLE I+GGT Sbjct: 1 MAKVRLDKLRKVYPNGHVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGGT 60 Query: 60 LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119 L I VVND+ P R IAMVFQ+YALYPHMTV EN+ F LK+ + +AEI+ V AA Sbjct: 61 LSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAAR 120 Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179 L+L Q LD P ALSGGQRQRVA+GR++VRDPKV+L DEPLSNLDA LR++ R+EIA++ Sbjct: 121 MLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIARI 180 Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239 + + ++TMVYVTHDQ+EAMTL RIVVL GG I Q+ +P+ LY+ P N FVA F+GSP Sbjct: 181 HQRL-KATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPA 239 Query: 240 MNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSL---MGAAVNVGVRPEDMVEAAPGGD 296 MNLL G + G + M G + + P +L + VG+RPED++ A Sbjct: 240 MNLLRGILYRDGG-WKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDLLLCADAAG 298 Query: 297 YVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354 ++ + E +G L GE + ++ G P ++H F Sbjct: 299 AALAAQLEVVEPVGNEVFLNLR--HGELALVSRMPPRELPAPGSTLHFGFAPERLHFF 354 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: 429 Number of extensions: 21 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: 364 Length adjustment: 30 Effective length of query: 343 Effective length of database: 334 Effective search space: 114562 Effective search space used: 114562 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