Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate H281DRAFT_02629 H281DRAFT_02629 carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-)
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Burk376:H281DRAFT_02629 Length = 381 Score = 313 bits (801), Expect = 6e-90 Identities = 184/371 (49%), Positives = 244/371 (65%), Gaps = 15/371 (4%) Query: 1 MADLKLTGVEKAY-GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59 MA + L G++K + G+ VL ++NL+I + E VF+GPSGCGKSTLLR++AGLE T G Sbjct: 1 MAAISLRGIQKTFDGNAPVLRDLNLEIGEHEFCVFLGPSGCGKSTLLRIVAGLEDQTDGD 60 Query: 60 LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119 + I G +N VP A+RG+AMVFQSYAL+PHMTV ENM+F LK+A+ +AEID V AA Sbjct: 61 VSIGGRTMNSVPAAERGVAMVFQSYALFPHMTVYENMAFGLKLARTPKAEIDRKVREAAH 120 Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179 LQL L R P+ LSGGQRQRVAIGR+IVR+P V+LFDEPLSNLDAALR TR+EIA+L Sbjct: 121 VLQLDALLARKPRELSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDAALRGQTRIEIARL 180 Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVL-AG------GGIAQVGSPLELYEKPENEFVA 232 + ++++VYVTHDQ+EAMTLA +IV+L AG G IAQ+G+PLELY +P ++FVA Sbjct: 181 HQRYAQASVVYVTHDQIEAMTLADKIVLLHAGAETQRLGSIAQIGAPLELYHRPRSKFVA 240 Query: 233 QFIGSPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLM-GAAVNVGVRPEDMVEA 291 FIGSP+MN + G ++ A +VE++ G A+ L G V +G+RPE + Sbjct: 241 GFIGSPRMNFIDG-VVERIADDSVEVSMPGTALRVLVDGRRLKPGQRVTLGIRPEHV--R 297 Query: 292 APGGDYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKV 351 GG +TE LGE + L+ + G I K G G+ L Sbjct: 298 FDGGTQTLAVNALLTEQLGEHSYLHADHAGG--TLIAKAPGDLHVRNGERLALHLPADAC 355 Query: 352 HVF-KDGVSLH 361 H+F +DG++LH Sbjct: 356 HLFDEDGIALH 366 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: 437 Number of extensions: 19 Number of successful extensions: 2 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: 381 Length adjustment: 30 Effective length of query: 343 Effective length of database: 351 Effective search space: 120393 Effective search space used: 120393 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