Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate SM_b21106 SM_b21106 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Smeli:SM_b21106 Length = 365 Score = 319 bits (818), Expect = 7e-92 Identities = 173/370 (46%), Positives = 238/370 (64%), Gaps = 12/370 (3%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + + L K Y G V+H +DL + D EF+ L+GPSGCGKST LRMIAGLE++SGG Sbjct: 1 MAPVTLKKLVKRY-GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 + IGG VNDLP R RN++MVFQ+YALYPHM+V +N+ F L+ RPA EI RV E AA Sbjct: 60 IEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L+L LLER+P +SGGQ+QR A+ RAI++ P VFLFDEPLSNLDAKLR Q+R +IK+L Sbjct: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H R++ T +YVTHDQ+EAMTL+DR+++M+DG I Q G+P +++R P F AGFIG+P M Sbjct: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPM 239 Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPD------HVRIAGER 294 N + DG+L + L S +R V +RPD H AG+ Sbjct: 240 NMEEAVL--TDGKLAFASG-ATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDA 296 Query: 295 EPAASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHV 354 + + PV++ E LG + L+ T+ + + + R +PG + ++ D H+ Sbjct: 297 DAVHEIELPVTI--TEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHL 354 Query: 355 FDVESGENLS 364 FD E+G L+ Sbjct: 355 FDGETGRALA 364 Lambda K H 0.321 0.137 0.403 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: 386 Number of extensions: 16 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: 406 Length of database: 365 Length adjustment: 30 Effective length of query: 376 Effective length of database: 335 Effective search space: 125960 Effective search space used: 125960 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: 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