Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 135 bits (341), Expect = 1e-36 Identities = 84/243 (34%), Positives = 138/243 (56%), Gaps = 17/243 (6%) Query: 4 IHCQALAKHY----AGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59 I + L K Y AGG + + I G+ V ++G SG GKST+L+ I GL G Sbjct: 6 ISVKNLTKQYQAEQAGG---IKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEG 62 Query: 60 TL-----RIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLK-RPAAEIDR 113 + R+ G +P ++ + MV Q+++L + VYDNIA L + AE Sbjct: 63 EIFFEDKRVKGPDEQLIPGHKQ-MKMVTQDFSLNIYAKVYDNIASQLSNTDLKTKAEKTL 121 Query: 114 RVREVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQL 173 ++ E +L L+ +K +SGG+QQR AIA+A++ V L DEP S +DA L+ QL Sbjct: 122 QIMEHLRILPLQ---NKKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQL 178 Query: 174 RGDIKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAG 233 R DIKR+ T + V+HD + + LAD+++++++G ++Q G P+E+Y++P++++ A Sbjct: 179 RADIKRVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQ 238 Query: 234 FIG 236 +G Sbjct: 239 ILG 241 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: 250 Number of extensions: 9 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: 406 Length of database: 330 Length adjustment: 30 Effective length of query: 376 Effective length of database: 300 Effective search space: 112800 Effective search space used: 112800 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: 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