Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 135 bits (340), Expect = 2e-36 Identities = 79/240 (32%), Positives = 132/240 (55%), Gaps = 8/240 (3%) Query: 4 VTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIF 63 ++ K+ + Y + +K + EI G+ + ++G SG GKST L+ + GL +G IF Sbjct: 6 ISVKNLTKQYQAEQAGGIKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGEIF 65 Query: 64 IGDKDVT----HVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAG-KSQDEINKRVDE 118 DK V + P + + MV Q+++L + V +N+ L K++ E ++ E Sbjct: 66 FEDKRVKGPDEQLIPGHKQMKMVTQDFSLNIYAKVYDNIASQLSNTDLKTKAEKTLQIME 125 Query: 119 AAATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQI 178 L L +K LSGG++QRVA+ +A+V + QV L+DEP S +DA L+ Q R I Sbjct: 126 HLRILPLQN---KKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRADI 182 Query: 179 AALQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGS 238 + + GVT + V+HD + L + D++ +LK+G L Q G P E+Y P +++ A +G+ Sbjct: 183 KRVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQILGN 242 Lambda K H 0.316 0.135 0.380 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: 228 Number of extensions: 5 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: 376 Length of database: 330 Length adjustment: 29 Effective length of query: 347 Effective length of database: 301 Effective search space: 104447 Effective search space used: 104447 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