Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 134 bits (337), Expect = 3e-36 Identities = 77/242 (31%), Positives = 139/242 (57%), Gaps = 9/242 (3%) Query: 2 TGLLLKDIRKSYGAVDV--IHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59 T + +K++ K Y A I + +IK+G+ V +G SG GKSTLL+ I GL + G+ Sbjct: 4 TIISVKNLTKQYQAEQAGGIKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGE 63 Query: 60 MFIDGERVN----DVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVR 115 +F + +RV + P + + MV Q ++L + VYDN+A +++ + + Sbjct: 64 IFFEDKRVKGPDEQLIPGHKQMKMVTQDFSLNIYAKVYDNIA--SQLSNTDLKTKAEKTL 121 Query: 116 GAADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIE 175 + L++ P ++ LSGG++QRVAI +A+ + +V L DEP S +DA L+ R + Sbjct: 122 QIMEHLRILPLQNKKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRAD 181 Query: 176 IAKLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFI 235 I +++ + T+I V+HD + + LAD++++L G + Q G P E+Y+ P +++ A+ + Sbjct: 182 IKRVASE-TGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQIL 240 Query: 236 GS 237 G+ Sbjct: 241 GN 242 Lambda K H 0.320 0.137 0.387 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: 224 Number of extensions: 13 Number of successful extensions: 4 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: 362 Length of database: 330 Length adjustment: 29 Effective length of query: 333 Effective length of database: 301 Effective search space: 100233 Effective search space used: 100233 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