Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Phaeo:GFF1645 Length = 355 Score = 302 bits (773), Expect = 1e-86 Identities = 170/344 (49%), Positives = 219/344 (63%), Gaps = 21/344 (6%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVF 83 +++ I+DGEF+VLVGPSGCGKST LRM+AGLE + G I + + + P+DRDIAMVF Sbjct: 22 INLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDFEIDGQRMNDVRPRDRDIAMVF 81 Query: 84 QNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQR 143 Q+YALYPHM VA NMGF+++I P E R +V AA+ L L+ +DR PKALSGGQRQR Sbjct: 82 QSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAETLGLSSLVDRLPKALSGGQRQR 141 Query: 144 VAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMG 203 VAMGRAI+R+P+ FL DEPLSNLDA LRV R +IA L ++LG T +YVTHDQVEA+T+ Sbjct: 142 VAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLHKQLGATMIYVTHDQVEALTLA 201 Query: 204 DRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSVVPVN 263 DR+ VL G +QQV SP +Y++PAN FVA FIGSP MN++ V GV N ++ Sbjct: 202 DRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMNILPVSGAASGVMATNGMM--- 258 Query: 264 REALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEELGAD 323 L V +G+RPEH DVVE G L +VVE LG+D Sbjct: 259 -LTLDHMHDTAAAVELGIRPEHLDVVEPG--------------EGHLIAVADVVERLGSD 303 Query: 324 GYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVF 367 +Y A+V G + L+VR +G G L + + H+F Sbjct: 304 TNIY--AKVDG-LGPLMVRKHGNVPVRSGERLGLRVQAQNAHIF 344 Lambda K H 0.317 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: 396 Number of extensions: 21 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: 377 Length of database: 355 Length adjustment: 30 Effective length of query: 347 Effective length of database: 325 Effective search space: 112775 Effective search space used: 112775 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