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 WP_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::P96483 (377 letters) >NCBI__GCF_000018545.1:WP_164924745.1 Length = 355 Score = 333 bits (853), Expect = 6e-96 Identities = 190/382 (49%), Positives = 248/382 (64%), Gaps = 34/382 (8%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 M VT T+ Y + QL IEDGEF+VLVGPSGCGKST LRMLAGLE+++GG Sbjct: 1 MTDVTIRNVTKRYGALT--VIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEISGG 58 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 + +G + P K+RD+A+VFQNYALYPHMTVA+NMGFALK+ P+AEI ++V++AA Sbjct: 59 DLLMGADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKRPRAEIDERVDKAA 118 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 IL L + LDR P+ALSGGQRQRVAMGRAIVR+PQVFL DEPLSNLDAKLRV R +I + Sbjct: 119 AILGLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKA 178 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L +RL ITTVYVTHDQ+EAMTM D++ V+ +G ++Q+ +P +YD+PAN+FVAGFIGSP+ Sbjct: 179 LHQRLKITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFIGSPS 238 Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRT------VTVGVRPEHFDVVELGGA 294 MN +P T V N + E ++ G T VT G+RPEH + E Sbjct: 239 MNF--LPAT---VAATNGPLLKTPEGVALPIDGGPTLTGRSEVTYGIRPEHLQLGE---- 289 Query: 295 VAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGST 354 G+ V VVE G++ +Y T VGG +++V + R G Sbjct: 290 -------------TGIPAEVVVVEPTGSETQLYVT--VGG--REVVAVLRDRVDVRPGEK 332 Query: 355 LHVVPRPGETHVFSTSTGERLS 376 + + PR G H+F +TG R++ Sbjct: 333 IWLTPRKGCAHLFDPNTGARIA 354 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: 446 Number of extensions: 22 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 Apr 09 2024. 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