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 Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 304 bits (779), Expect = 2e-87 Identities = 166/353 (47%), Positives = 227/353 (64%), Gaps = 25/353 (7%) Query: 23 QLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMV 82 ++DI + GEFL+LVGPSGCGKST L ++AGL++ G IRIG ++V +PP+DRDIAMV Sbjct: 26 KVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKNVVGMPPRDRDIAMV 85 Query: 83 FQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQ 142 FQ+YALYP ++VADN+GFAL++ +PK E +++++E A +L ++ LDR+P LSGGQRQ Sbjct: 86 FQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQLSGGQRQ 145 Query: 143 RVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTM 202 RVAMGRA+ R+PQ+FL DEPLSNLDAKLRV R +I L + GIT+VYVTHDQVEAMT+ Sbjct: 146 RVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHDQVEAMTL 205 Query: 203 GDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSVVPV 262 G R+AV+K G++QQ+ +P +Y++PAN +VA FIGSP MNL+ +T G +FG + Sbjct: 206 GSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGAVTGG--QFGIQGAAL 263 Query: 263 NREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEELGA 322 N L+ V +GVRPEH + E A V+VVE G Sbjct: 264 N---LAPPPSSANEVLLGVRPEHLVMQE----------------TAPWRGRVSVVEPTGP 304 Query: 323 DGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFSTSTGERL 375 D YV G + +R + + + G + + P H F + ERL Sbjct: 305 DTYVMVDTAAG----SVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEERL 353 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: 394 Number of extensions: 19 Number of successful extensions: 1 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