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 SM_b20661 SM_b20661 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Smeli:SM_b20661 Length = 355 Score = 339 bits (869), Expect = 8e-98 Identities = 187/361 (51%), Positives = 238/361 (65%), Gaps = 28/361 (7%) Query: 19 PAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRD 78 P + ++I IEDGEF++LVGPSGCGKST LRMLAGLE++ G IRIG++ V LPPKDRD Sbjct: 17 PVIKGVNIEIEDGEFVILVGPSGCGKSTLLRMLAGLENITAGEIRIGNQVVNRLPPKDRD 76 Query: 79 IAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSG 138 IAMVFQNYALYPHMTVADNM F+L +A PK+EI ++V AA+IL L++ LDR P+ LSG Sbjct: 77 IAMVFQNYALYPHMTVADNMAFSLMLAARPKSEIDKRVGVAAEILGLSKLLDRYPRQLSG 136 Query: 139 GQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVE 198 GQRQRVAMGRAIVR+PQVFL DEPLSNLDAKLRV+ R +I L +RL TTVYVTHDQ+E Sbjct: 137 GQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVAMRAEIKELHQRLKTTTVYVTHDQIE 196 Query: 199 AMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGG----VK 254 AMTM D++ V+ DG+++Q+ +P +YD PANLFVAGFIGSPAMN+++ + + Sbjct: 197 AMTMADKIVVMHDGIVEQIGAPLELYDNPANLFVAGFIGSPAMNMLKGRLDPADPSVFLT 256 Query: 255 FGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSV 314 + +PV R A +A R + G+RPE+ A P GL + Sbjct: 257 ADGTALPVARPAAAAQ---GRDLVYGLRPEYM-----------------ALDPNGLPAEI 296 Query: 315 NVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFSTSTGER 374 V+E G + + A +GG V R P G T+H+ H+F TG R Sbjct: 297 AVIEPTGYETQL--IARLGGHDVTCVFRERVNAKP--GETIHLAIDAAHVHLFDAGTGRR 352 Query: 375 L 375 L Sbjct: 353 L 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: 420 Number of extensions: 20 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: 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