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_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::P96483 (377 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 298 bits (764), Expect = 1e-85 Identities = 177/383 (46%), Positives = 232/383 (60%), Gaps = 24/383 (6%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MA + D+ + + V + + D EF+VLVGPSGCGKST+LRM+AGLE+V G Sbjct: 1 MAEIKLDQVNKRF--KKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSG 58 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 I IG R V H+PPKDRDIAMVFQ+YALYPHM V NM F L GVP+ EI ++V++AA Sbjct: 59 EISIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAA 118 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 +IL ++ L R+P LSGGQRQRVAMGRAIVR+PQ FL DEPLSNLDAKLRV R ++A Sbjct: 119 EILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAK 178 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L RL T VYVTHDQ+EAMT+ DR+ V+KDG + QV P +Y++PAN FVAGFIGSP+ Sbjct: 179 LHERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPS 238 Query: 241 MNLVEVPITD-------GGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGG 293 MN ++V + + G F VP +R A + +R V G+RPE DV E G Sbjct: 239 MNFLDVRLVEEAGDLWVDGESF-RLKVPRHR-APAFRGHVNRPVIFGIRPE--DVKERPG 294 Query: 294 AVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGS 353 + L V+V E +G++ V TA VG R++ Sbjct: 295 DAL-------PEGVEPLRAEVDVREPIGSE--VIITATVGSHA--FTARISPNVAVRVHD 343 Query: 354 TLHVVPRPGETHVFSTSTGERLS 376 + + + H+F + + L+ Sbjct: 344 PIDLAVNMNKMHLFDPESEQALN 366 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: 416 Number of extensions: 16 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: 368 Length adjustment: 30 Effective length of query: 347 Effective length of database: 338 Effective search space: 117286 Effective search space used: 117286 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: 50 (23.9 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