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_086510097.1 BZY95_RS11680 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::P96483 (377 letters) >NCBI__GCF_002151265.1:WP_086510097.1 Length = 368 Score = 303 bits (775), Expect = 7e-87 Identities = 171/380 (45%), Positives = 231/380 (60%), Gaps = 24/380 (6%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MA+VT DK +++ + + +D+AI +GEF+V VGPSGCGKST LR++AGLE + G Sbjct: 1 MASVTLDKINKVFGSTH--IIKDVDLAIGEGEFVVFVGPSGCGKSTLLRLIAGLESITDG 58 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 + IGD+ V LPP++R + MVFQ+YALYPHMTV +NM F LK+A K + ++V A Sbjct: 59 ELSIGDQVVNELPPRERGVGMVFQSYALYPHMTVYENMAFGLKLAKTAKETVHERVMATA 118 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 +IL L + L+RKPKALSGGQRQRVAMGRA+ REP++ L DEPLSNLDA LRV R +IA Sbjct: 119 RILQLEELLERKPKALSGGQRQRVAMGRAMAREPRILLFDEPLSNLDASLRVQMRNEIAR 178 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L +RLG T VYVTHDQVEAMT+ D++ VL G ++QV SP+ +Y +PA FVAGFIGSP Sbjct: 179 LHKRLGSTMVYVTHDQVEAMTLADKIVVLDGGRVEQVGSPQELYQRPATKFVAGFIGSPT 238 Query: 241 MNLVEVPITDG---GVKFG-NSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVA 296 MN + + G + G + + ++ +T+G+RPEH + E G+ Sbjct: 239 MNFLPARLLGADATGCRIGATGLTELALPQDASGHAQGAALTLGIRPEHLRLSEAQGSEG 298 Query: 297 ASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLH 356 + VN VE LG + YVY + G + L+ R G + Sbjct: 299 FEI--------------VN-VEYLGNEVYVYLEPKEGETL--LIQRGEAPTTWRVGQRVT 341 Query: 357 VVPRPGETHVFSTSTGERLS 376 + P P H+F G LS Sbjct: 342 LAPDPEHVHLFDAG-GRALS 360 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: 18 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: 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 Sep 24 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