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_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::P96483 (377 letters) >NCBI__GCF_002115805.1:WP_085638943.1 Length = 350 Score = 314 bits (804), Expect = 3e-90 Identities = 174/375 (46%), Positives = 232/375 (61%), Gaps = 26/375 (6%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 M+ VT + + Y + +D+ ++DGEF V VGPSGCGKST LRM+AGLE+ G Sbjct: 1 MSGVTLESVIKRY--GQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEG 58 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 IRIG RDVT L P DR ++MVFQ YALYPHMTV +NMGF LK+ G +I++KV EA+ Sbjct: 59 TIRIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEAS 118 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 +IL L YL RKPKALSGGQRQRVA+GRAIVR P+VFL DEPLSNLDA+LRV R +IA Sbjct: 119 RILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIAR 178 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L + +G T +YVTHDQVEAMT+ D++ VL+ G ++QV +P +Y P N FVAGFIGSP+ Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPS 238 Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLS 300 MN + + G V V V++ A +A +G + V +G+RPEH ++ Sbjct: 239 MNFIRGRVQGGEVVSDGLVHSVSKTA--SAQEG-QEVLIGLRPEHLEL------------ 283 Query: 301 KDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPR 360 G + V++ E LG Y + +G + + ++V G G + +V Sbjct: 284 ------RPGSSHRVDLTESLGGVSYAH---LIGPDGEKIIVEERGDHRSSDGDMVDLVVD 334 Query: 361 PGETHVFSTSTGERL 375 P +F T RL Sbjct: 335 PDHMFLFDAKTEARL 349 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: 373 Number of extensions: 16 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: 350 Length adjustment: 29 Effective length of query: 348 Effective length of database: 321 Effective search space: 111708 Effective search space used: 111708 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 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