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 3607842 Dshi_1250 ABC transporter related (RefSeq)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Dino:3607842 Length = 351 Score = 322 bits (824), Expect = 1e-92 Identities = 185/376 (49%), Positives = 233/376 (61%), Gaps = 28/376 (7%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 M+ +T A + Y + V +D++I DGEF V VGPSGCGKST LRM+AGLE+ + G Sbjct: 1 MSGITLRGAVKRY--GETQVVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEG 58 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 +I IG RDVT L P +R +AMVFQ YALYPHMTVA+NMGF LK+ GVPKAEI+ KV A+ Sbjct: 59 SIHIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAAS 118 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 +IL L YL RKPKALSGGQRQRVA+GRAIVR P+VFL DEPLSNLDA+LRV R +IA Sbjct: 119 EILKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIAR 178 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L + +G T +YVTHDQVEAMT+ D++ VL+ G ++QV +P +Y P N+FVAGFIGSPA Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPA 238 Query: 241 MNLVEVPITDGGVKF-GNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASL 299 MN ++ I + V G +PV A VTVGVRP+H Sbjct: 239 MNFLDGRIENDAVHLAGLPPLPV-----PGAAGRSGPVTVGVRPQHI------------- 280 Query: 300 SKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVP 359 A P G V + E LG Y+Y G + L V +G+ + + Sbjct: 281 ----ALEPGGDGYLVELTESLGGVSYLYLR---GADGSRLTVEAGEEDPIAEGTPVGLSL 333 Query: 360 RPGETHVFSTSTGERL 375 P +F TG+RL Sbjct: 334 APDRVMLFEAETGQRL 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: 397 Number of extensions: 22 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: 351 Length adjustment: 29 Effective length of query: 348 Effective length of database: 322 Effective search space: 112056 Effective search space used: 112056 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