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_b21106 SM_b21106 sugar ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Smeli:SM_b21106 Length = 365 Score = 330 bits (845), Expect = 5e-95 Identities = 185/377 (49%), Positives = 247/377 (65%), Gaps = 14/377 (3%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MA VT K + Y + V +D+ ++D EF+ LVGPSGCGKST+LRM+AGLE+V+GG Sbjct: 1 MAPVTLKKLVKRYGALE--VVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGG 58 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 AI IG R V LPP+ R+I+MVFQ+YALYPHMTVA+NMGF+LKIAG P EI+ +V EAA Sbjct: 59 AIEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAA 118 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 ILDL L+R+P LSGGQRQRVAMGRAIVR+P VFL DEPLSNLDAKLR RT+I Sbjct: 119 AILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKK 178 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L R+ T +YVTHDQVEAMT+ DR+ +++DG ++QV +P +++ +PA FVAGFIGSP Sbjct: 179 LHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPP 238 Query: 241 MNLVEVPITDGGVKFGN-SVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASL 299 MN+ E +TDG + F + + +P+ S +G + VT G+RP+ DV G + A Sbjct: 239 MNMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQK-VTFGLRPD--DVYPSGHGLHAG- 294 Query: 300 SKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVP 359 ADA + + V + E LG + V+ + G +D V R+ + G + + Sbjct: 295 ---DADAVHEIELPVTITEPLGNETLVF--TQFNG--RDWVSRMLNPRPLRPGEAVPMSF 347 Query: 360 RPGETHVFSTSTGERLS 376 H+F TG L+ Sbjct: 348 DLARAHLFDGETGRALA 364 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: 409 Number of extensions: 19 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: 365 Length adjustment: 30 Effective length of query: 347 Effective length of database: 335 Effective search space: 116245 Effective search space used: 116245 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