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 H281DRAFT_05701 H281DRAFT_05701 glycerol 3-phosphate ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Burk376:H281DRAFT_05701 Length = 362 Score = 322 bits (825), Expect = 1e-92 Identities = 185/386 (47%), Positives = 238/386 (61%), Gaps = 34/386 (8%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MA +T + Y G + +D+ + DGEF+V+VGPSGCGKST LRM+AGLE ++ G Sbjct: 1 MAALTLQGVKKTYDGKQF-VLHGIDVDVNDGEFVVMVGPSGCGKSTLLRMVAGLERISEG 59 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 I I + V L PKDR+IAMVFQNYALYPHM+VA+NMG+ALKIAGV +A+I Q+V AA Sbjct: 60 TISIAGKVVNELEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAQRVNAAA 119 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 +IL+L L RKP+ LSGGQRQRVAMGRAIVREP VFL DEPLSNLDA+LRV R +I Sbjct: 120 QILELEPLLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQR 179 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L RL T++YVTHDQ+EAMT+ RV V+ G +Q+ +P +Y++PA +FVAGFIGSP Sbjct: 180 LHARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVAGFIGSPG 239 Query: 241 MNLVEVPITDGGVKF---GN-------SVVPVNREALSAADKGDRTVTVGVRPEHFDVVE 290 MNL+E ++D G F GN V + RE R T+G+RPEH Sbjct: 240 MNLLEGRVSDDGSTFDVAGNGPQLPLAGVASIGREVAKG-----REWTLGIRPEH----- 289 Query: 291 LGGAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPE 350 +S ADAP ++V+ E LGAD +G D+ R+ P Sbjct: 290 --------MSPGQADAP-HTTLTVDSCELLGADNLAHGR----WGKHDVTARLPHAHRPA 336 Query: 351 KGSTLHVVPRPGETHVFSTSTGERLS 376 G L V H F ++G R++ Sbjct: 337 AGEALQVALPARHLHFFDPASGRRVN 362 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: 388 Number of extensions: 9 Number of successful extensions: 3 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: 362 Length adjustment: 30 Effective length of query: 347 Effective length of database: 332 Effective search space: 115204 Effective search space used: 115204 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