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 HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 332 bits (851), Expect = 1e-95 Identities = 191/358 (53%), Positives = 235/358 (65%), Gaps = 25/358 (6%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVF 83 +DI I DGEF VLVGPSGCGKST LRMLAGLE++ GG I IG V ++ PKDRDIAMVF Sbjct: 22 VDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEILIGGTVVNNVQPKDRDIAMVF 81 Query: 84 QNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQR 143 QNYALYPHMTV DNM F+L +A KA + ++V++AA IL L Q LDR P+ LSGGQRQR Sbjct: 82 QNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAADILGLNQLLDRYPRQLSGGQRQR 141 Query: 144 VAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMG 203 VAMGRAIVR+PQVFL DEPLSNLDAKLRV RT+I L +RL T++YVTHDQ+EAMTM Sbjct: 142 VAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELHQRLKTTSIYVTHDQIEAMTMA 201 Query: 204 DRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPI----TDGGVKFGNSV 259 D++ V++DGL++Q P ++YD PANLFVAGFIGSPAMN + + T V+F + Sbjct: 202 DQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAMNFIPATLRRNATGAEVEFADGT 261 Query: 260 -VPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVE 318 VP A + G + VT GVRPEH + GA A G+A V VVE Sbjct: 262 RVPAPYGAALQGNDGQK-VTYGVRPEHLSI----GA-----------AGQGIATKVIVVE 305 Query: 319 ELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFSTSTGERLS 376 GAD V+ + G + R R G +H+VP TH+F +G+ L+ Sbjct: 306 PTGADTEVF--SRFGDTSLTSIFR--ERHDFGAGDVIHLVPDHSRTHLFDAESGKSLA 359 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: 414 Number of extensions: 22 Number of successful extensions: 4 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: 361 Length adjustment: 30 Effective length of query: 347 Effective length of database: 331 Effective search space: 114857 Effective search space used: 114857 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