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 AO356_28585 AO356_28585 ABC transporter
Query= TCDB::P96483 (377 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28585 Length = 379 Score = 280 bits (715), Expect = 6e-80 Identities = 150/311 (48%), Positives = 205/311 (65%), Gaps = 26/311 (8%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVF 83 + + I GEF+V VGPSGCGKST LR++AGL+ + GG + I R V L P++R + MVF Sbjct: 22 VSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDLEPRERGVGMVF 81 Query: 84 QNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQR 143 Q+YALYPHM+V DN+ F LK+A K +R++V + A+IL L + L RKP+ LSGGQRQR Sbjct: 82 QSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQILQLDKLLQRKPRELSGGQRQR 141 Query: 144 VAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMG 203 VAMGRA+ REP + L DEPLSNLDA LRV R +IA L RLG T +YVTHDQVEAMT+ Sbjct: 142 VAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGRLGSTMIYVTHDQVEAMTLA 201 Query: 204 DRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGG-------VKFG 256 D++ VL G ++QV SPR +Y++PA+ FVAGF+GSP MN + + G + G Sbjct: 202 DKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGSPRMNFLAAFLHTPGETSQVESLVLG 261 Query: 257 NSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNV 316 + +P + L+A + +++G+RPEH ++ +A AG+AVS Sbjct: 262 MTSLPFDSSGLAA----NTQLSLGIRPEH-------------IALKAAQGTAGIAVS--G 302 Query: 317 VEELGADGYVY 327 VE LG++ YV+ Sbjct: 303 VEYLGSETYVH 313 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: 412 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 377 Length of database: 379 Length adjustment: 30 Effective length of query: 347 Effective length of database: 349 Effective search space: 121103 Effective search space used: 121103 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: 50 (23.9 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