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 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 215 bits (547), Expect = 2e-60 Identities = 119/293 (40%), Positives = 173/293 (59%), Gaps = 4/293 (1%) Query: 20 AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79 AV+ + +E G F ++GPSGCGK+T LRM+AG E + G I I RD+ + P R + Sbjct: 43 AVNDVSFEVEQGRFFSILGPSGCGKTTLLRMIAGFESPDSGVIAIRGRDMAGIAPNRRPV 102 Query: 80 AMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGG 139 ++FQ+ AL+P M+VA+N+ F LK G+ EI ++V++ + + L Y + P LSGG Sbjct: 103 NLIFQHLALFPMMSVAENVAFGLKRRGMAGGEISRRVQDVLERVGLPGYGVKMPAQLSGG 162 Query: 140 QRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEA 199 Q+QRVA+ R +V EP V L+DEPL LD KLR + ++ +LQ +G T VY+THDQ EA Sbjct: 163 QKQRVAIARCLVLEPAVLLLDEPLGALDLKLREQMKVELKTLQAEVGTTFVYITHDQSEA 222 Query: 200 MTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAM--NLVEVPITDGGVKFGN 257 + M D VAV+ G +QVD+PRN+Y +PA+ FVAGF+G + +E D G+ + Sbjct: 223 LVMSDHVAVMNAGRFEQVDTPRNLYRRPASAFVAGFVGETNVWSGTLEEATGDAGLVRTD 282 Query: 258 SVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSA-DAPAG 309 + KG R V + +RPE + G + A + D A D AG Sbjct: 283 EGAVFRARVAAGLAKGTR-VDMFIRPEAVLIDPDGASCATDGATDGATDGAAG 334 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: 431 Number of extensions: 22 Number of successful extensions: 2 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: 418 Length adjustment: 31 Effective length of query: 346 Effective length of database: 387 Effective search space: 133902 Effective search space used: 133902 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