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 3607559 Dshi_0971 ABC transporter related (RefSeq)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Dino:3607559 Length = 334 Score = 302 bits (773), Expect = 1e-86 Identities = 171/378 (45%), Positives = 228/378 (60%), Gaps = 46/378 (12%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 M + ++ T+ + D + LD+ IEDGEF V VGPSGCGKST LR++AGLED+ G Sbjct: 1 MGQIKLNQVTKSF--GDVEVIPPLDLTIEDGEFAVFVGPSGCGKSTLLRLIAGLEDITSG 58 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 I I +D T++PP R +AMVFQ+YALYPHM+V N+ F +K+AG+ +AE +++++ AA Sbjct: 59 HIEIDGKDATNVPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIDEAEQQRRIDAAA 118 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 K L+LT YLDR+P LSGGQRQRVA+GRAIVREP FL DEPLSNLDA LRV R +I+ Sbjct: 119 KALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISE 178 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 L +RL T +YVTHDQVEAMTM D++ VL+ G ++QV SP +Y P N FVAGFIGSP Sbjct: 179 LHKRLETTMIYVTHDQVEAMTMADKIVVLRAGHIEQVGSPLELYHSPRNEFVAGFIGSPK 238 Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLS 300 MNL+ + AA G T+G+RPEH DV G Sbjct: 239 MNLI--------------------KGAEAAKHG--VATIGIRPEHTDVSTTEGLWEG--- 273 Query: 301 KDSADAPAGLAVSVNVVEELGADGY--VYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVV 358 V V E LG+D + ++G + + VRV+G + G + + Sbjct: 274 ------------RVGVAEHLGSDTFLHIHGVP----DCDPMTVRVDGELPVKHGDKIFLT 317 Query: 359 PRPGETHVFSTSTGERLS 376 P+ + H F + G R+S Sbjct: 318 PQLDKLHKFD-AQGLRVS 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: 351 Number of extensions: 12 Number of successful extensions: 2 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: 334 Length adjustment: 29 Effective length of query: 348 Effective length of database: 305 Effective search space: 106140 Effective search space used: 106140 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