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 208681 DVU3161 ABC transporter, ATP-binding protein
Query= TCDB::P96483 (377 letters) >MicrobesOnline__882:208681 Length = 349 Score = 286 bits (732), Expect = 6e-82 Identities = 165/374 (44%), Positives = 226/374 (60%), Gaps = 29/374 (7%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 M+T+ DK +R + D AVD + +E G+ LVL+GPSGCGKST+LR++AGLE V G Sbjct: 1 MSTIVLDKVSRHW--GDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSG 58 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 I IG RDVT+LPP R +AMVFQ+YAL+PH+TV DN+ F L + VP AE +++++ A Sbjct: 59 RILIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAV 118 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 +IL L + L+RKP LSGGQ+QRVA+GRA+V E V LMDEPLSNLDAKLR R +I + Sbjct: 119 EILGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRA 178 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 LQ+ LG+T VYVTHDQ EAM+M DR+ +++ G + Q +P MY +PA F FIG+P Sbjct: 179 LQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPP 238 Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLS 300 MNLV + D G++ S R G +G+RPEH +V+ Sbjct: 239 MNLVRLQGNDDGIRVAGS-----RSGRVTCHAG-ADCMLGIRPEHIRIVD---------- 282 Query: 301 KDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPR 360 G V VE LG++ + + VG E +L V V+G G+ +++ Sbjct: 283 -------DGWRAVVESVEYLGSNSVL--SCRVGSE--ELSVVVHGVTDTVVGAEIYLHCP 331 Query: 361 PGETHVFSTSTGER 374 H+F +TG R Sbjct: 332 EEHVHIFDAATGAR 345 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: 349 Number of extensions: 15 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: 349 Length adjustment: 29 Effective length of query: 348 Effective length of database: 320 Effective search space: 111360 Effective search space used: 111360 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