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 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 286 bits (731), Expect = 8e-82 Identities = 166/358 (46%), Positives = 215/358 (60%), Gaps = 27/358 (7%) Query: 17 DKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKD 76 D AVD + +E G LVL+GPSGCGKST+LR++AGLE V G I IG+RDVTHLPP Sbjct: 15 DVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRIMIGERDVTHLPPAQ 74 Query: 77 RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKAL 136 R +AMVFQ+YAL+PH+TV +N+ F L + VP+AE +++ A IL L+ L RKP L Sbjct: 75 RQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVDILGLSALLQRKPGEL 134 Query: 137 SGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQ 196 SGGQ+QRVA+GRA+V E V LMDEPLSNLDAKLR R +I +LQ+ LG+T VYVTHDQ Sbjct: 135 SGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRALQQTLGMTMVYVTHDQ 194 Query: 197 VEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFG 256 EAM+M DR+ +++ G + Q +P +Y +PA F FIG+P MNLV + G V Sbjct: 195 TEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPMNLVRLDDARGSVCVA 254 Query: 257 NSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNV 316 S +S D D +G+RPEH +V P G V Sbjct: 255 GS----RSGTVSVVDSAD--YVLGIRPEHIRIV-----------------PEGWRAVVES 291 Query: 317 VEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFSTSTGER 374 VE LG+ G V G VGGE +L V V+G G+ +++ H+F TGER Sbjct: 292 VEYLGS-GSVLG-CRVGGE--ELSVVVDGVPTIAVGAEIYLHCPDEHIHIFDAKTGER 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: 328 Number of extensions: 13 Number of successful extensions: 3 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: 350 Length adjustment: 29 Effective length of query: 348 Effective length of database: 321 Effective search space: 111708 Effective search space used: 111708 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