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 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= TCDB::P96483 (377 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 179 bits (455), Expect = 8e-50 Identities = 93/241 (38%), Positives = 153/241 (63%), Gaps = 8/241 (3%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 M+T+T ++ Y G + + LD+ + GE L+GPSGCGK+T L+ +AGL+ ++ G Sbjct: 1 MSTLTIEQVHSDYQG--QTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQG 58 Query: 61 AIRIGDRDV----THLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKV 116 I I R + T +P + R++ M+FQ+YAL+PH+TVA+N+ F +K G+ KA + ++ Sbjct: 59 RISINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVK--GLDKAARQARL 116 Query: 117 EEAAKILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRT 176 E ++ L R P LSGGQ+QRV++ RA+ EP++ L+DEP SN+DAK+R Sbjct: 117 GEMLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMV 176 Query: 177 QIASLQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFI 236 +I + ++ G++ V+VTH + EA D++A+ KDG + Q S ++Y +P + +VA F+ Sbjct: 177 EIREILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFL 236 Query: 237 G 237 G Sbjct: 237 G 237 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: 306 Number of extensions: 16 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: 342 Length adjustment: 29 Effective length of query: 348 Effective length of database: 313 Effective search space: 108924 Effective search space used: 108924 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