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 WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 201 bits (512), Expect = 2e-56 Identities = 110/233 (47%), Positives = 150/233 (64%), Gaps = 8/233 (3%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPK------DR 77 + + + GE + L+GPSG GK+T LR +AGLE + G+IRIG++ V K R Sbjct: 24 VSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRIGEQMVFESAKKIEVSVEKR 83 Query: 78 DIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALS 137 + VFQ+YAL+PH TV +N+ + LK+ VP EIRQ+V+E L L +R P LS Sbjct: 84 CLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQEVLANLGLGDLSERHPHQLS 143 Query: 138 GGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQV 197 GGQ+QRVA+ R++V PQV L+DEPLSNLDAKLR R + L L ++ V VTHDQ Sbjct: 144 GGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIWLRQLIIDLNLSAVCVTHDQA 203 Query: 198 EAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITD 250 EAM M D+V +LKDG+++Q +P+ MY P +LFVA F+G A N + +TD Sbjct: 204 EAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMG--ANNTISGLVTD 254 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: 329 Number of extensions: 11 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: 353 Length adjustment: 30 Effective length of query: 347 Effective length of database: 323 Effective search space: 112081 Effective search space used: 112081 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 Apr 09 2024. 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