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_011973055.1 MAEO_RS01670 ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >NCBI__GCF_000017185.1:WP_011973055.1 Length = 329 Score = 215 bits (548), Expect = 1e-60 Identities = 116/276 (42%), Positives = 172/276 (62%), Gaps = 13/276 (4%) Query: 30 DGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVFQNYALY 89 + E + L+GPSGCGK+T LR +AG E + G I + D+T++PP R+I MVFQ+YAL+ Sbjct: 27 ENELISLLGPSGCGKTTCLRTIAGFEIPSNGKIFLNGNDITNIPPNKRNIGMVFQSYALF 86 Query: 90 PHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQRVAMGRA 149 PH+ V +N+ + LKI + K EI++KV++A +++L + + LSGG +QRVA+ RA Sbjct: 87 PHLNVYENVAYGLKIKKLKKNEIKEKVKDALNMVNLEGFENYNINELSGGMQQRVAVARA 146 Query: 150 IVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMGDRVAVL 209 +V EP+V L+DEPLSNLDAKLR+ R ++ LQR L I ++YVTHDQ EA+T+ DR+ V+ Sbjct: 147 LVIEPEVLLLDEPLSNLDAKLRIKMRRELKKLQRDLDIPSIYVTHDQEEALTISDRIGVM 206 Query: 210 KDGLLQQVDSPRNMYDKPANLFVAGFIGS---PAMNLVEVPITDGGVKFGNSVVPVNREA 266 +G ++Q+D P N+Y P F+A FIG+ + N++ D K+ V P N Sbjct: 207 NNGKIEQLDRPENIYTYPKTEFIANFIGNINEVSKNILTYLNIDYDKKYKYFVRPEN--- 263 Query: 267 LSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKD 302 KGD T + D+ LG V ++ D Sbjct: 264 -VVVGKGDFTGKI------VDIEYLGNLVRYAIKYD 292 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: 290 Number of extensions: 9 Number of successful extensions: 1 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: 329 Length adjustment: 29 Effective length of query: 348 Effective length of database: 300 Effective search space: 104400 Effective search space used: 104400 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