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_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >NCBI__GCF_000182725.1:WP_008510542.1 Length = 333 Score = 295 bits (754), Expect = 2e-84 Identities = 165/344 (47%), Positives = 204/344 (59%), Gaps = 40/344 (11%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVF 83 +++ + DGEF++ VGPSGCGKST LR +AGLEDV+ G + I DVT PP R IAMVF Sbjct: 22 INLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAGQVLINGEDVTVTPPSRRGIAMVF 81 Query: 84 QNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQR 143 Q+YALYPH+TV NMG LK AG PK EI +V +A+ +L L YL R+P LSGGQRQR Sbjct: 82 QSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKASAMLALEPYLARRPAELSGGQRQR 141 Query: 144 VAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMG 203 VA+GRA+VR P++FL DEPLSNLDA LRV TR +IA L R L T +YVTHDQVEAMT+ Sbjct: 142 VAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAKLHRELKATMIYVTHDQVEAMTLA 201 Query: 204 DRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSVVPVN 263 DR+ VL G ++Q+ SP +Y++P NLFVAGFIGSP MN + Sbjct: 202 DRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFIGSPQMNFI------------------- 242 Query: 264 REALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEELGAD 323 EA G R T+G+RPEH V G V E LGAD Sbjct: 243 -EAARIGATGAR--TIGIRPEHLSVSRESGTWKG---------------KVIHAEHLGAD 284 Query: 324 GYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVF 367 +Y E G V R+ G Q + + + P G+TH F Sbjct: 285 TILYVETETAGLV---TARLFGEQHYNEDDVIFLTPEEGKTHYF 325 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: 335 Number of extensions: 15 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: 333 Length adjustment: 29 Effective length of query: 348 Effective length of database: 304 Effective search space: 105792 Effective search space used: 105792 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 24 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