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_068221987.1 AWW68_RS13720 ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >NCBI__GCF_001592965.1:WP_068221987.1 Length = 288 Score = 147 bits (372), Expect = 3e-40 Identities = 84/244 (34%), Positives = 142/244 (58%), Gaps = 11/244 (4%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDV-----THLPPKDRD 78 LD + GEFLV+ G SG GK++ LRM+AGL + + G I I +++ T++ P+ R+ Sbjct: 21 LDFKCQAGEFLVISGESGAGKTSLLRMIAGLMNPDSGNI-ISNQEPWFGHKTNIKPQQRN 79 Query: 79 IAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSG 138 +VFQ YAL+P+MTV N+ +ALK K++ +EE I+++ ++KP LSG Sbjct: 80 CGLVFQQYALFPNMTVEGNLRYALK-----KSQADSIIEELLDIMEIKGLRNQKPNQLSG 134 Query: 139 GQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVE 198 GQ+QRVA+ R +V++P++ L+DEPLS LD +R+ + + + ++ +TT+ VTHD E Sbjct: 135 GQQQRVALARTLVQKPKLLLLDEPLSALDRSMRIRLQEYLKKVHQQFELTTIMVTHDPSE 194 Query: 199 AMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNS 258 A+ + DR+ ++ G + + P ++ + F G+ E + V GN Sbjct: 195 ALRLADRIIEIEKGNITKDGKPTEVFGNKSLSGKFQFTGAVVDIQEEELLCIASVLVGNQ 254 Query: 259 VVPV 262 ++ V Sbjct: 255 LIKV 258 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: 241 Number of extensions: 14 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: 288 Length adjustment: 28 Effective length of query: 349 Effective length of database: 260 Effective search space: 90740 Effective search space used: 90740 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