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_086511770.1 BZY95_RS20650 ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >NCBI__GCF_002151265.1:WP_086511770.1 Length = 422 Score = 304 bits (779), Expect = 3e-87 Identities = 175/361 (48%), Positives = 229/361 (63%), Gaps = 26/361 (7%) Query: 17 DKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKD 76 D AVD + + GEF++L+GPSGCGKST+LRM+AGLE G I IG RDVTHLPP D Sbjct: 42 DTAAVDAIGFDVAPGEFVILLGPSGCGKSTTLRMIAGLEQATAGRIEIGGRDVTHLPPGD 101 Query: 77 RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKAL 136 R I+MVFQ+YAL+PH++VADN+ F L+ VPKAE R+++ A+++DL YL+RKP L Sbjct: 102 RGISMVFQSYALFPHLSVADNIVFGLRSRKVPKAERRERLARVAQLVDLEAYLERKPAQL 161 Query: 137 SGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQ 196 SGGQRQRVA+ RAI+ E + LMDEPLSNLDA+LR R +I +LQ+RLG+T +YVTHDQ Sbjct: 162 SGGQRQRVALARAIISEHPICLMDEPLSNLDARLRGEMRREIKALQQRLGMTVIYVTHDQ 221 Query: 197 VEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEV-PITDGGVKF 255 VEAM+MGDRV +++DG + Q +P +Y++PA+ F AGFIGSPAMNLV + DG V Sbjct: 222 VEAMSMGDRVILMQDGRIVQDATPSELYERPASAFAAGFIGSPAMNLVTLSAAADGAVID 281 Query: 256 GNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVN 315 G S A + +G+RPE ++ ADAP G+ V Sbjct: 282 G-------EPRCSVAPHEAKGHWLGLRPEEIRLL-------------PADAP-GVPAEVI 320 Query: 316 VVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFSTSTGERL 375 E LGAD V +VG + L R++GR GS + R H F S G+RL Sbjct: 321 DAEYLGADSIV--RLKVGSQ--QLRARLDGRPSLAAGSPCRLQWRRETAHFFDASDGQRL 376 Query: 376 S 376 + Sbjct: 377 A 377 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: 457 Number of extensions: 16 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: 422 Length adjustment: 31 Effective length of query: 346 Effective length of database: 391 Effective search space: 135286 Effective search space used: 135286 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: 50 (23.9 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