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_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 308 bits (788), Expect = 2e-88 Identities = 180/364 (49%), Positives = 228/364 (62%), Gaps = 48/364 (13%) Query: 20 AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79 A+ Q+ + I+ GEF+V VGPSGCGKST LRM+AGLE +NGG + + RD+T +PP RD+ Sbjct: 18 AIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILDGRDITEVPPSQRDL 77 Query: 80 AMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGG 139 AMVFQ+YALYPHMTV +NM FAL++A V A I++KV+ AA L+LT YL R PKALSGG Sbjct: 78 AMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADKLNLTAYLQRTPKALSGG 137 Query: 140 QRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEA 199 QRQRVA+GR+IVR P+VFL DEPLSNLDA LR +TR +IASL R LG TTVYVTHDQVEA Sbjct: 138 QRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLHRELGATTVYVTHDQVEA 197 Query: 200 MTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSV 259 MT+ DRV VL+DG+++QV +P +YD+P N FVA FIG P MN+ + FG Sbjct: 198 MTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMNVAPASL------FGQFP 251 Query: 260 VPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEE 319 V VG+RPEH +V + LA V +VE Sbjct: 252 AQV--------------AEVGIRPEHLQMVSPEDGL--------------LAGKVVLVEA 283 Query: 320 LGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPG-------ETHVFSTSTG 372 LG + V+ + + L+VR+ GR +T+HV R G H F T G Sbjct: 284 LGNETLVHVRPDKVQLEEPLIVRLYGR------TTVHVGDRVGLKWDDSKHIHYFDTK-G 336 Query: 373 ERLS 376 RL+ Sbjct: 337 MRLT 340 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: 409 Number of extensions: 14 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: 348 Length adjustment: 29 Effective length of query: 348 Effective length of database: 319 Effective search space: 111012 Effective search space used: 111012 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