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 SM_b21605 SM_b21605 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Smeli:SM_b21605 Length = 362 Score = 325 bits (833), Expect = 1e-93 Identities = 182/358 (50%), Positives = 229/358 (63%), Gaps = 24/358 (6%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVF 83 +DI I GEF V VGPSGCGKST LRM+AGLE+ GG IRI DVTH P R +AMVF Sbjct: 22 VDIEIGQGEFAVFVGPSGCGKSTLLRMIAGLEETTGGEIRIDAEDVTHKEPSKRGVAMVF 81 Query: 84 QNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQR 143 Q+YALYPH++V DNM F+L IA PKAEI QKV+ AA+IL L+ YLD KP LSGGQRQR Sbjct: 82 QSYALYPHLSVFDNMAFSLSIARRPKAEIEQKVKAAAEILRLSDYLDSKPSQLSGGQRQR 141 Query: 144 VAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMG 203 VA+GRAIVREP+VFL DEPLSNLDA+LRV R +IA L R++G T VYVTHDQVEAMT+ Sbjct: 142 VAIGRAIVREPRVFLFDEPLSNLDAELRVKMRMEIARLHRQIGATMVYVTHDQVEAMTLA 201 Query: 204 DRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGG-----VKFGNS 258 DR+ VLK G++QQ +P +Y P N+FVAGFIGSP MN ++ + G ++ ++ Sbjct: 202 DRIVVLKAGVVQQTGAPLELYRNPDNMFVAGFIGSPGMNFLKARVVPGSGDRLTIELHDA 261 Query: 259 V-VPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVV 317 VP A + G+ + VGVRPEH + E G V GL V+ + Sbjct: 262 PGVPFEIPARTGPAVGEE-IFVGVRPEHITLGEREGGV-------------GLDVTAEFI 307 Query: 318 EELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFSTSTGERL 375 EELG GY++ G +++ + G + P+ + + P E F S GERL Sbjct: 308 EELGGTGYLHALTVTG---EEMTIECRGEERPQPKQAVRLTLAPEEMFAFEGS-GERL 361 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: 423 Number of extensions: 16 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: 362 Length adjustment: 30 Effective length of query: 347 Effective length of database: 332 Effective search space: 115204 Effective search space used: 115204 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 17 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