Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate 3607472 Dshi_0885 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Dino:3607472 Length = 322 Score = 174 bits (442), Expect = 2e-48 Identities = 96/242 (39%), Positives = 145/242 (59%), Gaps = 8/242 (3%) Query: 20 KRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIK 79 K + AV +VSF+V+E+ + +LVGESGSGK+T KM++ LL P+ G + G D+ ++ Sbjct: 30 KAILTAVSDVSFDVEERTVYALVGESGSGKSTIGKMVVGLLQPSEGSVKIGGTDLARET- 88 Query: 80 DRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFR 139 D L R + +FQDPFAS NP + V + + +S E L L + Sbjct: 89 DPAKLDLVRADIQMIFQDPFASLNPRWRVRDIINEPVSARGGDVKGLAERL------LEQ 142 Query: 140 VGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEE 199 VG+ +D GK+PH+ SGGQ+QRI IAR P LIV DEPTS +D S + ++ L+ + Sbjct: 143 VGLAAEDA-GKFPHEFSGGQRQRICIARALASEPKLIVCDEPTSALDVSVQAQVLNLMSD 201 Query: 200 LREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIP 259 L++E G + +FI+HDL + +V+D I V+ G +VE PD + P H YT++L+ + P Sbjct: 202 LKDEFGLTYLFISHDLTVVQHVADRIGVLYLGRLVEEADPDTLFENPRHPYTQMLLAAAP 261 Query: 260 KL 261 K+ Sbjct: 262 KM 263 Lambda K H 0.319 0.139 0.397 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: 230 Number of extensions: 10 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: 268 Length of database: 322 Length adjustment: 26 Effective length of query: 242 Effective length of database: 296 Effective search space: 71632 Effective search space used: 71632 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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