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 WP_103234822.1 C1634_RS14760 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >NCBI__GCF_002899945.2:WP_103234822.1 Length = 416 Score = 110 bits (276), Expect = 4e-29 Identities = 83/275 (30%), Positives = 134/275 (48%), Gaps = 25/275 (9%) Query: 3 RLVVKNLTKIFSL-----------GFFSKRRIE------AVKNVSFEVKEKEIVSLVGES 45 +L V++LT IF GF K +E + SFE+ E E ++G S Sbjct: 11 KLKVEDLTIIFGKNKEKAQELLDKGFSKKEILEKTGCTIGINKASFEIYEGEFFVIMGLS 70 Query: 46 GSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPF 105 GSGK+T + + RL PTSG++Y DI K+ + L+E RR ++ F Sbjct: 71 GSGKSTLLRCLNRLNEPTSGKVYINDDDITS--KNNKELLEVRRTEMSMVFQKFG----L 124 Query: 106 YPVERTLWQAISLLENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMI 165 P L A LE + +K E +++L VG++ + +YP Q+SGG +QR+ + Sbjct: 125 LPHHTILDNAGFGLEIRGEDKASRNEKAQKALDIVGLNGFE--NQYPSQLSGGMQQRVGL 182 Query: 166 ARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNI 225 AR P +++ DE S +D + + + EL+ +I+FITHDL A + D I Sbjct: 183 ARALANDPEVLLMDEAFSALDPLIKSEMQDQMLELQNTLQKTIVFITHDLDEAIKIGDRI 242 Query: 226 FVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIPK 260 +MK+G I + G + ++ P +Y K V + + Sbjct: 243 VIMKDGVIEQIGTAEDILTNPASDYVKAFVEKVDR 277 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: 279 Number of extensions: 19 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: 268 Length of database: 416 Length adjustment: 28 Effective length of query: 240 Effective length of database: 388 Effective search space: 93120 Effective search space used: 93120 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: 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