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 17601 b3540 dipeptide transporter (NCBI)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Keio:17601 Length = 334 Score = 169 bits (428), Expect = 7e-47 Identities = 89/245 (36%), Positives = 150/245 (61%), Gaps = 5/245 (2%) Query: 17 FFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWK 76 F +R ++A+ VSF ++ + +++VGESG GK+T +++ + PT GE+Y++G+D+ K Sbjct: 29 FAPERLVKALDGVSFNLERGKTLAVVGESGCGKSTLGRLLTMIEMPTGGELYYQGQDLLK 88 Query: 77 DIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKES 136 + L R+K+ VFQ+P+ S NP V + L + LL N +K++ E Sbjct: 89 HDPQAQKLR--RQKIQIVFQNPYGSLNPRKKVGQILEEP--LLINTSLSKEQRREKALSM 144 Query: 137 LFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKL 196 + +VG+ + +YPH SGGQ+QRI IAR +L P +++ADEP S +D S R ++ L Sbjct: 145 MAKVGLKTEHY-DRYPHMFSGGQRQRIAIARGLMLDPDVVIADEPVSALDVSVRAQVLNL 203 Query: 197 LEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVG 256 + +L++E G S +FI+HDL + +++D + VM G VE+G D++ P H YT+ L+ Sbjct: 204 MMDLQQELGLSYVFISHDLSVVEHIADEVMVMYLGRCVEKGTKDQIFNNPRHPYTQALLS 263 Query: 257 SIPKL 261 + P+L Sbjct: 264 ATPRL 268 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: 228 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: 334 Length adjustment: 27 Effective length of query: 241 Effective length of database: 307 Effective search space: 73987 Effective search space used: 73987 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