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 BWI76_RS07535 BWI76_RS07535 dipeptide/oligopeptide/nickel ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Koxy:BWI76_RS07535 Length = 347 Score = 172 bits (437), Expect = 7e-48 Identities = 98/260 (37%), Positives = 156/260 (60%), Gaps = 9/260 (3%) Query: 4 LVVKNLTKIFSLGFFSKRRI-EAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPP 62 L V NL K F G R + +AV +VSF V + E + +VGESG GK+TTA+++++LL Sbjct: 17 LKVNNLLKHFPAGGGKAREVVQAVDDVSFAVIKGETLGVVGESGCGKSTTARLLMQLLKQ 76 Query: 63 TSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENK 122 SGE+ F+G ++ R + +RR+V VFQD +AS NP T+ ++I+ + Sbjct: 77 DSGELIFDGLEVGSS---RLPMKAYRRQVQMVFQDSYASLNP----RMTMEESIAFGQRV 129 Query: 123 PS-NKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEP 181 + KEA E + L VG++P+ +YPH +SGGQ+QR+ IAR ++P L++ DE Sbjct: 130 HGVSAKEASEYARYLLAHVGLEPERFAHRYPHALSGGQRQRVNIARALAMKPRLVILDEA 189 Query: 182 TSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDK 241 S +D S +++LL+EL+ + +FI+HDL + ++SD I VM GE+VE G ++ Sbjct: 190 VSALDKSVEAQVLQLLQELKRTLALTYVFISHDLHVVRWLSDRILVMYLGEVVEIGPAEQ 249 Query: 242 VVLEPTHEYTKLLVGSIPKL 261 + H YT+ L+ S+P + Sbjct: 250 LFTASAHPYTRALLSSMPSM 269 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: 198 Number of extensions: 9 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: 347 Length adjustment: 27 Effective length of query: 241 Effective length of database: 320 Effective search space: 77120 Effective search space used: 77120 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