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 GFF205 HP15_204 oligopeptide/dipeptide ABC transporter, ATPase subunit
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Marino:GFF205 Length = 336 Score = 162 bits (411), Expect = 7e-45 Identities = 91/251 (36%), Positives = 150/251 (59%), Gaps = 6/251 (2%) Query: 13 FSLGFFSKRR--IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFE 70 F G F +++ + A+ V EV++ E + +VGESG GK+T A+ ++ LL P++GEI+++ Sbjct: 27 FEGGRFRRKQEAVHAINGVDLEVQKGEALCVVGESGCGKSTVARTVMGLLSPSAGEIHYD 86 Query: 71 GKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEAL 130 G+ I D +R+ + +RRK+ +FQ+P+AS NP +++TL + I + + + Sbjct: 87 GQRI--DNLERKDSLPYRRKMQMIFQNPYASLNPRMTIQQTLEEPIRF-HHPDWSPVQVR 143 Query: 131 ELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSR 190 + I E + VGID +D ++ H+ SGGQ+QRI IAR + P IVADEP S +D S + Sbjct: 144 DKIHEVMHSVGID-QDWGNRFGHEFSGGQRQRIAIARALAVDPEFIVADEPISALDVSIQ 202 Query: 191 GGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEY 250 ++ LL + +E +G + +FITHDL + + + VM G + E + P H Y Sbjct: 203 AQVLNLLMDAQESRGLTYLFITHDLAVVEHFGTRVAVMYLGRVCELADTKTLFSAPRHPY 262 Query: 251 TKLLVGSIPKL 261 T+ L+ +IPKL Sbjct: 263 TQALLSAIPKL 273 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: 196 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: 336 Length adjustment: 27 Effective length of query: 241 Effective length of database: 309 Effective search space: 74469 Effective search space used: 74469 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