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 GFF668 PGA1_c06820 dipeptide transport ATP-binding protein DppF
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Phaeo:GFF668 Length = 321 Score = 177 bits (450), Expect = 2e-49 Identities = 99/265 (37%), Positives = 157/265 (59%), Gaps = 17/265 (6%) Query: 6 VKNLTKIFS---------LGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMI 56 V LT++F L K + AV +VSF++KEK + SLVGESGSGK+T KM+ Sbjct: 7 VNELTRVFDVSKPWLNRVLERLPKSHLTAVSDVSFDIKEKTVYSLVGESGSGKSTIGKMV 66 Query: 57 LRLLPPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAI 116 + LL +SG + G D+ ++ D ++ + R + +FQDP+AS NP + V + + + Sbjct: 67 VGLLENSSGAVKVSGVDLNRET-DAVAITKARDAIQMIFQDPYASMNPRWRVRDIIAEPV 125 Query: 117 SLLENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLI 176 + + E EL + L +VG+ +D K+PH+ SGGQ+QRI IAR +P LI Sbjct: 126 A------AKGGETKELAERLLEQVGLSAEDA-DKFPHEFSGGQRQRICIARSLASQPRLI 178 Query: 177 VADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVER 236 V DEPTS +D S + ++ L+ +L+++ G + +FI+HDL + ++SD I V+ G +VE Sbjct: 179 VCDEPTSALDVSVQAQVLNLMSDLKDDLGLTYLFISHDLTVVRHISDRIGVLYLGRLVEE 238 Query: 237 GHPDKVVLEPTHEYTKLLVGSIPKL 261 PD + P H YT++L+ + PK+ Sbjct: 239 AAPDDLFEAPKHPYTQMLLAAAPKM 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: 209 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: 321 Length adjustment: 26 Effective length of query: 242 Effective length of database: 295 Effective search space: 71390 Effective search space used: 71390 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