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 GFF3696 PGA1_262p01000 dipeptide transport ATP-binding protein DppF
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Phaeo:GFF3696 Length = 344 Score = 168 bits (426), Expect = 1e-46 Identities = 95/272 (34%), Positives = 152/272 (55%), Gaps = 18/272 (6%) Query: 4 LVVKNLTKIFSL--GFFS------------KRRIEAVKNVSFEVKEKEIVSLVGESGSGK 49 L +KNL K F L GF KR + AV NVS E + +VGESG GK Sbjct: 12 LELKNLEKRFELDKGFLETIKLRGGRITREKRAVHAVNNVSLSADRGEALCIVGESGCGK 71 Query: 50 TTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVE 109 +T A+++ LL P+ GEI+++G+ I D + R ++ R+K+ +FQ+P+AS NP ++ Sbjct: 72 STVARLVAGLLAPSGGEIHYDGERI--DDRSRGEMMPLRKKMQMIFQNPYASLNPRMTIQ 129 Query: 110 RTLWQAISLLENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCW 169 + L + + N ++ E + + E + VG+DP +YPH+ SGGQ+QRI IAR Sbjct: 130 QALEEPVRH-HNPSLSRGEVRDKVSEVMRSVGVDPS-WSSRYPHEFSGGQRQRIAIARAL 187 Query: 170 ILRPLLIVADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMK 229 + P I+ADEP S +D S + ++ L+ E ++++G + FITHDL + + + V+ Sbjct: 188 TVDPEFIIADEPISALDVSIQAQVLNLMLEAKDQRGLTYFFITHDLSVVEHFGTRVAVLY 247 Query: 230 NGEIVERGHPDKVVLEPTHEYTKLLVGSIPKL 261 G + E + P H YTK L+ ++P+L Sbjct: 248 LGTLCELADTQTLFENPKHPYTKALLSAVPQL 279 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: 216 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: 344 Length adjustment: 27 Effective length of query: 241 Effective length of database: 317 Effective search space: 76397 Effective search space used: 76397 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