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 Pf1N1B4_1127 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1127 Length = 326 Score = 159 bits (403), Expect = 6e-44 Identities = 90/262 (34%), Positives = 152/262 (58%), Gaps = 8/262 (3%) Query: 4 LVVKNLTKIFSLG---FFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL 60 L +NLT+ + + F + A+ VSFE++ + +++VGESG GK+T A+ + + Sbjct: 5 LTARNLTRHYEVSRGLFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLARALTLIE 64 Query: 61 PPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLE 120 P+SG + G+++ D+ + R+ V VFQ P+AS NP V L A LL Sbjct: 65 EPSSGSLKIAGQEVAG--ADKAQRKQLRKDVQMVFQSPYASLNPRQKVGDQL--AEPLLI 120 Query: 121 NKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADE 180 N + E E ++ + +VG+ P+ +YPH SGGQ+QRI +AR +L+P ++VADE Sbjct: 121 NTNLSASERREKVQAMMKQVGLRPEHYQ-RYPHMFSGGQRQRIALARAMMLQPKVLVADE 179 Query: 181 PTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPD 240 PTS +D S + ++ L +L++E T+ +FI+H+L + +V+D++ VM G VE G + Sbjct: 180 PTSALDVSIQAQVLNLFMDLQQEFNTAYVFISHNLAVVRHVADHVMVMYLGRPVEMGPKE 239 Query: 241 KVVLEPTHEYTKLLVGSIPKLY 262 + P H YT+ L+ + P ++ Sbjct: 240 DIYTRPLHPYTQALLSATPTIH 261 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: 218 Number of extensions: 11 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: 326 Length adjustment: 26 Effective length of query: 242 Effective length of database: 300 Effective search space: 72600 Effective search space used: 72600 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 Apr 09 2024. 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