Align TM0029, 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 GFF666 PGA1_c06800 dipeptide transport system permease protein DppC
Query= TCDB::Q9WXN6 (280 letters) >FitnessBrowser__Phaeo:GFF666 Length = 304 Score = 116 bits (291), Expect = 5e-31 Identities = 73/233 (31%), Positives = 129/233 (55%), Gaps = 14/233 (6%) Query: 57 LGTDTYGRDVLAQLLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGITNI 116 LGTD GRDV + +L+G+R SL +G L+ ++V+G I+G + G + ++M + ++ Sbjct: 75 LGTDDQGRDVFSTILYGMRISLMVGVLSVTFAMVLGIILGLLAGYVGGWTETIIMRVADV 134 Query: 117 VLTTPSILIAILIASYLK-VRSVE--------MVAVILGLFQWPWFARAIRAQLMSVMSR 167 LT PSIL+A+LI +K V VE ++ + +GL +W FAR +R + +R Sbjct: 135 QLTFPSILVAMLIFGIVKGVTPVEYRDQMAIWVLILAIGLGEWVQFARVVRGATLVEKNR 194 Query: 168 EYVYLSVMAGYSDLRLVIEDLIPTIATYAFMSFVLFINGGIMGEAGLSLIGLG--PTQGI 225 EYV + + G S ++I L+P + + + + + I+ EA LS +G+G PTQ Sbjct: 195 EYVQAARLIGRSKWVIMIRHLLPNVLSPVLVIATISLALAIIAEATLSFLGVGAPPTQP- 253 Query: 226 SLGIMLQWAVLMEAVRRGLWWWFVPPGLAIVAVTASLLVISTAMDEVFNPRLR 278 SLG +++ + + G WW + P L ++ + S+ ++ + + NP+LR Sbjct: 254 SLGTLIR--IGQGFLFSGEWWILLFPALTLLTLALSVNMLGDWLRDALNPKLR 304 Lambda K H 0.330 0.144 0.441 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: 201 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: 280 Length of database: 304 Length adjustment: 26 Effective length of query: 254 Effective length of database: 278 Effective search space: 70612 Effective search space used: 70612 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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