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 Ac3H11_4314 Dipeptide transport system permease protein DppC (TC 3.A.1.5.2)
Query= TCDB::Q9WXN6 (280 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4314 Length = 328 Score = 98.2 bits (243), Expect = 2e-25 Identities = 71/227 (31%), Positives = 112/227 (49%), Gaps = 15/227 (6%) Query: 49 QPPSSAHPLGTDTYGRDVLAQLLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDD 108 Q PS+AH LGTD GRD A+L+ G SL FLA + LV+GT++G + G V+D Sbjct: 106 QAPSAAHWLGTDALGRDGYARLVFGAVHSLSGAFLAVAVGLVLGTLLGVLAGSIGGWVED 165 Query: 109 VLMGITNIVLTTPSILIAILIASYLKVRSVEMVAVILGLFQWPWFARAIRAQLMSVMSRE 168 V+M +++L+ P +L+++ I L ++ AV +G+ FAR R++++ V E Sbjct: 166 VIMRTVDVLLSVPPLLLSLSIIIILGFGTLN-AAVAVGVASVASFARLTRSEVVRVRRSE 224 Query: 169 YVYLSVMAGYSDLRLVIEDLIPTIATYAFMSFVLFINGGIMGEAGLSLIGLG---PTQGI 225 YV + +G ++ ++P T L I+ + L +G G PT Sbjct: 225 YVEAAFGSGGRFGAVLWRHVLPNSLTSVIAMAALQFGSAILSISTLGFLGYGAPPPTP-- 282 Query: 226 SLGIMLQWAVLMEAVRRGL---WWWFVPPGLAIVAVTASLLVISTAM 269 +W +L+ R + WW PGL +VAV S IS A+ Sbjct: 283 ------EWGLLIAEGRNYIATAWWLTTVPGLVVVAVVLSANRISAAL 323 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: 227 Number of extensions: 14 Number of successful extensions: 4 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: 328 Length adjustment: 27 Effective length of query: 253 Effective length of database: 301 Effective search space: 76153 Effective search space used: 76153 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