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 PP_4454 PP_4454 putative Opine ABC transporter, permease protein
Query= TCDB::Q9WXN6 (280 letters) >FitnessBrowser__Putida:PP_4454 Length = 290 Score = 145 bits (367), Expect = 8e-40 Identities = 85/281 (30%), Positives = 158/281 (56%), Gaps = 10/281 (3%) Query: 4 TMIRPLFKNKKFIIGFSIFLFFLFLGIFGPMFYRVDPTEMTWDYE-QPPSSAHPLGTDTY 62 T+ + LF+N+ IG + + + + +F P+ DP + Y +PPS+ LGTDTY Sbjct: 14 TLWQALFQNRLSWIGIGLLVMIVLVALFAPLIAPYDPLQQNIAYRLEPPSAEFWLGTDTY 73 Query: 63 GRDVLAQLLHGIRSSLYIGFLAAIISLVIGTIIGSFSAVKRGIVDDVLMGITNIVLTTPS 122 GRDVL++L++G R SL +GF+A +I++V+G+ +G + GI D ++ G +++L+ P+ Sbjct: 74 GRDVLSRLIYGTRVSLLVGFVAVMIAMVVGSALGVIAGYVGGITDRLITGFVDVLLSFPT 133 Query: 123 ILIAILIASYLKVRSVEMVAVILGLFQWPWFARAIRAQLMSVMSREYVYLSVMAGYSDLR 182 +L+ +++A+ L S+E + + + + + F R RA +++ R++V GY R Sbjct: 134 LLLGLMVAAMLGA-SLENLIIAIAITEIAPFVRIARAPTIALKQRDFVEAGRSLGYGPGR 192 Query: 183 LVIEDLIPTIATYAFMSFVLFINGGIMGEAGLSLIGLG-PTQGISLGIMLQ--WAVLMEA 239 L+ ++P + + + L++ I EA LS IGLG P + G M++ + +++A Sbjct: 193 LMTVHILPNMISEVLVLGALWMATAIRTEASLSFIGLGVPPPAPTWGSMIREGFENILDA 252 Query: 240 VRRGLWWWFVPPGLAIVAVTASLLVISTAMDEVFNPRLREE 280 WW V P LAI+ +L ++ A+ + +P+ R E Sbjct: 253 -----WWLTVFPSLAILLTVLALSLLGDALRDANDPKTRSE 288 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: 196 Number of extensions: 12 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: 290 Length adjustment: 26 Effective length of query: 254 Effective length of database: 264 Effective search space: 67056 Effective search space used: 67056 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: 47 (22.7 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