Align TM0030, 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_1124 Dipeptide transport system permease protein DppB (TC 3.A.1.5.2)
Query= TCDB::Q9WXN7 (338 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1124 Length = 336 Score = 179 bits (455), Expect = 7e-50 Identities = 117/342 (34%), Positives = 170/342 (49%), Gaps = 23/342 (6%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 MF ++ RR L+ T+ T + F L R IPG+P+ +++ G RV +PE A Sbjct: 1 MFSFIARRLGLLIPTFFGITLLTFALIRMIPGDPV-EVMMGERRV---DPEMHAQA---- 52 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 ME GL KP Y QY ++I K GDLG S+ V + P TL L + A + A Sbjct: 53 MERLGLNKPLYAQYLDYIGKLAHGDLGESLRTR-ESVWTEFSSLFPATLELSMAALLFAG 111 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 ILG G +AA KR + D GV+ SL +P +W G+I I F V LGW PV G Sbjct: 112 ILGLLAGVIAALKRGSLFDHGVMGVSLAGYSMPIFWWGLILIMFFSVSLGWTPVSGRIDL 171 Query: 186 -------------GTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGS 232 T+ F D L H I+P + + A R ++ L Sbjct: 172 LYDIEPRTGFMLIDTLLADDVGAFFDALHHLILPAIVLGTIPLAVIARMTRSSMLEVLRE 231 Query: 233 DYAMFSEYLGMKDKRI-FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLL 291 DY + G+ R+ F + RN+L+P +T + L +G +L GA++TE +F++PG G L Sbjct: 232 DYIRTARAKGLSPSRVVFVHGLRNALIPVLTVVGLQVGTLLAGAVLTETIFSWPGIGKWL 291 Query: 292 FRALTTLDYPLIQGIFVILIASIYLANFIVDFLYALIDPRIR 333 A+ DYP++Q +++ + L NF+VD LY +PRIR Sbjct: 292 IEAIGARDYPVVQNGILLIACLVILVNFVVDILYGFANPRIR 333 Lambda K H 0.329 0.146 0.449 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: 324 Number of extensions: 18 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: 338 Length of database: 336 Length adjustment: 28 Effective length of query: 310 Effective length of database: 308 Effective search space: 95480 Effective search space used: 95480 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: 49 (23.5 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