Align Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate Pf6N2E2_1793 Inositol transport system sugar-binding protein
Query= TCDB::Q9X053 (323 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1793 Length = 308 Score = 111 bits (278), Expect = 2e-29 Identities = 84/250 (33%), Positives = 125/250 (50%), Gaps = 15/250 (6%) Query: 48 LAETAKQRAEQLGYEATIFDSQNDTAKESAHFDAIIAAGYDAIIFNPTDADGSIANVKRA 107 LAE AK+ Q+ +E D+Q D ++ I DA+I P D + + A Sbjct: 44 LAEAAKKENVQIQFE----DAQGDVVRQLNQVQGFINQKVDAVIVLPVDTSATANITRAA 99 Query: 108 KEAGIPVFCVDRGINARGL--AVAQIYSDNYYGGVLMGEYFVKFLKEKYPDAKEIPYAEL 165 EA P+ V+R + R L V + S++ G L +++L EK + A + Sbjct: 100 VEAKTPLVYVNRHPDERTLPKGVVTVASNDIEAGHLQ----MRYLAEKLGGKGNL--AII 153 Query: 166 LGILSAQPTWDRSNGFHSVVDQYPEFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWC 225 +G L+ T DR+ G V+ YP K+V QQSAE+ R+ +T L A AI Sbjct: 154 MGDLAQNATHDRTEGVKQVLKDYPGIKIVEQQSAEWQRNKGMDLTSNWLLAGSRFDAIVA 213 Query: 226 GNDAMALGAMKACEAAGRT--DIYIFGFDGAEDVINAIKEGKQIVATIMQFPKLMARLAV 283 ND MA+GA A + AG+T ++ I G DG D + AIK G +VA++ Q PK A AV Sbjct: 214 NNDEMAIGAAMALQQAGKTKGEVAIVGIDGLPDGLAAIKRG-MLVASVFQDPKAQATSAV 272 Query: 284 EWADQYLRGE 293 + A + ++GE Sbjct: 273 QAALKMIKGE 282 Lambda K H 0.319 0.135 0.393 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: 168 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 323 Length of database: 308 Length adjustment: 27 Effective length of query: 296 Effective length of database: 281 Effective search space: 83176 Effective search space used: 83176 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 (21.8 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