Align Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate SM_b20856 SM_b20856 sugar uptake ABC transporter substrate-binding protein precursor
Query= TCDB::Q9X053 (323 letters) >FitnessBrowser__Smeli:SM_b20856 Length = 322 Score = 145 bits (365), Expect = 2e-39 Identities = 104/325 (32%), Positives = 161/325 (49%), Gaps = 20/325 (6%) Query: 1 MKKSLFVVLVLVGLLLVSFTGLAQEQQKPKGKMAIVISTLNNPWFVVLAETAKQRAEQLG 60 MKKS+ ++ + + V+ G+A K+ I + TL P+F A+ +A++ G Sbjct: 1 MKKSIAGCMLAL-MASVASAGIANAADC---KVGIAMYTLGAPYFAAQVAAAEDQAKKAG 56 Query: 61 YEATIFDSQNDTAKESAHFDAIIAAGYDAIIFNPTDADGSIANVKRAKEAGIPVFCVDRG 120 E T D QND K+ A + ++A G + +I NP D +G +A A AG+ V +D Sbjct: 57 CEVTSADGQNDMTKQIADVEDMVARGVNLLILNPRDPEGLVAAADAATAAGVKVVVMDSS 116 Query: 121 INARGLAVAQIYSDNYYGGVLMGEYFVKFLKEKYPDAKEIPYAELLGILSAQPTWDRSNG 180 IN + V Q+ S N GVL+G++ +K K + L G + DR G Sbjct: 117 INTKANVVTQVRSSNDQNGVLVGQWLANAMK-----GKPMKIILLSGDKGNEVGRDRRLG 171 Query: 181 FHS-------VVDQYPEFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALG 233 V D F++V Q + + E +L AHP+ + ND+M LG Sbjct: 172 VFKGLVEGQLVNDGKVSFEVVGQGWGGWAHEGGLAAMEDLLTAHPDANVVLGENDSMVLG 231 Query: 234 AMKACEAAGRTDIY-IFGFDGAEDVINAIKEGKQIVATIMQFPKLMARLAVEWADQYLRG 292 AMKA EA G+TD+ + DG ++ + IKEGK AT + P L+AR AV+ + + G Sbjct: 232 AMKALEAQGKTDVLALAAADGQKEALALIKEGK-YGATGLNDPDLVARTAVDVGLKAVNG 290 Query: 293 E--RSFPEIVPVTVELVTRENIDKY 315 E FP++ T ++T+EN+DKY Sbjct: 291 ELPADFPKLNLTTPAVITKENVDKY 315 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: 205 Number of extensions: 9 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: 323 Length of database: 322 Length adjustment: 28 Effective length of query: 295 Effective length of database: 294 Effective search space: 86730 Effective search space used: 86730 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