Align Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate SM_b20349 SM_b20349 sugar ABC transporter
Query= TCDB::Q9X053 (323 letters) >FitnessBrowser__Smeli:SM_b20349 Length = 313 Score = 205 bits (521), Expect = 1e-57 Identities = 119/287 (41%), Positives = 172/287 (59%), Gaps = 8/287 (2%) Query: 33 MAIVISTLNNPWFVVLAETAKQRAEQLGYEATIFDSQNDTAKESAHFDAIIAAGYDAIIF 92 +AI+ + +NP+F A A+ +A++LGYE + +D K+S D I G AII Sbjct: 30 IAIITPSHDNPFFKAEAVGAEAKAKELGYETLVLVHDDDANKQSQLIDTAIGRGAKAIIL 89 Query: 93 NPTDADGSIANVKRAKEAGIPVFCVDRGINARGLAVAQIYSDNYYGGVLMGEYFVKFLKE 152 + ++ SIA V++AK+AG+P F +DR INA G+AV+QI S+NY G L E FVK + E Sbjct: 90 DNAGSEASIAAVQKAKDAGVPSFLIDREINATGVAVSQIVSNNYQGAQLGAEEFVKLMGE 149 Query: 153 KYPDAKEIPYAELLGILSAQPTWDRSNGFHSVVDQYPEFKMVAQQSAEFDRDTAYKVTEQ 212 Y ELLG + RS G+H V+D+YPE KMVAQQSA + + Y E Sbjct: 150 SGN------YVELLGREADLNAGIRSKGYHDVIDEYPEMKMVAQQSANWSQTEGYSKMET 203 Query: 213 ILQAHPEIKAIWCGNDAMALGAMKACEAAGRTDIYIFGFDGAEDVINAIKEGKQIVATIM 272 ILQA+P+IK + GND MA+GA+ A +AAGR D+ + GFDG+ DV ++IK G I AT++ Sbjct: 204 ILQANPDIKGVISGNDTMAMGAIAALQAAGRKDVIVVGFDGSNDVRDSIKSG-GIKATVL 262 Query: 273 QFPKLMARLAVEWADQYL-RGERSFPEIVPVTVELVTRENIDKYTAY 318 Q A++AV+ A +Y+ G+ E + L+ EN D+ + Sbjct: 263 QPAYAQAQMAVQQAHEYITTGKAPAEEKQLMDCVLINSENADQLETF 309 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: 239 Number of extensions: 14 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: 313 Length adjustment: 27 Effective length of query: 296 Effective length of database: 286 Effective search space: 84656 Effective search space used: 84656 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