Align High-affinity gluconate transporter; Gluconate permease; Gnt-I system (characterized)
to candidate CA265_RS01125 CA265_RS01125 gluconate permease
Query= SwissProt::P39835 (438 letters) >FitnessBrowser__Pedo557:CA265_RS01125 Length = 429 Score = 413 bits (1062), Expect = e-120 Identities = 211/438 (48%), Positives = 302/438 (68%), Gaps = 9/438 (2%) Query: 1 MPLVIVAIGVILLLLLMIRFKMNGFIALVLVALAVGLMQGMPLDKVIGSIKAGVGGTLGS 60 M L I+ G++LL +L+++ K+N IAL+ VA+ GL+ GMP KV+ SI G+G TLGS Sbjct: 1 MSLFILLFGILLLFVLILK-KINPMIALIAVAIITGLLLGMPATKVMASISNGIGSTLGS 59 Query: 61 LALIMGFGAMLGKMLADCGGAQRIATTLIAKFGKKHIQWAVVLTGFTVGFALFYEVGFVL 120 + +++ GAM+GK++ D G A++I LI FGKK+IQWAV+LTG VG LFY GFV+ Sbjct: 60 MVMVLALGAMMGKLIEDSGSAKKIVFILIGAFGKKNIQWAVLLTGLLVGIPLFYNAGFVV 119 Query: 121 MLPLVFTIAASANIPLLYVGVPMAAALSVTHGFLPPHPGPTAIATIFNADMGKTLLYGTI 180 ++PLVF I+A+ + LY+G+PMA ALSVTHGFLPPHPGP A+A IF+AD+GKTL+YG Sbjct: 120 LIPLVFAISATTGLSKLYIGIPMATALSVTHGFLPPHPGPVALAGIFHADIGKTLIYGLT 179 Query: 181 LAIPTVILAGPVYARVLKGIDKPIPEGLYSAKTFSEEEMPSFGVSVWTSLVPVVLMAMRA 240 L++P ++AG + R++ D+ + +S EE +PS S T+L+PV L+ Sbjct: 180 LSVPIAVIAGIYFPRLILKRDQSVTVQHFSIS--EEENLPSASRSFITALLPVFLIIAGT 237 Query: 241 IAEMILPKGHAFLPVAEFLGDPVMATLIAVLIAMFTFGLNRGRSMDQINDTLVSSIKIIA 300 I + P+ FL DP A LI+V+IA+ + S+ + ++ +K IA Sbjct: 238 IGSS-FKIDYICKPLFIFLADPTAALLISVIIALVV----QKTSITKAMESCAEGVKSIA 292 Query: 301 MMLLIIGGGGAFKQVLVDSGVDKYIASMMHETNISPLLMAWSIAAVLRIALGSATVAAIT 360 M++LII GGAFKQ+L+DSG+ + + + N+SPLL+AW I A LR+ LGSATVAA+T Sbjct: 293 MIILIIAAGGAFKQILIDSGMGETVKQLTGGLNLSPLLLAWLITASLRVTLGSATVAALT 352 Query: 361 AGGIAAPLIATTGVSPELMVIAVGSGSVIFSHVNDPGFWLFKEYFNLTIGETIKSWSMLE 420 A G+ PLI G PELMV++VG+GS++FSHVND GFW+FKEYFNL++ ET ++W+M+E Sbjct: 353 ASGMVLPLIG-PGTPPELMVLSVGAGSLMFSHVNDTGFWMFKEYFNLSLKETFRTWTMME 411 Query: 421 TIISVCGLVGCLLLNMVI 438 +++SV GLVG L+LN + Sbjct: 412 SLVSVLGLVGVLVLNQFV 429 Lambda K H 0.327 0.142 0.417 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: 543 Number of extensions: 38 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: 438 Length of database: 429 Length adjustment: 32 Effective length of query: 406 Effective length of database: 397 Effective search space: 161182 Effective search space used: 161182 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 (21.7 bits) S2: 51 (24.3 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