Align High-affinity gluconate transporter; Gluconate permease; Gnt-I system (characterized)
to candidate PP_0652 PP_0652 Gluconate transporter
Query= SwissProt::P39835 (438 letters) >FitnessBrowser__Putida:PP_0652 Length = 461 Score = 322 bits (825), Expect = 2e-92 Identities = 165/449 (36%), Positives = 274/449 (61%), Gaps = 13/449 (2%) Query: 3 LVIVAIGVILLLLLMIRFKMNGFIALVLVALAVGLMQGMPLDKVIGSIKAGVGGTLGSLA 62 L +A ++L+ L++ R KM+ +AL++V++ VG M ++ + G G TLG++ Sbjct: 10 LTALASVLVLVALIVSRLKMHPLLALLVVSIGVGFATHMAPGSIVSHLLTGAGKTLGAVG 69 Query: 63 LIMGFGAMLGKMLADCGGAQRIATTLIAKFGKKHIQWAVVLTGFTVGFALFYEVGFVLML 122 +++ GAMLGK+LAD G +++A ++ + + I WA++L F +G +F+EVG V+ML Sbjct: 70 VVIALGAMLGKILADAGVTEQVADVILKRTPDRMIPWAMMLVAFVIGIPMFFEVGLVIML 129 Query: 123 PLVFTIAASANIPL-------LYVGVPMAAALSVTHGFLPPHPGPTAIATIFNADMGKTL 175 PL+F++A +YVGVP+ +AL+ HG +PPHPGP + +G T+ Sbjct: 130 PLIFSVARKLESKARFKGSAYVYVGVPVISALAAMHGMVPPHPGPLTAIAVLKTSVGPTM 189 Query: 176 LYGTILAIPTVILAGPVYA-----RVLKGIDKPIPEGLYSAKTFSEEEMPSFGVSVWTSL 230 LYG + AIP +IL GP+Y R+ D+ + + A+ + P V + +L Sbjct: 190 LYGFLAAIPAMILGGPLYGMFISPRMNTRPDQALLDQFTLAEKADGQPRPGVMVGMLAAL 249 Query: 231 VPVVLMAMRAIAEMILPKGHAFLPVAEFLGDPVMATLIAVLIAMFTFGLNRGRSMDQIND 290 +P +LM + A+AEM+LPKG+A L +A FLG+P++A L+ VL A + L RG +Q+ D Sbjct: 250 LPAILMLVHAVAEMLLPKGNALLEMASFLGNPLIAMLLGVLFAGASLVLARGGDAEQLRD 309 Query: 291 TLVSSIKIIAMMLLIIGGGGAFKQVLVDSGVDKYIASMMHETNISPLLMAWSIAAVLRIA 350 L S+K IA +++II GGGAF+++L + V I + ++ PL++ W IA +L ++ Sbjct: 310 ALGKSLKPIASIIMIIAGGGAFQEMLTSAKVGDAIVHLTQQSAFPPLILGWLIAMLLSVS 369 Query: 351 LGSATVAAITAGGIAAPLI-ATTGVSPELMVIAVGSGSVIFSHVNDPGFWLFKEYFNLTI 409 GSATV + A G+ APL A ++ L+ +++G GS+ F++ N GFW+ KE F +T+ Sbjct: 370 TGSATVGIVGAAGLLAPLAGADPSLNLPLLALSIGCGSLFFNYANHAGFWMVKESFGMTM 429 Query: 410 GETIKSWSMLETIISVCGLVGCLLLNMVI 438 GE K+ S++++I++V GL+ L+LN I Sbjct: 430 GEATKTISVVQSIVAVVGLMVVLMLNAAI 458 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: 525 Number of extensions: 25 Number of successful extensions: 5 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: 461 Length adjustment: 33 Effective length of query: 405 Effective length of database: 428 Effective search space: 173340 Effective search space used: 173340 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