Align High-affinity gluconate transporter; Gluconate permease; Gnt-I system (characterized)
to candidate Echvi_2089 Echvi_2089 gluconate transporter
Query= SwissProt::P39835 (438 letters) >FitnessBrowser__Cola:Echvi_2089 Length = 438 Score = 431 bits (1107), Expect = e-125 Identities = 210/438 (47%), Positives = 311/438 (71%), Gaps = 1/438 (0%) Query: 1 MPLVIVAIGVILLLLLMIRFKMNGFIALVLVALAVGLMQGMPLDKVIGSIKAGVGGTLGS 60 M ++ V + ++LL+LL++ K+N FIA ++ ++ GL+ G+P ++V S++ G+G LG Sbjct: 1 MTILFVLLSILLLVLLIVWAKLNPFIAFLITSIVAGLLLGIPPEQVAVSVQQGMGSLLGD 60 Query: 61 LALIMGFGAMLGKMLADCGGAQRIATTLIAKFGKKHIQWAVVLTGFTVGFALFYEVGFVL 120 L +I+ GAMLGK++A+ G AQRIA L+ FGKK+I WA+++TG VG LFY VGFVL Sbjct: 61 LVIIITMGAMLGKLVAESGAAQRIADFLMRVFGKKYIHWAMMVTGLVVGIPLFYNVGFVL 120 Query: 121 MLPLVFTIAASANIPLLYVGVPMAAALSVTHGFLPPHPGPTAIATIFNADMGKTLLYGTI 180 ++PLVFT+A + +YVG+P+ AALSVTHGFLPPHP P A+ F+A+MG TLLYG + Sbjct: 121 LVPLVFTVAHQYKLSAVYVGIPLLAALSVTHGFLPPHPSPAALVAQFDANMGVTLLYGMM 180 Query: 181 LAIPTVILAGPVYARVLKGIDKPIPEGLYSAKTFSEEEMPSFGVSVWTSLVPVVLMAMRA 240 +AIPT+++AGP +AR LK I P + A + EEE+P S ++L+PVVL+ Sbjct: 181 VAIPTILVAGPFFARFLKHIPAS-PLKSFRASSKPEEELPGTINSFLSALLPVVLLVGTP 239 Query: 241 IAEMILPKGHAFLPVAEFLGDPVMATLIAVLIAMFTFGLNRGRSMDQINDTLVSSIKIIA 300 + M + A +F+ DP M L ++L+A FT GL++G MD + D V S+K +A Sbjct: 240 VLLMQTDEQSALYGYVKFIADPGMVMLFSLLVATFTLGLHQGMKMDHLMDIYVDSVKDVA 299 Query: 301 MMLLIIGGGGAFKQVLVDSGVDKYIASMMHETNISPLLMAWSIAAVLRIALGSATVAAIT 360 M++LI+ G GA KQVL+DSGV + IA + N+ PL++AW+I AV+R+ +GSATVA +T Sbjct: 300 MIILIVAGAGALKQVLLDSGVSQVIADGLEGWNVHPLVLAWTITAVIRVCVGSATVAGLT 359 Query: 361 AGGIAAPLIATTGVSPELMVIAVGSGSVIFSHVNDPGFWLFKEYFNLTIGETIKSWSMLE 420 GI APLI +GV P L+V+A+G+GS++FSH ND GFW++KE+FN++I +TI+SWS++E Sbjct: 360 TAGIIAPLIEGSGVDPNLVVLAIGAGSLMFSHFNDAGFWMYKEFFNVSIKDTIRSWSVME 419 Query: 421 TIISVCGLVGCLLLNMVI 438 TI++V GL G ++L+ V+ Sbjct: 420 TIVAVVGLAGVMVLDWVV 437 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: 21 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: 438 Length of database: 438 Length adjustment: 32 Effective length of query: 406 Effective length of database: 406 Effective search space: 164836 Effective search space used: 164836 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