Align gluconate:H+ symporter (gntT) (characterized)
to candidate AO353_25205 AO353_25205 permease DsdX
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25205 Length = 447 Score = 368 bits (945), Expect = e-106 Identities = 194/451 (43%), Positives = 285/451 (63%), Gaps = 5/451 (1%) Query: 4 VTGTTLLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGG 63 +T T LL +++ +VVLI KF+++PF++L+ S+L+G GM IV +FE G+G Sbjct: 1 MTPTYSLLTLGASILLIVVLIGKFRVHPFLSLIAASLLVGIGTGMAPTAIVSAFEKGMGS 60 Query: 64 TLGHIALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEV 123 TLG +A ++GLG++LGK++ ESGGA+RIA TL+ GEKN WAM+ + FI G+PVFFEV Sbjct: 61 TLGFLAGIIGLGSILGKLLEESGGAKRIATTLLRVLGEKNASWAMMLVGFIAGIPVFFEV 120 Query: 124 GFVLLVPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGKTIL 183 GFVLL+P+ + VA++T +++ +G+P+ L VVH ++PPHPAA ADIGK IL Sbjct: 121 GFVLLIPLIYVVARQTRINVLYLGVPLAISLMVVHCILPPHPAATAITGMLNADIGKVIL 180 Query: 184 YALIVGIPTAAIAGPLFAKL-MTRYVTLPDVNPLAAQFTEEDEGVKASHELPGFGITLFT 242 Y LIVG+PTA IAGP++ +L TR LAA+ E V + P FGI + T Sbjct: 181 YGLIVGLPTAVIAGPIWVRLTCTREAPEGQAQFLAAR----SEAVIDDSKAPSFGIAMVT 236 Query: 243 ILLPVILMLIGSWADLITTPKTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRENI 302 +LLP+ LM+ + A + T + +++ IGN +IAL ++ ++++ G RRG + Sbjct: 237 VLLPLALMVGKTLAAPLLTKGSMTLEWVSFIGNPLIALALSICFAYWSLGLRRGLGMGAL 296 Query: 303 LRFTNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVLIR 362 L TN C P A I L++GAGG F +L SGI A+ DV + ++ ++L WL+A L+ Sbjct: 297 LNLTNRCFPPLAGILLIIGAGGAFNDMLVGSGIGKALADVLGQSQINPIILAWLIAGLMH 356 Query: 363 IATGSATVAMTTAAGIVAPIAASVPGTRPELLVLTTGAGSLILSHVNDGGFWLVKEYFNM 422 A GSATVAM + AG+V PI P PE+LV+ GAG++ +HV D FW+VKEY + Sbjct: 357 FAVGSATVAMISTAGMVLPILGQHPEYSPEILVIAIGAGAIGWTHVTDSAFWVVKEYLGI 416 Query: 423 TVAQTFKTWSVCETLISVIALLLTLALATVV 453 +++ K ++ L S AL+ TL L+ V Sbjct: 417 PLSEAIKKFTGATVLASSAALVFTLILSRFV 447 Lambda K H 0.326 0.141 0.410 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: 718 Number of extensions: 41 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: 453 Length of database: 447 Length adjustment: 33 Effective length of query: 420 Effective length of database: 414 Effective search space: 173880 Effective search space used: 173880 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 (21.6 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