Align gluconate:H+ symporter (gntT) (characterized)
to candidate 5210089 Shew_2533 gluconate transporter (RefSeq)
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__PV4:5210089 Length = 452 Score = 211 bits (537), Expect = 4e-59 Identities = 147/461 (31%), Positives = 244/461 (52%), Gaps = 29/461 (6%) Query: 10 LLYALIAVIALVVLI-AKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGGTLGHI 68 L+ LIAVIA +V+ +KFKL+PF+TL++ S + FA G+P D+ K+ +G GG LG+I Sbjct: 3 LVLILIAVIAFIVIATSKFKLHPFLTLILASFIAAFAYGLPSADVAKTITSGFGGILGYI 62 Query: 69 ALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEVGFVLL 128 LV+ LGT++G ++ +SG A +A +I G++ M I ++V +PVF + GFV+L Sbjct: 63 GLVIVLGTIIGTILEKSGAAITMADVVIKVLGKRFPTLTMSIIGYLVSIPVFCDSGFVIL 122 Query: 129 VPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGKTILYALIV 188 + ++A R S V + + + GL H +PP P + A ++G L++ Sbjct: 123 NSLKQSMANRMKVSSVSMSVALATGLYATHTFVPPTPGPIAAA----GNLGLESNLGLVI 178 Query: 189 GI-----PTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEEDEGVKASH-ELPGFGITLFT 242 G+ AA+AG L+A + E+ E +KA++ ELP Sbjct: 179 GVGIFVAAVAALAGMLWANRFAHVEPDGEGAEELKNNVEDFEQLKAAYGELPSPAKAFAP 238 Query: 243 ILLPVILMLIGSWADLITTP--KTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRE 300 I +P++L+ +GS A + P D L +G V AL+I +S + K + +E Sbjct: 239 IFVPILLICLGSIAKFPSQPLGDGALFDTLAFLGQPVNALMIGLFLSL-SLLKSQDKIKE 297 Query: 301 NILRFTNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLG----WL 356 R ++ V A I L+ GAGG FG VL+ + I N + G+ +S L +G ++ Sbjct: 298 FSDRISHGLVV-AAPILLITGAGGAFGAVLKATEIGNFL-----GSSLSALGIGIFMPFI 351 Query: 357 VAVLIRIATGSATVAMTTAAGIVAPIAASVPGTRPE----LLVLTTGAGSLILSHVNDGG 412 VA ++ A GS+TVA+ + +VAP+ + G + L V+ GAG++ +SH ND Sbjct: 352 VAAALKSAQGSSTVALVATSALVAPMLGDI-GLASDMGRVLTVMAIGAGAMTVSHANDSF 410 Query: 413 FWLVKEYFNMTVAQTFKTWSVCETLISVIALLLTLALATVV 453 FW+V ++ M+V Q +K ++ + V A++L L+ V+ Sbjct: 411 FWVVTQFSRMSVKQAYKAQTMATLIQGVTAMILVYLLSLVL 451 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: 553 Number of extensions: 38 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: 453 Length of database: 452 Length adjustment: 33 Effective length of query: 420 Effective length of database: 419 Effective search space: 175980 Effective search space used: 175980 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