Align gluconate:H+ symporter (gntT) (characterized)
to candidate 7025533 Shewana3_2684 gluconate transporter (RefSeq)
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__ANA3:7025533 Length = 452 Score = 203 bits (516), Expect = 1e-56 Identities = 144/456 (31%), Positives = 237/456 (51%), Gaps = 19/456 (4%) Query: 10 LLYALIAVIALVVLI-AKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGGTLGHI 68 L+ LI VIA +V+ +KFKL+PF+TL++ + + FA G+P GDI K+ G G LG+I Sbjct: 3 LVLILIGVIAFIVIATSKFKLHPFLTLILAAFIAAFAYGLPSGDIAKTITTGFGNILGYI 62 Query: 69 ALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEVGFVLL 128 LV+ LGT++G ++ +SG A +A +I G++ M I ++V +PVF + GFV+L Sbjct: 63 GLVIVLGTIIGIILEKSGAAITMADVVIKVLGKRFPTLTMSIIGYLVSIPVFCDSGFVIL 122 Query: 129 VPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAV--TAYKADIGKTILYAL 186 + ++A R S V + + + GL H +PP P + A ++++G I L Sbjct: 123 NSLKQSMANRMKVSSVSMSVALATGLYATHTFVPPTPGPIAAAGNLGLESNLGLVIGVGL 182 Query: 187 IVGIPTAAIAGPLFAKLMTRYVTL-PD---VNPLAAQFTEEDEGVKASHELPGFGITLFT 242 +V AA+AG +A R+ ++ PD L AQ + + ++ LP Sbjct: 183 LVA-AVAALAGMFWA---NRFASVEPDGEGAEELKAQAADFEALKQSYGTLPSPLKAFAP 238 Query: 243 ILLPVILMLIGSWADLITTP--KTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRE 300 I +P++L+ +GS A+ + P K L +G V ALLI +S K E Sbjct: 239 IFVPILLICLGSIANFPSAPLGKEGLFSLLVFLGQPVNALLIGLFLSLLLL-KSDNKIAE 297 Query: 301 NILRFTNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVL 360 R + VA II L+ GAGG FG VL+ + I + + + V + + ++VA Sbjct: 298 FSERISQGLVAAAPII-LITGAGGAFGAVLKATPIGDFLGSSLSALGVGI-FMPFIVAAA 355 Query: 361 IRIATGSATVAMTTAAGIVAPIAASV---PGTRPELLVLTTGAGSLILSHVNDGGFWLVK 417 ++ A GS+TVA+ + +VAP+ + L V+ GAG++ +SH ND FW+V Sbjct: 356 LKSAQGSSTVALVATSALVAPMLGDIGLGSDMGRVLTVMAIGAGAMTVSHANDSFFWVVT 415 Query: 418 EYFNMTVAQTFKTWSVCETLISVIALLLTLALATVV 453 ++ M+V Q +K ++ + V A+L L+ V+ Sbjct: 416 QFSRMSVKQAYKAQTMATLIQGVTAMLTVYVLSLVL 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: 592 Number of extensions: 34 Number of successful extensions: 6 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