Align gluconate:H+ symporter (gntT) (characterized)
to candidate Ga0059261_1667 Ga0059261_1667 gluconate permease GntT (TC 2.A.8.1.4)
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__Korea:Ga0059261_1667 Length = 447 Score = 573 bits (1477), Expect = e-168 Identities = 294/445 (66%), Positives = 354/445 (79%), Gaps = 4/445 (0%) Query: 9 LLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGGTLGHI 68 L+L L +V L+ LIA+ KLNPFI L+V S+ LG + G+P+ ++ +EAGVG LGHI Sbjct: 7 LVLLGLASVGGLIFLIARLKLNPFIALLVTSLALGASAGLPLDKLLVIYEAGVGNALGHI 66 Query: 69 ALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEVGFVLL 128 ALVVGLGTM+GK+MAESGGAERIA+T+I FG VHWAM+ AF+VGLPVFFEVGFVLL Sbjct: 67 ALVVGLGTMMGKLMAESGGAERIAQTMIGWFGPARVHWAMMAAAFLVGLPVFFEVGFVLL 126 Query: 129 VPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGKTILYALIV 188 +PI F VA RTGTS++ VG+PMVAGLSVVHGLIPPHPAALLAV AYKADIG T+LYALIV Sbjct: 127 MPIVFTVAMRTGTSILKVGLPMVAGLSVVHGLIPPHPAALLAVGAYKADIGLTVLYALIV 186 Query: 189 GIPTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEEDEGVKASHELPGFGITLFTILLPVI 248 GIPTAA+AGP+FA L+ R+VT+ VNP+A TE S ELPGFGIT+ TILLPV Sbjct: 187 GIPTAALAGPIFATLIDRHVTVDGVNPMAEALTERKVD---SRELPGFGITVATILLPVA 243 Query: 249 LMLIGSWADLITTPKTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRENILRFTNE 308 LMLIGSWADL + ND ++ G+ V ALL L+SF TFG RGF RE+I RF + Sbjct: 244 LMLIGSWADLFAARGSLVNDAIRFSGHPVTALLAGLLLSFVTFGSARGFDRESIGRFLED 303 Query: 309 CVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVLIRIATGSA 368 C+APTA+ITL+VGAG GFG++L ++GIS ++V +A V +L+L WLVA ++RIATGSA Sbjct: 304 CLAPTALITLIVGAGAGFGKILMEAGISTSVVGMAQSVEVPLLVLAWLVAAMMRIATGSA 363 Query: 369 TVAMTTAAGIVAPIAASVPGTRPELLVLTTGAGSLILSHVNDGGFWLVKEYFNMTVAQTF 428 TVAM TAAGIVAP+AA G PELLVL TGAGSLILSHVNDGGFWLVK YF +T++QTF Sbjct: 364 TVAMATAAGIVAPVAAG-SGVSPELLVLATGAGSLILSHVNDGGFWLVKTYFGLTLSQTF 422 Query: 429 KTWSVCETLISVIALLLTLALATVV 453 KTW+VCETLIS++ALLLTLAL+ V+ Sbjct: 423 KTWTVCETLISIVALLLTLALSAVL 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: 773 Number of extensions: 43 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: 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