Align gluconate:H+ symporter (gntT) (characterized)
to candidate AO353_03245 AO353_03245 permease DsdX
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03245 Length = 450 Score = 492 bits (1266), Expect = e-143 Identities = 245/445 (55%), Positives = 323/445 (72%), Gaps = 4/445 (0%) Query: 9 LLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGGTLGHI 68 LLL A+I VI L+VLI KFKL+PFI L++ + LG GMP+G I+K+F+ G GG LG + Sbjct: 10 LLLDAVITVIGLIVLITKFKLHPFIALIIAAAFLGLTSGMPIGTIIKAFQDGFGGVLGFV 69 Query: 69 ALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEVGFVLL 128 +++ LGTMLGKMMAESGGA++IA+TLI AFG++ V WAM+ AF+VG+P+FFE+GFVLL Sbjct: 70 GIILALGTMLGKMMAESGGADQIAQTLIRAFGKERVQWAMMFAAFLVGIPLFFEIGFVLL 129 Query: 129 VPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGKTILYALIV 188 +P+ F VA+RTG S++ +GIP++AGLS VHGL+PPHP LLA+ + ADIGKTILY LIV Sbjct: 130 IPLVFIVARRTGVSIIKIGIPLLAGLSAVHGLVPPHPGPLLAIGVFGADIGKTILYGLIV 189 Query: 189 GIPTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEEDEGVKASHELPGFGITLFTILLPVI 248 +PTA IAGP++ + +Y+ L Q E S LP F ITL T+LLPV Sbjct: 190 ALPTAIIAGPIYGTFIAKYIPGHPNQELVDQLAREPH----SSTLPSFSITLITVLLPVF 245 Query: 249 LMLIGSWADLITTPKTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRENILRFTNE 308 LML+ ++AD+ F ++ +IG+ + ALL+A L+S YTFG R+G + IL+ + Sbjct: 246 LMLLKTFADIALPDGHFFRTWMDMIGHPISALLLALLLSLYTFGHRQGIGSKQILKLLDA 305 Query: 309 CVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVLIRIATGSA 368 +APTA I L++GAGGGF ++L SG+ + I +A A +S +LL WLVA +IR+ATGSA Sbjct: 306 SLAPTAAIILIIGAGGGFKQMLVTSGVGDVIGHMAVSAQISPILLAWLVAAVIRVATGSA 365 Query: 369 TVAMTTAAGIVAPIAASVPGTRPELLVLTTGAGSLILSHVNDGGFWLVKEYFNMTVAQTF 428 TVA T AGIV P+ +PG ELLVL TGAGSLILSHVND GFWLVK+YFNMTVA+TF Sbjct: 366 TVATITGAGIVVPVVGMIPGVNRELLVLATGAGSLILSHVNDAGFWLVKQYFNMTVAETF 425 Query: 429 KTWSVCETLISVIALLLTLALATVV 453 KTW+ ET++SV+AL L L+ VV Sbjct: 426 KTWTAMETILSVVALGFILLLSLVV 450 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: 752 Number of extensions: 42 Number of successful extensions: 4 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: 450 Length adjustment: 33 Effective length of query: 420 Effective length of database: 417 Effective search space: 175140 Effective search space used: 175140 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