Align gluconate:H+ symporter (gntT) (characterized)
to candidate AO353_05900 AO353_05900 permease DsdX
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05900 Length = 449 Score = 590 bits (1520), Expect = e-173 Identities = 297/448 (66%), Positives = 364/448 (81%), Gaps = 4/448 (0%) Query: 6 GTTLLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGGTL 65 G LL+YA IA+IAL+VLIA+++LNPFI + +VS+ L GMP +V ++EAGVG TL Sbjct: 6 GYWLLVYAAIAIIALIVLIARYRLNPFIVITLVSIGLALLAGMPPSGVVGAYEAGVGKTL 65 Query: 66 GHIALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEVGF 125 GHIALVV LGTMLGKMMAESGGAE++ARTLI+ FGEKN HWAMV IAF+VGLP+FFEVGF Sbjct: 66 GHIALVVALGTMLGKMMAESGGAEQMARTLIERFGEKNAHWAMVCIAFLVGLPLFFEVGF 125 Query: 126 VLLVPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGKTILYA 185 VLLVPIAF VA+R G S+++VG+PMVAGLSVVH L+PPHPAA+LAV AY+A +G+T+LYA Sbjct: 126 VLLVPIAFTVARRVGVSILMVGLPMVAGLSVVHALVPPHPAAMLAVQAYQASVGQTLLYA 185 Query: 186 LIVGIPTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEEDEGVKASHELPGFGITLFTILL 245 +++GIPTA IAGPL+AK + + LP NPL QF E + LPGFGIT+ TILL Sbjct: 186 ILIGIPTAIIAGPLYAKFIVPRIQLPAENPLERQFIERE----PRDRLPGFGITMATILL 241 Query: 246 PVILMLIGSWADLITTPKTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRENILRF 305 PV+LMLIG WA+LI+TP + N FL IGNSVIALL+A L+SF+T G +GF RE+IL+F Sbjct: 242 PVVLMLIGGWANLISTPGSGFNQFLLFIGNSVIALLLATLLSFWTLGLAQGFNRESILKF 301 Query: 306 TNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVLIRIAT 365 TNEC+APTA ITL+VGAGGG R+L D+G+++ IV +A H+S LL+GWL A L+RIAT Sbjct: 302 TNECLAPTASITLLVGAGGGLNRILVDAGVTDQIVGLAHEFHLSPLLMGWLFAALMRIAT 361 Query: 366 GSATVAMTTAAGIVAPIAASVPGTRPELLVLTTGAGSLILSHVNDGGFWLVKEYFNMTVA 425 GSATVAMTTA+G+VAP+A + PELLVL TGAGS+I SHVNDGGFWLVKEYFNMTV Sbjct: 362 GSATVAMTTASGVVAPVAIGLGYPHPELLVLATGAGSVIFSHVNDGGFWLVKEYFNMTVT 421 Query: 426 QTFKTWSVCETLISVIALLLTLALATVV 453 QTFKTW+V ETLIS++A LTL L+ V+ Sbjct: 422 QTFKTWTVLETLISLVAFGLTLGLSYVL 449 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: 801 Number of extensions: 49 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: 449 Length adjustment: 33 Effective length of query: 420 Effective length of database: 416 Effective search space: 174720 Effective search space used: 174720 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