Align gluconate:H+ symporter (gntT) (characterized)
to candidate BPHYT_RS13375 BPHYT_RS13375 permease
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__BFirm:BPHYT_RS13375 Length = 456 Score = 684 bits (1764), Expect = 0.0 Identities = 355/458 (77%), Positives = 396/458 (86%), Gaps = 7/458 (1%) Query: 1 MGAVTGTTLLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAG 60 M V G+ LL+YALIA+IALVVLIA+FK+NPFITL+VVSV L AVGMP I+KSFE G Sbjct: 1 MATVQGSLLLVYALIAIIALVVLIARFKMNPFITLMVVSVALALAVGMPATSILKSFETG 60 Query: 61 VGGTLGHIALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVF 120 VGGTLGHIA+VVGLGTMLGKMMAESGGAERIARTLID FG KNVHWAM+ IAF+VGLPVF Sbjct: 61 VGGTLGHIAIVVGLGTMLGKMMAESGGAERIARTLIDLFGPKNVHWAMMCIAFLVGLPVF 120 Query: 121 FEVGFVLLVPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGK 180 FEVGFVLL+PIAFNVA+RTGTSM+ VGIPMVAGLSVVHGLIPPHPAALLAVTAY ADIG Sbjct: 121 FEVGFVLLIPIAFNVAQRTGTSMIRVGIPMVAGLSVVHGLIPPHPAALLAVTAYNADIGH 180 Query: 181 TILYALIVGIPTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEEDEGVKASH-ELPGFGIT 239 TI YALIVGIPTAAIAGPLF+KL+ R+V L VNP+A QF E+D K SH ELPGFGIT Sbjct: 181 TIFYALIVGIPTAAIAGPLFSKLIARFVVLDGVNPMAQQFIEQD--AKRSHQELPGFGIT 238 Query: 240 LFTILLPVILMLIGSWADLITTPKTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTR 299 L T+LLPV+LML+GSWADLI K+ AN+ L+LIG+ +ALL+A L+SF TFGK RGF R Sbjct: 239 LLTVLLPVLLMLVGSWADLIVPAKSTANNVLRLIGHPDMALLLAVLLSFITFGKARGFNR 298 Query: 300 ENILRFTNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAV 359 + IL+FTNEC+APTA ITLVVGAG GFGR+L DSG S AIVDVATGAHV +L+L WLVA Sbjct: 299 DQILKFTNECLAPTASITLVVGAGAGFGRILIDSGASKAIVDVATGAHVPLLILAWLVAA 358 Query: 360 LIRIATGSATVAMTTAAGIVAPIAA----SVPGTRPELLVLTTGAGSLILSHVNDGGFWL 415 LIR+ATGSATVAM TAAGI+APIAA +V G RPELLVL TGAGSLILSHVNDGGFWL Sbjct: 359 LIRVATGSATVAMATAAGIIAPIAAAAASTVGGVRPELLVLATGAGSLILSHVNDGGFWL 418 Query: 416 VKEYFNMTVAQTFKTWSVCETLISVIALLLTLALATVV 453 VKEYF MTV QTFKTW+VCET+ISV ALLLTL L+TV+ Sbjct: 419 VKEYFGMTVPQTFKTWTVCETIISVTALLLTLGLSTVI 456 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: 819 Number of extensions: 47 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: 456 Length adjustment: 33 Effective length of query: 420 Effective length of database: 423 Effective search space: 177660 Effective search space used: 177660 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