Align gluconate:H+ symporter (gntT) (characterized)
to candidate PP_3417 PP_3417 D-gluconate transporter
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__Putida:PP_3417 Length = 450 Score = 505 bits (1300), Expect = e-147 Identities = 248/453 (54%), Positives = 335/453 (73%), Gaps = 6/453 (1%) Query: 2 GAVTGTTLLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGV 61 G T T LLL AL+ ++ L++LI FK++PF+ L + + LG GMP+ ++KSF+ G Sbjct: 3 GLATDTFLLLDALVTIVGLILLITHFKVHPFVALTLAAGFLGLTSGMPVAKVMKSFQDGF 62 Query: 62 GGTLGHIALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFF 121 GG LG + +V+ LGTMLGK+MA+SGGA++IA+TLI AFG+KNVHWAM+ AF+VG+P+FF Sbjct: 63 GGVLGFVGIVLALGTMLGKLMADSGGADQIAQTLIRAFGKKNVHWAMMFAAFLVGIPLFF 122 Query: 122 EVGFVLLVPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGKT 181 E+GFVLL+P+ F VA+R+G S+V +GIP++AGLSVVHGL+PPHP LLA+ + ADIGKT Sbjct: 123 EIGFVLLIPLVFIVARRSGVSLVKIGIPLLAGLSVVHGLVPPHPGPLLAIGIFHADIGKT 182 Query: 182 ILYALIVGIPTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEE-DEGVKASHELPGFGITL 240 I Y LIV +PTA IAGPLF ++RY+ L Q ++ D+G LP F ITL Sbjct: 183 IFYGLIVALPTAIIAGPLFGNFISRYIPGNPSQELMDQIAKDSDQG-----NLPSFSITL 237 Query: 241 FTILLPVILMLIGSWADLITTPKTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRE 300 T+LLPV LML+ ++AD++ + ++ LIG+ + ALL A L++FYTFG RGF R+ Sbjct: 238 VTVLLPVALMLLKTFADVVLPAEHIVRQWMDLIGHPITALLAALLLAFYTFGSARGFNRQ 297 Query: 301 NILRFTNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVL 360 I++ ++ +APTA I L+VGAGGGF ++L D+G+ N I +A A +S ++L WLVA + Sbjct: 298 QIMKMLDQSLAPTAAIVLIVGAGGGFKQMLVDTGVGNVIGQMAVQAEISPIMLAWLVAAV 357 Query: 361 IRIATGSATVAMTTAAGIVAPIAASVPGTRPELLVLTTGAGSLILSHVNDGGFWLVKEYF 420 IRIATGSATVA T AGIVAP+ VPG ELLVL TGAGSLILSHVND GFWLVK+YF Sbjct: 358 IRIATGSATVATITGAGIVAPVIDLVPGVNRELLVLATGAGSLILSHVNDAGFWLVKQYF 417 Query: 421 NMTVAQTFKTWSVCETLISVIALLLTLALATVV 453 NMTVA+TFKTWS+ ET++S++ ++ + L+ VV Sbjct: 418 NMTVAETFKTWSMMETILSIVGIIFIMLLSLVV 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: 760 Number of extensions: 43 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