Align gluconate:H+ symporter (gntT) (characterized)
to candidate HSERO_RS05470 HSERO_RS05470 permease
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__HerbieS:HSERO_RS05470 Length = 450 Score = 500 bits (1288), Expect = e-146 Identities = 250/454 (55%), Positives = 333/454 (73%), Gaps = 6/454 (1%) Query: 1 MGAVTGTTLLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAG 60 +G TLL A+IA++AL+++I + +++PFI L + S LLG GMP+ IVKSF+ G Sbjct: 2 LGMSHDATLLFNAVIAILALILMITRLRIHPFIALTITSGLLGLISGMPLPKIVKSFQDG 61 Query: 61 VGGTLGHIALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVF 120 GG LG + +V+GLGTMLGK+MAESGGA++IA+TL+ AFG + VHWAM+ AF+VG+P+F Sbjct: 62 FGGVLGFVGIVLGLGTMLGKLMAESGGADQIAQTLVRAFGRERVHWAMMMGAFLVGIPLF 121 Query: 121 FEVGFVLLVPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGK 180 FE+GFVLL+P+ F VA+R+G + +G+PM+A LSV+HGL+PPHP LLA+ + ADIGK Sbjct: 122 FEIGFVLLIPLVFIVARRSGVPLFKIGMPMLASLSVMHGLVPPHPGPLLAIGIFGADIGK 181 Query: 181 TILYALIVGIPTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEEDEGVKASHELPGFGITL 240 TI Y L+VG+PT IAGP+F ++RYV + L AQ E + K LPGF TL Sbjct: 182 TIFYGLLVGLPTVIIAGPMFGAFISRYVDIKPSEELMAQLVREPQTTK----LPGFATTL 237 Query: 241 FTILLPVILMLIGSWADLITTPKTFA-NDFLKLIGNSVIALLIAALVSFYTFGKRRGFTR 299 T+L PV LML+ + D +T P+ A D + IGN ++ALL A L++ +TFG RGFTR Sbjct: 238 ITVLAPVFLMLLKTLVD-VTLPEGHAMRDLMDFIGNPIVALLAALLLAIWTFGIARGFTR 296 Query: 300 ENILRFTNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAV 359 + +L+F ++ +APTA I L++GAGGGF ++L +SG+ AI +A A +S LLL W VA Sbjct: 297 QQVLKFVDQSLAPTAAIVLIIGAGGGFKQMLVNSGVGTAIGQLAVHAQISPLLLAWFVAG 356 Query: 360 LIRIATGSATVAMTTAAGIVAPIAASVPGTRPELLVLTTGAGSLILSHVNDGGFWLVKEY 419 +IR+ATGSATVA T AGIVAP+ A +PGT ELLVL TGAGSLILSHVND GFWLVKEY Sbjct: 357 VIRVATGSATVATITGAGIVAPLVALIPGTNKELLVLATGAGSLILSHVNDAGFWLVKEY 416 Query: 420 FNMTVAQTFKTWSVCETLISVIALLLTLALATVV 453 FNM+V +TFKTW+V ETLISV+A++ + L VV Sbjct: 417 FNMSVGETFKTWTVMETLISVVAIIFIMLLNLVV 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: 718 Number of extensions: 37 Number of successful extensions: 2 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