Align gluconate:H+ symporter (gntT) (characterized)
to candidate PfGW456L13_3649 D-serine permease DsdX
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3649 Length = 446 Score = 365 bits (937), Expect = e-105 Identities = 190/449 (42%), Positives = 286/449 (63%), Gaps = 5/449 (1%) Query: 5 TGTTLLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGGT 64 +G TLL+ A+I +V LI K +++ F+ L S ++G GMP+ + S+E GVGGT Sbjct: 3 SGPTLLVVLFSAIILIVFLIVKVRVHAFLALTAASFVVGIGSGMPLAQMASSYEKGVGGT 62 Query: 65 LGHIALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEVG 124 LG +A ++GLG +LGKM+ ESGGAERIA+TL+ G++ WAM+ + FI G+PVFFEVG Sbjct: 63 LGFLATIIGLGGILGKMLEESGGAERIAQTLLSTLGKERASWAMMLVGFIAGIPVFFEVG 122 Query: 125 FVLLVPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGKTILY 184 FVLL+P+ + VAK T +++ +G+P+ L VH ++PPHPAA+ AD+GK I+Y Sbjct: 123 FVLLIPLIYVVAKETRINLLYLGVPLAVSLMAVHCMLPPHPAAMAITGLLGADVGKVIVY 182 Query: 185 ALIVGIPTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEEDEGVKASHELPGFGITLFTIL 244 LI+ +PTA IAGPL+ KL+ + PD F +E A+ +LPG G+TL TIL Sbjct: 183 GLIIALPTAIIAGPLWIKLVCK-SEAPDTQ---EAFLDEHCVDSATRDLPGLGLTLLTIL 238 Query: 245 LPVILMLIGSWADLITTPKTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRENILR 304 LP++LM+ S+A + + + +G +IAL IA + +++ G RRG + ++L Sbjct: 239 LPLLLMVGKSFAAGLPHDSGLFS-IVSFLGTPLIALSIAVVFAYWALGLRRGLSMPDLLA 297 Query: 305 FTNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVLIRIA 364 T + P A I L++GAGG F +L DSG+ NA+ T +++ ++L WLVA L+ A Sbjct: 298 HTQKSFPPLASILLIIGAGGAFNGILVDSGVGNALSGSLTQLNMNPIVLAWLVAGLMHFA 357 Query: 365 TGSATVAMTTAAGIVAPIAASVPGTRPELLVLTTGAGSLILSHVNDGGFWLVKEYFNMTV 424 GSATVAM +AAG+V P+ ++ P E++ + GAG++ +HV D FW+VKEY +++ Sbjct: 358 VGSATVAMISAAGMVMPMLSAHPTVSKEIICIAIGAGAIGWTHVTDSAFWVVKEYLGVSL 417 Query: 425 AQTFKTWSVCETLISVIALLLTLALATVV 453 A+ K ++ L S+IAL LTL L+ V Sbjct: 418 AEALKKFTSATVLASLIALGLTLLLSQFV 446 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: 660 Number of extensions: 41 Number of successful extensions: 6 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: 446 Length adjustment: 33 Effective length of query: 420 Effective length of database: 413 Effective search space: 173460 Effective search space used: 173460 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