Align D-serine transporter DsdX (characterized)
to candidate Ac3H11_3740 Gluconate permease
Query= SwissProt::P08555 (445 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3740 Length = 456 Score = 225 bits (574), Expect = 2e-63 Identities = 133/442 (30%), Positives = 239/442 (54%), Gaps = 10/442 (2%) Query: 14 SIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFLAAVIGLG 73 SI L++L I++++ H F+A++L SF V GM D+++ + +G+GGTLG +A ++ LG Sbjct: 13 SIALLLLLIIRWQVHAFVAMMLVSFLVAFATGMPIGDIISTLIAGMGGTLGSVAILVALG 72 Query: 74 TILGKMMEVSGAAERIGLTL-QRCRWLSVDVIMVLVGLICGITLFVEVGVVLLIPLAFSI 132 ++LG+M+EVSG A + Q V + + L+ I +F +VG ++L+P+ + Sbjct: 73 SMLGRMIEVSGGAASLANRFTQLLGPTRVPMALTAAALVLAIPVFFDVGFIILVPIVYGF 132 Query: 133 AKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLLVGLMASLI 192 K + +K +P+ ++A H VVPPHP + A + DIG + + GL + + + + Sbjct: 133 CKAAGVNPIKFGLPVAGIMLAAHVVVPPHPGIVGGAAIVKGDIGWITIIGLAICIPLAAL 192 Query: 193 GGPLFLKFLGQRLPFKPVPTE-FADLKVRDEKTL------PSLGATLFTILLPIALMLVK 245 + + P P E FA ++ T PS+G + I++P+AL++ Sbjct: 193 SQVVAGWLNRKGYPMLPTTAEQFAAFGNSEDSTASKSGKAPSVGTIMALIIIPLALIMAG 252 Query: 246 TIAELNMARESGLYILVEFIGNPITAMFIAVFVAYYVLGIRQHMSMGTMLTHTENGFGSI 305 T + + L ++ FIG+PI A+ +AV +A ++LG Q + E+ Sbjct: 253 TTGATLLPKGDSLRNVLGFIGSPIFALMVAVGLAMFLLGRNQGWNRERTNAIMESALPPA 312 Query: 306 ANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSATVAMM 365 A ++L+ GAGG F +L +S + L+ L+ H+ ILLA++++L L AA GSATVA++ Sbjct: 313 ATVILVTGAGGVFAKVLTASGIGAALSQSLTATHLPLILLAFIISLALRAAQGSATVAII 372 Query: 366 GATAIVAPMLP--LYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFKYY 423 ++A + Y + ++ +AIG G++G + V DS FW+V +Y G ++ + + + Sbjct: 373 TTCGLLADAMAGGGYSPLQVALLTVAIGFGSLGLSHVNDSGFWIVTRYLGLSVGDGLRTW 432 Query: 424 TTATFIASVVALAGTFLLSFII 445 T T + + A T LL ++ Sbjct: 433 TVLTTVLGIAGFAMTALLWVLV 454 Lambda K H 0.329 0.143 0.418 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: 582 Number of extensions: 36 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: 445 Length of database: 456 Length adjustment: 33 Effective length of query: 412 Effective length of database: 423 Effective search space: 174276 Effective search space used: 174276 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 (21.8 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