Align D-serine transporter DsdX (characterized)
to candidate PP_3417 PP_3417 D-gluconate transporter
Query= SwissProt::P08555 (445 letters) >FitnessBrowser__Putida:PP_3417 Length = 450 Score = 317 bits (811), Expect = 6e-91 Identities = 174/437 (39%), Positives = 260/437 (59%), Gaps = 4/437 (0%) Query: 12 LISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFLAAVIG 71 L++IV ++L I FK HPF+AL LA+ F+G GM ++ + + G GG LGF+ V+ Sbjct: 15 LVTIVGLILLITHFKVHPFVALTLAAGFLGLTSGMPVAKVMKSFQDGFGGVLGFVGIVLA 74 Query: 72 LGTILGKMMEVSGAAERIGLTLQRCRWL-SVDVIMVLVGLICGITLFVEVGVVLLIPLAF 130 LGT+LGK+M SG A++I TL R +V M+ + GI LF E+G VLLIPL F Sbjct: 75 LGTMLGKLMADSGGADQIAQTLIRAFGKKNVHWAMMFAAFLVGIPLFFEIGFVLLIPLVF 134 Query: 131 SIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLLVGLMAS 190 +A+++ SL+K+ IPL L VH +VPPHP L ADIG I YGL+V L + Sbjct: 135 IVARRSGVSLVKIGIPLLAGLSVVHGLVPPHPGPLLAIGIFHADIGKTIFYGLIVALPTA 194 Query: 191 LIGGPLFLKFLGQRLPFKPVPTEFAD--LKVRDEKTLPSLGATLFTILLPIALMLVKTIA 248 +I GPLF F+ + +P P E D K D+ LPS TL T+LLP+ALML+KT A Sbjct: 195 IIAGPLFGNFISRYIPGNP-SQELMDQIAKDSDQGNLPSFSITLVTVLLPVALMLLKTFA 253 Query: 249 ELNMARESGLYILVEFIGNPITAMFIAVFVAYYVLGIRQHMSMGTMLTHTENGFGSIANI 308 ++ + E + ++ IG+PITA+ A+ +A+Y G + + ++ + A I Sbjct: 254 DVVLPAEHIVRQWMDLIGHPITALLAALLLAFYTFGSARGFNRQQIMKMLDQSLAPTAAI 313 Query: 309 LLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSATVAMMGAT 368 +LI+GAGG F +L + + + + + + PI+LAWLVA ++ A GSATVA + Sbjct: 314 VLIVGAGGGFKQMLVDTGVGNVIGQMAVQAEISPIMLAWLVAAVIRIATGSATVATITGA 373 Query: 369 AIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFKYYTTATF 428 IVAP++ L P ++ E++ +A G+G++ + V D+ FWLVKQY T+ ETFK ++ Sbjct: 374 GIVAPVIDLVPGVNRELLVLATGAGSLILSHVNDAGFWLVKQYFNMTVAETFKTWSMMET 433 Query: 429 IASVVALAGTFLLSFII 445 I S+V + LLS ++ Sbjct: 434 ILSIVGIIFIMLLSLVV 450 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: 581 Number of extensions: 38 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: 450 Length adjustment: 33 Effective length of query: 412 Effective length of database: 417 Effective search space: 171804 Effective search space used: 171804 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