Align D-serine transporter DsdX (characterized)
to candidate PfGW456L13_1927 Gluconate permease
Query= SwissProt::P08555 (445 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1927 Length = 450 Score = 332 bits (852), Expect = 1e-95 Identities = 179/448 (39%), Positives = 268/448 (59%), Gaps = 4/448 (0%) Query: 1 MHSQIWVVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIG 60 M + +++ +++++ +++ I KFK HPFLAL++A+ F+G GM ++ A + G G Sbjct: 4 MSHETFLLLDAVVTVIGLIVLITKFKLHPFLALIIAAAFLGLTSGMPIGTIIKAFQDGFG 63 Query: 61 GTLGFLAAVIGLGTILGKMMEVSGAAERIGLTLQRCRWLS-VDVIMVLVGLICGITLFVE 119 G LGF+ ++ LGT+LGKMM SG A++I TL R V M+ + GI LF E Sbjct: 64 GVLGFVGIILALGTMLGKMMAESGGADQIAQTLIRAFGKDKVQWAMMFAAFLVGIPLFFE 123 Query: 120 VGVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVI 179 +G VLLIPL F +A++T S++K+ IPL L AVH +VPPHP L GADIG I Sbjct: 124 IGFVLLIPLVFIVARRTGVSIIKIGIPLLAGLSAVHGLVPPHPGPLLAIGVFGADIGKTI 183 Query: 180 VYGLLVGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVR--DEKTLPSLGATLFTILL 237 +YGL+V L ++I GP+F F+ + +P P E D R D LPS G TL T+LL Sbjct: 184 LYGLIVALPTAIIAGPIFGTFIAKHIPGHP-NQELVDQLSRETDSAELPSFGITLVTVLL 242 Query: 238 PIALMLVKTIAELNMARESGLYILVEFIGNPITAMFIAVFVAYYVLGIRQHMSMGTMLTH 297 P+ LML+KT A++ + + ++ IG+PI+A+ +A+ ++ Y G +Q + M+ Sbjct: 243 PVFLMLLKTFADVVLPDGNIFRAFMDLIGHPISALLLALLLSLYTFGYKQGIGSSQMMKW 302 Query: 298 TENGFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAV 357 + A I+LIIGAGG F +L +S + D + + N + PILLAWLVA ++ A Sbjct: 303 LDASLAPTAAIILIIGAGGGFKQMLVTSGVGDVIGHMAVNAQISPILLAWLVAAVIRIAT 362 Query: 358 GSATVAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLN 417 GSATVA + IV P++ + P ++ E++ +A G+G++ + V D+ FWLVKQY T+ Sbjct: 363 GSATVATITGAGIVVPVVGMIPGVNRELLVLATGAGSLILSHVNDAGFWLVKQYFNMTVA 422 Query: 418 ETFKYYTTATFIASVVALAGTFLLSFII 445 ETFK +T I SVV L LLS + Sbjct: 423 ETFKTWTAMETILSVVGLGFILLLSLFV 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: 625 Number of extensions: 36 Number of successful extensions: 5 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