Align D-serine transporter DsdX (characterized)
to candidate PfGW456L13_3649 D-serine permease DsdX
Query= SwissProt::P08555 (445 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3649 Length = 446 Score = 413 bits (1061), Expect = e-120 Identities = 229/450 (50%), Positives = 302/450 (67%), Gaps = 15/450 (3%) Query: 1 MHSQIWVVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIG 60 MHS ++ L +I+LIV IVK + H FLAL ASF VG GM M ++ E G+G Sbjct: 1 MHSGPTLLVVLFSAIILIVFLIVKVRVHAFLALTAASFVVGIGSGMPLAQMASSYEKGVG 60 Query: 61 GTLGFLAAVIGLGTILGKMMEVSGAAERIGLTL------QRCRWLSVDVIMVLVGLICGI 114 GTLGFLA +IGLG ILGKM+E SG AERI TL +R W M+LVG I GI Sbjct: 61 GTLGFLATIIGLGGILGKMLEESGGAERIAQTLLSTLGKERASWA-----MMLVGFIAGI 115 Query: 115 TLFVEVGVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGAD 174 +F EVG VLLIPL + +AK+T +LL L +PL +LMAVHC++PPHPAA+ + LGAD Sbjct: 116 PVFFEVGFVLLIPLIYVVAKETRINLLYLGVPLAVSLMAVHCMLPPHPAAMAITGLLGAD 175 Query: 175 IGSVIVYGLLVGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVRDEKT--LPSLGATL 232 +G VIVYGL++ L ++I GPL++K + + F D D T LP LG TL Sbjct: 176 VGKVIVYGLIIALPTAIIAGPLWIKLVCKS-EAPDTQEAFLDEHCVDSATRDLPGLGLTL 234 Query: 233 FTILLPIALMLVKTIAELNMARESGLYILVEFIGNPITAMFIAVFVAYYVLGIRQHMSMG 292 TILLP+ LM+ K+ A + +SGL+ +V F+G P+ A+ IAV AY+ LG+R+ +SM Sbjct: 235 LTILLPLLLMVGKSFAA-GLPHDSGLFSIVSFLGTPLIALSIAVVFAYWALGLRRGLSMP 293 Query: 293 TMLTHTENGFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALI 352 +L HT+ F +A+ILLIIGAGGAFN IL S + + L+ L+ ++M+PI+LAWLVA + Sbjct: 294 DLLAHTQKSFPPLASILLIIGAGGAFNGILVDSGVGNALSGSLTQLNMNPIVLAWLVAGL 353 Query: 353 LHAAVGSATVAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYC 412 +H AVGSATVAM+ A +V PML +P +S EII IAIG+GAIG T VTDS FW+VK+Y Sbjct: 354 MHFAVGSATVAMISAAGMVMPMLSAHPTVSKEIICIAIGAGAIGWTHVTDSAFWVVKEYL 413 Query: 413 GATLNETFKYYTTATFIASVVALAGTFLLS 442 G +L E K +T+AT +AS++AL T LLS Sbjct: 414 GVSLAEALKKFTSATVLASLIALGLTLLLS 443 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: 600 Number of extensions: 27 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: 445 Length of database: 446 Length adjustment: 32 Effective length of query: 413 Effective length of database: 414 Effective search space: 170982 Effective search space used: 170982 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