Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate BWI76_RS27855 BWI76_RS27855 D-serine transporter DsdX
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__Koxy:BWI76_RS27855 Length = 445 Score = 781 bits (2017), Expect = 0.0 Identities = 406/445 (91%), Positives = 422/445 (94%) Query: 1 MHSQIWVVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIG 60 M SQIWVVSTLLISIVLIVLTIVK KFHPFLALLLASFFVG MMGM PLDMVNAIESGIG Sbjct: 1 MESQIWVVSTLLISIVLIVLTIVKLKFHPFLALLLASFFVGAMMGMSPLDMVNAIESGIG 60 Query: 61 GTLGFLAAVIGLGTILGKMMEVSGAAERIGLTLQRCRWLSADVIMVLVGLICGITLFVEV 120 GTLGFLAAVIGLGTILGKMMEVSGAAERIGLTLQRCRWLSADVIMVLVGLICGITLFVEV Sbjct: 61 GTLGFLAAVIGLGTILGKMMEVSGAAERIGLTLQRCRWLSADVIMVLVGLICGITLFVEV 120 Query: 121 GVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIV 180 GVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAAL+VANKLGADIG+VIV Sbjct: 121 GVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALFVANKLGADIGTVIV 180 Query: 181 YGLLVGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVRDEKTLPSLGATLFTVLLPIA 240 YGLLVGL+ASL+GGPLFL+ LG RLPFK VP EFA+L+VR E+TLPSLGATLFTVLLPI Sbjct: 181 YGLLVGLLASLVGGPLFLRLLGNRLPFKAVPAEFANLEVRKEETLPSLGATLFTVLLPIG 240 Query: 241 LMLVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTMLTHTEN 300 LMLVKTIAELNM + LY LLEFIGNPITA FIAVFVAYYVLGIRQ M M T+LTHTEN Sbjct: 241 LMLVKTIAELNMTKGGTLYMLLEFIGNPITAMFIAVFVAYYVLGIRQDMGMSTLLTHTEN 300 Query: 301 GFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSA 360 FGSIANILLIIGAGGAFNAILK+S LADTLAVILSN+ MHPILLAWLVALILHAAVGSA Sbjct: 301 CFGSIANILLIIGAGGAFNAILKTSGLADTLAVILSNLDMHPILLAWLVALILHAAVGSA 360 Query: 361 TVAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETF 420 TVAMMGATAIVAPMLPLYP +SPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGA+LNETF Sbjct: 361 TVAMMGATAIVAPMLPLYPGVSPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGASLNETF 420 Query: 421 KYYTTATFIASVIALAGTFLLSFII 445 KYYTTATFIAS++ALAGTFLLSFII Sbjct: 421 KYYTTATFIASLLALAGTFLLSFII 445 Lambda K H 0.328 0.142 0.417 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: 791 Number of extensions: 31 Number of successful extensions: 2 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: 445 Length adjustment: 32 Effective length of query: 413 Effective length of database: 413 Effective search space: 170569 Effective search space used: 170569 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