Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate GFF4292 PS417_21980 permease DsdX
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__WCS417:GFF4292 Length = 450 Score = 341 bits (874), Expect = 3e-98 Identities = 184/453 (40%), Positives = 275/453 (60%), Gaps = 14/453 (3%) Query: 1 MHSQIWVVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIG 60 M + +++ +++I+ +++ I KFK HPF+AL++A+ F+G GM ++ A + G G Sbjct: 4 MSHESYLLLDAVVTIIGLIVLITKFKVHPFIALIIAAGFLGLTSGMPVDKIIKAFQDGFG 63 Query: 61 GTLGFLAAVIGLGTILGKMMEVSGAAERIGLTL------QRCRWLSADVIMVLVGLICGI 114 G LGF+ ++ LGT+LGKMM SG A++I TL ++ +W M+ + GI Sbjct: 64 GVLGFVGIILALGTMLGKMMAESGGADQIAQTLIRAFGKEKVQWA-----MMFAAFLVGI 118 Query: 115 TLFVEVGVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGAD 174 LF E+G VLLIPL F +A++T SL+K+ IPL L AVH +VPPHP L GAD Sbjct: 119 PLFFEIGFVLLIPLVFIVARRTGVSLIKIGIPLLAGLSAVHGLVPPHPGPLLAIGVFGAD 178 Query: 175 IGSVIVYGLLVGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVR--DEKTLPSLGATL 232 IG I+YGL+V L ++I GP+F F+ + +P P E D R D K+LPS G TL Sbjct: 179 IGKTILYGLIVALPTAIIAGPIFGTFIAKYIPGNP-SQELVDQLARETDNKSLPSFGITL 237 Query: 233 FTVLLPIALMLVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMG 292 TVLLP+ LML+KT A++ A + + ++ IG+PITA +A+ ++ Y G RQ + Sbjct: 238 VTVLLPVFLMLLKTFADIAFAEGNVVRNWMDMIGHPITALLLALLLSLYTFGHRQGIHSK 297 Query: 293 TMLTHTENGFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALI 352 +L + A I+LIIGAGG F +L +S + D + + N ++PILLAWLVA + Sbjct: 298 QILKLLDASLAPTAAIILIIGAGGGFKQMLVTSGVGDVIGHMAVNAQINPILLAWLVAAV 357 Query: 353 LHAAVGSATVAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYC 412 + A GSATVA + IV P++ + P ++ E++ +A G+G++ + V D+ FWLVKQY Sbjct: 358 IRVATGSATVATITGAGIVVPVVGMIPGVNRELLVLATGAGSLILSHVNDAGFWLVKQYF 417 Query: 413 GATLNETFKYYTTATFIASVIALAGTFLLSFII 445 T+ ETFK +T I SV+AL LLS ++ Sbjct: 418 NMTVAETFKTWTAMETILSVVALIFIMLLSLVV 450 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: 591 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