Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate BPHYT_RS13375 BPHYT_RS13375 permease
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__BFirm:BPHYT_RS13375 Length = 456 Score = 304 bits (779), Expect = 3e-87 Identities = 171/448 (38%), Positives = 259/448 (57%), Gaps = 19/448 (4%) Query: 12 LISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFLAAVIG 71 LI+I+ +V+ I +FK +PF+ L++ S + +GM ++ + E+G+GGTLG +A V+G Sbjct: 14 LIAIIALVVLIARFKMNPFITLMVVSVALALAVGMPATSILKSFETGVGGTLGHIAIVVG 73 Query: 72 LGTILGKMMEVSGAAERIGLTL------QRCRWLSADVIMVLVGLICGITLFVEVGVVLL 125 LGT+LGKMM SG AERI TL + W M+ + + G+ +F EVG VLL Sbjct: 74 LGTMLGKMMAESGGAERIARTLIDLFGPKNVHWA-----MMCIAFLVGLPVFFEVGFVLL 128 Query: 126 IPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLLV 185 IP+AF++A++T TS++++ IP+ L VH ++PPHPAAL ADIG I Y L+V Sbjct: 129 IPIAFNVAQRTGTSMIRVGIPMVAGLSVVHGLIPPHPAALLAVTAYNADIGHTIFYALIV 188 Query: 186 GLMASLIGGPLFLKFLGQRLPF---KPVPTEFADLKV-RDEKTLPSLGATLFTVLLPIAL 241 G+ + I GPLF K + + + P+ +F + R + LP G TL TVLLP+ L Sbjct: 189 GIPTAAIAGPLFSKLIARFVVLDGVNPMAQQFIEQDAKRSHQELPGFGITLLTVLLPVLL 248 Query: 242 MLVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTMLTHTENG 301 MLV + A+L + +S +L IG+P A +AV +++ G + + +L T Sbjct: 249 MLVGSWADLIVPAKSTANNVLRLIGHPDMALLLAVLLSFITFGKARGFNRDQILKFTNEC 308 Query: 302 FGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSAT 361 A+I L++GAG F IL S + + + + H+ ++LAWLVA ++ A GSAT Sbjct: 309 LAPTASITLVVGAGAGFGRILIDSGASKAIVDVATGAHVPLLILAWLVAALIRVATGSAT 368 Query: 362 VAMMGATAIVAPMLPLYPD----ISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLN 417 VAM A I+AP+ + PE++ +A G+G++ + V D FWLVK+Y G T+ Sbjct: 369 VAMATAAGIIAPIAAAAASTVGGVRPELLVLATGAGSLILSHVNDGGFWLVKEYFGMTVP 428 Query: 418 ETFKYYTTATFIASVIALAGTFLLSFII 445 +TFK +T I SV AL T LS +I Sbjct: 429 QTFKTWTVCETIISVTALLLTLGLSTVI 456 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: 533 Number of extensions: 34 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: 456 Length adjustment: 33 Effective length of query: 412 Effective length of database: 423 Effective search space: 174276 Effective search space used: 174276 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