Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate AO356_07790 AO356_07790 permease DsdX
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07790 Length = 449 Score = 305 bits (781), Expect = 2e-87 Identities = 162/444 (36%), Positives = 258/444 (58%), Gaps = 6/444 (1%) Query: 6 WVVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGF 65 W++ I+I+ +++ I +++ +PF+ + L S + + GM P +V A E+G+G TLG Sbjct: 8 WLLVYAAIAIIALIVLIARYRLNPFIVITLVSIGLALLAGMPPSSVVGAYEAGVGKTLGH 67 Query: 66 LAAVIGLGTILGKMMEVSGAAERIGLTL-QRCRWLSADVIMVLVGLICGITLFVEVGVVL 124 +A V+ LGT+LGKMM SG AER+ TL +R +A MV + + G+ LF EVG VL Sbjct: 68 IALVVALGTMLGKMMAESGGAERMAQTLIERFGERNAHWAMVCIAFLVGLPLFFEVGFVL 127 Query: 125 LIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLL 184 L+P+AF+IA++ S+L + +P+ L VH +VPPHPAA+ A +G ++Y +L Sbjct: 128 LVPIAFTIARRVGVSILMVGLPMVAGLSVVHALVPPHPAAMLAVQAFQASVGQTLLYAIL 187 Query: 185 VGLMASLIGGPLFLKFLGQRLPF---KPVPTEFADLKVRDEKTLPSLGATLFTVLLPIAL 241 +G+ ++I GPL+ KF+ R+ P+ +F D + R LP G TL T+LLP+ L Sbjct: 188 IGIPTAIIAGPLYAKFIVPRIQLPAENPLERQFLDREPRAR--LPGFGVTLGTILLPVIL 245 Query: 242 MLVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTMLTHTENG 301 ML+ A L SG L FIGN + A +A ++++ LG+ Q + ++L T Sbjct: 246 MLIGGWANLISTPGSGFNQFLLFIGNSVIALLLATVLSFWTLGLAQGFNRESILKFTNEC 305 Query: 302 FGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSAT 361 A+I L++GAGG N IL + + + + + P+++ WL A ++ A GSAT Sbjct: 306 LAPTASITLLVGAGGGLNRILVDAGVTQQIVGLAQEFQLSPLVMGWLFAALMRVATGSAT 365 Query: 362 VAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFK 421 VAM A+ IVAP+ PE++ +A G+G++ + V D FWL+K+Y T+ +TFK Sbjct: 366 VAMTTASGIVAPVAIGLGYPHPELLVLATGAGSVIFSHVNDGGFWLIKEYFNMTVTQTFK 425 Query: 422 YYTTATFIASVIALAGTFLLSFII 445 +T + SV+A A T LS ++ Sbjct: 426 TWTVLETLISVVAFALTLGLSRLL 449 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: 543 Number of extensions: 33 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: 449 Length adjustment: 33 Effective length of query: 412 Effective length of database: 416 Effective search space: 171392 Effective search space used: 171392 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