Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate HSERO_RS08740 HSERO_RS08740 permease
Query= SwissProt::A0A0H2VAP9 (445 letters) >FitnessBrowser__HerbieS:HSERO_RS08740 Length = 450 Score = 320 bits (819), Expect = 8e-92 Identities = 169/443 (38%), Positives = 265/443 (59%), Gaps = 15/443 (3%) Query: 12 LISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLGFLAAVIG 71 L++++ +++ I KFK +PF+ L++ S +G +GM ++V A E+G+G LG +A V+G Sbjct: 14 LVAVIALIVLIAKFKMNPFIVLIVVSLVLGLAVGMPMGNIVKAFETGVGNALGHIALVVG 73 Query: 72 LGTILGKMMEVSGAAERIGLTL------QRCRWLSADVIMVLVGLICGITLFVEVGVVLL 125 LGT+LGKMM SG AERI T+ + W M+ V I G+ +F EVG VLL Sbjct: 74 LGTMLGKMMAESGGAERIANTMIKAFGEKNVHWA-----MMTVAFIVGLPVFFEVGFVLL 128 Query: 126 IPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVYGLLV 185 +P+AF++AK+T T+++ + IP+ L VH ++PPHPAAL ADIG I+Y L+V Sbjct: 129 VPIAFNVAKRTGTNMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYSADIGRTILYALIV 188 Query: 186 GLMASLIGGPLFLKFLGQRL---PFKPVPTEFADLKVRDEKTLPSLGATLFTVLLPIALM 242 G+ ++I GP+F K + + + P P+ ++F D +D + LP G TLFT+LLP+ALM Sbjct: 189 GIPTAIIAGPIFGKLISKVVIPNPDNPLISQFVDEGKKDRE-LPGFGITLFTILLPVALM 247 Query: 243 LVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTMLTHTENGF 302 L+ + A+L A ++ L IGN + A IA V+++ G + +L T Sbjct: 248 LIGSWADLFFAPKTFANDFLRLIGNSVIALLIATLVSFWTFGRARGFGADQILKFTNECL 307 Query: 303 GSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSATV 362 IA+I L++GAG F IL ++ + I ++ H+ P++L W VA ++ A GSATV Sbjct: 308 APIASITLVVGAGAGFGRILMDGGVSKAIVGIATDAHLSPLILGWFVAALIRVATGSATV 367 Query: 363 AMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETFKY 422 AM A IVAP++ + PE++ +A G+G++ + V D FWLVK+Y T+ +TFK Sbjct: 368 AMTTACGIVAPIVSTVGGVRPELMVLATGAGSLILSHVNDGGFWLVKEYFNMTVPQTFKT 427 Query: 423 YTTATFIASVIALAGTFLLSFII 445 +T + SV+AL T L+ ++ Sbjct: 428 WTVMETLVSVLALLFTLALATVV 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: 564 Number of extensions: 38 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: 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