GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdX in Burkholderia phytofirmans PsJN

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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