GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdX in Pseudomonas fluorescens FW300-N2C3

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.

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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