GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdX in Pseudomonas fluorescens FW300-N1B4

Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate Pf1N1B4_556 Gluconate permease

Query= SwissProt::A0A0H2VAP9
         (445 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_556
          Length = 450

 Score =  333 bits (853), Expect = 9e-96
 Identities = 180/450 (40%), Positives = 269/450 (59%), Gaps = 8/450 (1%)

Query: 1   MHSQIWVVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIG 60
           M  + +++   +++++ +++ I KFK HPFLAL++A+ F+G   GM    ++ A + G G
Sbjct: 4   MSHESFLLLDAVVTVIGLIVLITKFKLHPFLALIIAAAFLGLTSGMPIGTIIKAFQDGFG 63

Query: 61  GTLGFLAAVIGLGTILGKMMEVSGAAERIGLTLQRCRWLSADVI---MVLVGLICGITLF 117
           G LGF+  ++ LGT+LGKMM  SG A++I  TL R      D +   M+    + GI LF
Sbjct: 64  GVLGFVGIILALGTMLGKMMAESGGADQIAQTLIRA--FGKDKVQWAMMFAAFLVGIPLF 121

Query: 118 VEVGVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGS 177
            E+G VLLIPL F +A++T  S++K+ IPL   L AVH +VPPHP  L      GADIG 
Sbjct: 122 FEIGFVLLIPLVFIVARRTGVSIIKIGIPLLAGLSAVHGLVPPHPGPLLAIGVFGADIGK 181

Query: 178 VIVYGLLVGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVR--DEKTLPSLGATLFTV 235
            I+YGL+V L  ++I GP+F  F+ + +P  P   E  D   R  D   LPS G TL TV
Sbjct: 182 TILYGLIVALPTAIIAGPIFGTFIAKHIPGHP-NQELVDQLSRETDSAELPSFGITLVTV 240

Query: 236 LLPIALMLVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHMSMGTML 295
           LLP+ LML+KT A++ +   +   T ++ IG+PI+A  +A+ ++ Y  G +Q +    M+
Sbjct: 241 LLPVFLMLLKTFADVVLPDGNIFRTFMDLIGHPISALLLALLLSLYTFGYKQGIGSSQMM 300

Query: 296 THTENGFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHA 355
              +      A I+LIIGAGG F  +L +S + D +  +  N  + PILLAWLVA ++  
Sbjct: 301 KWLDASLAPTAAIILIIGAGGGFKQMLVTSGVGDVIGHMAVNAQISPILLAWLVAAVIRI 360

Query: 356 AVGSATVAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGAT 415
           A GSATVA +    IV P++ + P ++ E++ +A G+G++  + V D+ FWLVKQY   T
Sbjct: 361 ATGSATVATITGAGIVVPVVGMIPGVNRELLVLATGAGSLILSHVNDAGFWLVKQYFNMT 420

Query: 416 LNETFKYYTTATFIASVIALAGTFLLSFII 445
           + ETFK +T    I SV+ L    LLS  +
Sbjct: 421 VAETFKTWTAMETILSVVGLGFILLLSLFV 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: 634
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.

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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