GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Pseudomonas simiae WCS417

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate GFF2259 PS417_11520 sorbitol dehydrogenase

Query= SwissProt::Q1NEI6
         (249 letters)



>FitnessBrowser__WCS417:GFF2259
          Length = 257

 Score =  141 bits (356), Expect = 1e-38
 Identities = 83/252 (32%), Positives = 133/252 (52%), Gaps = 14/252 (5%)

Query: 7   RYAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDA-THVVALDVS 65
           R  G+ A++TG A G+G+  A   IAEG  VA+ D++     AT AE+    + VA+DV+
Sbjct: 3   RLEGKSALITGSARGIGRAFAQAYIAEGATVAIADIDLQRAQATAAELGPQAYAVAMDVT 62

Query: 66  DHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNRE 125
           D A++  A     A  GK+DILI +A +     P+ +   DS+ R+  IN+ G  +  + 
Sbjct: 63  DQASIDGAITAVVAQAGKLDILINNAALFDLA-PIVDITRDSYDRLFSINVAGTLFTLQA 121

Query: 126 VVPFMLENGYG-RIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANAL 184
               M+  G+G +I+N+AS AG+ G P  + Y A+KA VI  T+S G  L  +G+  NA+
Sbjct: 122 AARQMIRQGHGGKIINMASQAGRRGEPLVAIYCATKAAVISLTQSAGLNLIKQGINVNAI 181

Query: 185 TPATFESPILDQL-----------PQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECS 233
            P   +    D +           P  +   + +++P GR+G  E+   M  F+AS+E  
Sbjct: 182 APGVVDGEHWDGVDALFAKHEGLAPGEKKQRVGAEVPFGRMGTAEDLTGMAIFLASKEAD 241

Query: 234 FTTASTFDTSGG 245
           +  A T++  GG
Sbjct: 242 YVVAQTYNVDGG 253


Lambda     K      H
   0.318    0.132    0.381 

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: 142
Number of extensions: 7
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: 249
Length of database: 257
Length adjustment: 24
Effective length of query: 225
Effective length of database: 233
Effective search space:    52425
Effective search space used:    52425
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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