GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Pseudomonas simiae WCS417

Align BadH (characterized)
to candidate GFF1782 PS417_09065 short-chain dehydrogenase

Query= metacyc::MONOMER-893
         (255 letters)



>FitnessBrowser__WCS417:GFF1782
          Length = 253

 Score =  139 bits (349), Expect = 7e-38
 Identities = 90/248 (36%), Positives = 129/248 (52%), Gaps = 6/248 (2%)

Query: 7   KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIAD 66
           + A++TG   GIG AT   FA EG K+ V DL+    E     I  AGG A  VRC++  
Sbjct: 8   QVALVTGAAAGIGRATALAFAAEGLKVVVADLDATGGENTVALIHQAGGEALFVRCNVTL 67

Query: 67  RTSVDAAIATTTTTLGPVDILVNNAGWDIFK-PFTKTEPGEWERLIAINLTGA-LHMHHA 124
              V   +A T    G +D   NNAG +I K         E++ ++ +N+ G  L M H 
Sbjct: 68  EADVQQLMAQTLAAYGRLDYAFNNAGIEIEKGKLADGSLDEFDAIMGVNVKGVWLCMKHQ 127

Query: 125 VLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVC 184
            LP ++ +  G IVN AS A    +   ++YAA K  ++  +K+ A E+A+  I VN VC
Sbjct: 128 -LPLLLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSAAIEYAKKKIRVNAVC 186

Query: 185 PGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQV 244
           P   DT +     +  A+P K  E      P+GR+GK +++A A+ +  SD A F TGQ 
Sbjct: 187 PAVIDTDMFR--RAYEADPRK-AEFAAAMHPVGRIGKVEEIASAVLYLCSDGAAFTTGQA 243

Query: 245 LSVSGGLT 252
           L+V GG T
Sbjct: 244 LAVDGGAT 251


Lambda     K      H
   0.318    0.135    0.398 

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: 147
Number of extensions: 9
Number of successful extensions: 3
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: 255
Length of database: 253
Length adjustment: 24
Effective length of query: 231
Effective length of database: 229
Effective search space:    52899
Effective search space used:    52899
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: 47 (22.7 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