GapMind for catabolism of small carbon sources

 

Aligments for a candidate for badH in Burkholderia phytofirmans PsJN

Align BadH (characterized)
to candidate BPHYT_RS30440 BPHYT_RS30440 short-chain dehydrogenase

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS30440 BPHYT_RS30440 short-chain
           dehydrogenase
          Length = 254

 Score =  175 bits (443), Expect = 9e-49
 Identities = 102/256 (39%), Positives = 149/256 (58%), Gaps = 12/256 (4%)

Query: 4   LQNKTAVITGGGG--GIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVR 61
           L  K AVI+GG    GIG AT R+FA  GA+IA+FDL+  AA + A +I   G       
Sbjct: 7   LDGKVAVISGGASPRGIGMATARKFAAHGARIAIFDLDEKAAVEAAASI---GPEHRGYV 63

Query: 62  CDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHM 121
           C++ DR +  AA+  T    G +DIL+NNAG      F   +P  W+R++ +NL G L++
Sbjct: 64  CNVTDRGACQAAVERTVADFGSIDILINNAGITQAAKFLDIDPESWDRILDVNLRGVLYL 123

Query: 122 HHAVLPGMVERRHGRIVNIASDAARVGSS--GEAVYAACKGGLVAFSKTLAREHARHGIT 179
             AV+P M +++ G I  ++S +A+ G    G   Y+A K G++  +K +ARE    GI 
Sbjct: 124 SQAVVPQMKKQKSGSIGCMSSVSAQRGGGILGGPHYSAAKAGVLGLAKAMARELGNDGIR 183

Query: 180 VNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGF 239
           VN V PG   T    D+ +G  + +K +E  +  IPL RLG PDD+AGA  F  SD + +
Sbjct: 184 VNCVTPGLIQT----DINAGKISDDKRVEILS-GIPLNRLGVPDDVAGAFLFLASDLSSY 238

Query: 240 ITGQVLSVSGGLTMNG 255
           ITG V+ V+GG+ ++G
Sbjct: 239 ITGAVIDVNGGMLIHG 254


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: 184
Number of extensions: 10
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: 255
Length of database: 254
Length adjustment: 24
Effective length of query: 231
Effective length of database: 230
Effective search space:    53130
Effective search space used:    53130
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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