GapMind for catabolism of small carbon sources

 

Aligments for a candidate for badH in Pseudomonas putida KT2440

Align BadH (characterized)
to candidate PP_1946 PP_1946 Oxidoreductase, short chain dehydrogenase/reductase family

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



>lcl|FitnessBrowser__Putida:PP_1946 PP_1946 Oxidoreductase, short
           chain dehydrogenase/reductase family
          Length = 262

 Score =  151 bits (381), Expect = 1e-41
 Identities = 83/248 (33%), Positives = 129/248 (52%), Gaps = 7/248 (2%)

Query: 7   KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIAD 66
           K  ++TG G GIG AT   FAQ GA +AV D++ D   K    ++  GG A     D+  
Sbjct: 10  KVVLVTGAGSGIGRATALAFAQSGASVAVADISTDHGLKTVELVKAEGGEATFFHVDVGS 69

Query: 67  RTSVDAAIATTTTTLGPVDILVNNAGWDI-FKPFTKTEPGEWERLIAINLTGALHMHHAV 125
             SV + +A      G +DI  NNAG +    P  + +   W R+I +NL+   +     
Sbjct: 70  EPSVQSMLAGVVAHYGGLDIAHNNAGIEANIVPLAELDSDNWRRVIDVNLSSVFYCLKGE 129

Query: 126 LPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCP 185
           +P M++R  G IVN AS +  +G    + Y A K G+V  +K  A ++A   I +N VCP
Sbjct: 130 IPLMLKRGGGAIVNTASASGLIGGYRLSGYTATKHGVVGLTKAAAIDYANQNIRINAVCP 189

Query: 186 GPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVL 245
           GP D+  LAD+      P+ + +      P+GRL   +++A ++ +  SDDA ++ G  +
Sbjct: 190 GPVDSPFLADM------PQPMRDRLLFGTPIGRLATAEEIARSVLWLCSDDAKYVVGHSM 243

Query: 246 SVSGGLTM 253
           SV GG+ +
Sbjct: 244 SVDGGVAV 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: 177
Number of extensions: 12
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: 262
Length adjustment: 24
Effective length of query: 231
Effective length of database: 238
Effective search space:    54978
Effective search space used:    54978
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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