GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaB in Pseudomonas fluorescens GW456-L13

Align ring 1,2-phenylacetyl-CoA epoxidase PaaB subunit (EC 1.14.13.149) (characterized)
to candidate PfGW456L13_2426 Phenylacetate-CoA oxygenase, PaaH subunit

Query= metacyc::MONOMER-15948
         (93 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2426
          Length = 93

 Score =  182 bits (462), Expect = 8e-52
 Identities = 86/93 (92%), Positives = 90/93 (96%)

Query: 1  MSEWTLFEVFVRSKHGLNHKHVGSVHAADAAMAIDNARELYTRRNEGVSLWVVPSALITA 60
          MSEWTLFEVFVRSKHGLNHKHVGSVHAAD  MAI+NARELYTRR+EGVSLWVVPSALITA
Sbjct: 1  MSEWTLFEVFVRSKHGLNHKHVGSVHAADTTMAIENARELYTRRSEGVSLWVVPSALITA 60

Query: 61 SSPDEKEPLFDPAQDKVYRHASFYELPAEVGHM 93
          SSPDEK+PLFDP+ DKVYRHASFYELPAEVGHM
Sbjct: 61 SSPDEKDPLFDPSDDKVYRHASFYELPAEVGHM 93


Lambda     K      H
   0.318    0.130    0.395 

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: 90
Number of extensions: 1
Number of successful extensions: 1
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: 93
Length of database: 93
Length adjustment: 10
Effective length of query: 83
Effective length of database: 83
Effective search space:     6889
Effective search space used:     6889
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: 39 (20.8 bits)
S2: 39 (19.6 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