GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaG in Pseudomonas fluorescens FW300-N2E2

Align protocatechuate 3,4-dioxygenase type II β subunit (EC 1.13.11.3) (characterized)
to candidate Pf6N2E2_997 Catechol 1,2-dioxygenase 1 (EC 1.13.11.1)

Query= metacyc::MONOMER-14210
         (241 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_997
          Length = 242

 Score = 68.6 bits (166), Expect = 1e-16
 Identities = 48/140 (34%), Positives = 65/140 (46%), Gaps = 17/140 (12%)

Query: 69  DLTKQGEGEPIGERIFVHGQVMDEDGRAIPNTLIEIWQANAAGRYIHALDSHPAPLDPNF 128
           DL +   G   G   FV G V  +DG  IPN  IE+WQA+ AG Y         P   ++
Sbjct: 69  DLGEDISGGLPGVPWFVKGTVTAKDGTPIPNATIEVWQADDAGFY-----DVQKPDMGDY 123

Query: 129 YGAGRTVTADDGTYTFTTIKPGPYPI----------MGLNNY-WRPAHIHLSLFGPSFLT 177
           +G        +G Y F TI P  YPI            LN + WRPAH+H  +  P +  
Sbjct: 124 HGRAVIQADANGHYYFRTIVPECYPIPHDGPVGKMLEALNRHPWRPAHLHFMITAPGY-Q 182

Query: 178 RLVTQLYFEGDPLIQHDMIY 197
           RLVT ++ EG   +  D ++
Sbjct: 183 RLVTHVFREGGDYLDSDAVF 202


Lambda     K      H
   0.319    0.136    0.422 

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: 206
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: 241
Length of database: 242
Length adjustment: 23
Effective length of query: 218
Effective length of database: 219
Effective search space:    47742
Effective search space used:    47742
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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