GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Pseudomonas fluorescens FW300-N2E3

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate AO353_00510 AO353_00510 multifunctional fatty acid oxidation complex subunit alpha

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_00510
          Length = 715

 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 61/175 (34%), Positives = 88/175 (50%), Gaps = 22/175 (12%)

Query: 24  VNVLDMETMKEIISAIDEVEG----VDVIVFSGEGKSFSAGAEIKEHFPD-KAPEMIRWF 78
           VN  +  T+ E+ SA+D ++       VIV SG+   F  GA+I E   + K P+     
Sbjct: 29  VNKFNRLTLNELRSAVDAIKADASVKGVIVSSGKDV-FIVGADITEFVDNFKLPD----- 82

Query: 79  TQLIDKVLRCKAI----------TVAAVKGFALGGGFELAIACDFVLASKNAKLGVPEIT 128
            +L+   L    I          TVAA+ G ALGGG E+ +A D+ + S  AK+G+PE+ 
Sbjct: 83  AELVAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLEMCLAADYRVMSTTAKIGLPEVK 142

Query: 129 LAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEES 182
           L  YP       LPR+IG  NA E I  G+    E A ++G V+ V   E  +E+
Sbjct: 143 LGIYPGFGGTVRLPRIIGADNAIEWIAAGKENRPEDALKVGAVDAVVAPEQLQEA 197


Lambda     K      H
   0.318    0.136    0.382 

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: 437
Number of extensions: 24
Number of successful extensions: 2
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: 252
Length of database: 715
Length adjustment: 32
Effective length of query: 220
Effective length of database: 683
Effective search space:   150260
Effective search space used:   150260
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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