GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Marivita geojedonensis DPG-138

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_085640004.1 MGEO_RS15835 FAD-dependent oxidoreductase

Query= BRENDA::D3RXI0
         (252 letters)



>NCBI__GCF_002115805.1:WP_085640004.1
          Length = 695

 Score =  108 bits (269), Expect = 4e-28
 Identities = 57/171 (33%), Positives = 101/171 (59%), Gaps = 6/171 (3%)

Query: 6   IKVEKDERVARIKIANPPVNVLDMETMKEIISAID--EVEGVDVIVFSGEGKSFSAGAEI 63
           I+  +D  +A I I NPPVN L     + ++ A++  E +G    +  GEG+SF AGA+I
Sbjct: 5   IRYNRDGDIAMIAIDNPPVNALGQAVRQGLVEAVEKAEADGARAALIYGEGRSFPAGADI 64

Query: 64  KEHFPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKLG 123
           +E      P +  W   + +++     + V+A+ G ALGGG E+A+A D+ +A+  AK+G
Sbjct: 65  REF---GKPPLEPWLPDVCNRLETSPVLVVSALHGTALGGGLEIALASDYRIATPAAKVG 121

Query: 124 VPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKV 173
           +PE+ +   P       LPR++G + + ++I +G  I+A  AF++G++++V
Sbjct: 122 LPEVLIGVMPGAGGTQRLPRLVGVETSIDVITSGRQISAGEAFDLGIIDRV 172


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: 358
Number of extensions: 22
Number of successful extensions: 4
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: 695
Length adjustment: 31
Effective length of query: 221
Effective length of database: 664
Effective search space:   146744
Effective search space used:   146744
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 24 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