GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praC in Pedobacter sp. GW460-11-11-14-LB5

Align 2-hydroxymuconate tautomerase (EC 5.3.2.6) (characterized)
to candidate CA265_RS13720 CA265_RS13720 4-oxalocrotonate tautomerase

Query= BRENDA::Q01468
         (63 letters)



>FitnessBrowser__Pedo557:CA265_RS13720
          Length = 72

 Score = 38.1 bits (87), Expect = 1e-08
 Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 1  MPIAQIHIL-EGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELAS 59
          MP  +I +  EG + EQK+TLI  +++ IS  LD       ++I E+    +G  GE  S
Sbjct: 1  MPYVKIEVTREGVTREQKQTLISGITKLISEVLDKDPKLTHIVIQEIELDDWGYAGEQVS 60

Query: 60 KVRR 63
           +R+
Sbjct: 61 VLRK 64


Lambda     K      H
   0.317    0.134    0.352 

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: 10
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: 63
Length of database: 72
Length adjustment: 5
Effective length of query: 58
Effective length of database: 67
Effective search space:     3886
Effective search space used:     3886
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: 37 (19.8 bits)
S2: 37 (18.9 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