GapMind for catabolism of small carbon sources


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

Align Pyrimidine/purine nucleoside phosphorylase; Adenosine phosphorylase; Cytidine phosphorylase; Guanosine phosphorylase; Inosine phosphorylase; Thymidine phosphorylase; Uridine phosphorylase; Xanthosine phosphorylase; EC; EC; EC; EC; EC (characterized)
to candidate CA265_RS10695 CA265_RS10695 hypothetical protein

Query= SwissProt::P0C037
         (94 letters)

          Length = 93

 Score = 98.6 bits (244), Expect = 1e-26
 Identities = 46/93 (49%), Positives = 66/93 (70%), Gaps = 1/93 (1%)

          M+  N+YF G VKS+G+ ++  G++++GV+  GEYTF TA+ E M VI G L  LLPDAT

          +WQ  +AGS F VP +S F ++ +  T+YLC+Y

Lambda     K      H
   0.314    0.129    0.372 

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: 48
Number of extensions: 2
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: 94
Length of database: 93
Length adjustment: 10
Effective length of query: 84
Effective length of database: 83
Effective search space:     6972
Effective search space used:     6972
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (20.6 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