GapMind for catabolism of small carbon sources


Aligments for a candidate for deoD in Pseudomonas fluorescens FW300-N2E3

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 AO353_19295 AO353_19295 hypothetical protein

Query= SwissProt::P0C037
         (94 letters)

>lcl|FitnessBrowser__pseudo3_N2E3:AO353_19295 AO353_19295
          hypothetical protein
          Length = 94

 Score =  105 bits (263), Expect = 9e-29
 Identities = 51/93 (54%), Positives = 67/93 (72%), Gaps = 1/93 (1%)

          M + NEYF G VKSI F ++  G A++GVM  GEY F T++ E M V+SGAL V LPD++

          DW+ + AGS FNVP +S+F L+VA  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: 45
Number of extensions: 3
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: 94
Length adjustment: 10
Effective length of query: 84
Effective length of database: 84
Effective search space:     7056
Effective search space used:     7056
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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