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69  structures 4388  species 0  interactions 12207  sequences 234  architectures

Family: 2OG-FeII_Oxy_2 (PF13532)

Summary: 2OG-Fe(II) oxygenase superfamily

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2OG-Fe(II) oxygenase superfamily Provide feedback

No Pfam abstract.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR027450

AlkB is a DNA repair enzyme that removes methyl adducts and some larger alkylation lesions from endocyclic positions on purine and pyrimidine bases. It is a dioxygenase that requires molecular oxygen, alpha-ketoglutarate and iron [ PUBMED:12226668 , PUBMED:21068844 ]. The catalytic core of AlkB is homologous to other Fe-2OG dioxygenases [ PUBMED:16513174 ]. Two discrete global conformations have been observed for AlkB, differing in accessibility of a putative oxygen-diffusion tunnel [ PUBMED:19706517 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(36)
Full
(12207)
Representative proteomes UniProt
(35858)
RP15
(1974)
RP35
(5493)
RP55
(10614)
RP75
(16749)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(36)
Full
(12207)
Representative proteomes UniProt
(35858)
RP15
(1974)
RP35
(5493)
RP55
(10614)
RP75
(16749)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(36)
Full
(12207)
Representative proteomes UniProt
(35858)
RP15
(1974)
RP35
(5493)
RP55
(10614)
RP75
(16749)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:A1B8L5
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 36
Number in full: 12207
Average length of the domain: 192.60 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 54.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 31.2 31.2
Trusted cut-off 31.2 31.2
Noise cut-off 31.1 31.1
Model length: 194
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the 2OG-FeII_Oxy_2 domain has been found. There are 69 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2K5G5 View 3D Structure Click here
A0A0R0F4U2 View 3D Structure Click here
A0A0R0G401 View 3D Structure Click here
A0A0R0GIH9 View 3D Structure Click here
A0A0R0GNF3 View 3D Structure Click here
A0A0R0HM03 View 3D Structure Click here
A0A0R0IFY8 View 3D Structure Click here
A0A1D6F7Y2 View 3D Structure Click here
A0A1D6KUW3 View 3D Structure Click here
A0A1D6NVU9 View 3D Structure Click here
A0A1D6NYV0 View 3D Structure Click here
A0A1Q0YC58 View 3D Structure Click here
A3QK41 View 3D Structure Click here
A4HSZ8 View 3D Structure Click here
A4HWT4 View 3D Structure Click here
A4I1X6 View 3D Structure Click here
A4IB22 View 3D Structure Click here
B4FTR4 View 3D Structure Click here
B6T2N7 View 3D Structure Click here
C6TKW1 View 3D Structure Click here
D3Z8W2 View 3D Structure Click here
D3ZK29 View 3D Structure Click here
D3ZKD3 View 3D Structure Click here
E0DBL0 View 3D Structure Click here
E9QB52 View 3D Structure Click here
E9QHS2 View 3D Structure Click here
F1QRD8 View 3D Structure Click here
F4JFR7 View 3D Structure Click here
F4JFR7 View 3D Structure Click here
F4KAV2 View 3D Structure Click here
G3V9E2 View 3D Structure Click here
I1KUL8 View 3D Structure Click here
I1L044 View 3D Structure Click here
I1L5A9 View 3D Structure Click here
I1MFT0 View 3D Structure Click here
I1MX21 View 3D Structure Click here
I1MYF0 View 3D Structure Click here
K7K3K1 View 3D Structure Click here
L7N6A4 View 3D Structure Click here
M0R7T2 View 3D Structure Click here
P0CB42 View 3D Structure Click here
Q08BA6 View 3D Structure Click here
Q0ISN2 View 3D Structure Click here
Q10BI5 View 3D Structure Click here
Q13686 View 3D Structure Click here
Q17527 View 3D Structure Click here
Q1ECQ5 View 3D Structure Click here
Q2R067 View 3D Structure Click here
Q3KRA9 View 3D Structure Click here
Q3TSG4 View 3D Structure Click here
Q4D8T3 View 3D Structure Click here
Q4D9X3 View 3D Structure Click here
Q4DDF6 View 3D Structure Click here
Q4DDZ6 View 3D Structure Click here
Q4DF98 View 3D Structure Click here
Q4DTN6 View 3D Structure Click here
Q54BK8 View 3D Structure Click here
Q54N08 View 3D Structure Click here
Q5RJC7 View 3D Structure Click here
Q5VPG7 View 3D Structure Click here
Q5XIC8 View 3D Structure Click here
Q5XVJ1 View 3D Structure Click here
Q6IQE9 View 3D Structure Click here
Q6NS38 View 3D Structure Click here
Q6P6C2 View 3D Structure Click here
Q6P6J4 View 3D Structure Click here
Q7KUZ2 View 3D Structure Click here
Q7XTQ3 View 3D Structure Click here
Q7YWP5 View 3D Structure Click here
Q80Y20 View 3D Structure Click here
Q8K1E6 View 3D Structure Click here
Q8K2U2 View 3D Structure Click here
Q8MNT9 View 3D Structure Click here
Q8RWY1 View 3D Structure Click here
Q96BT7 View 3D Structure Click here
Q96Q83 View 3D Structure Click here
Q9BT30 View 3D Structure Click here
Q9D6Z0 View 3D Structure Click here
Q9LJH2 View 3D Structure Click here
Q9SIE0 View 3D Structure Click here
Q9SUP1 View 3D Structure Click here