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81  structures 1740  species 0  interactions 2853  sequences 99  architectures

Family: Protoglobin (PF11563)

Summary: Protoglobin

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Protoglobin Provide feedback

This family includes protoglobin from Methanosarcina acetivorans C2A. It is also found near the N-terminus of the Haem-based aerotactic transducer HemAT in Bacillus subtilis (O07621). It is part of the haemoglobin superfamily. Protoglobin has specific loops and an amino-terminal extension which leads to the burying of the haem within the matrix of the protein. Protoglobin-specific apolar tunnels allow the access of O2, CO and NO to the haem distal site [1]. In HemAT it acts as an oxygen sensor domain [2]. It can also recognise cyanide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).

Literature references

  1. Nardini M, Pesce A, Thijs L, Saito JA, Dewilde S, Alam M, Ascenzi P, Coletta M, Ciaccio C, Moens L, Bolognesi M; , EMBO Rep. 2008;9:157-163.: Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity. PUBMED:18188182 EPMC:18188182

  2. Zhang W, Phillips GN Jr;, Structure. 2003;11:1097-1110.: Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry. PUBMED:12962628 EPMC:12962628

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR044398

This domain is found at the N-terminal of globin-containing proteins mainly from bacteria, archaea and fungi [ PUBMED:15096613 ]. It is found in protoglobin, a single-domain globin of yet unknown biological function [ PUBMED:17540514 ], which has specific loops and an amino-terminal extension which leads to the burying of the heme within the matrix of the protein. Protoglobin-specific apolar tunnels allow the access of O2, CO and NO to the haem distal site [ PUBMED:18188182 , PUBMED:24054795 ].

Proteins containing this domain include protoglobins from the strictly anaerobic methanogen Methanosarcina acetivorans and from the obligate aerobic hyperthermophile Aeropyrum pernix [ PUBMED:17540514 ]. This domain is also found in the N-terminal regions of HemAT from the archaeon Halobacterium salinarum (HemAT-Hs) and from the Gram-positive bacterium Bacillus subtilis (HemAT-Bs) [ PUBMED:12962628 ]. It contains a myoglobin-like motif, displays characteristic heme-protein absorption spectra, and binds oxygen reversibly [ PUBMED:11481493 ]. This domain is present in Diguanylate cyclase DosC (also known as YddV) from E. coli which is coupled with a C-terminal diguanylate cyclase (DGC/GGDEF) domain, which likely functions as a c-di-GMP cyclase in the synthesis of the second messenger cyclic-di-GMP (c-di-GMP) [ PUBMED:26148715 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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

This family is a member of clan Globin (CL0090), which has the following description:

The globin fold is an evolutionary conserved six helical fold that is found in bacteria and eukaryotes.

The clan contains the following 8 members:

Bac_globin Globin HisK-N-like HisK_N Phycobilisome Protoglobin Rsbr_N RsbRD_N


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...

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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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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...


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: pdb_2veb
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Pollington J , Eberhardt R
Number in seed: 72
Number in full: 2853
Average length of the domain: 161.3 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 39.4 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 158
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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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The tree shows the occurrence of this domain across different species. More...


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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 Protoglobin domain has been found. There are 81 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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