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2733  structures 3270  species 12  interactions 7458  sequences 100  architectures

Family: Globin (PF00042)

Summary: Globin

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

This is the Wikipedia entry entitled "Globin". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Globin Provide feedback

No Pfam abstract.

Literature references

  1. Bashford D, Chothia C, Lesk AM; , J Mol Biol 1987;196:199-216.: Determinants of a protein fold. Unique features of the globin amino acid sequences. PUBMED:3656444 EPMC:3656444

  2. Neuwald AF, Liu JS, Lipman DJ, Lawrence CE; , Nucleic Acids Res 1997;25:1665-1677.: Extracting protein alignment models from the sequence database. PUBMED:9108146 EPMC:9108146

  3. Bogusz D, Appleby CA, Landsmann J, Dennis ES, Trinick MJ, Peacock WJ; , Nature 1988;331:178-180.: Functioning haemoglobin genes in non-nodulating plants. PUBMED:2448639 EPMC:2448639

  4. Kinniburgh AJ, Maquat LE, Schedl T, Rachmilewitz E, Ross J; , Nucleic Acids Res 1982;10:5421-5427.: mRNA-deficient beta o-thalassemia results from a single nucleotide deletion. PUBMED:6292840 EPMC:6292840


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000971

Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms [PUBMED:17540514]. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors [PUBMED:16600051]. Several functionally different haemoglobins can coexist in the same species. The major types of globins include:

  • Haemoglobin (Hb): tetramer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates [PUBMED:16888280]. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors [PUBMED:15598493].
  • Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle [PUBMED:15339940].
  • Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia [PUBMED:12962627]. Neuroglobin belongs to a branch of the globin family that diverged early in evolution.
  • Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin [PUBMED:15804833].
  • Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers [PUBMED:17084861].
  • Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation.
  • Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants [PUBMED:17540516].
  • Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin [PUBMED:11092893].
  • Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [PUBMED:11481493, PUBMED:15598488].
  • Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors [PUBMED:15096613].
  • Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features [PUBMED:17701548].

This entry covers most of the globin family of proteins, but it omits some bacterial globins and the protoglobins.

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 7 members:

Bac_globin Globin HisK_N Phycobilisome Protoglobin Rsbr_N RsbRD_N

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(73)
Full
(7458)
Representative proteomes UniProt
(20560)
NCBI
(27846)
Meta
(34)
RP15
(1678)
RP35
(4017)
RP55
(6657)
RP75
(9134)
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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
(73)
Full
(7458)
Representative proteomes UniProt
(20560)
NCBI
(27846)
Meta
(34)
RP15
(1678)
RP35
(4017)
RP55
(6657)
RP75
(9134)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(73)
Full
(7458)
Representative proteomes UniProt
(20560)
NCBI
(27846)
Meta
(34)
RP15
(1678)
RP35
(4017)
RP55
(6657)
RP75
(9134)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: Structure_superposition
Previous IDs: globin;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Chothia C
Number in seed: 73
Number in full: 7458
Average length of the domain: 99.70 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 34.63 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 110
Family (HMM) version: 22
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

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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Interactions

There are 12 interactions for this family. More...

AHSP Trypsin NAD_binding_1 Globin NEAT AHSP FAD_binding_6 Ldl_recept_a NEAT FAD_binding_6 MHC_I NAD_binding_1

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 Globin domain has been found. There are 2733 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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