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76  structures 1353  species 0  interactions 15036  sequences 351  architectures

Family: PB1 (PF00564)

Summary: PB1 domain

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.

PB1 domain Provide feedback

No Pfam abstract.

Literature references

  1. Ponting CP; , Protein Sci 1996;5:2353-2357.: Novel domains in NADPH oxidase subunits, sorting nexins, and PtdIns 3-kinases: binding partners of SH3 domains? PUBMED:8931154 EPMC:8931154

  2. Zhou G, Bao ZQ, Dixon JE; , J Biol Chem 1995;270:12665-12669.: Components of a new human protein kinase signal transduction pathway. PUBMED:7759517 EPMC:7759517

  3. English JM, Vanderbilt CA, Xu S, Marcus S, Cobb MH; , J Biol Chem 1995;270:28897-28902.: Isolation of MEK5 and differential expression of alternatively spliced forms. PUBMED:7499418 EPMC:7499418


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000270

The PB1 (Phox and Bem1) domain, comprising about 80 amino acid residues, is conserved among animals, fungi, amoebas, and plants. It functions as a protein binding module through PB1-mediated heterodimerization or homo-oligomerization [ PUBMED:17726178 , PUBMED:15590654 , PUBMED:11483498 , PUBMED:24706860 ].

The PB1 domains adopt an ubiquitin-like beta-grasp fold, containing two alpha helices and a mixed five-stranded beta sheet. The beta-sheet has a convex surface, and alpha1 fits into the cavity formed by the sheet. PB1 domains may display an acidic surface (type I), a basic surface (tape II), or both surfaces (type I/II) on opposite faces of the domain structure to allow for front-to-back orientation of multiple PB1 domains [ PUBMED:17726178 , PUBMED:15590654 , PUBMED:11483498 , PUBMED:24706860 , PUBMED:24710426 ].

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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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
(46)
Full
(15036)
Representative proteomes UniProt
(23679)
RP15
(2032)
RP35
(7105)
RP55
(12224)
RP75
(16459)
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
(46)
Full
(15036)
Representative proteomes UniProt
(23679)
RP15
(2032)
RP35
(7105)
RP55
(12224)
RP75
(16459)
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
(46)
Full
(15036)
Representative proteomes UniProt
(23679)
RP15
(2032)
RP35
(7105)
RP55
(12224)
RP75
(16459)
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: Alignment kindly provided by SMART
Previous IDs: OPR;
Type: Domain
Sequence Ontology: SO:0000417
Author: SMART
Number in seed: 46
Number in full: 15036
Average length of the domain: 84.50 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 12.78 %

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 23.6 23.6
Trusted cut-off 23.6 23.6
Noise cut-off 23.5 23.5
Model length: 84
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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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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 PB1 domain has been found. There are 76 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
A0A096PY84 View 3D Structure Click here
A0A096QBS7 View 3D Structure Click here
A0A096SVP6 View 3D Structure Click here
A0A0N7KDA4 View 3D Structure Click here
A0A0P0VEJ5 View 3D Structure Click here
A0A0P0XJ24 View 3D Structure Click here
A0A0P0XQL5 View 3D Structure Click here
A0A0P0YBU6 View 3D Structure Click here
A0A0R0GWJ1 View 3D Structure Click here
A0A0R0HMX7 View 3D Structure Click here
A0A0R0IRI6 View 3D Structure Click here
A0A0R0J1Q5 View 3D Structure Click here
A0A0R0JYS7 View 3D Structure Click here
A0A0R0KHG6 View 3D Structure Click here
A0A0R4ITX2 View 3D Structure Click here
A0A1D6DRY2 View 3D Structure Click here
A0A1D6E793 View 3D Structure Click here
A0A1D6ECR4 View 3D Structure Click here
A0A1D6EHN3 View 3D Structure Click here
A0A1D6EUG0 View 3D Structure Click here
A0A1D6EY10 View 3D Structure Click here
A0A1D6GZW1 View 3D Structure Click here
A0A1D6HML9 View 3D Structure Click here
A0A1D6HP12 View 3D Structure Click here
A0A1D6HZL1 View 3D Structure Click here
A0A1D6IAN8 View 3D Structure Click here
A0A1D6IB27 View 3D Structure Click here
A0A1D6J9B4 View 3D Structure Click here
A0A1D6JMR3 View 3D Structure Click here
A0A1D6KF52 View 3D Structure Click here
A0A1D6KXW8 View 3D Structure Click here
A0A1D6L051 View 3D Structure Click here
A0A1D6L063 View 3D Structure Click here
A0A1D6LIX0 View 3D Structure Click here
A0A1D6LIX2 View 3D Structure Click here
A0A1D6M0H8 View 3D Structure Click here
A0A1D6MET6 View 3D Structure Click here
A0A1D6MPN6 View 3D Structure Click here
A0A1D6P3G6 View 3D Structure Click here
A0A1D6PSW2 View 3D Structure Click here
A0A1I9LN82 View 3D Structure Click here
A0A2R8Q7H2 View 3D Structure Click here
A0A368UI00 View 3D Structure Click here
A0A368UKN3 View 3D Structure Click here
A1Z9X0 View 3D Structure Click here
A3C1D8 View 3D Structure Click here
A4HZD3 View 3D Structure Click here
A7E3N2 View 3D Structure Click here
A7E3N7 View 3D Structure Click here
A9JRD0 View 3D Structure Click here
B0S4T7 View 3D Structure Click here
B2RZ98 View 3D Structure Click here
B5DF98 View 3D Structure Click here
B6SXQ4 View 3D Structure Click here
B7ZY51 View 3D Structure Click here
C0HG45 View 3D Structure Click here
C0PDQ4 View 3D Structure Click here
C0PHI9 View 3D Structure Click here
C4JAN7 View 3D Structure Click here
D4A2F2 View 3D Structure Click here
E7EXX1 View 3D Structure Click here
E7F683 View 3D Structure Click here
E9PT71 View 3D Structure Click here
E9QEG9 View 3D Structure Click here
F1M7Y5 View 3D Structure Click here
F1M9D0 View 3D Structure Click here
F1Q5Z8 View 3D Structure Click here
F1R2I7 View 3D Structure Click here
F1R754 View 3D Structure Click here
F4I5S1 View 3D Structure Click here
F4IRM4 View 3D Structure Click here
F4JTI1 View 3D Structure Click here
F4K487 View 3D Structure Click here
F8W4T2 View 3D Structure Click here
I1J535 View 3D Structure Click here
I1JC75 View 3D Structure Click here
I1JH30 View 3D Structure Click here
I1JJW0 View 3D Structure Click here
I1JUA6 View 3D Structure Click here
I1JXB3 View 3D Structure Click here
I1JXX1 View 3D Structure Click here
I1K529 View 3D Structure Click here
I1KBQ2 View 3D Structure Click here
I1KCB9 View 3D Structure Click here
I1KL73 View 3D Structure Click here
I1KLC1 View 3D Structure Click here
I1KNI0 View 3D Structure Click here
I1KNY3 View 3D Structure Click here
I1KQR2 View 3D Structure Click here
I1KQV6 View 3D Structure Click here
I1KTY1 View 3D Structure Click here
I1KTY2 View 3D Structure Click here
I1L282 View 3D Structure Click here
I1L491 View 3D Structure Click here
I1LES5 View 3D Structure Click here
I1LQB5 View 3D Structure Click here
I1LTB7 View 3D Structure Click here
I1LZU9 View 3D Structure Click here
I1M2J9 View 3D Structure Click here
I1MB27 View 3D Structure Click here
I1MI76 View 3D Structure Click here
I1MJC0 View 3D Structure Click here
I1MJC1 View 3D Structure Click here
I1MJU8 View 3D Structure Click here
I1MPM2 View 3D Structure Click here
I1MR20 View 3D Structure Click here
I1MTC8 View 3D Structure Click here
I1MTZ3 View 3D Structure Click here
I1MU15 View 3D Structure Click here
I1N2C5 View 3D Structure Click here
I1NFP9 View 3D Structure Click here
K7KHB3 View 3D Structure Click here
K7KHM7 View 3D Structure Click here
K7KMT5 View 3D Structure Click here
K7KMZ0 View 3D Structure Click here
K7KPD3 View 3D Structure Click here
K7KSI9 View 3D Structure Click here
K7KWA7 View 3D Structure Click here
K7L4C5 View 3D Structure Click here
K7L9F8 View 3D Structure Click here
K7LAT7 View 3D Structure Click here
K7LD90 View 3D Structure Click here
K7LDR9 View 3D Structure Click here
K7LJE7 View 3D Structure Click here
K7LKC2 View 3D Structure Click here
K7LL19 View 3D Structure Click here
K7LPE3 View 3D Structure Click here
K7LWW4 View 3D Structure Click here
K7M3K8 View 3D Structure Click here
K7M979 View 3D Structure Click here
K7M9W4 View 3D Structure Click here
K7MCM1 View 3D Structure Click here
K7MJV8 View 3D Structure Click here
K7MK79 View 3D Structure Click here
K7MKM1 View 3D Structure Click here
K7N2H4 View 3D Structure Click here
K7N3R8 View 3D Structure Click here
K7N4J1 View 3D Structure Click here
K7TQE3 View 3D Structure Click here
K7U8M9 View 3D Structure Click here
K7UQN1 View 3D Structure Click here
K7V271 View 3D Structure Click here
K7VE43 View 3D Structure Click here
K7VFE6 View 3D Structure Click here
K7VRG4 View 3D Structure Click here
K7VV70 View 3D Structure Click here
O08623 View 3D Structure Click here
O13965 View 3D Structure Click here
O22864 View 3D Structure Click here
O48802 View 3D Structure Click here
O64768 View 3D Structure Click here
O70145 View 3D Structure Click here
O97111 View 3D Structure Click here
P09217 View 3D Structure Click here
P0DH79 View 3D Structure Click here
P14199 View 3D Structure Click here
P19878 View 3D Structure Click here
P40995 View 3D Structure Click here
P41743 View 3D Structure Click here
P97369 View 3D Structure Click here
P97432 View 3D Structure Click here
Q02956 View 3D Structure Click here
Q05513 View 3D Structure Click here
Q0D5J6 View 3D Structure Click here
Q0D6U7 View 3D Structure Click here
Q0DAT1 View 3D Structure Click here
Q0DE33 View 3D Structure Click here
Q0E362 View 3D Structure Click here
Q0ISL7 View 3D Structure Click here
Q0IZD0 View 3D Structure Click here
Q0JC27 View 3D Structure Click here
Q0WLC7 View 3D Structure Click here
Q10K10 View 3D Structure Click here
Q10S83 View 3D Structure Click here
Q13163 View 3D Structure Click here
Q13501 View 3D Structure Click here
Q14596 View 3D Structure Click here
Q15080 View 3D Structure Click here
Q19266 View 3D Structure Click here
Q1LUW2 View 3D Structure Click here
Q27GK5 View 3D Structure Click here
Q2QX49 View 3D Structure Click here
Q2RA11 View 3D Structure Click here
Q4DB71 View 3D Structure Click here
Q4E1T7 View 3D Structure Click here
Q501R9 View 3D Structure Click here
Q53KV1 View 3D Structure Click here
Q53KV7 View 3D Structure Click here
Q54R82 View 3D Structure Click here
Q55CE3 View 3D Structure Click here
Q5A3N2 View 3D Structure Click here
Q5JMT5 View 3D Structure Click here
Q5NB82 View 3D Structure Click here
Q5ZDH9 View 3D Structure Click here
Q61083 View 3D Structure Click here
Q61084 View 3D Structure Click here
Q62074 View 3D Structure Click here
Q62862 View 3D Structure Click here
Q64337 View 3D Structure Click here
Q67W58 View 3D Structure Click here
Q69QX2 View 3D Structure Click here
Q6AYR1 View 3D Structure Click here
Q6B4M5 View 3D Structure Click here
Q6P0G5 View 3D Structure Click here
Q6TNS1 View 3D Structure Click here
Q6ZH84 View 3D Structure Click here
Q75HQ9 View 3D Structure Click here
Q7X9B9 View 3D Structure Click here
Q7XK43 View 3D Structure Click here
Q84TH9 View 3D Structure Click here
Q86UR1 View 3D Structure Click here
Q8CJ00 View 3D Structure Click here
Q8H111 View 3D Structure Click here
Q8RWY4 View 3D Structure Click here
Q90XF2 View 3D Structure Click here
Q92734 View 3D Structure Click here
Q940N7 View 3D Structure Click here
Q99759 View 3D Structure Click here
Q9BYG4 View 3D Structure Click here
Q9BYG5 View 3D Structure Click here
Q9FGF3 View 3D Structure Click here
Q9FKL3 View 3D Structure Click here
Q9FML0 View 3D Structure Click here
Q9FMV3 View 3D Structure Click here
Q9FRH9 View 3D Structure Click here
Q9GRV1 View 3D Structure Click here
Q9JK83 View 3D Structure Click here
Q9JK84 View 3D Structure Click here
Q9LE38 View 3D Structure Click here
Q9LF06 View 3D Structure Click here
Q9LF97 View 3D Structure Click here
Q9LJQ7 View 3D Structure Click here
Q9LRY7 View 3D Structure Click here
Q9LTX8 View 3D Structure Click here
Q9LXC6 View 3D Structure Click here
Q9M1B0 View 3D Structure Click here
Q9M9L2 View 3D Structure Click here
Q9NAN2 View 3D Structure Click here
Q9NPB6 View 3D Structure Click here
Q9S843 View 3D Structure Click here
Q9SA26 View 3D Structure Click here
Q9SAJ2 View 3D Structure Click here
Q9SB64 View 3D Structure Click here
Q9SFW8 View 3D Structure Click here
Q9SJQ5 View 3D Structure Click here
Q9STK4 View 3D Structure Click here
Q9SVF1 View 3D Structure Click here
Q9U1W1 View 3D Structure Click here
Q9WVS7 View 3D Structure Click here
Q9Y2U5 View 3D Structure Click here
Q9Z101 View 3D Structure Click here
Q9Z1A1 View 3D Structure Click here
Q9ZU48 View 3D Structure Click here