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110  structures 7129  species 0  interactions 59445  sequences 274  architectures

Family: Usp (PF00582)

Summary: Universal stress protein family

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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.

Universal stress protein family Provide feedback

The universal stress protein UspA P28242 [1] is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [3] reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP [2] though UspA lacks ATP-binding activity.

Literature references

  1. Nystrom T, Neidhardt FC; , Mol Microbiol 1994;11:537-544.: Expression and role of the universal stress protein, UspA, of Escherichia coli during growth arrest. PUBMED:8152377 EPMC:8152377

  2. Zarembinski TI, Hung LW, Mueller-Dieckmann HJ, Kim KK, Yokota H, Kim R, Kim SH; , Proc Natl Acad Sci U S A 1998;95:15189-15193.: Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. PUBMED:9860944 EPMC:9860944

  3. Sousa MC, McKay DB; , Structure (Camb) 2001;9:1135-1141.: Structure of the universal stress protein of Haemophilus influenzae. PUBMED:11738040 EPMC:11738040


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006016

This entry represents a domain found in the universal stress protein UspA SWISSPROT [ PUBMED:8152377 ], which is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [ PUBMED:11738040 ] reveals an alpha/beta fold similar to that of the Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0577 protein, which binds ATP [ PUBMED:9860944 ], though UspA lacks ATP-binding activity.

Proteins containing this domain include the TeaD protein from Halomonas elongata. TeaD regulates the ectoine uptake by the transporter TeaABC. TeaD shows an ATP-dependent oligomerisation [ PUBMED:20113006 ].

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 HUP (CL0039), which has the following description:

The HUP class contains the HIGH-signature proteins, UspA superfamily and the PP-ATPase superfamily [1]. The HIGH superfamily has the HIGH Nucleotidyl transferases and the class I tRNA synthetases both of which have the HIGH and the KMSKS motif [1],[2]. The PP-loop ATPase named after the ATP PyroPhosphatase domain, was initially identified as a conserved amino acid sequence motif in four distinct groups of enzymes that catalyse the hydrolysis of the alpha-beta phosphate bond of ATP, namely GMP synthetases, argininosuccinate synthetases, asparagine synthetases, and ATP sulfurylases [3]. The USPA superfamily contains USPA, ETFP and Photolyases [1]

The clan contains the following 31 members:

Arginosuc_synth Asn_synthase ATP-sulfurylase ATP_bind_3 BshC CDPS Citrate_ly_lig CTP_transf_like Diphthami_syn_2 DNA_photolyase DPRP ETF FAD_syn HIGH_NTase1 HIGH_NTase1_ass NAD_synthase Pantoate_ligase PAPS_reduct QueC ThiI tRNA-synt_1 tRNA-synt_1_2 tRNA-synt_1b tRNA-synt_1c tRNA-synt_1d tRNA-synt_1e tRNA-synt_1f tRNA-synt_1g tRNA_Me_trans UDPG_MGDP_dh_C Usp

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
(159)
Full
(59445)
Representative proteomes UniProt
(221634)
RP15
(6042)
RP35
(25389)
RP55
(59235)
RP75
(103454)
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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
(159)
Full
(59445)
Representative proteomes UniProt
(221634)
RP15
(6042)
RP35
(25389)
RP55
(59235)
RP75
(103454)
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
(159)
Full
(59445)
Representative proteomes UniProt
(221634)
RP15
(6042)
RP35
(25389)
RP55
(59235)
RP75
(103454)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: MRC-LMB Genome group
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Griffiths-Jones SR , Kerk D , Studholme DJ
Number in seed: 159
Number in full: 59445
Average length of the domain: 136.00 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 60.65 %

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 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 141
Family (HMM) version: 28
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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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 Usp domain has been found. There are 110 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
A0A0N7KH89 View 3D Structure Click here
A0A0N7KI21 View 3D Structure Click here
A0A0P0VB72 View 3D Structure Click here
A0A0P0VMX2 View 3D Structure Click here
A0A0P0Y4W2 View 3D Structure Click here
A0A0P0Y881 View 3D Structure Click here
A0A0R0FC91 View 3D Structure Click here
A0A0R0G4A7 View 3D Structure Click here
A0A0R0JFL7 View 3D Structure Click here
A0A0R0K8D7 View 3D Structure Click here
A0A0R0L4D0 View 3D Structure Click here
A0A0R0L852 View 3D Structure Click here
A0A0R4J3L4 View 3D Structure Click here
A0A178VQ59 View 3D Structure Click here
A0A1D6G8D5 View 3D Structure Click here
A0A1D6GA16 View 3D Structure Click here
A0A1D6GHY9 View 3D Structure Click here
A0A1D6GPF6 View 3D Structure Click here
A0A1D6GPU8 View 3D Structure Click here
A0A1D6HL18 View 3D Structure Click here
A0A1D6I421 View 3D Structure Click here
A0A1D6IEQ6 View 3D Structure Click here
A0A1D6J571 View 3D Structure Click here
A0A1D6JZ20 View 3D Structure Click here
A0A1D6KWQ4 View 3D Structure Click here
A0A1D6L4K8 View 3D Structure Click here
A0A1D6LXE8 View 3D Structure Click here
A0A1D6LZ57 View 3D Structure Click here
A0A1D6M5M2 View 3D Structure Click here
A0A1D6M7K3 View 3D Structure Click here
A0A1D6MXG9 View 3D Structure Click here
A0A1D6N9T5 View 3D Structure Click here
A0A1D6NG77 View 3D Structure Click here
A0A1D6QCL0 View 3D Structure Click here
A0A1D6QQF6 View 3D Structure Click here
A0A1D8PMV1 View 3D Structure Click here
A0A1P8APG6 View 3D Structure Click here
A0A1P8AW87 View 3D Structure Click here
A0A1P8BD07 View 3D Structure Click here
A0A368UGS8 View 3D Structure Click here
B4FFW5 View 3D Structure Click here
B4FGW4 View 3D Structure Click here
B4FH43 View 3D Structure Click here
B4FL00 View 3D Structure Click here
B4FT81 View 3D Structure Click here
B4FVQ8 View 3D Structure Click here
B6TLF8 View 3D Structure Click here
B6TLW3 View 3D Structure Click here
B7EME6 View 3D Structure Click here
B9DG73 View 3D Structure Click here
B9DG73 View 3D Structure Click here
C0PFI7 View 3D Structure Click here
C0PL43 View 3D Structure Click here
C0Z2J1 View 3D Structure Click here
C6SVB6 View 3D Structure Click here
C6SVT0 View 3D Structure Click here
C6SVX3 View 3D Structure Click here
C6SXR1 View 3D Structure Click here
C6SZN6 View 3D Structure Click here
C6SZS5 View 3D Structure Click here
C6T3L1 View 3D Structure Click here
C6T3X9 View 3D Structure Click here
F4I5M8 View 3D Structure Click here
F4IDG2 View 3D Structure Click here
F4IK85 View 3D Structure Click here
F4JYN2 View 3D Structure Click here
F4JZT9 View 3D Structure Click here
I1J728 View 3D Structure Click here
I1JBG7 View 3D Structure Click here
I1JEJ0 View 3D Structure Click here
I1JFI9 View 3D Structure Click here
I1JFX0 View 3D Structure Click here
I1JLY5 View 3D Structure Click here
I1JR56 View 3D Structure Click here
I1JSN4 View 3D Structure Click here
I1JTY6 View 3D Structure Click here
I1JUN7 View 3D Structure Click here
I1JXZ6 View 3D Structure Click here
I1JZ69 View 3D Structure Click here
I1K466 View 3D Structure Click here
I1K653 View 3D Structure Click here
I1KAF1 View 3D Structure Click here
I1KBL7 View 3D Structure Click here
I1KD67 View 3D Structure Click here
I1KJW8 View 3D Structure Click here
I1KK69 View 3D Structure Click here
I1KNM2 View 3D Structure Click here
I1KSL4 View 3D Structure Click here
I1L048 View 3D Structure Click here
I1L7V6 View 3D Structure Click here
I1LSY9 View 3D Structure Click here
I1LUA5 View 3D Structure Click here
I1LVU3 View 3D Structure Click here
I1LW65 View 3D Structure Click here
I1LXD7 View 3D Structure Click here
I1M3Z4 View 3D Structure Click here
I1M4R0 View 3D Structure Click here
I1M619 View 3D Structure Click here
I1MA31 View 3D Structure Click here
I1MAZ6 View 3D Structure Click here
I1MBS4 View 3D Structure Click here
I1MC77 View 3D Structure Click here
I1MFT4 View 3D Structure Click here
I1MGF3 View 3D Structure Click here
I1MSE8 View 3D Structure Click here
I1N5P1 View 3D Structure Click here
I1NBB8 View 3D Structure Click here
I1NBR9 View 3D Structure Click here
K7K9W6 View 3D Structure Click here
K7KM53 View 3D Structure Click here
K7KMT2 View 3D Structure Click here
K7KNH0 View 3D Structure Click here
K7KTR1 View 3D Structure Click here
K7L4M8 View 3D Structure Click here
K7M3L4 View 3D Structure Click here
K7M6M7 View 3D Structure Click here
K7M712 View 3D Structure Click here
K7MK86 View 3D Structure Click here
K7MMP2 View 3D Structure Click here
K7MNU0 View 3D Structure Click here
K7U3I3 View 3D Structure Click here
K7U8V9 View 3D Structure Click here
K7UQP3 View 3D Structure Click here
K7UZG9 View 3D Structure Click here
K7V2N6 View 3D Structure Click here
O74782 View 3D Structure Click here
O82240 View 3D Structure Click here
P0AAB8 View 3D Structure Click here
P0AAC0 View 3D Structure Click here
P0AAC0 View 3D Structure Click here
P0AED0 View 3D Structure Click here
P37903 View 3D Structure Click here
P39177 View 3D Structure Click here
P46888 View 3D Structure Click here
P87132 View 3D Structure Click here
P9WFC9 View 3D Structure Click here
P9WFD1 View 3D Structure Click here
P9WFD1 View 3D Structure Click here
P9WFD3 View 3D Structure Click here
P9WFD5 View 3D Structure Click here
P9WFD7 View 3D Structure Click here
P9WFD7 View 3D Structure Click here
P9WFD9 View 3D Structure Click here
P9WGL3 View 3D Structure Click here
P9WLB5 View 3D Structure Click here
P9WLB5 View 3D Structure Click here
P9WLN1 View 3D Structure Click here
P9WLN1 View 3D Structure Click here
P9WLP1 View 3D Structure Click here
P9WLP1 View 3D Structure Click here
Q0DEQ5 View 3D Structure Click here
Q0WVJ0 View 3D Structure Click here
Q10MK7 View 3D Structure Click here
Q10PA1 View 3D Structure Click here
Q1G363 View 3D Structure Click here
Q1PE30 View 3D Structure Click here
Q1PF03 View 3D Structure Click here
Q2FXL6 View 3D Structure Click here
Q2FXM1 View 3D Structure Click here
Q2QNV2 View 3D Structure Click here
Q2QNV3 View 3D Structure Click here
Q2QQA6 View 3D Structure Click here
Q336S5 View 3D Structure Click here
Q33BK6 View 3D Structure Click here
Q54CH2 View 3D Structure Click here
Q54L57 View 3D Structure Click here
Q54SV7 View 3D Structure Click here
Q556D4 View 3D Structure Click here
Q55CS1 View 3D Structure Click here
Q55FP9 View 3D Structure Click here
Q57951 View 3D Structure Click here
Q57997 View 3D Structure Click here
Q5A0W0 View 3D Structure Click here
Q5Z7K5 View 3D Structure Click here
Q5ZAV7 View 3D Structure Click here
Q5ZB74 View 3D Structure Click here
Q60EJ0 View 3D Structure Click here
Q657H4 View 3D Structure Click here
Q65XS4 View 3D Structure Click here
Q67UV9 View 3D Structure Click here
Q67Y32 View 3D Structure Click here
Q681A5 View 3D Structure Click here
Q6AVR9 View 3D Structure Click here
Q6K4Q1 View 3D Structure Click here
Q6K8D2 View 3D Structure Click here
Q6Z2G8 View 3D Structure Click here
Q6Z6L3 View 3D Structure Click here
Q6ZHE6 View 3D Structure Click here
Q75HQ2 View 3D Structure Click here
Q75M01 View 3D Structure Click here
Q7XE49 View 3D Structure Click here
Q7XHV1 View 3D Structure Click here
Q84JS5 View 3D Structure Click here
Q84R08 View 3D Structure Click here
Q86K96 View 3D Structure Click here
Q8GWU3 View 3D Structure Click here
Q8H454 View 3D Structure Click here
Q8H907 View 3D Structure Click here
Q8L4N1 View 3D Structure Click here
Q8LFK2 View 3D Structure Click here
Q8LGG8 View 3D Structure Click here
Q8S292 View 3D Structure Click here
Q8VYN9 View 3D Structure Click here
Q8VZG4 View 3D Structure Click here
Q8W1D3 View 3D Structure Click here
Q93W91 View 3D Structure Click here
Q94E74 View 3D Structure Click here
Q94II5 View 3D Structure Click here
Q9C9G5 View 3D Structure Click here
Q9FI65 View 3D Structure Click here
Q9LF45 View 3D Structure Click here
Q9LQ92 View 3D Structure Click here
Q9LQB2 View 3D Structure Click here
Q9LSP5 View 3D Structure Click here
Q9LVN9 View 3D Structure Click here
Q9LYJ2 View 3D Structure Click here
Q9M328 View 3D Structure Click here
Q9M9P7 View 3D Structure Click here
Q9SW11 View 3D Structure Click here