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72  structures 6186  species 0  interactions 9366  sequences 71  architectures

Family: Pro_dh (PF01619)

Summary: Proline dehydrogenase

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.

Proline dehydrogenase Provide feedback

No Pfam abstract.

Literature references

  1. Ling M, Allen SW, Wood JM; , J Mol Biol 1994;243:950-956.: Sequence analysis identifies the proline dehydrogenase and delta 1- pyrroline-5-carboxylate dehydrogenase domains of the multifunctional Escherichia coli PutA protein. PUBMED:7966312 EPMC:7966312


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002872

The proline oxidase/dehydrogenase EC is responsible for the first step in the conversion of proline to glutamate for use as a carbon and nitrogen source. The enzyme requires FAD as a cofactor, and is induced by proline.

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 FAD_oxidored (CL0086), which has the following description:

The members of this clan adopt a TIM barrel fold, which is reminiscent of flavin mononucleotide binding proteins, rather than one similar to other flavin adenine dinucleotide binding domains. However, the way the FAD cofactor binds in quite different compared to the binding of FMN in the TIM-barrel structures [1].

The clan contains the following 3 members:

MTHFR MTHFR_2 Pro_dh

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
(197)
Full
(9366)
Representative proteomes UniProt
(37284)
RP15
(1187)
RP35
(4109)
RP55
(8845)
RP75
(14903)
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
(197)
Full
(9366)
Representative proteomes UniProt
(37284)
RP15
(1187)
RP35
(4109)
RP55
(8845)
RP75
(14903)
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
(197)
Full
(9366)
Representative proteomes UniProt
(37284)
RP15
(1187)
RP35
(4109)
RP55
(8845)
RP75
(14903)
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: Pfam-B_1092 (release 4.1)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 197
Number in full: 9366
Average length of the domain: 301.7 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 45.01 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.2
Noise cut-off 26.7 26.9
Model length: 282
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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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 Pro_dh domain has been found. There are 72 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
A0A044TSB3 View 3D Structure Click here
A0A0D2DJ37 View 3D Structure Click here
A0A0D2F408 View 3D Structure Click here
A0A0D2GQ51 View 3D Structure Click here
A0A0H3GRA2 View 3D Structure Click here
A0A0H4IVH0 View 3D Structure Click here
A0A0H5SCE5 View 3D Structure Click here
A0A0K0EE58 View 3D Structure Click here
A0A0N4U568 View 3D Structure Click here
A0A175WHB8 View 3D Structure Click here
A0A1C1C848 View 3D Structure Click here
A0A1C1CNN4 View 3D Structure Click here
A0A1D6K864 View 3D Structure Click here
A0A1D8PNH4 View 3D Structure Click here
A0A3P7DMK3 View 3D Structure Click here
A0A3P7FUS0 View 3D Structure Click here
A0A3Q0KST5 View 3D Structure Click here
A0A5K4EWI8 View 3D Structure Click here
A0A5S6PFK4 View 3D Structure Click here
A4I294 View 3D Structure Click here
A6QQ74 View 3D Structure Click here
B6STU5 View 3D Structure Click here
C0NBI5 View 3D Structure Click here
C0NSV7 View 3D Structure Click here
C1H7N6 View 3D Structure Click here
E7FEU8 View 3D Structure Click here
E7FFM5 View 3D Structure Click here
F1MAR6 View 3D Structure Click here
F1QCH4 View 3D Structure Click here
I1KWN9 View 3D Structure Click here
I1N4V3 View 3D Structure Click here
I1N6L0 View 3D Structure Click here
K0EUS1 View 3D Structure Click here
K0FC47 View 3D Structure Click here
K7LXR0 View 3D Structure Click here
K7MWG9 View 3D Structure Click here
O24897 View 3D Structure Click here
O32179 View 3D Structure Click here
O43272 View 3D Structure Click here
O45228 View 3D Structure Click here