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8  structures 854  species 0  interactions 944  sequences 13  architectures

Family: Nnf1 (PF03980)

Summary: Nnf1

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.

Nnf1 Provide feedback

NNF1 is an essential yeast gene that is necessary for chromosome segregation. It is associated with the spindle poles [1] and forms part of a kinetochore subcomplex called MIND [2].

Literature references

  1. Euskirchen GM; , Eukaryot Cell 2002;1:229-240.: Nnf1p, Dsn1p, Mtw1p, and Nsl1p: a new group of proteins important for chromosome segregation in Saccharomyces cerevisiae. PUBMED:12455957 EPMC:12455957

  2. De Wulf P, McAinsh AD, Sorger PK; , Genes Dev 2003;17:2902-2921.: Hierarchical assembly of the budding yeast kinetochore from multiple subcomplexes. PUBMED:14633972 EPMC:14633972

  3. Meraldi P, McAinsh AD, Rheinbay E, Sorger PK; , Genome Biol. 2006;7:R23.: Phylogenetic and structural analysis of centromeric DNA and kinetochore proteins. PUBMED:16563186 EPMC:16563186


This tab holds annotation information from the InterPro database.

InterPro entry IPR007128

This entry includes polyamine-modulated factor 1 (PMF1) from animals and Nnf1 from yeasts. PMF1 is part of the MIS12 complex which is required for normal chromosome alignment and segregation and kinetochore formation during mitosis [PUBMED:16585270]. Nnf1 is an essential component of the MIND kinetochore complex required for accurate chromosome segregation [PUBMED:12455957].

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, 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
(113)
Full
(944)
Representative proteomes UniProt
(1454)
NCBI
(1883)
Meta
(3)
RP15
(146)
RP35
(390)
RP55
(646)
RP75
(940)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(113)
Full
(944)
Representative proteomes UniProt
(1454)
NCBI
(1883)
Meta
(3)
RP15
(146)
RP35
(390)
RP55
(646)
RP75
(940)
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
(113)
Full
(944)
Representative proteomes UniProt
(1454)
NCBI
(1883)
Meta
(3)
RP15
(146)
RP35
(390)
RP55
(646)
RP75
(940)
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: Wood V
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Wood V , Mistry J
Number in seed: 113
Number in full: 944
Average length of the domain: 104.30 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 45.18 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.7 23.7
Trusted cut-off 23.7 23.7
Noise cut-off 23.5 23.5
Model length: 110
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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 Nnf1 domain has been found. There are 8 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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