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46  structures 1659  species 0  interactions 14957  sequences 296  architectures

Family: NIF (PF03031)

Summary: NLI interacting factor-like phosphatase

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.

NLI interacting factor-like phosphatase Provide feedback

This family contains a number of NLI interacting factor isoforms (eg. Q9PTJ8) and also an N-terminal regions of RNA polymerase II CTC phosphatase (Q9Y5BO) and FCP1 serine phosphatase (Q9PT70). This region has been identified as the minimal phosphatase domain [1].

Literature references

  1. Hausmann S, Shuman S; , J Biol Chem 2003;0:0-0.: Defining the active site of Schizosaccharomyces pombe CTD phosphatase Fcp1. PUBMED:12556522 EPMC:12556522


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004274

Yeast FCP1 is an essential protein serine phosphatase ( EC ) that dephosphorylates the C-terminal domain (CTD) of RNA polymerase II. FCP1 orthologs are present in all known eukaryote proteomes. The N-terminal domain of FCP1 corresponds to the catalytic unit of the phosphatase and has been refered to as the FCP1 homology domain. The FCP1 homology domain, which is a ~180-residue module, is also found in many other proteins of unknown function. It contains a DxDx(T/V) motif preceded by four hydrophobic residues characteristic of a large family of metal-dependent phosphohydrolases and phosphotransferases. The first aspartate residue is likely to participate in catalysis, whereas the second could have a role in substrate recognition [ PUBMED:9405607 , PUBMED:10445027 , PUBMED:12556522 , PUBMED:10385623 ].

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 HAD (CL0137), which has the following description:

This clan represents the haloacid dehalogenase (HAD) superfamily that includes a diverse range of enzymes that use an asp carboxylate as a nucleophile [1].

The clan contains the following 24 members:

5_nucleotid Acid_phosphat_B Acid_PPase Cation_ATPase DHH DUF2608 DUF705 HAD HAD_2 Hydrolase Hydrolase_3 Hydrolase_6 Hydrolase_like LNS2 NIF NT5C PGP_phosphatase PhoLip_ATPase_C PMM PNK3P Put_Phosphatase S6PP Trehalose_PPase UMPH-1

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
(116)
Full
(14957)
Representative proteomes UniProt
(26161)
RP15
(3206)
RP35
(7487)
RP55
(12198)
RP75
(16065)
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
(116)
Full
(14957)
Representative proteomes UniProt
(26161)
RP15
(3206)
RP35
(7487)
RP55
(12198)
RP75
(16065)
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
(116)
Full
(14957)
Representative proteomes UniProt
(26161)
RP15
(3206)
RP35
(7487)
RP55
(12198)
RP75
(16065)
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_1405 (release 6.4)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Griffiths-Jones SR
Number in seed: 116
Number in full: 14957
Average length of the domain: 157.40 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 32.87 %

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 21.8 21.8
Trusted cut-off 21.8 21.8
Noise cut-off 21.7 21.7
Model length: 156
Family (HMM) version: 20
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 NIF domain has been found. There are 46 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
A0A096S016 View 3D Structure Click here
A0A0G2K0J7 View 3D Structure Click here
A0A0G2L5M5 View 3D Structure Click here
A0A0P0V8I5 View 3D Structure Click here
A0A0P0VQL1 View 3D Structure Click here
A0A0P0W3F9 View 3D Structure Click here
A0A0P0WCN4 View 3D Structure Click here
A0A0P0WNH0 View 3D Structure Click here
A0A0P0WQX3 View 3D Structure Click here
A0A0P0X1H8 View 3D Structure Click here
A0A0P0Y2X9 View 3D Structure Click here
A0A0R0F5G2 View 3D Structure Click here
A0A0R0FIM3 View 3D Structure Click here
A0A0R0G5G3 View 3D Structure Click here
A0A0R0G7K6 View 3D Structure Click here
A0A0R0GL98 View 3D Structure Click here
A0A0R0H1R6 View 3D Structure Click here
A0A0R0ID32 View 3D Structure Click here
A0A0R4IC10 View 3D Structure Click here
A0A0R4IYK3 View 3D Structure Click here
A0A1D6FAE7 View 3D Structure Click here
A0A1D6FS55 View 3D Structure Click here
A0A1D6FT99 View 3D Structure Click here
A0A1D6FZZ3 View 3D Structure Click here
A0A1D6G8W2 View 3D Structure Click here
A0A1D6GB26 View 3D Structure Click here
A0A1D6GGV4 View 3D Structure Click here
A0A1D6HEE3 View 3D Structure Click here
A0A1D6HN72 View 3D Structure Click here
A0A1D6HWB6 View 3D Structure Click here
A0A1D6HZS7 View 3D Structure Click here
A0A1D6J2I1 View 3D Structure Click here
A0A1D6J2I1 View 3D Structure Click here
A0A1D6M367 View 3D Structure Click here
A0A1D6N5U1 View 3D Structure Click here
A0A1D6N6V8 View 3D Structure Click here
A0A1D6PTK9 View 3D Structure Click here
A0A1D6Q5S7 View 3D Structure Click here
A0A1D8PL92 View 3D Structure Click here
A0A1D8PL92 View 3D Structure Click here
A0A2R8QHL3 View 3D Structure Click here
A2RVS1 View 3D Structure Click here
A4HRX5 View 3D Structure Click here
A4HRX5 View 3D Structure Click here
A4HW67 View 3D Structure Click here
A4I1Q1 View 3D Structure Click here
A4I1V3 View 3D Structure Click here
A4I314 View 3D Structure Click here
A4I4V4 View 3D Structure Click here
A4I7H3 View 3D Structure Click here
A4I8U3 View 3D Structure Click here
A4I9T8 View 3D Structure Click here
A4IAG1 View 3D Structure Click here
A4IAS0 View 3D Structure Click here
A4IB52 View 3D Structure Click here
A4IBC9 View 3D Structure Click here
A4IBP7 View 3D Structure Click here
A4IBP7 View 3D Structure Click here
A4ICB8 View 3D Structure Click here
A4QNX6 View 3D Structure Click here
B0S5V5 View 3D Structure Click here
B1WC24 View 3D Structure Click here
B4FS56 View 3D Structure Click here
B6T776 View 3D Structure Click here
B6TE36 View 3D Structure Click here
C6T717 View 3D Structure Click here
C7EYT0 View 3D Structure Click here
D3ZJX5 View 3D Structure Click here
E7F3H1 View 3D Structure Click here
E7FFL3 View 3D Structure Click here
E9AH40 View 3D Structure Click here
F4JCB2 View 3D Structure Click here
F4JCB2 View 3D Structure Click here
F4JQR6 View 3D Structure Click here
F4JU71 View 3D Structure Click here
F4KHG9 View 3D Structure Click here
I1JGN5 View 3D Structure Click here
I1JI92 View 3D Structure Click here
I1JJI9 View 3D Structure Click here
I1KLI0 View 3D Structure Click here
I1KSQ5 View 3D Structure Click here
I1KWR8 View 3D Structure Click here
I1LN83 View 3D Structure Click here
I1M0C8 View 3D Structure Click here
I1MEW5 View 3D Structure Click here
I1NAI1 View 3D Structure Click here
K7KJU9 View 3D Structure Click here
K7KW77 View 3D Structure Click here
K7KYH6 View 3D Structure Click here
K7L1T3 View 3D Structure Click here
K7L8P7 View 3D Structure Click here
K7LXM9 View 3D Structure Click here
K7M175 View 3D Structure Click here
K7MCJ2 View 3D Structure Click here
K7MKD8 View 3D Structure Click here
K7MP89 View 3D Structure Click here
K7MTG8 View 3D Structure Click here
K7MUZ3 View 3D Structure Click here
K7MW97 View 3D Structure Click here
K7UKE2 View 3D Structure Click here
K7UUU7 View 3D Structure Click here
M0R4W4 View 3D Structure Click here
M0R5X1 View 3D Structure Click here
M9PFN0 View 3D Structure Click here
O13636 View 3D Structure Click here
O14595 View 3D Structure Click here
O15194 View 3D Structure Click here
O59718 View 3D Structure Click here
O94336 View 3D Structure Click here
O95476 View 3D Structure Click here
P38757 View 3D Structure Click here
P58465 View 3D Structure Click here
P58466 View 3D Structure Click here
Q00IB6 View 3D Structure Click here
Q02776 View 3D Structure Click here
Q03254 View 3D Structure Click here
Q05D32 View 3D Structure Click here
Q07800 View 3D Structure Click here
Q07949 View 3D Structure Click here
Q08BB5 View 3D Structure Click here
Q09695 View 3D Structure Click here
Q0DGT4 View 3D Structure Click here
Q0JL24 View 3D Structure Click here
Q20432 View 3D Structure Click here
Q22647 View 3D Structure Click here
Q3B7T6 View 3D Structure Click here
Q3E7I8 View 3D Structure Click here
Q3ECX9 View 3D Structure Click here
Q3TP92 View 3D Structure Click here
Q3ZCQ8 View 3D Structure Click here
Q4CPR0 View 3D Structure Click here
Q4CUL1 View 3D Structure Click here
Q4CWP4 View 3D Structure Click here
Q4D4E5 View 3D Structure Click here
Q4D9B2 View 3D Structure Click here
Q4DA86 View 3D Structure Click here
Q4DAK8 View 3D Structure Click here
Q4DGU0 View 3D Structure Click here
Q4DK23 View 3D Structure Click here
Q4DLG0 View 3D Structure Click here
Q4DML9 View 3D Structure Click here
Q4DP31 View 3D Structure Click here
Q4DQK3 View 3D Structure Click here
Q4DR97 View 3D Structure Click here
Q4DRW7 View 3D Structure Click here
Q4DS85 View 3D Structure Click here
Q4DSR0 View 3D Structure Click here
Q4DT50 View 3D Structure Click here
Q4DTS4 View 3D Structure Click here
Q4DX36 View 3D Structure Click here
Q4E0W7 View 3D Structure Click here
Q4E136 View 3D Structure Click here
Q4E2U9 View 3D Structure Click here
Q4E609 View 3D Structure Click here
Q4E669 View 3D Structure Click here
Q54GB2 View 3D Structure Click here
Q54IJ8 View 3D Structure Click here
Q54M72 View 3D Structure Click here
Q54M73 View 3D Structure Click here
Q556S4 View 3D Structure Click here
Q55C70 View 3D Structure Click here
Q59W44 View 3D Structure Click here
Q5A7R0 View 3D Structure Click here
Q5ADU9 View 3D Structure Click here
Q5FWT7 View 3D Structure Click here
Q5N890 View 3D Structure Click here
Q5QLC5 View 3D Structure Click here
Q5SN52 View 3D Structure Click here
Q5U395 View 3D Structure Click here
Q5U3T3 View 3D Structure Click here
Q5W6J1 View 3D Structure Click here
Q5XIK8 View 3D Structure Click here
Q5YDB5 View 3D Structure Click here
Q5YDB6 View 3D Structure Click here
Q6DI37 View 3D Structure Click here
Q6H5U8 View 3D Structure Click here
Q6K8Y2 View 3D Structure Click here
Q6NWD4 View 3D Structure Click here
Q6P3I6 View 3D Structure Click here
Q75JA4 View 3D Structure Click here
Q75KI1 View 3D Structure Click here
Q7JY68 View 3D Structure Click here
Q7TSG2 View 3D Structure Click here
Q84K83 View 3D Structure Click here
Q84WY5 View 3D Structure Click here
Q8BG15 View 3D Structure Click here
Q8BGR9 View 3D Structure Click here
Q8BX07 View 3D Structure Click here
Q8I3U9 View 3D Structure Click here
Q8IBI8 View 3D Structure Click here
Q8IDE5 View 3D Structure Click here
Q8IJR8 View 3D Structure Click here
Q8LL04 View 3D Structure Click here
Q8RYY0 View 3D Structure Click here
Q8T3G2 View 3D Structure Click here
Q8VYE2 View 3D Structure Click here
Q8W3M6 View 3D Structure Click here
Q8WVY7 View 3D Structure Click here
Q95QG8 View 3D Structure Click here
Q9D880 View 3D Structure Click here
Q9FHL1 View 3D Structure Click here
Q9FK73 View 3D Structure Click here
Q9FL74 View 3D Structure Click here
Q9FXF4 View 3D Structure Click here
Q9GZU7 View 3D Structure Click here
Q9LN24 View 3D Structure Click here
Q9LRQ0 View 3D Structure Click here
Q9LUP3 View 3D Structure Click here
Q9LY49 View 3D Structure Click here
Q9LYI7 View 3D Structure Click here
Q9N4V4 View 3D Structure Click here
Q9P376 View 3D Structure Click here
Q9SI33 View 3D Structure Click here
Q9SJQ4 View 3D Structure Click here
Q9V9P3 View 3D Structure Click here
Q9VRG7 View 3D Structure Click here
Q9VZS0 View 3D Structure Click here
Q9W0S3 View 3D Structure Click here
Q9W147 View 3D Structure Click here
Q9W4V8 View 3D Structure Click here
Q9XYL0 View 3D Structure Click here
Q9XZ16 View 3D Structure Click here
Q9Y5B0 View 3D Structure Click here
Q9ZVR2 View 3D Structure Click here