Summary: Nucleotidyltransferase substrate binding protein like
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Nucleotidyltransferase substrate binding protein like Provide feedback
Nucleotidyltransferases (EC 2.7.7) comprise a large enzyme family with diverse roles in polynucleotide synthesis and modification. This domain is structurally related to kanamycin nucleotidyltransferase (KNTase) and forms a complex with HI0073, a sequence homolog of the nucleotide-binding domain of this nucleotidyltransferase superfamily [1].
Literature references
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Lehmann C, Lim K, Chalamasetty VR, Krajewski W, Melamud E, Galkin A, Howard A, Kelman Z, Reddy PT, Murzin AG, Herzberg O; , Proteins. 2003;50:249-260.: The HI0073/HI0074 protein pair from Haemophilus influenzae is a member of a new nucleotidyltransferase family: structure, sequence analyses, and solution studies. PUBMED:12486719 EPMC:12486719
Internal database links
SCOOP: | DNA_topoisoIV DUF86 |
Similarity to PfamA using HHSearch: | DUF86 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR010235
The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins [ PUBMED:12486719 ]. It forms a complex with HI0073 ( SWISSPROT ), encoded by the adjacent gene, which contains a nucleotidyltransferase nucleotide binding domain ( INTERPRO ). Double- and single-stranded DNA binding assays showed no evidence of DNA binding to HI0074 or to HI0073/HI0074 complex despite the suggestive shape of the putative binding cleft formed by the HI0074 dimer [ PUBMED:12486719 ].
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 KNTase_C (CL0291), which has the following description:
This alpha helical domain is found associated with a variety of nucleotidyltransferase domains.
The clan contains the following 27 members:
AadA_C DUF294_C DUF4145 DUF5667 DUF86 GlnD_UR_UTase HEPN HEPN-like_int HEPN_AbiA_CTD HEPN_AbiU2 HEPN_AbiV HEPN_Apea HEPN_Cthe2314 HEPN_DZIP3 HEPN_LA2681 HEPN_MAE_28990 HEPN_RiboL-PSP HEPN_RnaseLS HEPN_SAV2148 HEPN_SAV_6107 HEPN_STY4199 HEPN_Swt1 KNTase_C NTase_sub_bind PaREP1 pEK499_p136 RnlA-toxin_DBDAlignments
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...
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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 (24) |
Full (970) |
Representative proteomes | UniProt (4403) |
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RP15 (187) |
RP35 (532) |
RP55 (973) |
RP75 (1589) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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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 (24) |
Full (970) |
Representative proteomes | UniProt (4403) |
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RP15 (187) |
RP35 (532) |
RP55 (973) |
RP75 (1589) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | pdb_1wwp |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Mistry J |
Number in seed: | 24 |
Number in full: | 970 |
Average length of the domain: | 120.50 aa |
Average identity of full alignment: | 28 % |
Average coverage of the sequence by the domain: | 87.83 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 125 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
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 NTase_sub_bind domain has been found. There are 14 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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