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0  structures 2328  species 0  interactions 3631  sequences 36  architectures

Family: NicO (PF03824)

Summary: High-affinity nickel-transport protein

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High-affinity nickel-transport protein Provide feedback

High affinity nickel transporters involved in the incorporation of nickel into H2-uptake hydrogenase [2] and urease [3] enzymes. Essential for the expression of catalytically active hydrogenase and urease. Ion uptake is dependent on proton motive force. HoxN in Alcaligenes eutrophus is thought to be an integral membrane protein with seven transmembrane helices [4]. The family also includes a cobalt transporter.

Literature references

  1. Maeda M, Hidaka M, Nakamura A, Masaki H, Uozumi T; , J Bacteriol 1994;176:432-442.: Cloning, sequencing, and expression of thermophilic Bacillus sp. strain TB-90 urease gene complex in Escherichia coli. PUBMED:8288539 EPMC:8288539

  2. Fu C, Javedan S, Moshiri F, Maier RJ; , Proc Natl Acad Sci U S A 1994;91:5099-5103.: Bacterial genes involved in incorporation of nickel into a hydrogenase enzyme. PUBMED:8197192 EPMC:8197192

  3. Mobley HL, Garner RM, Bauerfeind P; , Mol Microbiol 1995;16:97-109.: Helicobacter pylori nickel-transport gene nixA: synthesis of catalytically active urease in Escherichia coli independent of growth conditions. PUBMED:7651142 EPMC:7651142

  4. Eitinger T, Friedrich B; , Mol Microbiol 1994;12:1025-1032.: A topological model for the high-affinity nickel transporter of Alcaligenes eutrophus. PUBMED:7934894 EPMC:7934894

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011541

High affinity nickel transporters are involved in the incorporation of nickel into H2-uptake hydrogenase [ PUBMED:7934894 , PUBMED:7651142 ] and urease [ PUBMED:8197192 ] enzymes and are essential for the expression of catalytically active hydrogenase and urease. Ion uptake is dependent on proton motive force. HoxN in Ralstonia eutropha (Alcaligenes eutrophus) is thought to be an integral membrane protein with seven transmembrane helices [ PUBMED:8288539 ]. The transporter RcnA has been implicated in Ni(II) and Co(II) detoxification in E. coli, probably through efflux [ PUBMED:17120142 ].

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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Pfam Clan

This family is a member of clan LysE (CL0292), which has the following description:

This clan includes a diverse range of transporter families [1].

The clan contains the following 19 members:

BacA Cad Colicin_V DsbD DsbD_2 DUF475 DUF6044 FTR1 HupE_UreJ HupE_UreJ_2 LysE MarC Mntp NicO OFeT_1 SfLAP TauE TerC UPF0016


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.

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Representative proteomes UniProt

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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...


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.

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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: Manual
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Griffiths-Jones SR , Kerrison ND , Finn RD , Eberhardt R
Number in seed: 13
Number in full: 3631
Average length of the domain: 220.9 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 67.42 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.7 27.7
Trusted cut-off 27.7 27.7
Noise cut-off 27.6 27.6
Model length: 287
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence


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