Summary: Transposase zinc-ribbon domain
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Transposase zinc-ribbon domain Provide feedback
This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It is likely a zinc-binding beta ribbon domain that could bind the DNA.
Internal database links
SCOOP: | DUF2089 DUF2387 Lar_restr_allev Mur_ligase_M OrfB_Zn_ribbon PhnA_Zn_Ribbon ribosomal_L24 Ribosomal_L37ae Ribosomal_S27 TF_Zn_Ribbon TFIIS_C zf-FPG_IleRS zf-ISL3 Zn_Tnp_IS1 |
Similarity to PfamA using HHSearch: | TFIIS_C Ribosomal_L37ae zf-RRN7 |
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 Zn_Beta_Ribbon (CL0167), which has the following description:
A clan of zinc-binding ribbon domains.
The clan contains the following 85 members:
A2L_zn_ribbon Auto_anti-p27 Baculo_LEF5_C CpXC DNA_RNApol_7kD DUF1451 DUF1610 DUF1936 DUF2072 DUF2116 DUF2180 DUF2387 DUF2614 DUF35_N DUF4379 DZR Elf1 GATA Lar_restr_allev LIM Mu-like_Com NinF NOB1_Zn_bind Nudix_N_2 Ogr_Delta OrfB_Zn_ribbon PhnA_Zn_Ribbon PriA_CRR Prim_Zn_Ribbon RecO_C Ribosomal_L32p Ribosomal_L33 Ribosomal_L37ae Ribosomal_L37e Ribosomal_L40e Ribosomal_L44 Ribosomal_S27 Ribosomal_S27e RNA_POL_M_15KD Rubredoxin_2 Spt4 Stc1 TF_Zn_Ribbon TFIIS_C Tnp_zf-ribbon_2 Topo_Zn_Ribbon Toprim_Crpt Trm112p UPF0547 zf-C4 zf-C4_ClpX zf-C4_Topoisom zf-CHC2 zf-CSL zf-dskA_traR zf-FPG_IleRS zf-GRF zf-ISL3 zf-NADH-PPase zf-PARP zf-RanBP zf-ribbon_3 zf-RING_7 zf-RRN7 zf-TFIIB zf-trcl zf-ZPR1 zf_PR_Knuckle zf_Rg zinc-ribbon_6 zinc-ribbons_6 zinc_ribbon_10 zinc_ribbon_11 zinc_ribbon_12 zinc_ribbon_13 zinc_ribbon_15 zinc_ribbon_2 zinc_ribbon_4 zinc_ribbon_5 zinc_ribbon_9 Zn-ribbon_8 Zn_ribbon_recom Zn_ribbon_SprT Zn_Tnp_IS1 Zn_Tnp_IS1595Alignments
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 (37) |
Full (1387) |
Representative proteomes | UniProt (3353) |
NCBI (5653) |
Meta (164) |
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RP15 (380) |
RP35 (935) |
RP55 (1439) |
RP75 (1936) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (37) |
Full (1387) |
Representative proteomes | UniProt (3353) |
NCBI (5653) |
Meta (164) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (380) |
RP35 (935) |
RP55 (1439) |
RP75 (1936) |
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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: | Pfam-B_3 (Release 24.0) |
Previous IDs: | Zn_ribbon_3; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 37 |
Number in full: | 1387 |
Average length of the domain: | 48.20 aa |
Average identity of full alignment: | 28 % |
Average coverage of the sequence by the domain: | 17.11 % |
HMM information
HMM build commands: |
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 46 | ||||||||||||
Family (HMM) version: | 7 | ||||||||||||
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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