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19  structures 1361  species 0  interactions 12781  sequences 163  architectures

Family: Homeobox_KN (PF05920)

Summary: Homeobox KN domain

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.

Homeobox KN domain Provide feedback

This is a homeobox transcription factor KN domain conserved from fungi to human and plants. They were first identified as TALE homeobox genes in eukaryotes, (including KNOX and MEIS genes) [1,2,3]. They have been recently classified [4,5,6].

Literature references

  1. Hirayama Y, Yamada T, Oya Y, Ito M, Kato M, Imaichi R;, Dev Genes Evol. 2007;217:363-372.: Expression patterns of class I KNOX and YABBY genes in Ruscus aculeatus (Asparagaceae) with implications for phylloclade homology. PUBMED:17429685 EPMC:17429685

  2. Bertolino E, Reimund B, Wildt-Perinic D, Clerc RG;, J Biol Chem. 1995;270:31178-31188: A novel homeobox protein which recognizes a TGT core and functionally interferes with a retinoid-responsive motif. PUBMED:8537382 EPMC:8537382

  3. Burglin TR; , Nucleic Acids Res 1997;25:4173-4180.: Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals. PUBMED:9336443 EPMC:9336443

  4. Mukherjee K, Burglin TR;, J Mol Evol. 2007;65:137-153.: Comprehensive analysis of animal TALE homeobox genes: new conserved motifs and cases of accelerated evolution. PUBMED:17665086 EPMC:17665086

  5. Mukherjee K, Brocchieri L, Burglin TR;, Mol Biol Evol. 2009;26:2775-2794.: A comprehensive classification and evolutionary analysis of plant homeobox genes. PUBMED:19734295 EPMC:19734295

  6. Burglin TR;, Subcell Biochem. 2011;52:95-122.: Homeodomain subtypes and functional diversity. PUBMED:21557080 EPMC:21557080


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008422

This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [ PUBMED:17429685 ]. Genes encoding these proteins were first identified as TALE homeobox proteins in eukaryotes, (including KNOX and MEIS genes) [ PUBMED:17429685 , PUBMED:8537382 , PUBMED:9336443 ]. They have been classified [ PUBMED:17665086 , PUBMED:19734295 , PUBMED:21557080 ].

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 HTH (CL0123), which has the following description:

This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.

The clan contains the following 353 members:

AbiEi_3_N AbiEi_4 ANAPC2 AphA_like AraR_C Arg_repressor ARID ArsR B-block_TFIIIC B5 Bac_DnaA_C Baculo_PEP_N BetR BHD_3 BLACT_WH Bot1p BrkDBD BsuBI_PstI_RE_N C_LFY_FLO CaiF_GrlA CarD_CdnL_TRCF CDC27 Cdc6_C Cdh1_DBD_1 CDT1 CDT1_C CENP-B_N Costars CPSase_L_D3 Cro Crp CSN4_RPN5_eIF3a CSN8_PSD8_EIF3K CtsR Cullin_Nedd8 CUT CUTL CvfB_WH DBD_HTH DDRGK DEP Dimerisation Dimerisation2 DNA_meth_N DpnI_C DprA_WH DsrC DsrD DUF1016_N DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1819 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF2513 DUF2582 DUF3116 DUF3253 DUF3853 DUF3860 DUF3908 DUF433 DUF4364 DUF4423 DUF4447 DUF480 DUF4817 DUF5635 DUF573 DUF6088 DUF6262 DUF6362 DUF6432 DUF6462 DUF6471 DUF722 DUF739 DUF742 DUF977 E2F_TDP EAP30 eIF-5_eIF-2B ELL ESCRT-II Ets EutK_C Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC FokI_C FokI_N Forkhead FtsK_gamma FUR GcrA GerE GntR GP3_package HARE-HTH HemN_C HNF-1_N Homeobox_KN Homeodomain Homez HPD HrcA_DNA-bdg HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_15 HTH_16 HTH_17 HTH_18 HTH_19 HTH_20 HTH_21 HTH_22 HTH_23 HTH_24 HTH_25 HTH_26 HTH_27 HTH_28 HTH_29 HTH_3 HTH_30 HTH_31 HTH_32 HTH_33 HTH_34 HTH_35 HTH_36 HTH_37 HTH_38 HTH_39 HTH_40 HTH_41 HTH_42 HTH_43 HTH_45 HTH_46 HTH_47 HTH_48 HTH_49 HTH_5 HTH_50 HTH_51 HTH_52 HTH_53 HTH_54 HTH_55 HTH_56 HTH_57 HTH_58 HTH_59 HTH_6 HTH_7 HTH_8 HTH_9 HTH_ABP1_N HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_micro HTH_OrfB_IS605 HTH_PafC HTH_ParB HTH_psq HTH_SUN2 HTH_Tnp_1 HTH_Tnp_1_2 HTH_Tnp_4 HTH_Tnp_IS1 HTH_Tnp_IS630 HTH_Tnp_ISL3 HTH_Tnp_Mu_1 HTH_Tnp_Mu_2 HTH_Tnp_Tc3_1 HTH_Tnp_Tc3_2 HTH_Tnp_Tc5 HTH_WhiA HxlR IBD IF2_N IRF KicB KilA-N Kin17_mid KORA KorB La LacI LexA_DNA_bind Linker_histone LZ_Tnp_IS481 MADF_DNA_bdg MAGE MARF1_LOTUS MarR MarR_2 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 MogR_DNAbind Mor MotA_activ MqsA_antitoxin MRP-L20 MukE Myb_DNA-bind_2 Myb_DNA-bind_3 Myb_DNA-bind_4 Myb_DNA-bind_5 Myb_DNA-bind_6 Myb_DNA-bind_7 Myb_DNA-binding Neugrin NFRKB_winged NOD2_WH NUMOD1 ORC_WH_C OST-HTH P22_Cro PaaX PadR PapB PAX PCI Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_NinH Phage_Nu1 Phage_rep_O Phage_rep_org_N Phage_terminase PheRS_DBD1 PheRS_DBD2 PheRS_DBD3 Pou Pox_D5 PqqD PRC2_HTH_1 PUFD PuR_N Put_DNA-bind_N pXO2-72 Raf1_HTH Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S18 Ribosomal_S19e Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RNA_pol_Rpc82 RNase_H2-Ydr279 ROQ_II RP-C RPA RPA_C RQC Rrf2 RTP RuvB_C S10_plectin SAC3_GANP SANT_DAMP1_like SatD SelB-wing_1 SelB-wing_2 SelB-wing_3 SgrR_N Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_ner Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 SinI Ski_Sno SLIDE Slx4 SMC_Nse1 SMC_ScpB SoPB_HTH SpoIIID SRP19 SRP_SPB STN1_2 Sulfolobus_pRN Suv3_N Swi6_N SWIRM Tau95 TBPIP TEA Terminase_5 TetR_N TFA2_Winged_2 TFIIE_alpha TFIIE_beta TFIIF_alpha TFIIF_beta Tn7_Tnp_TnsA_C Tn916-Xis TraI_2_C Trans_reg_C TrfA TrmB tRNA_bind_2 tRNA_bind_3 Trp_repressor UPF0122 UPF0175 Vir_act_alpha_C YdaS_antitoxin YjcQ YokU z-alpha

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
(59)
Full
(12781)
Representative proteomes UniProt
(23297)
RP15
(1732)
RP35
(5508)
RP55
(10472)
RP75
(14299)
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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
(59)
Full
(12781)
Representative proteomes UniProt
(23297)
RP15
(1732)
RP35
(5508)
RP55
(10472)
RP75
(14299)
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
(59)
Full
(12781)
Representative proteomes UniProt
(23297)
RP15
(1732)
RP35
(5508)
RP55
(10472)
RP75
(14299)
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_4610 (release 8.0)
Previous IDs: Coprinus_mating;
Type: Family
Sequence Ontology: SO:0100021
Author: Moxon SJ
Number in seed: 59
Number in full: 12781
Average length of the domain: 39.70 aa
Average identity of full alignment: 53 %
Average coverage of the sequence by the domain: 8.64 %

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 19.8 19.8
Trusted cut-off 19.8 19.8
Noise cut-off 19.7 19.7
Model length: 40
Family (HMM) version: 13
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 Homeobox_KN domain has been found. There are 19 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
A0A096PXB1 View 3D Structure Click here
A0A0P0VTG7 View 3D Structure Click here
A0A0P0XZ22 View 3D Structure Click here
A0A0R0FAX6 View 3D Structure Click here
A0A0R0GC11 View 3D Structure Click here
A0A0R0GL54 View 3D Structure Click here
A0A0R0HAW9 View 3D Structure Click here
A0A0R0K2Y7 View 3D Structure Click here
A0A0R0KMH2 View 3D Structure Click here
A0A0R0KZM6 View 3D Structure Click here
A0A0R4J5J4 View 3D Structure Click here
A0A1D6DYM0 View 3D Structure Click here
A0A1D6FP22 View 3D Structure Click here
A0A1D6GKJ4 View 3D Structure Click here
A0A1D6H2P2 View 3D Structure Click here
A0A1D6H6M1 View 3D Structure Click here
A0A1D6K7I1 View 3D Structure Click here
A0A1D6KYQ9 View 3D Structure Click here
A0A1D6KYU8 View 3D Structure Click here
A0A1D6L2Y9 View 3D Structure Click here
A0A1D6L365 View 3D Structure Click here
A0A1D6L675 View 3D Structure Click here
A0A1D6PKW2 View 3D Structure Click here
A0A1D6QRZ9 View 3D Structure Click here
A0A2R8QIZ3 View 3D Structure Click here
A0A2R8QKE9 View 3D Structure Click here
A0A2R8QPY7 View 3D Structure Click here
A0A2R8QU68 View 3D Structure Click here
A0A368UGQ4 View 3D Structure Click here
A0A368UJU3 View 3D Structure Click here
A1Z913 View 3D Structure Click here
A1Z916 View 3D Structure Click here
A6NDR6 View 3D Structure Click here
A7J0W0 View 3D Structure Click here
A8K0S8 View 3D Structure Click here
A9UGK1 View 3D Structure Click here
B1WC31 View 3D Structure Click here
B3DH47 View 3D Structure Click here
B3DKL9 View 3D Structure Click here
B4F8C3 View 3D Structure Click here
B4FBI0 View 3D Structure Click here
B4FS21 View 3D Structure Click here
B5DEL6 View 3D Structure Click here
B6SZ15 View 3D Structure Click here
B6TPJ2 View 3D Structure Click here
C4IYV8 View 3D Structure Click here
C4J9N0 View 3D Structure Click here
C6TEF2 View 3D Structure Click here
C7G045 View 3D Structure Click here
D3ZEM3 View 3D Structure Click here
D3ZGA0 View 3D Structure Click here
D3ZNE0 View 3D Structure Click here
D3ZRI4 View 3D Structure Click here
D3ZUL2 View 3D Structure Click here
D4A2T5 View 3D Structure Click here
D4A7R4 View 3D Structure Click here
D4A9L1 View 3D Structure Click here
D4A9U2 View 3D Structure Click here
E7FBG0 View 3D Structure Click here
F1Q7T5 View 3D Structure Click here
G3V7I4 View 3D Structure Click here
I1J568 View 3D Structure Click here
I1J907 View 3D Structure Click here
I1JA22 View 3D Structure Click here
I1JA88 View 3D Structure Click here
I1JC49 View 3D Structure Click here
I1JGH7 View 3D Structure Click here
I1JQ89 View 3D Structure Click here
I1JTU5 View 3D Structure Click here
I1JU99 View 3D Structure Click here
I1K0E5 View 3D Structure Click here
I1K6F5 View 3D Structure Click here
I1K7P2 View 3D Structure Click here
I1K7P3 View 3D Structure Click here
I1KPE2 View 3D Structure Click here
I1KXC9 View 3D Structure Click here
I1L2B3 View 3D Structure Click here
I1L9K6 View 3D Structure Click here
I1LGE2 View 3D Structure Click here
I1LTZ9 View 3D Structure Click here
I1LZN4 View 3D Structure Click here
I1M493 View 3D Structure Click here
I1M880 View 3D Structure Click here
I1M8Y1 View 3D Structure Click here
I1M9G1 View 3D Structure Click here
I1MFK9 View 3D Structure Click here
I1MWX1 View 3D Structure Click here
I1MXZ4 View 3D Structure Click here
I1N2N9 View 3D Structure Click here
I1NAU4 View 3D Structure Click here
K7K0T9 View 3D Structure Click here
K7K312 View 3D Structure Click here
K7KGK3 View 3D Structure Click here
K7KHH8 View 3D Structure Click here
K7KHT4 View 3D Structure Click here
K7KI69 View 3D Structure Click here
K7KKY5 View 3D Structure Click here
K7KSE7 View 3D Structure Click here
K7KT71 View 3D Structure Click here
K7KTF9 View 3D Structure Click here
K7LJG7 View 3D Structure Click here
K7LNB7 View 3D Structure Click here
K7LQD5 View 3D Structure Click here
K7LTM0 View 3D Structure Click here
K7LTX2 View 3D Structure Click here
K7LVK3 View 3D Structure Click here
K7M356 View 3D Structure Click here
K7MHC0 View 3D Structure Click here
K7MJC6 View 3D Structure Click here
K7MNH9 View 3D Structure Click here
K7N2L1 View 3D Structure Click here
K7UPH8 View 3D Structure Click here
K7VF27 View 3D Structure Click here
M0RCY5 View 3D Structure Click here
O00470 View 3D Structure Click here
O14770 View 3D Structure Click here
O46339 View 3D Structure Click here
O65685 View 3D Structure Click here
O70477 View 3D Structure Click here
O80416 View 3D Structure Click here
P24345 View 3D Structure Click here
P41817 View 3D Structure Click here
P46608 View 3D Structure Click here
P46609 View 3D Structure Click here
P46639 View 3D Structure Click here
P46640 View 3D Structure Click here
P48000 View 3D Structure Click here
P48001 View 3D Structure Click here
P48002 View 3D Structure Click here
P48731 View 3D Structure Click here
P53147 View 3D Structure Click here
P54269 View 3D Structure Click here
P55347 View 3D Structure Click here
P56659 View 3D Structure Click here
P56660 View 3D Structure Click here
P56661 View 3D Structure Click here
P56662 View 3D Structure Click here
P56663 View 3D Structure Click here
P56664 View 3D Structure Click here
P56665 View 3D Structure Click here
P56666 View 3D Structure Click here
P56667 View 3D Structure Click here
P56668 View 3D Structure Click here
P56669 View 3D Structure Click here
P70284 View 3D Structure Click here
P78411 View 3D Structure Click here
P78412 View 3D Structure Click here
P78413 View 3D Structure Click here
P78414 View 3D Structure Click here
P78415 View 3D Structure Click here
P81066 View 3D Structure Click here
P81067 View 3D Structure Click here
P81068 View 3D Structure Click here
P97367 View 3D Structure Click here
P97368 View 3D Structure Click here
Q0DBI4 View 3D Structure Click here
Q0DF87 View 3D Structure Click here
Q0E3C3 View 3D Structure Click here
Q0J6N4 View 3D Structure Click here
Q10DD6 View 3D Structure Click here
Q10EC6 View 3D Structure Click here
Q10ED2 View 3D Structure Click here
Q10SF7 View 3D Structure Click here
Q15583 View 3D Structure Click here
Q1LWG1 View 3D Structure Click here
Q1LXU5 View 3D Structure Click here
Q1PFD1 View 3D Structure Click here
Q24248 View 3D Structure Click here
Q2QLM6 View 3D Structure Click here
Q38874 View 3D Structure Click here
Q38897 View 3D Structure Click here
Q41853 View 3D Structure Click here
Q45EK2 View 3D Structure Click here
Q503Z8 View 3D Structure Click here
Q54F11 View 3D Structure Click here
Q54LB3 View 3D Structure Click here
Q54VB4 View 3D Structure Click here
Q5AH24 View 3D Structure Click here
Q5BJP1 View 3D Structure Click here
Q5BJZ9 View 3D Structure Click here
Q5I8Y1 View 3D Structure Click here
Q5KQP1 View 3D Structure Click here
Q60954 View 3D Structure Click here
Q60EM7 View 3D Structure Click here
Q6DEL0 View 3D Structure Click here
Q6H6J2 View 3D Structure Click here
Q6NZU4 View 3D Structure Click here
Q75LX7 View 3D Structure Click here
Q75LX9 View 3D Structure Click here
Q7GDL5 View 3D Structure Click here
Q7SZP3 View 3D Structure Click here
Q7XYR8 View 3D Structure Click here
Q803F0 View 3D Structure Click here
Q84JS6 View 3D Structure Click here
Q84N16 View 3D Structure Click here
Q84N17 View 3D Structure Click here
Q86IH1 View 3D Structure Click here
Q8AYN1 View 3D Structure Click here
Q8BG99 View 3D Structure Click here
Q8BIA3 View 3D Structure Click here
Q8C0Y1 View 3D Structure Click here
Q8IUE0 View 3D Structure Click here
Q8IUE1 View 3D Structure Click here
Q8IX15 View 3D Structure Click here
Q8IYA7 View 3D Structure Click here
Q8K5B9 View 3D Structure Click here
Q8LN25 View 3D Structure Click here
Q8S897 View 3D Structure Click here
Q90VY7 View 3D Structure Click here
Q90YX8 View 3D Structure Click here
Q90Z68 View 3D Structure Click here
Q90ZE3 View 3D Structure Click here
Q93348 View 3D Structure Click here
Q941S9 View 3D Structure Click here
Q948L5 View 3D Structure Click here
Q94KL5 View 3D Structure Click here
Q94LW3 View 3D Structure Click here
Q94LW4 View 3D Structure Click here
Q96KN3 View 3D Structure Click here
Q99687 View 3D Structure Click here
Q9AYD8 View 3D Structure Click here
Q9BZI1 View 3D Structure Click here
Q9ER75 View 3D Structure Click here
Q9FP29 View 3D Structure Click here
Q9FPQ8 View 3D Structure Click here
Q9FWS9 View 3D Structure Click here
Q9FXG8 View 3D Structure Click here
Q9GZN2 View 3D Structure Click here
Q9JKQ4 View 3D Structure Click here
Q9LZM8 View 3D Structure Click here
Q9N5D6 View 3D Structure Click here
Q9QY61 View 3D Structure Click here
Q9SIW1 View 3D Structure Click here
Q9SJ56 View 3D Structure Click here
Q9SJJ3 View 3D Structure Click here
Q9SW80 View 3D Structure Click here
Q9SYT6 View 3D Structure Click here
Q9VPL4 View 3D Structure Click here