JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  636 WVYVGMIFSTFCWHNEDHHAYSANYQHFGATKTWYGIPAADTEKFENAMKDavpELFETQPDLLFQLVTLLTPEQLKKAG 715
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSD---HFGGEQPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1570000057  716 VRVYALDQRAGQLVITFPQAYHAGFNHGFNFNEAVNF 752
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114

PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins; The family includes Saccharomyces cerevisiae Ecm5p, Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins. Ecm5p is a JmjC domain-containing protein that directly removes histone lysine methylation via a hydroxylation reaction. It associates with the yeast Snt2p and Rpd3 deacetylase, which may play a role in regulating transcription in response to oxidative stress. Ecm5p promotes oxidative stress tolerance, while Snt2p ultimately decreases tolerance. Ecm5p contains an N-terminal ARID domain, a JmjC domain, and a C-terminal plant homeodomain (PHD) finger. Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model includes the second PHD finger of Lid2p.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1570000057 1335 FCICRRVEAGMMIECPLCHEWYHGKCLKIARGKVKEDDKYTCPIC 1379
Cdd:cd15518      1 YCFCRQGEGGTMIECEICKEWYHVKCIKNGRWKLDDDDKFVCPIC 45

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1570000057  464 CETCGKGEDVGFLAVCETCDNGYHGACVDPPLKQKPEGEWNCPRC 508
Cdd:cd15519      2 CEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  636 WVYVGMIFSTFCWHNEDHHAYSANYQHFGATKTWYGIPAADTEKFENAMKDavpELFETQPDLLFQLVTLLTPEQLKKAG 715
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSD---HFGGEQPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1570000057  716 VRVYALDQRAGQLVITFPQAYHAGFNHGFNFNEAVNF 752
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114

ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  162 ANLTYLDALSKFHKQQGTNLNRLPYVDKKPLDLYRLKKAVESRGGFEKVCKTKKWAEIGRDLGYSgKIMSSLSTSLKNSY 241
Cdd:pfam01388    1 EKELFLKSLRKFHEKRGTPLKQIPVIGGKPVDLYKLYKAVQKLGGYDKVTEKNLWREVAEKLGFP-PSAASAATQLKQIY 79

                   ....*...
gi 1570000057  242 DRWLNPYE 249
Cdd:pfam01388   80 EKYLLPYE 87

PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins; The family includes Saccharomyces cerevisiae Ecm5p, Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins. Ecm5p is a JmjC domain-containing protein that directly removes histone lysine methylation via a hydroxylation reaction. It associates with the yeast Snt2p and Rpd3 deacetylase, which may play a role in regulating transcription in response to oxidative stress. Ecm5p promotes oxidative stress tolerance, while Snt2p ultimately decreases tolerance. Ecm5p contains an N-terminal ARID domain, a JmjC domain, and a C-terminal plant homeodomain (PHD) finger. Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model includes the second PHD finger of Lid2p.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1570000057 1335 FCICRRVEAGMMIECPLCHEWYHGKCLKIARGKVKEDDKYTCPIC 1379
Cdd:cd15518      1 YCFCRQGEGGTMIECEICKEWYHVKCIKNGRWKLDDDDKFVCPIC 45

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1570000057  464 CETCGKGEDVGFLAVCETCDNGYHGACVDPPLKQKPEGEWNCPRC 508
Cdd:cd15519      2 CEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46

C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1570000057  861 CSYCKCYAYLSRFKCQR-SGKVLCLLHAgSHPCCDAPESQRFageehsLFYRKSNEEL 917
Cdd:pfam02928    1 CSFCKAYCYLSAVTCSKcSGKVVCLRHA-KELCSDCPPSKRT------LLYRYTDDEL 51

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1570000057  464 CETCGKGEDVGFLAVCETCDNGYHGACVDPPL--KQKPEGEWNCPRCLV 510
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLdpAEIPSGEWLCPECKP 50

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1570000057 1335 FC-ICRRVEA-GMMIECPLCHEWYHGKCLKIA-RGKVKEDDKYTCPICD 1380
Cdd:pfam00628    1 YCaVCGKSDDgGELVQCDGCDDWFHLACLGPPlDPAEIPSGEWLCPECK 49

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057 1018 QEQKERELRRVENIYRLIDEAERigfdcpEIQQLQERAHAIRSFQKNAEQALEhilgQSQESIEELIEegrtfnidipEL 1097
Cdd:TIGR02168  280 EEEIEELQKELYALANEISRLEQ------QKQILRERLANLERQLEELEAQLE----ELESKLDELAE----------EL 339

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057 1098 DKLCDVLEQLRWNAKARANRnvfmtLSEARELIEEGTRLEIPLYNDHMKFYTEKYQAGLQWEAKAKELINAEMT------ 1171
Cdd:TIGR02168  340 AELEEKLEELKEELESLEAE-----LEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARlerled 414

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057 1172 ----HYPQLEALSNQVQVNALPVSAETLASVDQILHKQREAHRQIIDLTERSRNpdySKRPKYSEVAEIMKKLEDLNSKP 1247
Cdd:TIGR02168  415 rrerLQQEIEELLKKLEEAELKELQAELEELEEELEELQEELERLEEALEELRE---ELEEAEQALDAAERELAQLQARL 491

                          250       260
                   ....*....|....*....|....
gi 1570000057 1248 TGtldLEREQKRHEDWMRKGKKLF 1271
Cdd:TIGR02168  492 DS---LERLQENLEGFSEGVKALL 512

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  636 WVYVGMIFSTFCWHNEDHHAYSANYQHFGATKTWYGIPAADTEKFENAMKDavpELFETQPDLLFQLVTLLTPEQLKKAG 715
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSD---HFGGEQPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1570000057  716 VRVYALDQRAGQLVITFPQAYHAGFNHGFNFNEAVNF 752
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114

ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  162 ANLTYLDALSKFHKQQGTNLNRLPYVDKKPLDLYRLKKAVESRGGFEKVCKTKKWAEIGRDLGYSgKIMSSLSTSLKNSY 241
Cdd:pfam01388    1 EKELFLKSLRKFHEKRGTPLKQIPVIGGKPVDLYKLYKAVQKLGGYDKVTEKNLWREVAEKLGFP-PSAASAATQLKQIY 79

                   ....*...
gi 1570000057  242 DRWLNPYE 249
Cdd:pfam01388   80 EKYLLPYE 87

ARID/BRIGHT DNA binding domain family; The AT-rich interaction domain (ARID) family of transcription factors, found in a broad array of organisms from fungi to mammals, is characterized by a highly conserved, helix-turn-helix DNA binding domain that binds to the major groove of DNA. The ARID domain, also called BRIGHT, was first identified in the mouse B-cell-specific transcription factor Bright and in the product of the dead ringer (dri) gene of Drosophila melanogaster. ARID family members are implicated in normal development, differentiation, cell cycle regulation, transcriptional activation and chromatin remodeling. Different family members exhibit different DNA-binding properties. Drosophila Dri, mammalian ARID3A/3B/3C and ARID5A/5B, selectively bind AT-rich sites. However, ARID1A/1B, Drosophila Osa, yeast SWI1, ARID2, ARID4A/4B, JARID1A/1B/1C/1D, and JARID2, bind DNA without sequence specificity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  166 YLDALSKFHKQQGTNLNRLPYVDKKPLDLYRLKKAVESRGGFEKVCKTKKWAEIGRDLGYSgKIMSSLSTSLKNSYDRWL 245
Cdd:cd16100      5 FLEQLRAFLESRGTPLLKPPTIGGKPLDLYKLYRAVVSRGGYEKVTEKKLWKEVARKLGLP-TSSTSAAQALKRIYEKYL 83

                   ....
gi 1570000057  246 NPYE 249
Cdd:cd16100     84 LPFE 87

PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins; The family includes Saccharomyces cerevisiae Ecm5p, Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins. Ecm5p is a JmjC domain-containing protein that directly removes histone lysine methylation via a hydroxylation reaction. It associates with the yeast Snt2p and Rpd3 deacetylase, which may play a role in regulating transcription in response to oxidative stress. Ecm5p promotes oxidative stress tolerance, while Snt2p ultimately decreases tolerance. Ecm5p contains an N-terminal ARID domain, a JmjC domain, and a C-terminal plant homeodomain (PHD) finger. Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model includes the second PHD finger of Lid2p.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1570000057 1335 FCICRRVEAGMMIECPLCHEWYHGKCLKIARGKVKEDDKYTCPIC 1379
Cdd:cd15518      1 YCFCRQGEGGTMIECEICKEWYHVKCIKNGRWKLDDDDKFVCPIC 45

ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D; This group includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C, also called histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, protein SmcX, or protein Xe169, is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D, also called histocompatibility Y antigen (H-Y), histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or protein SmcY, is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as two plant homeodomain (PHD) fingers.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  160 TRANLTYLDALSKFHKQQGTNLnRLPYVDKKPLDLYRLKKAVESRGGFEKVCKTKKWAEIGRDLGY-SGKIMSSLstsLK 238
Cdd:cd16875      1 TRVKLNYLDQIAKFWEIQGSSL-KIPNVERRILDLYSLSKIVQEEGGYEAICKDRRWARVAQRLGYpPGKNIGSL---LR 76

                           90
                   ....*....|...
gi 1570000057  239 NSYDRWLNPYENY 251
Cdd:cd16875     77 SHYERIIYPYEMY 89

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 1570000057    94 EAPTYRPTDEEWKDPFEYVRKITPEAKEYGLCKIIPPDSWNP 135
Cdd:smart00545    1 EIPVFYPTMEEFKDPLAYISKIRPQAEKYGICKVVPPKSWKP 42

ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, HMGB10, HMGB11, HMGB15 and similar proteins; This subfamily includes a group of conserved plant DNA-binding proteins, including HMGB9 (or ARID-HMG1), HMGB10 (or ARID-HMG2), HMGB11, and HMGB15. They have been termed ARID-HMG proteins, due to containing two DNA-binding domains, an N-terminal AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and a C-terminal high mobility group (HMG)-box domain. They are widely expressed in Arabidopsis and localize primarily to the nucleus. HMGB9/ARID-HMG1 binds specifically to A/T-rich DNA. HMGB15 is a transcription factor predominantly expressed in mature pollen grains and pollen tubes. It may work in the form of a homodimer, or interact with HMGB9, HMGB10 and HMGB11 to form heteromultimers in plant cells. HMGB15 is required for pollen tube growth in Arabidopsis and is involved in transcriptional regulation through the interaction with AGL66 and AGL104.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  166 YLDALSKFHKQQGTNLnRLPYVDKKPLDLYRLKKAVESRGGFEKVCKTKKWAEIGRDLGYSGKImSSLSTSLKNSYDRWL 245
Cdd:cd16872      5 FWETLRKFHESLGTKF-RIPIVGGKELDLHRLYKEVTSRGGLEKVIKDRKWKEVAAVFNFPPTI-TNASFVLRKYYLSLL 82

                   ....
gi 1570000057  246 NPYE 249
Cdd:cd16872     83 HHYE 86

jmjN domain;

                           10        20        30
                   ....*....|....*....|....*....|....
gi 1570000057   96 PTYRPTDEEWKDPFEYVRKITPEAKEYGLCKIIP 129
Cdd:pfam02375    1 PVFYPTEEEFKDPLKYIEKIRPLGEKYGICKIVP 34

ARID/BRIGHT DNA binding domain of yeast SWI/SNF chromatin-remodeling complex subunit Swi1p and similar proteins; Saccharomyces cerevisiae Swi1p, also called SWI/SNF chromatin-remodeling complex subunit SWI1, regulatory protein GAM3, or transcription regulatory protein ADR6, is a transcription regulatory protein that is a subunit of the SWI/SNF complex, which plays critical roles in the regulation of gene transcription and expression. It can exist as a prion, [SWI(+)], which demonstrates a link between prionogenesis and global transcriptional regulation. Swi1p contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT) that binds DNA nonspecifically. This subfamily also includes Schizosaccharomyces pombe SWI/SNF chromatin-remodeling complex subunit sol1 (sol1p, also known as switch one-like protein). sol1p is a homolog of S. cerevisiae Swi1p and is also a part of SWI/SNF chromatin-remodeling complex.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  166 YLDALSKFHKQQGTNLNRLPYVDKKPLDLYRLKKAVESRGGFEKVCKTKKWAEIGRDLGYSGKIMSSLSTSLKNSYDRWL 245
Cdd:cd16871      6 FMKSLREFMAKRGTPIEQQPVIGGRPVNLFRLYQLVQKLGGSRQVTQNNQWPRVAQKLGFPPEQNPQVAQQLAQIYQRYL 85

                   ....
gi 1570000057  246 NPYE 249
Cdd:cd16871     86 LPYE 89

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1570000057   607 DPWNLNILPLHpESLFRHIKTDISGMTV-PWVYVGMIFSTFCWHNEDHHaySANYQHFGAT 666
Cdd:smart00558    1 QLWNLAKLPFK-LNLLSDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYD--LVNYLHQGAG 58

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID3A, ARID3B, ARID3C, dead ringer (Dri) from Drosophila melanogaster, and similar proteins; The ARID3 subfamily includes AT-rich interactive domain (ARID, also known as BRIGHT)-containing proteins ARID3A, ARID3B and ARID3C, which are the most direct mammalian counterparts of the Drosophila "dead ringer" protein Dri. They consist of an acidic N-terminal region of unknown function, the central ARID matrix association (or attachment) region (MAR)-DNA binding domain, a SUMO-I conjugation (SUMO) motif, and a multifunctional homomerization/nuclear export REKLES domain in the C-terminal third of the molecule. The ARID domain in this subfamily has been described as the "extended" or e-ARID due to additional conserved sequences at both the N and C termini of the core ARID region. The REKLES domain is found only in the ARID3 subfamily. It has co-evolved with and regulates functional properties of the ARID DNA-binding domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  166 YLDALSKFHKQQGTNLNRLPYVDKKPLDLYRLKKAVESRGGFEKVCKTKKWAEIGRDLGYSGKIMSSLSTsLKNSYDRWL 245
Cdd:cd16867     16 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLYELYRLVVEKGGLVEVINKKIWREITKGLNLPSSITSAAFT-LRTQYMKYL 94

                   ....
gi 1570000057  246 NPYE 249
Cdd:cd16867     95 YPYE 98

ARID/BRIGHT DNA binding domain of dead ringer (Dri) from Drosophila melanogaster and similar proteins; Dri, also termed retained (retn), is a nuclear protein with a sequence-specific DNA-binding domain termed AT-rich DNA-interacting domain (ARID, also known as BRIGHT). It is a founding member of the ARID family. Sequence comparison shows that DRI belongs to the "extended" or e-ARID subfamily, which exhibits an extended region of similarity either side of the ARID. Dri plays an important role in embryogenesis. It functions as an essential transcription factor involved in aspects of dorsal/ventral and anterior/posterior axis patterning, as well as myogenesis and hindgut development.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  166 YLDALSKFHKQQGTNLNRLPYVDKKPLDLYRLKKAVESRGGFEKVCKTKKWAEIGRDLGYSGKIMSSLSTsLKNSYDRWL 245
Cdd:cd16881     23 FLDDLFSFMQKRGTPVNRIPIMAKQVLDLYELYNLVVARGGLVEVINKKLWREITKGLHLPSSITSAAFT-LRTQYMKYL 101

                   ....
gi 1570000057  246 NPYE 249
Cdd:cd16881    102 YPYE 105

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins; ARID1B, also called BRG1-associated factor 250b (BAF250B), BRG1-binding protein ELD/OSA1, Osa homolog 2 (Osa2), or p250R, is the largest subunit of ATP-dependent SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, which plays a critical role in transcriptional control and gene expression. ARID1B exhibits tumour-suppressor activities in pancreatic cancer cell lines. Mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Moreover, mutations in the ARID1B gene have been found in many cancers. ARID1B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner similar to ARID1A.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  166 YLDALSKFHKQQGTNLNRLPYVDKKPLDLYRLKKAVESRGGFEKVCKTKKWAEIGRDL--GYSgkimSSLSTSLKNSYDR 243
Cdd:cd16877      6 WVDRYLTFMEERGTPVASLPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLnvGTS----SSAASSLKKQYIQ 81

                   ....*.
gi 1570000057  244 WLNPYE 249
Cdd:cd16877     82 YLFAFE 87

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID4A, ARID4B and similar proteins; This subfamily contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (Rb)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and Rb transcriptional activity, and play important roles in the AR and Rb pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570000057  166 YLDALSKFHKQQGTNLNRLPYVDKKPLDLYRLKKAVESRGGFEKVCKTKKWAEIGRDLGYSgKIMSSLSTSLKNSYDRWL 245
Cdd:cd16868      5 FLEQLYKFMEDRGTPINKPPVLGYKDLDLFKLYKLVQELGGMERVSQGAKWRSIYQQLGIP-VLNSAASHNIKQAYKKYL 83

                   ....
gi 1570000057  246 NPYE 249
Cdd:cd16868     84 YAFE 87

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1570000057  464 CETCGKGEDVGFLAVCETCDNGYHGACVDPPLKQKPEGEWNCPRC 508
Cdd:cd15515      2 CQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1570000057  464 CETCGKGEDVGFLAVCETCDNGYHGACVDPPLKQKPEGEWNCPRC 508
Cdd:cd15513      2 CEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 1570000057   464 CETCGKGEDVGFLAVCETCDNGYHGACVDPPLKQK-PEGEWNCPRC 508
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEePDGKWYCPKC 47