PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15233766 192 FCAECNSREAFPDNDIILCDGTCNRAFHQKCLDPPLETESIPPGDQGWFCKFC 244
Cdd:cd15504   1 FCAKCQSGEASPDNDILLCDGGCNRAYHQKCLEPPLLTEDIPPEDEGWLCPLC 53

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766    386 MFGKDAVLQEQGSEDEDWGPNDRRKRKRES----DAGS----TLVTMCESSKKDQD--------------------VVET 437
Cdd:TIGR00600  353 LLAKQAAMSESSSEDSDESEWERQELKRNNvafvDDGSlsprTLQAIGQALDDDEDkkvsassddqaspskktkmlLISR 432

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766    438 LEQSERDSVSVENKGGRRRMFRLPRNAVEKLRQVFAET----ELPSKAVRDRLAKELSLDPEKVNKWFKNTRYMALrNRK 513
Cdd:TIGR00600  433 IEVEDDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTkiarEVTSSGHEAVPKAVQSLLLGATNDSPIPSEFTIL-DRK 511

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766    514 TESVkqPGDSKTVSGGDSGPEAVMENNTE---TNEVQDTLDDTVPPGFDATN---------------------------- 562
Cdd:TIGR00600  512 SELS--IERTVKPVSSEFGLPSQREDKLAiptEGTQNLQGISDHPEQFEFQNelspletknnesnlssdaetegspnpem 589

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766    563 ---------QNILSPCNNNQEEFQQENVSFPSPTDESQQYLEQNDSSFVLVPH-------EKQSSE-----ISLKTAVEE 621
Cdd:TIGR00600  590 pswssvtvpSEALDNYETTNPSNAKEVRNFAETGIQTTNVGESADLLLISNPMevepmesEKEESEsdgsfIEVDSVSST 669

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766    622 NETESKMMKEPHEELSSEMSLKTAAEEKETESKMIEEPHEELSREMSLKTAVEEKETESKMMEEPHDELNSEMSLSTAVE 701
Cdd:TIGR00600  670 LELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEEKDADDFKNEWQDISLEELEALEANLL 749

                          410       420       430
                   ....*....|....*....|....*....|
gi 15233766    702 EKETGSKMTEESHEELSNE----MSLEEKE 727
Cdd:TIGR00600  750 AEQNSLKAQKQQQKRIAAEvtgqMILESQE 779

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15233766 192 FCAECNSREAFPDNDIILCDGTCNRAFHQKCLDPPLETESIPPGDQGWFCKFC 244
Cdd:cd15504   1 FCAKCQSGEASPDNDILLCDGGCNRAYHQKCLEPPLLTEDIPPEDEGWLCPLC 53

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        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 15233766    192 FCAECNSREAfpDNDIILCDGtCNRAFHQKCLDPPLEtESIPPGDqgWFCKFC 244
Cdd:smart00249   1 YCSVCGKPDD--GGELLQCDG-CDRWYHQTCLGPPLL-EEEPDGK--WYCPKC 47

Homeodomain; DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 15233766    453 GRRRMFRLPRNAVEKLRQVFAETELPSKAVRDRLAKELSLDPEKVNKWFKNTRY 506
Cdd:smart00389   1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRA 54

Homeodomain-containing transcription factor [Transcription];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766 451 KGGRRRMFRLprnAVEKLRQVFAETELPSKAVRDRLAKELSLDPEKVNKWFKNTRYMALRNRKTESVKQPGDSKTVSGGD 530
Cdd:COG5576  52 KSKRRRTTDE---QLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQRPGEEEADLAKI 128

                        90
                ....*....|....*..
gi 15233766 531 SGPEAVMENNTETNEVQ 547
Cdd:COG5576 129 GSLSTGQISIIETLEFS 145

PHD zinc finger-containing protein [General function prediction only];

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNSREAFPDNDIILCDGtCNRAFHQKCLDPPLetesIPPGDqgWFCKFC 244
Cdd:COG5141 196 CTKCTSTHNENSNAIVFCDG-CEICVHQSCYGIQF----LPEGF--WLCRKC 240

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15233766 192 FCAECNSREAFPDNDIILCDGTCNRAFHQKCLDPPLETESIPPGDQGWFCKFC 244
Cdd:cd15504   1 FCAKCQSGEASPDNDILLCDGGCNRAYHQKCLEPPLLTEDIPPEDEGWLCPLC 53

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15233766 192 FCAECNSREAFPDNDIILCDGtCNRAFHQKCLDPPLETESIPPGDQGWFCKFC 244
Cdd:cd15502   1 VCIVCQRGHSPKSNRIVFCDG-CNTPYHQLCHDPSIDDEVVEDPDAEWFCKKC 52

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        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNSREAfpDNDIILCDGtCNRAFHQKCLDPPLetESIPPGDqgWFCKFC 244
Cdd:cd15519   2 CEVCGLDDN--EGEVLLCDG-CDAEYHTSCLDPPL--GEIPPGT--WFCPSC 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        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 15233766    192 FCAECNSREAfpDNDIILCDGtCNRAFHQKCLDPPLEtESIPPGDqgWFCKFC 244
Cdd:smart00249   1 YCSVCGKPDD--GGELLQCDG-CDRWYHQTCLGPPLL-EEEPDGK--WYCPKC 47

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNSREAfPDNdIILCDgTCNRAFHQKCLDPPLetESIPPGDqgWFCKFC 244
Cdd:cd15543   2 CRKCGLSDH-PEW-ILLCD-RCDAGYHTACLRPPL--MIIPDGN--WFCPPC 46

Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15233766 454 RRRMFRLPRNAVEKLRQVFAETELPSKAVRDRLAKELSLDPEKVNKWFKNTRY 506
Cdd:cd00086   1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRA 53

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNsREAFPDNdIILCDGtCNRAFHQKCLDPPLETesIPPGDqgWFCKFC 244
Cdd:cd15544   2 CKVCR-KKGDPDN-MILCDG-CDKAFHLYCLRPALRE--VPSGD--WFCPAC 46

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        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15233766 192 FCAECNsREAFPDNDIILCDGtCNRAFHQKCLDPPLETesiPPGDQGWFCKFC 244
Cdd:cd15489   1 SCIVCG-KGGDLGGELLQCDG-CGKWFHADCLGPPLSS---FVPNGKWICPVC 48

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNSREAFpdNDIILCDgTCNRAFHQKCLDPPLetESIPPGDQgWFCKFC 244
Cdd:cd15525   2 CHVCGGKQDP--EKQLLCD-ECDMAYHLYCLDPPL--TSLPDDDE-WYCPDC 47

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 15233766 207 IILCDGtCNRAFHQKCLDPPLetESIPPGDqgWFCKFC 244
Cdd:cd15627  14 MLLCDG-CDRGHHMYCLRPPL--KKVPEGD--WFCPDC 46

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNSREAfPDNDIiLCDgTCNRAFHQKCLDPPLETesiPPGDQGWFCKFC 244
Cdd:cd15616   2 CHVCGGKQD-PDKQL-MCD-ECDMAFHIYCLNPPLSS---IPDDEDWYCPEC 47

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15233766 192 FCAECNSreafpDND---IILCDgTCNRAFHQKCLDPPLETESIPPGDQGWFCKFC 244
Cdd:cd15562   1 SCGICKK-----SNDqhlLALCD-TCKLYYHLGCLDPPLTRMPKKTKNSGWQCSEC 50

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15233766 192 FCAECNSreafpDNDIILCDGtCNRAFHQKCLDPPLetESIPPGDqgWFCKFC 244
Cdd:cd15532   1 FCRVCKD-----GGELLCCDG-CPSSYHLHCLNPPL--AEIPDGD--WFCPRC 43

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNSREAfpDNDIILCDgTCNRAFHQKCLDPPLETESIPPGdQGWFCKFC 244
Cdd:cd15563   2 CCVCKQTGD--NSQLVRCD-ECKLCYHFGCLDPPLKKSPKQRG-YGWVCEEC 49

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 15233766 192 FCAECNsREAFPDNdIILCDgTCNRAFHQKCLDPPLETesiPPGDQGWFC 241
Cdd:cd15534   1 VCFKCN-RSCRVAP-LIQCD-YCPLLFHLDCLDPPLTH---PPATGRWMC 44

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); 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. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECnsREAFPDNDIILCDgTCNRAFHQKCLDPPLETesIPpgDQGWFCKFC 244
Cdd:cd15594   2 CQTC--RQPGDDNKMLVCD-TCDKGYHTFCLQPVMTT--IP--KNGWKCKNC 46

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15233766 192 FCAECNSREAFPDNDIILCDgTCNRAFHQKCLDPPLetesIPPGDqgWFCKFC 244
Cdd:cd15572   3 VCCICLDGECQNSNVILFCD-MCNLAVHQECYGVPY----IPEGQ--WLCRRC 48

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECnsREAFPDNDIILCDgTCNRAFHQKCLDPPLetESIPPGDqgWFCKFC 244
Cdd:cd15628   2 CKVC--RKKGEDDKLILCD-ECNQAFHLFCLRPAL--YEVPDGE--WMCPAC 46

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15233766 192 FCAECNSREAfpDNDIILCDGtCNRAFHQKCLDPPLETESIppgdQGWFCKFC 244
Cdd:cd15536   1 YCEVCGRSDR--EDRLLLCDG-CDAGYHMECLTPPLDEVPI----EEWFCPEC 46

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNSrEAFPDNdIILCDgTCNRAFHQKCLDPPLetESIPPGDqgWFCKFC 244
Cdd:cd15527   2 CSVCQD-SGNADN-LLFCD-ACDKGFHMECHDPPL--TRMPKGK--WVCQIC 46

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766    386 MFGKDAVLQEQGSEDEDWGPNDRRKRKRES----DAGS----TLVTMCESSKKDQD--------------------VVET 437
Cdd:TIGR00600  353 LLAKQAAMSESSSEDSDESEWERQELKRNNvafvDDGSlsprTLQAIGQALDDDEDkkvsassddqaspskktkmlLISR 432

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766    438 LEQSERDSVSVENKGGRRRMFRLPRNAVEKLRQVFAET----ELPSKAVRDRLAKELSLDPEKVNKWFKNTRYMALrNRK 513
Cdd:TIGR00600  433 IEVEDDDLDYLDQGEGIPLMAALQLSSVNSKPEAVASTkiarEVTSSGHEAVPKAVQSLLLGATNDSPIPSEFTIL-DRK 511

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766    514 TESVkqPGDSKTVSGGDSGPEAVMENNTE---TNEVQDTLDDTVPPGFDATN---------------------------- 562
Cdd:TIGR00600  512 SELS--IERTVKPVSSEFGLPSQREDKLAiptEGTQNLQGISDHPEQFEFQNelspletknnesnlssdaetegspnpem 589

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766    563 ---------QNILSPCNNNQEEFQQENVSFPSPTDESQQYLEQNDSSFVLVPH-------EKQSSE-----ISLKTAVEE 621
Cdd:TIGR00600  590 pswssvtvpSEALDNYETTNPSNAKEVRNFAETGIQTTNVGESADLLLISNPMevepmesEKEESEsdgsfIEVDSVSST 669

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15233766    622 NETESKMMKEPHEELSSEMSLKTAAEEKETESKMIEEPHEELSREMSLKTAVEEKETESKMMEEPHDELNSEMSLSTAVE 701
Cdd:TIGR00600  670 LELQVPSKSQPTDESEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEEKDADDFKNEWQDISLEELEALEANLL 749

                          410       420       430
                   ....*....|....*....|....*....|
gi 15233766    702 EKETGSKMTEESHEELSNE----MSLEEKE 727
Cdd:TIGR00600  750 AEQNSLKAQKQQQKRIAAEvtgqMILESQE 779

PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNSREAFPDNDIILCDgTCNRAFHQKCLDPPleteSIPPGDqgWFCKFC 244
Cdd:cd15677   4 CCICMDGECQNSNVILFCD-MCNLAVHQECYGVP----YIPEGQ--WLCRHC 48

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 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 asHOXA1-3 and NESTIN. It 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 KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two 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 second PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECnsREAFPDNDIILCDgTCNRAFHQKCLDPPLetESIPPgdQGWFCKFC 244
Cdd:cd15595   2 CQTC--RKPGEDSKMLVCE-ACDKGYHTFCLKPAM--ESLPT--DSWKCKAC 46

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the ATX1 and ATX2 family. They are multi-domain containing proteins that consist of an N-terminal PWWP domain, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNSREAFPDNDIILCDGtCNRAFHQKCLDPpleTESIPPGDqgWFCKFC 244
Cdd:cd15495   2 CAVCNEGEDDDNNPLITCNR-CQISVHQKCYGI---REVDPDGS--WVCRAC 47

PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; BRPF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15233766 192 FCAECNSREAFPDNDIILCDgTCNRAFHQKCLDPPLetesIPPGDqgWFCKFC 244
Cdd:cd15678   3 FCCVCLDDECHNSNVILFCD-ICNLAVHQECYGVPY----IPEGQ--WLCRCC 48

PHD finger found in pygopus homolog 2 (PYGO2); PYGO2 is a homolog of Drosophila melanogaster protein pygopus (dPYGO), which is a fundamental Wnt signaling transcriptional component in Drosophila. It functions as a context-dependent beta-catenin coactivator, as well as a histone methylation reader that binds di-and trimethylated lysine 4 of histone H3 (H3K4me2/3). Moreover, PYGO2 acts as a chromatin remodeler in a testis-specific and Wnt-unrelated manner. It also mediates chromatin regulation and links Wnt signaling and Notch signaling to suppress the luminal/alveolar differentiation competence of mammary stem and basal cells. Furthermore, PYGO2 plays a new role in rRNA transcription during cancer cell growth. It regulates mammary tumor initiation and heterogeneity in MMTV-Wnt1 mice. PYGO2 contains a plant homeodomain (PHD) finger, which is important for Lgs/Bcl9 recognition as well as for the regulation of the Wnt/beta-catenin signaling pathway.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15233766 193 CAECNSrEAFPDNDIILCDGTCNRAFHQKC--LDPP----LETESippgDQGWFCKFC 244
Cdd:cd15636   2 CGACRS-EVNDDQDAILCEASCQKWFHRECtgMTESayglLTTEA----SAVWACDFC 54

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 15233766 208 ILCDGTCNRAFHQKCLDppleTESIPPGDqgWFCKFC 244
Cdd:cd15567  11 LICCESCPASFHPECLG----LEPPPEGK--FYCEDC 41

PHD zinc finger-containing protein [General function prediction only];

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15233766 193 CAECNSREAFPDNDIILCDGtCNRAFHQKCLDPPLetesIPPGDqgWFCKFC 244
Cdd:COG5141 196 CTKCTSTHNENSNAIVFCDG-CEICVHQSCYGIQF----LPEGF--WLCRKC 240