BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760  130 KQLLLSDGSAVLKKDEHIFMVSEPPGEPYYIGRIVEFVPKKEFRSLISrslhlATSFPAIYFQLKMNWYYRPRDIQERTN 209
Cdd:cd04710    1 VGSLVLKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIH-----ARVFPASYFQVRLNWYYRPRDISRRVV 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49640760  210 sTSSRMLYASLHNDVCPIYSFRGKCNVKFQKEftsIDQLTEYVSRPNCFYFNQLFDRYTLKYYQ 273
Cdd:cd04710   76 -ADSRLLYASMHSDICPIGSVRGKCTVRHRDQ---IPDLEEYKKRPNHFYFDQLFDRYILRYYD 135

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 49640760  330 RCGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPAKGVVWICSNC 377
Cdd:cd15497    1 SCKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGFVWSCAPC 48

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 49640760  561 SQEEIKKFEEGVSLYGSELHPVCKH-VGTQSMSMIVRYYYYWKK 603
Cdd:cd11661    3 SESEAKLFEEGLRKYGKDFHDIRQDfLPWKSVGELVEFYYMWKK 46

BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760  130 KQLLLSDGSAVLKKDEHIFMVSEPPGEPYYIGRIVEFVPKKEFRSLISrslhlATSFPAIYFQLKMNWYYRPRDIQERTN 209
Cdd:cd04710    1 VGSLVLKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIH-----ARVFPASYFQVRLNWYYRPRDISRRVV 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49640760  210 sTSSRMLYASLHNDVCPIYSFRGKCNVKFQKEftsIDQLTEYVSRPNCFYFNQLFDRYTLKYYQ 273
Cdd:cd04710   76 -ADSRLLYASMHSDICPIGSVRGKCTVRHRDQ---IPDLEEYKKRPNHFYFDQLFDRYILRYYD 135

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 49640760  330 RCGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPAKGVVWICSNC 377
Cdd:cd15497    1 SCKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGFVWSCAPC 48

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760 1102 CRVCFSDYRSKTTNELSCSNCGMKVHASCYGIKctnqyhaSLKGKLWLCDPCSNDRNPVVStnyqCVLCSTRDihnesak 1181
Cdd:COG5141  196 CTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQ-------FLPEGFWLCRKCIYGEYQIRC----CSFCPSSD------- 257

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760 1182 kvtarslpNALKCTADGSWCHILCAIYRSMTKFASIETLQPIIGTECSLLNRNNINCNVCNLSGGLLVKC--QSCDDQFH 1259
Cdd:COG5141  258 --------GAFKQTSDGRWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCsyFNCTRAYH 329

                        170       180
                 ....*....|....*....|.
gi 49640760 1260 PSCGADKeGFFfgFKKQVKSN 1280
Cdd:COG5141  330 VTCARRA-GYF--DLNIYSHN 347

PHD finger 2 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; This group corresponds to Snt2p and similar proteins. Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the second canonical Cys4HisCys3 PHD finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 49640760 1101 FCRVCFSDYRSKTTNELSCSNCGMKVHASCYGIK--CTNQYHASLKGKLWLCDPC 1153
Cdd:cd15498    1 KCSVCSEQFASNFNTSLSCYNCGLNVHASCYGITvpGKMNKVKNLKSYKWLCDPC 55

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        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 49640760    330 RCGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPAKGVVWICSNCVGK 380
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGEWLCPECKPK 51

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 49640760     330 RCGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPAKGvVWICSNC 377
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDG-KWYCPKC 47

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 49640760    561 SQEEIKKFEEGVSLYGSELHPVCKHVGTQSMSMIVRYYYYWK 602
Cdd:pfam00249    5 TPEEDELLLEAVEKLGNRWKKIAKLLPGRTDNQCKNRWQNYL 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
                    ....*....|....*....|....*..
gi 49640760    1238 CNVCNLS--GGLLVKCQSCDDQFHPSC 1262
Cdd:smart00249    2 CSVCGKPddGGELLQCDGCDRWYHQTC 28

BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760  130 KQLLLSDGSAVLKKDEHIFMVSEPPGEPYYIGRIVEFVPKKEFRSLISrslhlATSFPAIYFQLKMNWYYRPRDIQERTN 209
Cdd:cd04710    1 VGSLVLKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIH-----ARVFPASYFQVRLNWYYRPRDISRRVV 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49640760  210 sTSSRMLYASLHNDVCPIYSFRGKCNVKFQKEftsIDQLTEYVSRPNCFYFNQLFDRYTLKYYQ 273
Cdd:cd04710   76 -ADSRLLYASMHSDICPIGSVRGKCTVRHRDQ---IPDLEEYKKRPNHFYFDQLFDRYILRYYD 135

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 49640760  330 RCGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPAKGVVWICSNC 377
Cdd:cd15497    1 SCKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGFVWSCAPC 48

BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760    147 IFMVSEPPGEPYYIGRIVEfvpkkefrslisrsLHLATSFPaiYFQLKMNWYYRPRDIQER-TNSTSSRMLYASLHNDVC 225
Cdd:pfam01426    9 VLVEPDDADEPYYVARIEE--------------LFEDTKNG--KKMVRVQWFYRPEETVHRaGKAFNKDELFLSDEEDDV 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 49640760    226 PIYSFRGKCNVKFQKEFTSIDQltEYVSRPNCFYFNQLFDRYTLKY 271
Cdd:pfam01426   73 PLSAIIGKCSVLHKSDLESLDP--YKIKEPDDFFCELLYDPKTKSF 116

Bromo adjacent homology domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760     147 IFMVSEPPGEPYYIGRIVEFVPKKEFRSlisrslhlatsfpaiYFQLKMNWYYRPRDIQ-ERTNSTSSRMLYASLHNDVC 225
Cdd:smart00439    8 VLVEPDDADEPYYIGRIEEIFETKKNSE---------------SKMVRVRWFYRPEETVlEKAALFDKNEVFLSDEYDTV 72

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 49640760     226 PIYSFRGKCNVKFQKEFTSIDQlTEYVSRPNCFYFNQLFDR 266
Cdd:smart00439   73 PLSDIIGKCNVLYKSDYPGLRP-EGSIGEPDVFFCESAYDP 112

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760 1167 CVLCSTRDihnesakkvTARSLPNALKCTADGSWCHILCAIYRSMTKFASIETLQpIIGTECSLLNRNNINCNVCNLSGG 1246
Cdd:cd15571    1 CALCPRSG---------GALKGGGALKTTSDGLWVHVVCALWSPEVYFDDGTLLE-VEGVSKIPKRRKKLKCSICGKRGG 70

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 49640760 1247 LLVKCQ--SCDDQFHPSCGADKeGFFFGFkkqvksnvtnnseisfvedqKDYTASPVILCPKH 1307
Cdd:cd15571   71 ACIQCSypGCPRSFHVSCAIRA-GCLFEF--------------------EDGPGNFVVYCPKH 112

PHD-zinc-finger like domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760   1166 QCVLCSTRDihnesakkvtarslpNALKCTADGSWCHILCAIYRSMTKFASIETLQPiIGTECSLLNRNNINCNVCNLSG 1245
Cdd:pfam13832    2 RCCLCPLRG---------------GALKQTSDGRWVHVLCAIFVPEVRFGNVATMEP-IDVSRIPPERWKLKCVFCKKRS 65

                           90       100
                   ....*....|....*....|....*...
gi 49640760   1246 GLLVKC--QSCDDQFHPSCgADKEGFFF 1271
Cdd:pfam13832   66 GACIQCskGRCTTAFHVTC-AQAAGVYM 92

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        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 49640760    330 RCGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPAKGVVWICSNCVGK 380
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGEWLCPECKPK 51

Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX1, -2, and similar proteins. ATX1 and -2 are sister paralogs originating from a segmental chromosomal duplication; they are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1 (also known as protein SET domain group 27, or trithorax-homolog protein 1/TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2 (also known as protein SET domain group 30, or trithorax-homolog protein 2/TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). ATX1 and ATX2 are multi-domain proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical PHD finger, this non-canonical ePHD finger, and a C-terminal SET domain.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 49640760 1191 ALKCTADGSWCHILCAIYRSMTKFASIETLQPIIGTECSLLNRNNINCNVCNLSGGLLVKC--QSCDDQFHPSCG 1263
Cdd:cd15662   10 ALKPTTDGRWAHLACAIWIPETCLLDVKTMEPVDGINAISKERWELSCTICKQRYGACIQCsnNSCRVAYHPLCA 84

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 49640760  331 CGECRDwchQSSSIKCDDCKISIHLWCMDPPLEKKPAKGvvWICSNCV 378
Cdd:cd15513    5 CGKASD---ESRLLLCDDCDISYHTYCLDPPLQTVPKGG--WKCKWCV 47

Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF14. 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 this non-canonical ePHD finger. It can interact with histones through its PHD fingers.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760 1189 PN---ALKCTADGSWCHILCAIYRSMTKFASIETLQPIIGTECSLLNRNNINCNVC---NLS-GGLLVKCQS--CDDQFH 1259
Cdd:cd15674    5 PNrggIFKETDTGRWVHLVCALYTPGVAFGDVDKLSPVTLTEMNYSKWGARECSLCedpRFArTGVCISCDAgmCKSYFH 84

                         90
                 ....*....|
gi 49640760 1260 PSCgADKEGF 1269
Cdd:cd15674   85 VTC-AQREGL 93

Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle. MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 49640760  561 SQEEIKKFEEGVSLYGSELHPVCKH-VGTQSMSMIVRYYYYWKK 603
Cdd:cd11661    3 SESEAKLFEEGLRKYGKDFHDIRQDfLPWKSVGELVEFYYMWKK 46

Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins 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. These proteins show distinct phylogenetic origins from the family of ATX1 and ATX2. They are multi-domain proteins that consist of an N-terminal PWWP domain, a canonical PHD finger, this non-canonical extended PHD finger, and a C-terminal SET domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760 1191 ALKCT-ADGSWCHILCAIYRSMTKFASIETLQPIIGTECSLLNRNNINCNVCNLSGGLLVKCQSCDDQFHPSCgADKEGF 1269
Cdd:cd15663   10 ALKPTdVEGLWVHVTCAWFRPEVCFKNEEKMEPAVGLLRIPLSTFLKACVICKQIHGSCTQCCKCATYFHAMC-ASRAGY 88

Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49640760 1167 CVLCSTRDihnesakkvtarslpNALKCTADGSWCHILCAIYRSMTKFASIETLQPIIGTECSlLNRNNINCNVCNLSG- 1245
Cdd:cd15672    1 CELCPHKD---------------GALKRTDNGGWAHVVCALYIPEVRFGNVATMEPIILQDVP-QDRFNKTCYICEEQGr 64

                         90       100
                 ....*....|....*....|....*
gi 49640760 1246 ------GLLVKC--QSCDDQFHPSC 1262
Cdd:cd15672   65 eskastGACMQCnkSGCKQSFHVTC 89

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.

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gi 49640760  331 CGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPAKGvVWICSN 376
Cdd:cd15534    2 CFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATG-RWMCPN 46

Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF2. BRPF2 also termed bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, 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 plant homeodomain (PHD) finger followed by a non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.

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gi 49640760 1167 CVLCSTRDihnesakkvtarslpNALKCTADGSWCHILCAIYRSMTKFASIETLQPIIGTECSLLNRNNINCNVCNLSG- 1245
Cdd:cd15702    1 CVLCPNKG---------------GAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGv 65

                         90       100
                 ....*....|....*....|....*..
gi 49640760 1246 GLLVKCQ--SCDDQFHPSCgADKEGFF 1270
Cdd:cd15702   66 GACIQCHkaNCYTAFHVTC-AQKAGLY 91

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.

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                 ....*....|....*....|....*....|....*....|....*...
gi 49640760  330 RCGECRDWCHQsssIKCDDCKISIHLWCMDPPLEKKPAKGvVWICSNC 377
Cdd:cd15525    4 VCGGKQDPEKQ---LLCDECDMAYHLYCLDPPLTSLPDDD-EWYCPDC 47

PHD finger 1 found in PHD finger protein 12 (PHF12); 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 model corresponds to the first PHD finger.

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gi 49640760  346 CDDCKISIHLWCMDPPLEKKPAKGVVWICSNC 377
Cdd:cd15533   14 CDRCPASFHLQCCNPPLDEEDLPPGEWLCHRC 45

Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-2. Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.

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gi 49640760 1167 CVLCSTRDihnesakkvtarslpNALKCTADGS-WCHILCAIYRSMTKFASIETLQPIIGTECSLLNRNNINCNVCNLSG 1245
Cdd:cd15705    1 CLLCPKRG---------------GALKPTRSGTkWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECT 65

                         90       100       110       120
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gi 49640760 1246 GLLVKCQ--SCDDQFHPSCGadkegffFGFKKQVKSNVTNNSEISF 1289
Cdd:cd15705   66 GTCIQCSmpSCITAFHVTCA-------FDHGLEMRTTLADNDEVKF 104

PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a Cys4HisCys3 canonical PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth. This model corresponds to the Cys4HisCys3 canonical PHD finger.

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gi 49640760 1117 LSCSNCGMKVHASCYGIKctnqyHASLKGKLWLCDPC 1153
Cdd:cd15493   11 LVCSRCCVCVHASCYGVP-----DIPGDGEGWKCDRC 42

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX1, ATX2, and similar proteins; The family includes A. thaliana ATX1 and ATX2, both of which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also termed protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also termed protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, 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.

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                 ....*....|....*....|....*....|....*....|....*....|..
gi 49640760 1102 CRVCFSDYRSKTTNELSCSNCGMKVHASCYGIKctnqyhASLKGKLWLCDPC 1153
Cdd:cd15494    2 CSVCGEDEEYEDNLLLQCDKCRMMVHMRCYGVL------EPPPGALWLCNLC 47

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.

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gi 49640760  330 RCGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPAKGvvWICSNC 377
Cdd:cd15544    1 RCKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGD--WFCPAC 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
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gi 49640760 1102 CRVCFSDYRSKTTNELSCSNCGMKVHASCYGIkctnqyHASLKGKLWLCDPC 1153
Cdd:cd15495    2 CAVCNEGEDDDNNPLITCNRCQISVHQKCYGI------REVDPDGSWVCRAC 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.

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                 ....*....|....*....|....*....|....*....|....*...
gi 49640760  330 RCGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPAKGvvWICSNC 377
Cdd:cd15627    1 RCRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGD--WFCPDC 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
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gi 49640760  331 CGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPaKGvVWICSNC 377
Cdd:cd15527    2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMP-KG-KWVCQIC 46

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.

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gi 49640760  331 CGECRDWCHQSSSIKCDDCKISIHLWCMDPPLEKKPAKGvvWICSNC 377
Cdd:cd15595    2 CQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDS--WKCKAC 46