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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  203 RPLAYYRFIEKSLEELDGE-VEYDVDEEDSAWLEHMNEERQRlglNAVGIDTMELLMDRLEKE----SHFQAAANGTPTG 277
Cdd:COG5141  111 SHDEGKKFIDIEPPRGLFFsVIYDLDEYDTMWLRYLNESAID---ENVSEEAFEIIVTRLEKEwfffEHGLPDKHVEPIE 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  278 VEVDDDAVCCICLDGECQNTNVILFCDMCNLAVHQDCYGVPYIPEGQWLCRRCLQSPSKPVNCVLCPNAGGAFKQTDHGQ 357
Cdd:COG5141  188 PSDEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGR 267

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  358 WAHVVCALWIPEVRFANTVFLEPIDSIETIPPARWRLTCYVCKEKGlGACIQCHRNSCYAAFHVTCAQQAGLYMTMDTvk 437
Cdd:COG5141  268 WGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFG-GTCIQCSYFNCTRAYHVTCARRAGYFDLNIY-- 344

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  438 dGHNDSSMHVQKFAYCHAHTPAD------------AKLKMNVPDFEDTRH-KMKEARKALAKKRstapVVLIPTIPPDRV 504
Cdd:COG5141  345 -SHNGISYCIDHEPLCRKHYPLGygrmnglryfgyEKLRYKNPPTAIPRKvRAARPRATLFMKL----CWKQPPATPSVL 419

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  505 QEIATMVTMQRKKEFLDRII----AYWTLKRHYRNGVPLLRrlqSQGNNHGVIQRNGIEGSPDTGELYRQLkywqclrQD 580
Cdd:COG5141  420 SRVEACDLKEKDRQDLPVNIfdicKYWEMKRKSEIGGPLVI---LPDIVYSLKTLEDWMSKRRMREVAKAL-------QD 489

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*.
gi 20129741  581 LERARLLCELVRKREKLKVAFVRISEEVVMLQLNPLEAALN-KLLD 625
Cdd:COG5141  490 QYQLLTLVESTAKRQLLKCQLSNLRKKFLNLNYFPAQRLLQvKIID 535

PWWP domain found in the bromodomain and PHD finger-containing (BRPF) protein family; The BRPF family of 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 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741 1303 LEPLQLVWAKCRGYPWYPALILDPKTPKGfvYNGVPLPAPPTDVLalrkNCLDEIVFLVLFFDVKRTWQWLPANKLDILG 1382
Cdd:cd05839    1 LEPGDLVWAKCRGYPWYPAEIVDPKDPKE--GNGVPIPVPPDRVL----KKSNEKLYLVLFFDAKRTWGWLPRNKLRPLG 74

                         90       100       110
                 ....*....|....*....|....*....|..
gi 20129741 1383 IDKQLDQQKLVESRKPAERKAVKKAYQDALHY 1414
Cdd:cd05839   75 VDEELDKLKLSEAKKSKRRKEVRKAYERACKH 106

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  1080 SDSDDAPSQSSSPCSSCSDFSMSGSCSDFDSDEASEGDADGDPDRDGGRSRSEERDSTSQEGTTDAMDMQHASLNNVQ-G 1158
Cdd:NF033609  788 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSESDSNSDSEsG 867

                  ....*
gi 20129741  1159 NNGNM 1163
Cdd:NF033609  868 SNNNV 872

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  203 RPLAYYRFIEKSLEELDGE-VEYDVDEEDSAWLEHMNEERQRlglNAVGIDTMELLMDRLEKE----SHFQAAANGTPTG 277
Cdd:COG5141  111 SHDEGKKFIDIEPPRGLFFsVIYDLDEYDTMWLRYLNESAID---ENVSEEAFEIIVTRLEKEwfffEHGLPDKHVEPIE 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  278 VEVDDDAVCCICLDGECQNTNVILFCDMCNLAVHQDCYGVPYIPEGQWLCRRCLQSPSKPVNCVLCPNAGGAFKQTDHGQ 357
Cdd:COG5141  188 PSDEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGR 267

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  358 WAHVVCALWIPEVRFANTVFLEPIDSIETIPPARWRLTCYVCKEKGlGACIQCHRNSCYAAFHVTCAQQAGLYMTMDTvk 437
Cdd:COG5141  268 WGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFG-GTCIQCSYFNCTRAYHVTCARRAGYFDLNIY-- 344

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  438 dGHNDSSMHVQKFAYCHAHTPAD------------AKLKMNVPDFEDTRH-KMKEARKALAKKRstapVVLIPTIPPDRV 504
Cdd:COG5141  345 -SHNGISYCIDHEPLCRKHYPLGygrmnglryfgyEKLRYKNPPTAIPRKvRAARPRATLFMKL----CWKQPPATPSVL 419

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  505 QEIATMVTMQRKKEFLDRII----AYWTLKRHYRNGVPLLRrlqSQGNNHGVIQRNGIEGSPDTGELYRQLkywqclrQD 580
Cdd:COG5141  420 SRVEACDLKEKDRQDLPVNIfdicKYWEMKRKSEIGGPLVI---LPDIVYSLKTLEDWMSKRRMREVAKAL-------QD 489

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*.
gi 20129741  581 LERARLLCELVRKREKLKVAFVRISEEVVMLQLNPLEAALN-KLLD 625
Cdd:COG5141  490 QYQLLTLVESTAKRQLLKCQLSNLRKKFLNLNYFPAQRLLQvKIID 535

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  615 PLEAALNKLLDALEARDSMQIFREPVDTSEVPDYTDIVKQPMDLGTMRAKLKECQYNSLEQLEADFDLMIQNCLAYNNKD 694
Cdd:cd05512    1 PLEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKD 80

                         90
                 ....*....|....*...
gi 20129741  695 TVFYRAGIRMRDQAAPLF 712
Cdd:cd05512   81 TIFYRAAVRLRDQGGAIL 98

PWWP domain found in the bromodomain and PHD finger-containing (BRPF) protein family; The BRPF family of 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 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741 1303 LEPLQLVWAKCRGYPWYPALILDPKTPKGfvYNGVPLPAPPTDVLalrkNCLDEIVFLVLFFDVKRTWQWLPANKLDILG 1382
Cdd:cd05839    1 LEPGDLVWAKCRGYPWYPAEIVDPKDPKE--GNGVPIPVPPDRVL----KKSNEKLYLVLFFDAKRTWGWLPRNKLRPLG 74

                         90       100       110
                 ....*....|....*....|....*....|..
gi 20129741 1383 IDKQLDQQKLVESRKPAERKAVKKAYQDALHY 1414
Cdd:cd05839   75 VDEELDKLKLSEAKKSKRRKEVRKAYERACKH 106

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741    620 LNKLLDALEARDSMQIFREPVDTSEVPDYTDIVKQPMDLGTMRAKLKECQYNSLEQLEADFDLMIQNCLAYNNKDTVFYR 699
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   .
gi 20129741    700 A 700
Cdd:pfam00439   81 A 81

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741   1307 QLVWAKCRGYPWYPALILDPktpkgfvyngvplPAPPTDVLALRKnclDEIVFLVLFFDVKRTwQWLPANKLDILGIDKQ 1386
Cdd:pfam00855    2 DLVWAKLKGYPWWPARVVDP-------------EELPENVLKPKK---KDGEYLVRFFGDSEF-AWVKPKDLKPFDEGDE 64

                           90       100
                   ....*....|....*....|....*...
gi 20129741   1387 LDQQKLVESRKPaeRKAVKKAYQDALHY 1414
Cdd:pfam00855   65 FEYLKKKKKKKK--KKAFKKALEEAEEA 90

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 20129741     285 VCCICldGECQNTNVILFCDMCNLAVHQDCYGVPY---IPEGQWLCRRC 330
Cdd:smart00249    1 YCSVC--GKPDDGGELLQCDGCDRWYHQTCLGPPLleeEPDGKWYCPKC 47

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  1080 SDSDDAPSQSSSPCSSCSDFSMSGSCSDFDSDEASEGDADGDPDRDGGRSRSEERDSTSQEGTTDAMDMQHASLNNVQ-G 1158
Cdd:NF033609  788 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSESDSNSDSEsG 867

                  ....*
gi 20129741  1159 NNGNM 1163
Cdd:NF033609  868 SNNNV 872

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 20129741  1080 SDSDDAPSQSSSPCSSCSDFSMSGSCSDFDSDEASEGDADGDPDRDGGRSRSEERDSTSQEGTTDAMD 1147
Cdd:NF033609  734 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 801

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 20129741  1080 SDSDDAPSQSSSPCSSCSDFSMSGSCSDFDSDEASEGDADGDPDRDGGRSRSEERDSTSQEGTTDAMDMQHAS 1152
Cdd:NF033609  736 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 808

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 20129741  1080 SDSDDAPSQSSSPCSSCSDFSMSGSCSDFDSDEASEGDADGDPDRDGGRSRSEERDSTSQEGTTDAMD 1147
Cdd:NF033609  732 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 799

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 20129741  1080 SDSDDAPSQSSSPCSSCSDFSMSGSCSDFDSDEASEGDADGDPDRDGGRSRSEERDSTSQEGTTDAMDMQHAS 1152
Cdd:NF033609  666 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 738

Aberrant zinc-finger; This is a family of largely microsporidia-specific proteins with an aberrant zinc-finger motif of Cx(4)C2H repeated.

                           10        20
                   ....*....|....*....|....*..
gi 20129741     23 FACPVRGCDRSYKTIMGLQYHLMKYDH 49
Cdd:pfam17017  130 IYCRIPGCGKQFKSLMAYKYHCGNYTH 156

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  203 RPLAYYRFIEKSLEELDGE-VEYDVDEEDSAWLEHMNEERQRlglNAVGIDTMELLMDRLEKE----SHFQAAANGTPTG 277
Cdd:COG5141  111 SHDEGKKFIDIEPPRGLFFsVIYDLDEYDTMWLRYLNESAID---ENVSEEAFEIIVTRLEKEwfffEHGLPDKHVEPIE 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  278 VEVDDDAVCCICLDGECQNTNVILFCDMCNLAVHQDCYGVPYIPEGQWLCRRCLQSPSKPVNCVLCPNAGGAFKQTDHGQ 357
Cdd:COG5141  188 PSDEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGR 267

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  358 WAHVVCALWIPEVRFANTVFLEPIDSIETIPPARWRLTCYVCKEKGlGACIQCHRNSCYAAFHVTCAQQAGLYMTMDTvk 437
Cdd:COG5141  268 WGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFG-GTCIQCSYFNCTRAYHVTCARRAGYFDLNIY-- 344

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  438 dGHNDSSMHVQKFAYCHAHTPAD------------AKLKMNVPDFEDTRH-KMKEARKALAKKRstapVVLIPTIPPDRV 504
Cdd:COG5141  345 -SHNGISYCIDHEPLCRKHYPLGygrmnglryfgyEKLRYKNPPTAIPRKvRAARPRATLFMKL----CWKQPPATPSVL 419

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  505 QEIATMVTMQRKKEFLDRII----AYWTLKRHYRNGVPLLRrlqSQGNNHGVIQRNGIEGSPDTGELYRQLkywqclrQD 580
Cdd:COG5141  420 SRVEACDLKEKDRQDLPVNIfdicKYWEMKRKSEIGGPLVI---LPDIVYSLKTLEDWMSKRRMREVAKAL-------QD 489

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*.
gi 20129741  581 LERARLLCELVRKREKLKVAFVRISEEVVMLQLNPLEAALN-KLLD 625
Cdd:COG5141  490 QYQLLTLVESTAKRQLLKCQLSNLRKKFLNLNYFPAQRLLQvKIID 535

Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF1. BRPF1, also termed peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ) -dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to methylated lysine 4 of histone H3 (H3K4me), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  340 CVLCPNAGGAFKQTDHGQWAHVVCALWIPEVRFANTVFLEPIDSIETIPPARWRLTCYVCKEKGLGACIQCHRNSCYAAF 419
Cdd:cd15701    1 CALCPNKGGAFKQTDDGRWAHVVCALWIPEVCFANTVFLEPIDSIEHIPPARWKLTCYICKQRGSGACIQCHKANCYTAF 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 20129741  420 HVTCAQQAGLYMTMDTVKD-GHNDSSMHVQKFAYCHAHTPA 459
Cdd:cd15701   81 HVTCAQQAGLYMKMEPVREtGANGTSFSVRKTAYCDIHTPP 121

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  340 CVLCPNAGGAFKQTDHGQWAHVVCALWIPEVRFANTVFLEPIDSIETIPPARWRLTCYVCKEKGLGACIQCHRNSCYAAF 419
Cdd:cd15702    1 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGVGACIQCHKANCYTAF 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 20129741  420 HVTCAQQAGLYMTMDTVKD-GHNDSSMHVQKFAYCHAH 456
Cdd:cd15702   81 HVTCAQKAGLYMKMEPVKEvTGGGTTFSVRKTAYCDAH 118

PHD-zinc-finger like domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741    338 VNCVLCPNAGGAFKQTDHGQWAHVVCALWIPEVRFANTVFLEPIDsIETIPPARWRLTCYVCKEKGlGACIQCHRNSCYA 417
Cdd:pfam13832    1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPID-VSRIPPERWKLKCVFCKKRS-GACIQCSKGRCTT 78

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 20129741    418 AFHVTCAQQAGLYMTMDTVKdghndssmHVQKFAYCHAH 456
Cdd:pfam13832   79 AFHVTCAQAAGVYMEPEDWP--------NVVVIAYCQKH 109

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins 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, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  340 CVLCPNAGGAFKQTDHG-QWAHVVCALWIPEVRFANTVFLEPIDSIETIPPARWRLTCYVCKEKgLGACIQCHRNSCYAA 418
Cdd:cd15671    1 CVLCPKKGGAMKSTKSGtKWVHVSCALWIPEVSIGCPEKMEPITKISHIPMSRWALVCVLCKEK-TGACIQCSVKSCKTA 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 20129741  419 FHVTCAQQAGLymTMDTVKDGHNDSsmhVQKFAYCHAH 456
Cdd:cd15671   80 FHVTCAFQHGL--EMKTILEDEDDE---VKFKSYCPKH 112

PWWP domain found in bromodomain and PHD finger-containing protein 1 (BRPF1); BRPF1, also called peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It may be involved in chromatin remodeling. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to methylated lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741 1303 LEPLQLVWAKCRGYPWYPALILDPKTPK-GFVYNGVPLPAPPTDVLALRKNCLDEI---VFLVLFFDVKRTWQWLPANKL 1378
Cdd:cd20156    1 LDALDLVWAKCRGYPSYPALIIDPKMPReGMFHHGVPIPVPPLEVLKLGEQMTQEArehLYLVLFFDNKRTWQWLPRTKL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 20129741 1379 DILGIDKQLDQQKLVESRKPAERKAVKKAYQDALHYQSQV 1418
Cdd:cd20156   81 VPLGVNQDLDKEKMLEGRKSNIRKSVQIAYHRAMQHRNKV 120

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 20129741  340 CVLCPNAGGAFKQ------TDHGQWAHVVCALWIPEVRFANTVFLEPIDsIETIPPARWRLTCYVCKEKGlGACIQCHRN 413
Cdd:cd15571    1 CALCPRSGGALKGggalktTSDGLWVHVVCALWSPEVYFDDGTLLEVEG-VSKIPKRRKKLKCSICGKRG-GACIQCSYP 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 20129741  414 SCYAAFHVTCAQQAGLYMTMDTvkdghndssMHVQKFAYCHAH 456
Cdd:cd15571   79 GCPRSFHVSCAIRAGCLFEFED---------GPGNFVVYCPKH 112

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741    360 HVVCALWIPEVRFANTVFL-EPIDSIETIPPARWRLTCYVCKEKGlGACIQCHRNSCYAAFHVTCAQQAGLYMTMDtvkd 438
Cdd:pfam13771    1 HVVCALWSPELVQRGNDSMgFPIEDIEKIPKRRWKLKCYLCKKKG-GACIQCSKKNCRRAFHVTCALEAGLLMQFD---- 75

                           90
                   ....*....|....*...
gi 20129741    439 ghndsSMHVQKFAYCHAH 456
Cdd:pfam13771   76 -----EDNGTFKSYCKKH 88

PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; BRPF1, also termed peregrin or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains 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. BRPF1 may be involved in chromatin remodeling. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 20129741  280 VDDDAVCCICLDGECQNTNVILFCDMCNLAVHQDCYGVPYIPEGQWLCRRCLQSPSKPV 338
Cdd:cd15676    4 IDEDAVCCICNDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRCLQSPSRAV 62

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 20129741  340 CVLCPNAGGAFKQTDHGQWAHVVCALWIPEVRFANTVFLEPIdSIETIPPARWRLTCYVCKEKG------LGACIQCHRN 413
Cdd:cd15672    1 CELCPHKDGALKRTDNGGWAHVVCALYIPEVRFGNVATMEPI-ILQDVPQDRFNKTCYICEEQGreskasTGACMQCNKS 79

                         90       100
                 ....*....|....*....|....*....
gi 20129741  414 SCYAAFHVTCAQQAGLY-----MTMDTVK 437
Cdd:cd15672   80 GCKQSFHVTCAQMAGLLceeagNYSDNVK 108

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  340 CVLCPNAGGAFKQTDHGQWAHVVCALWIPEVRFANTVFLEPIDSIETIPPARWRLTCYVCKEKgLGACIQCHRNSCYAAF 419
Cdd:cd15662    1 CCLCPVVGGALKPTTDGRWAHLACAIWIPETCLLDVKTMEPVDGINAISKERWELSCTICKQR-YGACIQCSNNSCRVAY 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 20129741  420 HVTCAQQAGLYMTMdTVKDGHNDSSMHVQKFAYCHAH 456
Cdd:cd15662   80 HPLCARAAGLCMEV-ADEGGEDPGDQGLRLLSYCPRH 115

Extended PHD finger found in protein AF-10 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10. 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 human counterpart of the 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-10 contains an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  338 VNCVLCPNAGGAFKQTDHGQWAHVVCALWIPEVRFANTVFLEPIdSIETIPPARWRLTCYVCKEKG------LGACIQCH 411
Cdd:cd15708    3 VRCELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVSTMEPI-VLQSVPHERYNKTCYICDEQGreskaaTGACMTCN 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 20129741  412 RNSCYAAFHVTCAQQAGLymtmdtVKDGHNDSSMHVQKFAYCHAH 456
Cdd:cd15708   82 KHGCRQAFHVTCAQLAGL------LCEEEGNGADNVQYCGYCKYH 120

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 20129741  340 CVLCPNAGGAFKQTDHGQWAHVVCALWIPEVRFANTVFLEPIdSIETIPPARW-RLTCYVCKEKGL---GACIQCHRNSC 415
Cdd:cd15674    1 CELCPNRGGIFKETDTGRWVHLVCALYTPGVAFGDVDKLSPV-TLTEMNYSKWgARECSLCEDPRFartGVCISCDAGMC 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 20129741  416 YAAFHVTCAQQAGLymtmdtVKDGHNDSSMHVQKFAYCHAH 456
Cdd:cd15674   80 KSYFHVTCAQREGL------LSEATDEEDIADPFYAYCKQH 114

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20129741  340 CVLCPNAGGAFKQTDHG-QWAHVVCALWIPEVRFANTVFLEPIDSIETIPPARWRLTCYVCKEKGlGACIQCHRNSCYAA 418
Cdd:cd15705    1 CLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECT-GTCIQCSMPSCITA 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 20129741  419 FHVTCAQQAGLYMTMdTVKDghNDssmHVQKFAYCHAH 456
Cdd:cd15705   80 FHVTCAFDHGLEMRT-TLAD--ND---EVKFKSFCLEH 111