Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775   820 DQIRQSVRHSLKDILMKRLTDSNlkipEEKSAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGE 899
Cdd:pfam07500    3 DKVRDKCRELLYDALAKDSTEAS----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGE 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 564367775   900 VTPDHLIRMSPEELASKELAAWRRRENRHTIEMI 933
Cdd:pfam07500   79 ISPEKLVTMSPEEMASEELKKEREKIEKEALKEA 112

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775  1795 GRQDQQQPDRPFNRGKGDRQRFYSDSHHLKRDR-HDKEWEQESERHRHRDRSQEKDRDRKSKEEAHKDKERPRLSHSDRA 1873
Cdd:TIGR01622    1 RYRDRERERLRDSSSAGDRDRRRDKGRERSRDRsRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYRPREKRRRRG 80

                           90
                   ....*....|....*...
gi 564367775  1874 ADGKANRESKSADKKPDR 1891
Cdd:TIGR01622   81 DSYRRRRDDRRSRREKPR 98

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775  1097 FLARLNFIWKGFINMPSVAKFVTKAYPVSGSPEYLtedLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEE 1176
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGVAEFSVRAHLVSGDIDSL---LPSLLRITGRIRLDAVWKYLDEVRRSITRDVLVVRFFPSSES 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564367775  1177 DQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAadkIPHPLVPFdGPGLELHRPNLLLGLIIRQ 1245
Cdd:pfam07744   78 DESAFDELIDYLQSKQRAGVIHAKSADVKDLYLFPPCE---FLELLLPV-GLSLEVSEPNLLLGVVVRK 142

Domain in the central regions of transcription elongation factor S-II (and elsewhere);

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775    824 QSVRHSLKDILMKRLTDSNLKIPEE-KSAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTP 902
Cdd:smart00510    1 DKVRDKCQEMLYKALQKISDPEEIElDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                            90       100
                    ....*....|....*....|..
gi 564367775    903 DHLIRMSPEELASKELAAWRRR 924
Cdd:smart00510   81 EKLATMTAEELASAELKEKREK 102

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775   761 RSSEEKSEKIAKDSAALTCAGEKAARSGTHEKQETKKKKveKGGPNVHPPAAAAIKPSADQIRQSVRHSLKDILMKRLTD 840
Cdd:TIGR01385   79 KSDHPGGNPEDKTTVGESVNSVKQEAKSQSDKIEQPKYV--SSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDH 156

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775   841 S-NLKIPEEKsakvATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELa 919
Cdd:TIGR01385  157 PpQSIDPEAK----AIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAEL- 231

                          170       180
                   ....*....|....*....|....*..
gi 564367775   920 awRRRENRHTIEMIEKEQREVERRPIT 946
Cdd:TIGR01385  232 --KQEREEITKENLFEAQGAKIQKAVT 256

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 564367775    611 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSqaqqMGEEDKEYVCIRC 660
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLL----EEEPDGKWYCPKC 47

MAEBL; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775  662 AEEDKKTDILDTETLETQASlEAHSEDKRVECGKLTSSSSKHSVTEDKHRHMD----DPGRHKVKIVKRDSGEGKTSSDS 737
Cdd:PTZ00121 1338 AEEAKKAAEAAKAEAEAAAD-EAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEkkkaDEAKKKAEEDKKKADELKKAAAA 1416

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775  738 RD--NEIKKwQLAPLRKLGQplLPRRSSEEKSEKIAKDSAALTCAGEKAARSGTHEKQ--ETKKKKVEKGGPNVHPPAAA 813
Cdd:PTZ00121 1417 KKkaDEAKK-KAEEKKKADE--AKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKadEAKKKAEEAKKADEAKKKAE 1493

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775  814 AIKPSADQIRQSVR-----HSLKDILMKRLTDSNLKIPEEKSAKVATKIEK-----ELFSFFRDTDAKYKNKYRSLMFNL 883
Cdd:PTZ00121 1494 EAKKKADEAKKAAEakkkaDEAKKAEEAKKADEAKKAEEAKKADEAKKAEEkkkadELKKAEELKKAEEKKKAEEAKKAE 1573

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775  884 KDPKNNILFKKVLKG--EVTPDHLIRMSPEELASKELAAWRRRENRHTIEMIEKEqrEVERRPITKITHKGEIEIESDAP 961
Cdd:PTZ00121 1574 EDKNMALRKAEEAKKaeEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKA--EEEKKKVEQLKKKEAEEKKKAEE 1651

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*.
gi 564367775  962 MKEQEAAMEIQEPSSANKSSEKPEASEKQKEELDSTSKDTTSQHRQ 1007
Cdd:PTZ00121 1652 LKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKE 1697

SPOC (Spen paralog and ortholog C-terminal) domain found in PHD finger protein 3 (PHF3), death-inducer obliterator (Dido) variants, and similar proteins; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. This group also includes the protein products of the Dido gene that encodes three alternative splicing variants (Dido1, 2, and 3), which have been implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. The Dido gene is a bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. This model corresponds to the SPOC domain of the PHF3-like group; the SPOC domain is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775 1104 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1183
Cdd:cd21541     1 VWKGFISMQEVAKFVASAYHVSGPCEDLSEDLPDTLEVCGRISPEQVWDYLSKLKQSGTKEIIVIRFHPANEEEKVSYIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564367775 1184 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRPNLLLGLIIR 1244
Cdd:cd21541    81 LYSYLSSRKRCGVVGNNSKHVKDMYLIPLASHQPIPQVLLPFDGPGLEETRPHMLLGIIVR 141

SPOC (Spen paralog and ortholog C-terminal) domain found in Drosophila melanogaster protein partner of Sans-fille and similar proteins; Drosophila melanogaster protein partner of Sans-fille (PPS), also called protein partner of Snf, is a homolog of human DIDO. It mediates diverse chromatin activities, including the regulation of stemness genes in embryonic stem cells and splicing. PPS associates with spliceosomal RNAs including the U1 snRNP protein Sans-fille (Snf) to mediate sex determination gene Sex-lethal (Sxl) splicing autoregulation. Alternative splicing of the Sxl pre-mRNA determines gender during development in Drosophila, producing protein-encoding mRNAs in females but yielding inactive and truncated mRNAs in males. PPS contains a plant homeodomain (PHD) finger, Brahma and Kismet (BRK), a transcription elongation factor S-II subunit M (TFSIIM) domain, and a SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775 1104 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1183
Cdd:cd22581     1 VWKGTINMPDVAKFNVSAQVVSGNSDDLSLDLPKVLDVVGRIAPETVWDYIGKLKKSPTKEIVVVRLTPASEEDEMSYNT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564367775 1184 LFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGL-ELHRPNLLLGLIIR 1244
Cdd:cd22581    81 FFEYLSSRNRLGVIGSVSKAIKDFYILPLPKESPIPEVLLPLDGPGLfENRRPNLLLGIIVR 142

SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II (TFIIS) family; The transcription factor S-II (TFIIS) family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling. SPOCD1 acts as a tumor-related factor that promotes cell proliferation and metastasis. Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). PHF3 is a human homolog of the yeast protein Bye1p. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. The Dido/DIDO1 gene is implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775 1104 IWKGFINMPSVAKFVTKAYPVSG---SPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTE-EDQI 1179
Cdd:cd21538     1 VWSGKLTMPGVASFPASARQVGGpdlSSTWWTDLLPSTLEIKGRIPLDKAEKYLCELRFSSSRDVVVVSLEPPDSsSDKA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564367775 1180 SYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIPHPLVPFDGPGLELHRP-NLLLGLIIR 1244
Cdd:cd21538    81 AFDELFDYFVSRDRYGVVGPKGLAVKDLYLVPLPAGDPLPPFLLLLDDGPGPEPRDeDLLLGVIVL 146

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775   820 DQIRQSVRHSLKDILMKRLTDSNlkipEEKSAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGE 899
Cdd:pfam07500    3 DKVRDKCRELLYDALAKDSTEAS----EEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGE 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 564367775   900 VTPDHLIRMSPEELASKELAAWRRRENRHTIEMI 933
Cdd:pfam07500   79 ISPEKLVTMSPEEMASEELKKEREKIEKEALKEA 112

PHD finger found in PHD finger protein 3 (PHF3); PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 564367775  610 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCIRC 660
Cdd:cd15638     1 QCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMEEEDKEYVCVKC 51

SPOC (Spen paralog and ortholog C-terminal) domain superfamily; The SPOC domain is involved in developmental signalling and has also been proposed to be a phosphorylation binding module. It has been found mainly in two protein families: transcription factor S-II (TFIIS) and Spen (split end). The TFIIS family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. The Spen protein family includes SMART/HDAC1-associated repressor protein (SHARP) and RNA binding motif protein 15 (RBM15)-like proteins from metazoans, as well as plant flowering time control protein FPA and yeast chromo domain-containing protein 1 (Chp1p). They are characterized by containing RNA recognition motifs (RRMs) and a SPOC domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775 1104 IWKGFINMPSVAKFVTKAYPVSGSPEYLTEDLPDSIQVGGRISPQTVWDYVEKIKASGTKEICVVRFTPVTEEDQISYTL 1183
Cdd:cd21520     1 VWQGLLALKNDPTAAARLHFVSGNNVLALSELPPVLRIAQRMRLNATQLEGVARRMAVATDYCLVLALPCGRDDESLKAA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564367775 1184 LFAYFSSRKRYGVAANnmkQVKDMYLIPLGAADKIPHPLVPF-DGPGLELHRPNLLLGLII 1243
Cdd:cd21520    81 FITYLQAKQRAGIASN---QPAYVLQLFPPCEFSESHLSRLApDLLASIVTISPHLMIVIL 138

PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family includes three alternative splicing variants (Dido1, 2, and 3) encoded by the Dido gene, which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1, also termed DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved plant homeodomain (PHD) finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). Gene Dido is a Bonemorphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, aspen paralog and ortholog (SPOC) module, and a long C-terminal region (CT) of unknown homology. Its PHD finger interacts with H3K4me3.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 564367775  607 PSKQCGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCIRC 660
Cdd:cd15639     1 PNALYCICRQPHNNRFMICCDRCEEWFHGDCVGITEARGRLLERNGEDYICPNC 54

SPOC (Spen paralog and ortholog C-terminal) domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p) and similar proteins; Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS. It plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. This model corresponds to the SPOC domain which is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775 1104 IWKGFINMPSV-AKFVTKAYPVSGS--------PEYLTEDLPDSIQVGGRISPQTVWDYVEKIKAsgTKEICVVRFTPVT 1174
Cdd:cd21542     1 VWKGTLEYPEInAEFSGKIKFVGSStklskqnvKEQQDALGDKKLEVEGRLSAETADKYLNQIMS--SRDLLVYELEPNE 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 564367775 1175 E-EDQISYTLLFAYFSSRKRYGVAANNMKQVKDMYLIPLGAADKIP 1219
Cdd:cd21542    79 SsEDKTNFDKLFDYLHSRERYGVLKNKPSYVKDAYLIPLSAGDKPP 124

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 564367775    611 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSqaqqMGEEDKEYVCIRC 660
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLL----EEEPDGKWYCPKC 47

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 564367775  611 CGFCKKPH-GNRFMVGCGRCDDWFHGDCVGLSLSqaqqMGEEDKEYVCIRC 660
Cdd:cd15489     2 CIVCGKGGdLGGELLQCDGCGKWFHADCLGPPLS----SFVPNGKWICPVC 48

PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 564367775  614 CKKPHGNRFMVGCGRCDDWFHGDCVglslsqaqQMGEEDKE----YVCIRC 660
Cdd:cd16039     4 CQKPDDGRWMIACDGCDEWYHFTCV--------NIPEADVElvdsFFCPPC 46

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 564367775  611 CGFCKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQaqqmgEEDKEYVCIRC 660
Cdd:cd15522     2 CPICKKPDDGSPMIGCDECDDWYHWECVGITDEP-----PEEDDWFCPKC 46

PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 564367775  614 CKKPHG-NRFMVGCGRCDDWFHGDCVGLSLSQA 645
Cdd:cd15640     4 CRQPYDvNRFMIECDICKDWFHGSCVQVEEHHA 36

PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 564367775  614 CKKPHGNrFMVGCGRCDDWFHGDCVGLSLSQAQQ-------MGEEDKEYVCIRC 660
Cdd:cd15606     4 CRKPFSG-FMLQCELCKDWFHSSCVPLPKSSSQKkggngsgQGAKELKFLCPLC 56

PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It contains a single plant homeodomain (PHD) finger followed by a catalytic SET domain. MLL5 can be recruited to E2F1-responsive promoters to stimulate H3K4 trimethylation and transcriptional activation by binding to the cell cycle regulator host cell factor (HCF-1), thereby facilitating the cell cycle G1 to S phase transition. It is also involved in mitotic fidelity and genomic integrity by modulating the stability of the chromosomal passenger complex (CPC) via the interaction with Borealin. Moreover, MLL5 is a component of a complex associated with retinoic acid receptor that requires GlcN Acylation of its SET domain in order to activate its histone lysine methyltransferase activity. It also participates in the camptothecin (CPT)-induced p53 activation. Furthermore, MLL5 indirectly regulates H3K4 methylation, represses cyclin A2 (CycA) expression, and promotes myogenic differentiation.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 564367775  611 CGFckkPHGNRFMVGCGRCDDWFHGDCVGLSlsqaQQMGEEDkeYVCIRC 660
Cdd:cd15550     4 CGF---EHDDGFMICCDKCSVWQHGDCMGID----RENIPDS--YLCEQC 44

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775  1813 RQRFYSDSHHLKRDRhDKEWEQESERHRHRDRSQEKDRDRKSKEEAHKDKERPR-----LSHSDRAADGKANRESKSADK 1887
Cdd:TIGR01642    1 RDEEPDREREKSRGR-DRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRdrrryDSRSPRSLRYSSVRRSRDRPR 79

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 564367775  1888 KPDRP--KGEDHEKEKEREKSKHREGEKDRERYHKDR 1922
Cdd:TIGR01642   80 RRSRSvrSIEQHRRRLRDRSPSNQWRKDDKKRSLWDI 116

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775  1824 KRDRhdkeweqESERHR----------HRDRSQEKDRDRKSKEEAHKDKERPRLSHSDRAADGKANRESKSADKKP-DRP 1892
Cdd:TIGR01622    2 YRDR-------ERERLRdsssagdrdrRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYrPRE 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 564367775  1893 KGEDHEKEKEREKSKHREG-EKDRERYHKDRDHTDRAKSKR 1932
Cdd:TIGR01622   75 KRRRRGDSYRRRRDDRRSRrEKPRARDGTPEPLTEDERDRR 115

PHD finger 3 found in lysine-specific demethylase 5B (KDM5B); KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 564367775  614 CKKPHGNRF-MVGC-GRCDDWFHGDCVGLSLSQAqqmgeEDKEYVCIRC 660
Cdd:cd15687     7 CLQPEGEEVdWVQCdGSCNRWFHQVCVGVSAEMA-----EKEDYICVSC 50

PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins; Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. The PHD domain binds to a histone H3 tail peptide containing trimethylated lysine 4 (H3K4me3). The TLD domain is responsible for the association with chromatin. Plant SIZ1 protein is a SUMO (small ubiquitin-related modifier) E3 ligase that facilitates conjugation of SUMO to substrate target proteins (sumoylation) and belongs to the protein inhibitor of activated STAT (PIAS) protein family. It negatively regulates abscisic acid (ABA) signaling, which is dependent on the bZIP transcripton factor ABI5. It also modulates plant growth and plays a role in drought stress response likely through the regulation of gene expression. SIZ1 functions as a floral repressor that not only represses the salicylic acid (SA)-dependent pathway, but also promotes FLOWERING LOCUS C (FLC) expression by repressing FLOWERING LOCUS D (FLD) activity through sumoylation. SIZ1 contains a PHD finger, which specifically binds methylated histone H3 at lysine 4 and arginine 2.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 564367775  614 CKKPHGNRFMVGCGRCDDWFHGDCVGLSLSQAQQMGEEDKEYVCIRC 660
Cdd:cd15570     4 CGSSMEDGSMIQCEGCKTWQHMDCVLIPDKPADGLPELPSKFYCELC 50

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 564367775  623 MVGCGRCDDWFHGDCVGLSLSQAQQMGE--EDKEYVCIRC 660
Cdd:cd15508    18 MMQCSQCDHWVHAKCEGLSDEMYEILSYlpESIEYTCSLC 57

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 564367775  613 FCKKPHGNrFMVGCGRCDDWFHGDCVGlslsQAQQMGEEDKEYVCIRC 660
Cdd:cd15518     3 FCRQGEGG-TMIECEICKEWYHVKCIK----NGRWKLDDDDKFVCPIC 45

PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A); KDM5A, also termed Histone demethylase JARID1A, or Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 564367775  614 CKKPHGNRF-MVGC-GRCDDWFHGDCVGLSLSQAqqmgeEDKEYVCIRC 660
Cdd:cd15686     8 CQRPCKDKVdWVQCdGGCDEWFHQVCVGVSPEMA-----ENEDYICINC 51

capsid maturational protease; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775  899 EVTPDHLIRMSPEELASKELAAWRRRE----NRHTIEMIE-----KEQREVERRPITKITHKGEIEIEsdapMKEQEAAM 969
Cdd:PHA03369  444 YVMPISMANMVYPGHPQEHGHERKRKRggelKEELIETLKlvkklKEEQESLAKELEATAHKSEIKKI----AESEFKNA 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367775  970 EIQEPSSANK-SSEKPEASEKQKEELDSTSKDTTSQHRQhlfdlncKICIGRMAPPVDDLSPKTVKVVVGGARkhSDNEA 1048
Cdd:PHA03369  520 GAKTAAANIEpNCSADAAAPATKRARPETKTELEAVVRF-------PYQIRNMESPAFVHSFTSTTLAAAAGQ--GSDTA 590

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 564367775 1049 ESIADALSSTTNIlASEFFEEEKQESP-----KSTFSPTPRPEMPGTVEVESTFLARL 1101
Cdd:PHA03369  591 EALAGAIETLLTQ-ASAQPAGLSLPAPavpvnASTPASTPPPLAPQEPPQPGTSAPSL 647

PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog protein, little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. The family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 564367775  622 FMVGCGRCDDWFHGDCVGLSLSQAQQMG----EEDKEYVCIRC 660
Cdd:cd15516    11 GMLQCELCQDWFHGSCVAVPRISSSPRPlawwEGDRKFLCPLC 53