ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ARID1B and similar proteins; This subfamily contains ARID1A and its paralog ARID1B. They are mutually exclusive components of human SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complexes, but display different functions in development and cell-cycle control. SWI/SNF complexes containing ARID1A have an antiproliferative function, whereas the one harboring ARID1B shows a pro-proliferative function. ARID1A functions as an important tumor suppressor in various tumor types. It has been implicated in cell-cycle arrest, as well as in the interactions with p53 and BRG1/BRM and with topoisomerase II alpha. ARID1B may be considered as a potential therapeutic target for ARID1A-mutant cancers. Moreover, mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Mutations in the ARID1B gene also have been found in many cancers. Both ARID1A and ARID1B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  317 AERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANPDlaESSAAGYQLRKH 396
Cdd:cd16865     1 PERRPFLDRLLRFMEERGSPITNCPQISKQPLDLFRLYVTVKERGGVAEVTKNKKWKEICTELNIG--ASSSAAFTLRKN 78

                          90
                  ....*....|....*
gi 808354853  397 YQRHLLMLECRETGR 411
Cdd:cd16865    79 YIKYLLAYECRFDRG 93

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  598 PAPSTTPAPQAASSSQAAPT---SGANTQPATPSASNQPPTPASAS--ASTTLHVEPASVAG-GSQAGSRAPSAGPGPSA 671
Cdd:PHA03247 2704 PPPTPEPAPHALVSATPLPPgpaAARQASPALPAAPAPPAVPAGPAtpGGPARPARPPTTAGpPAPAPPAAPAAGPPRRL 2783

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  672 TPDSSTIPSASAAA------DAQTTTSSETSTPGEPTSSTPSDTPAPSTSVPPPTSVQPPQPQQPPQGPPGPPGPQQHPG 745
Cdd:PHA03247 2784 TRPAVASLSESRESlpspwdPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVR 2863

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  746 PYPGYPGYGPPGAMRPPAGFAPPPGAPYGYPPGAPPPAGFHPSHPQHPQHAQylawqqqryhqqQQHQQQQQQGAPGGPR 825
Cdd:PHA03247 2864 RRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPP------------PPQPQPQPPPPPQPQP 2931

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 808354853  826 PPYPYPGGPVPPGPPQNRMPPPPPAQGAPSPSGAAGSNGKQPRYGTPAPPSRASAPTPQPLSST 889
Cdd:PHA03247 2932 PPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPP 2995

ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ARID1B and similar proteins; This subfamily contains ARID1A and its paralog ARID1B. They are mutually exclusive components of human SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complexes, but display different functions in development and cell-cycle control. SWI/SNF complexes containing ARID1A have an antiproliferative function, whereas the one harboring ARID1B shows a pro-proliferative function. ARID1A functions as an important tumor suppressor in various tumor types. It has been implicated in cell-cycle arrest, as well as in the interactions with p53 and BRG1/BRM and with topoisomerase II alpha. ARID1B may be considered as a potential therapeutic target for ARID1A-mutant cancers. Moreover, mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Mutations in the ARID1B gene also have been found in many cancers. Both ARID1A and ARID1B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  317 AERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANPDlaESSAAGYQLRKH 396
Cdd:cd16865     1 PERRPFLDRLLRFMEERGSPITNCPQISKQPLDLFRLYVTVKERGGVAEVTKNKKWKEICTELNIG--ASSSAAFTLRKN 78

                          90
                  ....*....|....*
gi 808354853  397 YQRHLLMLECRETGR 411
Cdd:cd16865    79 YIKYLLAYECRFDRG 93

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853   318 ERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANPDlAESSAAGYQLRKHY 397
Cdd:pfam01388    1 EKELFLKSLRKFHEKRGTPLKQIPVIGGKPVDLYKLYKAVQKLGGYDKVTEKNLWREVAEKLGFP-PSAASAATQLKQIY 79

                   ....*...
gi 808354853   398 QRHLLMLE 405
Cdd:pfam01388   80 EKYLLPYE 87

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853   596 STPAPSTTPAPQAASSSQAAPTSGANTQPA--TPSASNQPPTPASASASTTLHVEPASVAggsqagSRAPSAGpGPSATP 673
Cdd:pfam17823   98 SEPATREGAADGAASRALAAAASSSPSSAAqsLPAAIAALPSEAFSAPRAAACRANASAA------PRAAIAA-ASAPHA 170

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 808354853   674 DSSTIPSASAAADAQTTTSSETSTPGEPTSSTPSD-TPAPSTS 715
Cdd:pfam17823  171 ASPAPRTAASSTTAASSTTAASSAPTTAASSAPATlTPARGIS 213

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  598 PAPSTTPAPQAASSSQAAPT---SGANTQPATPSASNQPPTPASAS--ASTTLHVEPASVAG-GSQAGSRAPSAGPGPSA 671
Cdd:PHA03247 2704 PPPTPEPAPHALVSATPLPPgpaAARQASPALPAAPAPPAVPAGPAtpGGPARPARPPTTAGpPAPAPPAAPAAGPPRRL 2783

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  672 TPDSSTIPSASAAA------DAQTTTSSETSTPGEPTSSTPSDTPAPSTSVPPPTSVQPPQPQQPPQGPPGPPGPQQHPG 745
Cdd:PHA03247 2784 TRPAVASLSESRESlpspwdPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVR 2863

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  746 PYPGYPGYGPPGAMRPPAGFAPPPGAPYGYPPGAPPPAGFHPSHPQHPQHAQylawqqqryhqqQQHQQQQQQGAPGGPR 825
Cdd:PHA03247 2864 RRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPP------------PPQPQPQPPPPPQPQP 2931

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 808354853  826 PPYPYPGGPVPPGPPQNRMPPPPPAQGAPSPSGAAGSNGKQPRYGTPAPPSRASAPTPQPLSST 889
Cdd:PHA03247 2932 PPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPP 2995

ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ARID1B and similar proteins; This subfamily contains ARID1A and its paralog ARID1B. They are mutually exclusive components of human SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complexes, but display different functions in development and cell-cycle control. SWI/SNF complexes containing ARID1A have an antiproliferative function, whereas the one harboring ARID1B shows a pro-proliferative function. ARID1A functions as an important tumor suppressor in various tumor types. It has been implicated in cell-cycle arrest, as well as in the interactions with p53 and BRG1/BRM and with topoisomerase II alpha. ARID1B may be considered as a potential therapeutic target for ARID1A-mutant cancers. Moreover, mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Mutations in the ARID1B gene also have been found in many cancers. Both ARID1A and ARID1B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  317 AERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANPDlaESSAAGYQLRKH 396
Cdd:cd16865     1 PERRPFLDRLLRFMEERGSPITNCPQISKQPLDLFRLYVTVKERGGVAEVTKNKKWKEICTELNIG--ASSSAAFTLRKN 78

                          90
                  ....*....|....*
gi 808354853  397 YQRHLLMLECRETGR 411
Cdd:cd16865    79 YIKYLLAYECRFDRG 93

ARID/BRIGHT DNA binding domain; Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853    318 ERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANPDLAESSaAGYQLRKHY 397
Cdd:smart01014    2 ERELFLDRLRKFMEKRGTPLDKIPVIGGKPLDLYRLYRAVQKRGGFDKVTKKKKWKQVARELGIPPSATS-AGTSLRKHY 80

                    ....*...
gi 808354853    398 QRHLLMLE 405
Cdd:smart01014   81 EKYLLPYE 88

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  318 ERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANPDLAESSAAgYQLRKHY 397
Cdd:cd16100     1 EREEFLEQLRAFLESRGTPLLKPPTIGGKPLDLYKLYRAVVSRGGYEKVTEKKLWKEVARKLGLPTSSTSAA-QALKRIY 79

                  ....*
gi 808354853  398 QRHLL 402
Cdd:cd16100    80 EKYLL 84

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins; ARID1A, also called B120, BRG1-associated factor 250a (BAF250A), Osa homolog 1(OSA1), SWI-like protein, SWI/SNF complex protein p270, or SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1 (SWI1), has been identified as a novel tumor suppressor in various tumor types. It interacts with BRG1 adenosine triphosphatase to form a SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complex, which plays a critical role in transcriptional control and gene expression. ARID1A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and Eld/Osa homology domains (EHD) 1 and 2 within the C-terminus. The ARID in ARID1A binds nonspecific DNA in general and plays an important role in targeting SWI/SNF to chromatin. The EHD1 may be capable of mediating an intramolecular association with EHD2, and/or an intermolecular association resulting in homo- or hetero-dimerization. The EHD2 binds Swi2/Brahma homologue Brahma-related gene 1 (BRG1, also known as Snf2b), a human homologue of yeast Swi2.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  318 ERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANpdLAESSAAGYQLRKHY 397
Cdd:cd16876     2 ERKMWVDRYLAFTEEKAMGMTNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLN--VGTSSSAASSLKKQY 79

                          90
                  ....*....|
gi 808354853  398 QRHLLMLECR 407
Cdd:cd16876    80 IQCLYAFECK 89

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  317 AERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWK------NLCTEANPDLAEssaag 390
Cdd:cd16871     1 AQPEQFMKSLREFMAKRGTPIEQQPVIGGRPVNLFRLYQLVQKLGGSRQVTQNNQWPrvaqklGFPPEQNPQVAQ----- 75

                          90
                  ....*....|....*
gi 808354853  391 yQLRKHYQRHLLMLE 405
Cdd:cd16871    76 -QLAQIYQRYLLPYE 89

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3B (ARID3B) and similar proteins; ARID3B, also called Bright and dead ringer protein, or Bright-Dri-like protein (Bdp), is a DNA binding protein involved in cellular immortalization, epithelial-mesenchymal transition (EMT), and tumorigenesis. Its expression is differentially regulated in normal and malignant tissues. It is required for heart development by regulating the motility and differentiation of heart progenitors. ARID3B is overexpressed in neuroblastoma and ovarian cancer. It acts as a novel target with roles in cell motility in breast cancer cells, promotes migration of mouse embryo fibroblasts (MEFs) and breast cancer cells, and induces tumor necrosis factor alpha (TNFalpha)-mediated apoptosis. ARID3B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  318 ERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANPDLAESSAAgYQLRKHY 397
Cdd:cd16879    14 KRKEFLDDLFAFMQKRGTPINRIPIMAKQVLDLYMLYKLVTEKGGLVEVINKKIWREITKGLNLPTSITSAA-FTLRTQY 92

                          90       100       110
                  ....*....|....*....|....*....|....
gi 808354853  398 QRHLLMLECRETGRNPEDEVAFADKMKRQRKREP 431
Cdd:cd16879    93 MKYLYPYECEKKSLSSPAELQAAIDGNRREGRRP 126

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  317 AERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANPDLAESSAAgYQLRKH 396
Cdd:cd16867    11 PKRKEFLDDLFSFMQKRGTPVNRIPIMAKQVLDLYELYRLVVEKGGLVEVINKKIWREITKGLNLPSSITSAA-FTLRTQ 89

                          90       100
                  ....*....|....*....|
gi 808354853  397 YQRHLLMLEC-RETGRNPED 415
Cdd:cd16867    90 YMKYLYPYECeKEKLSSPSE 109

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  318 ERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEAN-PDLAesSAAGYQLRKH 396
Cdd:cd16868     1 EKENFLEQLYKFMEDRGTPINKPPVLGYKDLDLFKLYKLVQELGGMERVSQGAKWRSIYQQLGiPVLN--SAASHNIKQA 78

                  ....*....
gi 808354853  397 YQRHLLMLE 405
Cdd:cd16868    79 YKKYLYAFE 87

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  318 ERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANPDLAESSAAgYQLRKHY 397
Cdd:cd16881    19 KRKEFLDDLFSFMQKRGTPVNRIPIMAKQVLDLYELYNLVVARGGLVEVINKKLWREITKGLHLPSSITSAA-FTLRTQY 97

                          90       100
                  ....*....|....*....|...
gi 808354853  398 QRHLLMLECRETGRNPEDEVAFA 420
Cdd:cd16881    98 MKYLYPYECEKLKLSTPAELQAA 120

DNA polymerase III subunit gamma/tau;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  599 APSTTPAPQAASSSQAAPTSGANTQPATPSASNQPPTPASASASTTLHVEPASVAGGSQAGSRAPSAGPGPSATPDSSti 678
Cdd:PRK12323  380 APVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAA-- 457

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 808354853  679 PSASAAADAQTTTSSETSTPGEPTSSTPSDTPAPST 714
Cdd:PRK12323  458 PAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPAD 493

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins; ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1, or RBBP1L1), is a tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating cell cycle. ARID4B contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  318 ERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEAN-PDLaeSSAAGYQLRKH 396
Cdd:cd16883     1 ERENFLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGiPVL--NSAAGYNVKCA 78

                  ....*....
gi 808354853  397 YQRHLLMLE 405
Cdd:cd16883    79 YRKYLYGFE 87

cytoskeleton protein RodZ;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  596 STPAPSTTPAPQAASSSQAAPTSGANTQ----PATPSASNQPPTPASASASTTLHVEPASVAgGSQAGSRAPSAGPGPSA 671
Cdd:PRK10856  168 TTTDPATTPAPAAPVDTTPTNSQTPAVAtapaPAVDPQQNAVVAPSQANVDTAATPAPAAPA-TPDGAAPLPTDQAGVST 246

                  ....*
gi 808354853  672 TPDSS 676
Cdd:PRK10856  247 PAADP 251

ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called cancer/testis antigen 31 (CT31), histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), 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 earlygene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as three plant homeodomain (PHD) fingers.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  322 FFERLIEFCEHNGEPLTmVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANpdLAESSAAGYQLRKHYQRHL 401
Cdd:cd16874    10 FLDQIAKFWELQGCTLK-IPHVERKILDLFQLNKLVAEEGGFDLVCKERKWTKIATKMG--FAPGKAVGSHIRAHYERIL 86

DNA polymerase III subunits gamma and tau; Validated

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  599 APSTTPAPQAASSSQAAPTSGANTQPATPSASNQPPTPA--SASASTTLHVEPASVAGGSQAGSRAPSAGPGPSATPDSS 676
Cdd:PRK07764  596 GGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAapAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGG 675

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 808354853  677 TIPSASAAADAQTTTSSETSTPGEPTSSTPSDTPAPSTS 715
Cdd:PRK07764  676 AAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQA 714

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) and similar proteins; ARID5B, also called MRF1-like protein or modulator recognition factor 2 (MRF-2), is a DNA-binding protein that directly interacts with plant homeodomain (PHD) finger 2 (PHF2) to form a protein kinase A (PKA)-dependent PHF2-ARID5B histone H3K9Me2 demethylase complex, which is a signal-sensing modulator of histone methylation and gene transcription. It also functions as a transcriptional co-regulator for the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) and promotes chondrogenesis through histone modification. Moreover, ARID5B is highly expressed in the cardiovascular system and may play essential roles in the phenotypic change of smooth muscle cells (SMCs) through its regulation of SMC differentiation. Its polymorphism has been associated with risk for pediatric acute lymphoblastic leukemia (ALL). ARID5B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which can bind both the major and minor grooves of its target sequences.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  318 ERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANPDLAESSAAGYQlRKHY 397
Cdd:cd16885     1 DEQAFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCT-RRHY 79

                  ....*...
gi 808354853  398 QRHLLMLE 405
Cdd:cd16885    80 ERLILPYE 87

Chitinase [Carbohydrate transport and metabolism];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  596 STPAPSTTPAPQAASSSQAAPTSGANTQPATPSASNQPPTPASASASTTLHVEPASVAGGSQAGSRAPSAGPGPSATPDS 675
Cdd:COG3469    78 TTATATAAAAAATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSGTE 157

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 808354853  676 STIPSASAAADAQTTTSSETSTPGEPTSSTPSDTPAPSTSVPPPTS-V 722
Cdd:COG3469   158 TATGGTTTTSTTTTTTSASTTPSATTTATATTASGATTPSATTTATtT 205

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins; ARID4A, also called retinoblastoma-binding protein 1 (RBBP1, or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B (also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC-dependent and -independent repression activities. It is also involved in the pocket domain of pRb-mediated repression of E2F-dependent transcription and cellular proliferation. Moreover, it acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  318 ERRGFFERLIEFCEHNGEPLTMVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEAN-PDLaeSSAAGYQLRKH 396
Cdd:cd16882     1 ERDNFLQQLYKFMEDRGTPINKPPVLGYKDLNLFKLFRLVYQQGGCDNIESGSVWKQIYMDLGiPIL--NSAASYNVKTA 78

                  ....*....
gi 808354853  397 YQRHLLMLE 405
Cdd:cd16882    79 YRKYLYGFE 87

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  322 FFERLIEFCEHNGEPLTmVPQVSKQSIDLHRLYIGVRAKGGFQQVTKDKYWKNLCTEANpdLAESSAAGYQLRKHYQRHL 401
Cdd:cd16875     7 YLDQIAKFWEIQGSSLK-IPNVERRILDLYSLSKIVQEEGGYEAICKDRRWARVAQRLG--YPPGKNIGSLLRSHYERII 83

                  ....*....
gi 808354853  402 LMLECRETG 410
Cdd:cd16875    84 YPYEMYQSG 92

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808354853  596 STPAPSTTPAPQAASSSQAAPTSGANTQPATPSASNQPPTPASASASTtlhvePASVAGGSQAGSRAPSAGPGPSATPDS 675
Cdd:PRK12270   42 AAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAA-----AAAAAAPAAPPAAAAAAAPAAAAVEDE 116

                          90
                  ....*....|...
gi 808354853  676 STIPSASAAADAQ 688
Cdd:PRK12270  117 VTPLRGAAAAVAK 129