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Conserved domains on  [gi|56549668|ref|NP_689854|]
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AT-rich interactive domain-containing protein 2 isoform 1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ARID_ARID2 cd16866
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and ...
 15-102 4.51e-56

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and similar proteins; ARID2, also called BRG1-associated factor 200 (BAF200) or zinc finger protein with activation potential (Zipzap/p200), is a novel serum response factor (SRF)-binding protein with multiple conserved domains, including an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), RFX DNA-binding domain, a glutamine-rich domain, and two C2H2 zinc fingers. It binds DNA without sequence specificity. ARID2 is an intrinsic subunit of PBAF (SWI/SNF-B) remodeling complex, which needs ARID2 to play an essential role in promoting osteoblast differentiation, maintaining cellular identity and activating tissue-specific gene expression. Moreover, ARID2 may function as a tumor suppressor in many cancers. It may also serve as a transcription co-activator for the regulation of cardiac gene expression, and is required for heart morphogenesis and coronary artery development.


:

Pssm-ID: 350630  Cd Length: 88  Bit Score: 189.01  E-value: 4.51e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   15 KGLAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYL 94
Cdd:cd16866    1 EYDAFLNELRQFHASRGTPFKKIPVVGGKELDLYLLYSKVTALGGWAKVTDKNKWEEILEDFNFPRGCSNAAFALKQIYL 80


                 ....*...
gi 56549668   95 RYLEKYEK 102
Cdd:cd16866   81 RYLEAYEK 88
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 521-603 4.30e-31

RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer. It recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD).


:

Pssm-ID: 460512  Cd Length: 79  Bit Score: 117.27  E-value: 4.30e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668    521 EKFACQWLNAHFEVNPDCSVSRAEMYSEYLSTCSKLARgGILTSTGFYKCLRTVFPNHTVKRVEdssSNGQAHIHVVGVK 600
Cdd:pfam02257    1 QVFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGI-KPLNAASFGKLIRQVFPNLKTRRLG---TRGQSKYHYCGIR 76


                   ...
gi 56549668    601 RRA 603
Cdd:pfam02257   77 LKA 79
SP1-4_N super family cl41773
N-terminal domain of transcription factor Specificity Proteins (SP) 1-4; Specificity Proteins ...
 663-1152 4.19e-08

N-terminal domain of transcription factor Specificity Proteins (SP) 1-4; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. SPs belong to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP1-4.


The actual alignment was detected with superfamily member cd22540:

Pssm-ID: 425404 [Multi-domain]  Cd Length: 511  Bit Score: 58.01  E-value: 4.19e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  663 TATQMSFPvQGVHTVAQTVSRIPQNP-----SPHTHQQQNAPVTVIQSKAPIPCEVVKAtvIQNSIPQTGVPVSIavggg 737
Cdd:cd22540   17 STTQDSQP-SPLALLAATCSKIGPPAveaavTPPAPPQPTPRKLVPIKPAPLPLGPGKN--SIGFLSAKGNIIQL----- 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  738 pPQSSVVQNHSTGPQPVTVVNSQTLLHHPSVIPQQSPLHTVVPG-QIPSGTPVTVIQQAVPqshmfGRVQNI---PACTS 813
Cdd:cd22540   89 -QGSQLSSSAPGGQQVFAIQNPTMIIKGSQTRSSTNQQYQISPQiQAAGQINNSGQIQIIP-----GTNQAIitpVQVLQ 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  814 TVSQGQQLITTSPQPVQTSsQQTSAGSQSQDTVIiappqyVTTSASNIVSATSVQNFQVA--TGQMVTIAGVPSPQASRV 891
Cdd:cd22540  163 QPQQAHKPVPIKPAPLQTS-NTNSASLQVPGNVI------KLQSGGNVALTLPVNNLVGTqdGATQLQLAAAPSKPSKKI 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  892 GFQ--NIAPKPLPSQQVSSTVVQQPIQQPQQPTQQSVVIVSQPaqqGQTYAPAIHQIVLANPAALPagQTVQLTGQPnit 969
Cdd:cd22540  236 RKKsaQAAQPAVTVAEQVETVLIETTADNIIQAGNNLLIVQSP---GTGQPAVLQQVQVLQPKQEQ--QVVQIPQQA--- 307

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  970 pSSSPSPVPATNNQVPTamSSSSTPQSQGPPPTVSQMLSVKRQ-----QQQQHSPAPPPQQVQVQVQQPQQVQmqvqpqq 1044
Cdd:cd22540  308 -LRVVQAASATLPTVPQ--KPLQNIQIQNSEPTPTQVYIKTPSgevqtVLLQEAPAATATPSSSTSTVQQQVT------- 377

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668 1045 SNAGVGQPASGeSSLIKQLLLPKRGPStpGGKLILPAPQIpppnnarAPSPQVVYQVASNqaaGFGVQGQTPAQQLLVGQ 1124
Cdd:cd22540  378 ANNGTGTSKPN-YNVRKERTLPKIAPA--GGIISLNAAQL-------AAAAQAIQTININ---GVQVQGVPVTITNAGGQ 444

                        490       500
                 ....*....|....*....|....*...
gi 56549668 1125 QNvqlvpsamppsGGVQTVPISNLQILP 1152
Cdd:cd22540  445 QQ-----------LTVQTVSSNNLTISG 461
 
Name Accession Description Interval E-value
ARID_ARID2 cd16866
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and ...
 15-102 4.51e-56

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and similar proteins; ARID2, also called BRG1-associated factor 200 (BAF200) or zinc finger protein with activation potential (Zipzap/p200), is a novel serum response factor (SRF)-binding protein with multiple conserved domains, including an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), RFX DNA-binding domain, a glutamine-rich domain, and two C2H2 zinc fingers. It binds DNA without sequence specificity. ARID2 is an intrinsic subunit of PBAF (SWI/SNF-B) remodeling complex, which needs ARID2 to play an essential role in promoting osteoblast differentiation, maintaining cellular identity and activating tissue-specific gene expression. Moreover, ARID2 may function as a tumor suppressor in many cancers. It may also serve as a transcription co-activator for the regulation of cardiac gene expression, and is required for heart morphogenesis and coronary artery development.


Pssm-ID: 350630  Cd Length: 88  Bit Score: 189.01  E-value: 4.51e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   15 KGLAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYL 94
Cdd:cd16866    1 EYDAFLNELRQFHASRGTPFKKIPVVGGKELDLYLLYSKVTALGGWAKVTDKNKWEEILEDFNFPRGCSNAAFALKQIYL 80


                 ....*...
gi 56549668   95 RYLEKYEK 102
Cdd:cd16866   81 RYLEAYEK 88
ARID pfam01388
ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, ...
 17-101 2.03e-35

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


Pssm-ID: 460187  Cd Length: 87  Bit Score: 130.05  E-value: 2.03e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668     17 LAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRY 96
Cdd:pfam01388    3 ELFLKSLRKFHEKRGTPLKQIPVIGGKPVDLYKLYKAVQKLGGYDKVTEKNLWREVAEKLGFPPSAASAATQLKQIYEKY 82


                   ....*
gi 56549668     97 LEKYE 101
Cdd:pfam01388   83 LLPYE 87
ARID smart01014
ARID/BRIGHT DNA binding domain; Members of the recently discovered ARID (AT-rich interaction ...
 14-101 1.51e-31

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.


Pssm-ID: 198082 [Multi-domain]  Cd Length: 88  Bit Score: 118.87  E-value: 1.51e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668      14 RKGLAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYY 93
Cdd:smart01014    1 RERELFLDRLRKFMEKRGTPLDKIPVIGGKPLDLYRLYRAVQKRGGFDKVTKKKKWKQVARELGIPPSATSAGTSLRKHY 80


                    ....*...
gi 56549668      94 LRYLEKYE 101
Cdd:smart01014   81 EKYLLPYE 88
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 521-603 4.30e-31

RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer. It recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD).


Pssm-ID: 460512  Cd Length: 79  Bit Score: 117.27  E-value: 4.30e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668    521 EKFACQWLNAHFEVNPDCSVSRAEMYSEYLSTCSKLARgGILTSTGFYKCLRTVFPNHTVKRVEdssSNGQAHIHVVGVK 600
Cdd:pfam02257    1 QVFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGI-KPLNAASFGKLIRQVFPNLKTRRLG---TRGQSKYHYCGIR 76


                   ...
gi 56549668    601 RRA 603
Cdd:pfam02257   77 LKA 79
SP2_N cd22540
N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins ...
 663-1152 4.19e-08

N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP2 contains the least conserved DNA-binding domain within the SP subfamily of proteins, and its DNA sequence specificity differs from the other SP proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate, or in some cases, repress expression from different promoters. The transcription factor SP2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. SP2 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP2.


Pssm-ID: 411776 [Multi-domain]  Cd Length: 511  Bit Score: 58.01  E-value: 4.19e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  663 TATQMSFPvQGVHTVAQTVSRIPQNP-----SPHTHQQQNAPVTVIQSKAPIPCEVVKAtvIQNSIPQTGVPVSIavggg 737
Cdd:cd22540   17 STTQDSQP-SPLALLAATCSKIGPPAveaavTPPAPPQPTPRKLVPIKPAPLPLGPGKN--SIGFLSAKGNIIQL----- 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  738 pPQSSVVQNHSTGPQPVTVVNSQTLLHHPSVIPQQSPLHTVVPG-QIPSGTPVTVIQQAVPqshmfGRVQNI---PACTS 813
Cdd:cd22540   89 -QGSQLSSSAPGGQQVFAIQNPTMIIKGSQTRSSTNQQYQISPQiQAAGQINNSGQIQIIP-----GTNQAIitpVQVLQ 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  814 TVSQGQQLITTSPQPVQTSsQQTSAGSQSQDTVIiappqyVTTSASNIVSATSVQNFQVA--TGQMVTIAGVPSPQASRV 891
Cdd:cd22540  163 QPQQAHKPVPIKPAPLQTS-NTNSASLQVPGNVI------KLQSGGNVALTLPVNNLVGTqdGATQLQLAAAPSKPSKKI 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  892 GFQ--NIAPKPLPSQQVSSTVVQQPIQQPQQPTQQSVVIVSQPaqqGQTYAPAIHQIVLANPAALPagQTVQLTGQPnit 969
Cdd:cd22540  236 RKKsaQAAQPAVTVAEQVETVLIETTADNIIQAGNNLLIVQSP---GTGQPAVLQQVQVLQPKQEQ--QVVQIPQQA--- 307

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  970 pSSSPSPVPATNNQVPTamSSSSTPQSQGPPPTVSQMLSVKRQ-----QQQQHSPAPPPQQVQVQVQQPQQVQmqvqpqq 1044
Cdd:cd22540  308 -LRVVQAASATLPTVPQ--KPLQNIQIQNSEPTPTQVYIKTPSgevqtVLLQEAPAATATPSSSTSTVQQQVT------- 377

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668 1045 SNAGVGQPASGeSSLIKQLLLPKRGPStpGGKLILPAPQIpppnnarAPSPQVVYQVASNqaaGFGVQGQTPAQQLLVGQ 1124
Cdd:cd22540  378 ANNGTGTSKPN-YNVRKERTLPKIAPA--GGIISLNAAQL-------AAAAQAIQTININ---GVQVQGVPVTITNAGGQ 444

                        490       500
                 ....*....|....*....|....*...
gi 56549668 1125 QNvqlvpsamppsGGVQTVPISNLQILP 1152
Cdd:cd22540  445 QQ-----------LTVQTVSSNNLTISG 461
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 694-843 2.05e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.30  E-value: 2.05e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668    694 QQQNAPVTVIQSKAPIPCE--VVKATVIQNSIPQTGVPvSIAVGGGPPQSSVVQNHSTGPQPVTVVNSQTLLHHPSVIPQ 771
Cdd:pfam03154  167 LQTQPPVLQAQSGAASPPSppPPGTTQAATAGPTPSAP-SVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSP 245

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668    772 QSPLHTVVPGQIPSGTPVtviqQAVPQSHMFGRVQNIP-------------------ACTSTVSQGQQLITTSPQ-PVQT 831
Cdd:pfam03154  246 HPPLQPMTQPPPPSQVSP----QPLPQPSLHGQMPPMPhslqtgpshmqhpvppqpfPLTPQSSQSQVPPGPSPAaPGQS 321

                          170
                   ....*....|..
gi 56549668    832 SSQQTSAGSQSQ 843
Cdd:pfam03154  322 QQRIHTPPSQSQ 333
PHA03247 PHA03247
large tegument protein UL36; Provisional
 626-1097 3.55e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 45.70  E-value: 3.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   626 SVPDVSPAPSPAGIPHGSQtignhfQRTPVANQSSNLTATQM----SFPVQGVHTVAQTVSRIPQNPSPHTHQQQNAPVT 701
Cdd:PHA03247 2567 SVPPPRPAPRPSEPAVTSR------ARRPDAPPQSARPRAPVddrgDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDP 2640

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   702 VIQSKAPIPCEVVKATviqnSIPQTGVPVSIAVGGGPPQSSVVQNHSTGPQPVTVVNSQTLLHHPsviPQQSPLHTVVPG 781
Cdd:PHA03247 2641 HPPPTVPPPERPRDDP----APGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADP---PPPPPTPEPAPH 2713

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   782 QIPSGTPVTVIQQAVPQSHMFGRVQNIPACTSTVSQGQQLITTSPQPVQTSSQQTSAGSQSQdtviIAPPQYVTTSASNI 861
Cdd:PHA03247 2714 ALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAP----AAGPPRRLTRPAVA 2789

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   862 VSATSVQNFQVATGQMVTIAGVPSPQASRVGFQNIAP--KPLPSQQVSSTVVQQPIQQPQQPTQQSVVIVSQPAQQGQTY 939
Cdd:PHA03247 2790 SLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGplPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSR 2869

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   940 APAihqivlANPAAlPAGQTVQLTGQPNITPSSSPSPVPATNNQVPTAMSSSSTPQSQGPPPTVSQMLSVKRQQQQQHSP 1019
Cdd:PHA03247 2870 SPA------AKPAA-PARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPP 2942

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  1020 APPPQQVqvqvqqpqqvqmqvqpqqsnAGVGQPASGESSLIKQLLLPKRGPS----TPGGKLILPAPQIPPPNNARAPSP 1095
Cdd:PHA03247 2943 LAPTTDP--------------------AGAGEPSGAVPQPWLGALVPGRVAVprfrVPQPAPSREAPASSTPPLTGHSLS 3002


                  ..
gi 56549668  1096 QV 1097
Cdd:PHA03247 3003 RV 3004
 
Name Accession Description Interval E-value
ARID_ARID2 cd16866
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and ...
 15-102 4.51e-56

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and similar proteins; ARID2, also called BRG1-associated factor 200 (BAF200) or zinc finger protein with activation potential (Zipzap/p200), is a novel serum response factor (SRF)-binding protein with multiple conserved domains, including an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), RFX DNA-binding domain, a glutamine-rich domain, and two C2H2 zinc fingers. It binds DNA without sequence specificity. ARID2 is an intrinsic subunit of PBAF (SWI/SNF-B) remodeling complex, which needs ARID2 to play an essential role in promoting osteoblast differentiation, maintaining cellular identity and activating tissue-specific gene expression. Moreover, ARID2 may function as a tumor suppressor in many cancers. It may also serve as a transcription co-activator for the regulation of cardiac gene expression, and is required for heart morphogenesis and coronary artery development.


Pssm-ID: 350630  Cd Length: 88  Bit Score: 189.01  E-value: 4.51e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   15 KGLAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYL 94
Cdd:cd16866    1 EYDAFLNELRQFHASRGTPFKKIPVVGGKELDLYLLYSKVTALGGWAKVTDKNKWEEILEDFNFPRGCSNAAFALKQIYL 80


                 ....*...
gi 56549668   95 RYLEKYEK 102
Cdd:cd16866   81 RYLEAYEK 88
ARID pfam01388
ARID/BRIGHT DNA binding domain; This domain is know as ARID for AT-Rich Interaction Domain, ...
 17-101 2.03e-35

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


Pssm-ID: 460187  Cd Length: 87  Bit Score: 130.05  E-value: 2.03e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668     17 LAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRY 96
Cdd:pfam01388    3 ELFLKSLRKFHEKRGTPLKQIPVIGGKPVDLYKLYKAVQKLGGYDKVTEKNLWREVAEKLGFPPSAASAATQLKQIYEKY 82


                   ....*
gi 56549668     97 LEKYE 101
Cdd:pfam01388   83 LLPYE 87
ARID smart01014
ARID/BRIGHT DNA binding domain; Members of the recently discovered ARID (AT-rich interaction ...
 14-101 1.51e-31

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.


Pssm-ID: 198082 [Multi-domain]  Cd Length: 88  Bit Score: 118.87  E-value: 1.51e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668      14 RKGLAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYY 93
Cdd:smart01014    1 RERELFLDRLRKFMEKRGTPLDKIPVIGGKPLDLYRLYRAVQKRGGFDKVTKKKKWKQVARELGIPPSATSAGTSLRKHY 80


                    ....*...
gi 56549668      94 LRYLEKYE 101
Cdd:smart01014   81 EKYLLPYE 88
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 521-603 4.30e-31

RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer. It recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD).


Pssm-ID: 460512  Cd Length: 79  Bit Score: 117.27  E-value: 4.30e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668    521 EKFACQWLNAHFEVNPDCSVSRAEMYSEYLSTCSKLARgGILTSTGFYKCLRTVFPNHTVKRVEdssSNGQAHIHVVGVK 600
Cdd:pfam02257    1 QVFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGI-KPLNAASFGKLIRQVFPNLKTRRLG---TRGQSKYHYCGIR 76


                   ...
gi 56549668    601 RRA 603
Cdd:pfam02257   77 LKA 79
BRIGHT smart00501
BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a ...
 14-106 1.11e-30

BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structure


Pssm-ID: 128777 [Multi-domain]  Cd Length: 93  Bit Score: 116.61  E-value: 1.11e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668      14 RKGLAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYY 93
Cdd:smart00501    1 RERVLFLDRLYKFMEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHY 80

                            90
                    ....*....|...
gi 56549668      94 LRYLEKYEKVHHF 106
Cdd:smart00501   81 ERYLLPYERFLRG 93
ARID cd16100
ARID/BRIGHT DNA binding domain family; The AT-rich interaction domain (ARID) family of ...
 17-101 9.63e-30

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.


Pssm-ID: 350627  Cd Length: 87  Bit Score: 113.99  E-value: 9.63e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   17 LAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRY 96
Cdd:cd16100    3 EEFLEQLRAFLESRGTPLLKPPTIGGKPLDLYKLYRAVVSRGGYEKVTEKKLWKEVARKLGLPTSSTSAAQALKRIYEKY 82


                 ....*
gi 56549668   97 LEKYE 101
Cdd:cd16100   83 LLPFE 87
ARID_HMGB9-like cd16872
ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, ...
 19-101 2.67e-22

ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, HMGB10, HMGB11, HMGB15 and similar proteins; This subfamily includes a group of conserved plant DNA-binding proteins, including HMGB9 (or ARID-HMG1), HMGB10 (or ARID-HMG2), HMGB11, and HMGB15. They have been termed ARID-HMG proteins, due to containing two DNA-binding domains, an N-terminal AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and a C-terminal high mobility group (HMG)-box domain. They are widely expressed in Arabidopsis and localize primarily to the nucleus. HMGB9/ARID-HMG1 binds specifically to A/T-rich DNA. HMGB15 is a transcription factor predominantly expressed in mature pollen grains and pollen tubes. It may work in the form of a homodimer, or interact with HMGB9, HMGB10 and HMGB11 to form heteromultimers in plant cells. HMGB15 is required for pollen tube growth in Arabidopsis and is involved in transcriptional regulation through the interaction with AGL66 and AGL104.


Pssm-ID: 350636  Cd Length: 86  Bit Score: 92.71  E-value: 2.67e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   19 FLDELRQFHHSRGSPFKkIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRYLE 98
Cdd:cd16872    5 FWETLRKFHESLGTKFR-IPIVGGKELDLHRLYKEVTSRGGLEKVIKDRKWKEVAAVFNFPPTITNASFVLRKYYLSLLH 83


                 ...
gi 56549668   99 KYE 101
Cdd:cd16872   84 HYE 86
ARID_ARID1A-like cd16865
ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ...
 12-101 8.09e-19

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.


Pssm-ID: 350629  Cd Length: 93  Bit Score: 83.10  E-value: 8.09e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   12 ERRkglAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRScSNAAFALKQ 91
Cdd:cd16865    2 ERR---PFLDRLLRFMEERGSPITNCPQISKQPLDLFRLYVTVKERGGVAEVTKNKKWKEICTELNIGAS-SSAAFTLRK 77

                         90
                 ....*....|
gi 56549668   92 YYLRYLEKYE 101
Cdd:cd16865   78 NYIKYLLAYE 87
ARID_Swi1p-like cd16871
ARID/BRIGHT DNA binding domain of yeast SWI/SNF chromatin-remodeling complex subunit Swi1p and ...
 19-102 1.27e-18

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.


Pssm-ID: 350635  Cd Length: 90  Bit Score: 82.30  E-value: 1.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   19 FLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPR-SCSNAAFALKQYYLRYL 97
Cdd:cd16871    6 FMKSLREFMAKRGTPIEQQPVIGGRPVNLFRLYQLVQKLGGSRQVTQNNQWPRVAQKLGFPPeQNPQVAQQLAQIYQRYL 85


                 ....*
gi 56549668   98 EKYEK 102
Cdd:cd16871   86 LPYEE 90
ARID_ARID3 cd16867
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID3A, ...
 11-101 3.90e-18

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.


Pssm-ID: 350631  Cd Length: 118  Bit Score: 81.76  E-value: 3.90e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   11 DERRKglAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALK 90
Cdd:cd16867   10 DPKRK--EFLDDLFSFMQKRGTPVNRIPIMAKQVLDLYELYRLVVEKGGLVEVINKKIWREITKGLNLPSSITSAAFTLR 87

                         90
                 ....*....|.
gi 56549668   91 QYYLRYLEKYE 101
Cdd:cd16867   88 TQYMKYLYPYE 98
ARID_ARID3C cd16880
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3C (ARID3C) ...
 11-101 1.93e-17

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3C (ARID3C) and similar proteins; ARID3C, also called Brightlike, is a new ARID3 family transcription factor that co-activates ARID3A-mediated immunoglobulin gene transcription. It also functions as a potential regulator of early events in B cell antigen receptor (BCR) signaling. ARID3C 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.


Pssm-ID: 350644  Cd Length: 127  Bit Score: 80.46  E-value: 1.93e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   11 DERRKglAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALK 90
Cdd:cd16880   13 DPKRK--EFLDDLFSFMQKRGTPVNRIPIMAKQVLDLYTLYRLVTDKGGLVEVINKKIWREITKGLSLPTSITSAAFTLR 90

                         90
                 ....*....|.
gi 56549668   91 QYYLRYLEKYE 101
Cdd:cd16880   91 TQYMKYLYPYE 101
ARID_Dri-like cd16881
ARID/BRIGHT DNA binding domain of dead ringer (Dri) from Drosophila melanogaster and similar ...
 11-101 2.93e-17

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.


Pssm-ID: 350645  Cd Length: 125  Bit Score: 79.55  E-value: 2.93e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   11 DERRKglAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALK 90
Cdd:cd16881   17 DPKRK--EFLDDLFSFMQKRGTPVNRIPIMAKQVLDLYELYNLVVARGGLVEVINKKLWREITKGLHLPSSITSAAFTLR 94

                         90
                 ....*....|.
gi 56549668   91 QYYLRYLEKYE 101
Cdd:cd16881   95 TQYMKYLYPYE 105
ARID_ARID3A cd16878
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3A (ARID3A) ...
 11-101 5.15e-17

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3A (ARID3A) and similar proteins; ARID3A, also called B-cell regulator of IgH transcription (Bright), dead ringer-like protein 1 (Dril1), or E2F-binding protein 1 (E2FBP1), is an ubiquitously expressed DNA-binding protein that has been implicated in embryonic patterning, cell lineage gene regulation, and cell cycle control, chromatin remodeling and transcriptional regulation. It was originally identified as a B cell-specific trans-activator of immunoglobulin heavy-chain (IgH) transcription, which increases immunoglobulin transcription in antigen-activated B cells and plays regulatory roles in hematopoiesis. It also functions as an E2F transcription regulator, inducing promyelocytic leukemia protein (PML) reduction and suppressing the formation of PML-nuclear bodies. It antagonizes the p16(INK4A)-Rb tumor suppressor machinery by regulating PML stability. ARID3A transcriptional activity can be modulated by SUMO (Small Ubiquitin-related Modifier) modification through the interaction with the SUMO-conjugating enzyme Ubc9. ARID3A also plays an important role in marginal zone B lymphocyte development and autoantibody production. Furthermore, ARID3A is a direct p53 target gene. It controls cell growth in a p53-dependent manner. ARID3A 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.


Pssm-ID: 350642  Cd Length: 133  Bit Score: 79.34  E-value: 5.15e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   11 DERRKglAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALK 90
Cdd:cd16878   20 DPKRK--EFLDDLFSFMQKRGTPVNRIPIMAKQVLDLYMLYVLVTEKGGLVEVINKKLWREITKGLNLPTSITSAAFTLR 97

                         90
                 ....*....|.
gi 56549668   91 QYYLRYLEKYE 101
Cdd:cd16878   98 TQYMKYLYPYE 108
ARID_ARID3B cd16879
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3B (ARID3B) ...
 11-101 1.35e-16

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.


Pssm-ID: 350643  Cd Length: 126  Bit Score: 77.75  E-value: 1.35e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   11 DERRKglAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALK 90
Cdd:cd16879   12 DPKRK--EFLDDLFAFMQKRGTPINRIPIMAKQVLDLYMLYKLVTEKGGLVEVINKKIWREITKGLNLPTSITSAAFTLR 89

                         90
                 ....*....|.
gi 56549668   91 QYYLRYLEKYE 101
Cdd:cd16879   90 TQYMKYLYPYE 100
ARID_ARID4 cd16868
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID4A, ...
 18-101 3.73e-15

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.


Pssm-ID: 350632  Cd Length: 87  Bit Score: 72.42  E-value: 3.73e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   18 AFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRYL 97
Cdd:cd16868    4 NFLEQLYKFMEDRGTPINKPPVLGYKDLDLFKLYKLVQELGGMERVSQGAKWRSIYQQLGIPVLNSAASHNIKQAYKKYL 83


                 ....
gi 56549668   98 EKYE 101
Cdd:cd16868   84 YAFE 87
ARID_ARID5 cd16869
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID5A, ...
 18-101 6.54e-15

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID5A, ARID5B, and similar proteins; This subfamily contains ARID5A and its paralog ARID5B. ARID5A, also called modulator recognition factor 1 (MRF-1), is an estrogen receptor alpha (ER alpha)-interacting protein that is expressed abundantly in cardiovascular tissues and suppresses ER alpha-induced transactivation. It also plays an important role in the promotion of inflammatory processes and autoimmune diseases. 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. 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. Both ARID5A and ARID5B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT).


Pssm-ID: 350633  Cd Length: 87  Bit Score: 71.56  E-value: 6.54e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   18 AFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRYL 97
Cdd:cd16869    4 AFLKLLYKFMKDRGTPIERIPHLGFKQIDLYTFFKLVQKLGGYEQVTAKRLWKHVYDELGGNPSSTSAATCTRRHYEKLL 83


                 ....
gi 56549668   98 EKYE 101
Cdd:cd16869   84 LPYE 87
ARID_ARID1B cd16877
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) ...
 12-101 8.23e-14

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins; ARID1B, also called BRG1-associated factor 250b (BAF250B), BRG1-binding protein ELD/OSA1, Osa homolog 2 (Osa2), or p250R, is the largest subunit of ATP-dependent SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, which plays a critical role in transcriptional control and gene expression. ARID1B exhibits tumour-suppressor activities in pancreatic cancer cell lines. Mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Moreover, mutations in the ARID1B gene have been found in many cancers. ARID1B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner similar to ARID1A.


Pssm-ID: 350641  Cd Length: 93  Bit Score: 68.86  E-value: 8.23e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   12 ERRkglAFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRScSNAAFALKQ 91
Cdd:cd16877    2 ERK---LWVDRYLTFMEERGTPVASLPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVGTS-SSAASSLKK 77

                         90
                 ....*....|
gi 56549668   92 YYLRYLEKYE 101
Cdd:cd16877   78 QYIQYLFAFE 87
ARID_JARID cd16864
ARID/BRIGHT DNA binding domain of JARID proteins; The JARID subfamily within the JmjC protein ...
 14-101 1.42e-13

ARID/BRIGHT DNA binding domain of JARID proteins; The JARID subfamily within the JmjC protein family 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 of this subfamily contain the catalytic JmjC domain, JmjN, the AT-rich domain interacting domain (ARID)/BRIGHT domain, a C5HC2 zinc finger, as well as two or three plant homeodomain (PHD) fingers.


Pssm-ID: 350628  Cd Length: 87  Bit Score: 67.72  E-value: 1.42e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   14 RKGLAFLDELRQFHHSRGSPFKkIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPrSCSNAAFALKQYY 93
Cdd:cd16864    2 RVKLNFLDQIAKFWELQGSSLK-IPNVERKALDLFTLHKIVQEEGGFEEVTKERKWSKVARRLGYP-PGKGVGSLLRGHY 79


                 ....*...
gi 56549668   94 LRYLEKYE 101
Cdd:cd16864   80 ERILYPYD 87
ARID_ARID4B cd16883
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) ...
 19-101 1.31e-10

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.


Pssm-ID: 350647  Cd Length: 92  Bit Score: 59.60  E-value: 1.31e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   19 FLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRYLE 98
Cdd:cd16883    5 FLQQLYKFMEDRGTPINKRPVLGYRNLNLFKLFRLVHKLGGFDNIESGAVWKQVYQDLGIPVLNSAAGYNVKCAYRKYLY 84


                 ...
gi 56549668   99 KYE 101
Cdd:cd16883   85 GFE 87
ARID_ARID5B cd16885
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) ...
 18-110 1.57e-09

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.


Pssm-ID: 350649  Cd Length: 95  Bit Score: 56.62  E-value: 1.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   18 AFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRYL 97
Cdd:cd16885    4 AFLVALYKYMKERKTPIERIPYLGFKQINLWTMFQAAQKLGGYETITARRQWKHIYDELGGNPGSTSAATCTRRHYERLI 83

                         90
                 ....*....|...
gi 56549668   98 EKYEKVHHfGEDD 110
Cdd:cd16885   84 LPYERFIK-GEED 95
ARID_ARID1A cd16876
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) ...
 19-101 3.34e-09

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.


Pssm-ID: 350640  Cd Length: 93  Bit Score: 55.82  E-value: 3.34e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   19 FLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRScSNAAFALKQYYLRYLE 98
Cdd:cd16876    6 WVDRYLAFTEEKAMGMTNLPAVGRKPLDLYRLYVSVKEIGGLTQVNKNKKWRELATNLNVGTS-SSAASSLKKQYIQCLY 84


                 ...
gi 56549668   99 KYE 101
Cdd:cd16876   85 AFE 87
ARID_JARD2 cd16870
ARID/BRIGHT DNA binding domain of Jumonji/ARID domain-containing protein 2 (JARID2) and ...
 19-112 4.47e-09

ARID/BRIGHT DNA binding domain of Jumonji/ARID domain-containing protein 2 (JARID2) and similar proteins; JARID2, also called protein Jumonji, is a DNA-binding protein that contains both the Jumonji C (JmjC) domain and AT-rich DNA-interacting domain (ARID, also known as BRIGHT). It is an interacting component of Polycomb repressive complex-2 (PRC2) that catalyzes methylation of lysine 27 of histone H3 (H3K27) and regulates important gene expression patterns during development. It exhibits nucleosome-binding activity that contributes to PRC2 stimulation. However, unlike other JmjC domain-containing proteins, JARID2 is catalytically inactive due to the lack of conserved residues essential for histone demethylase activity. JARID2 is also involved in transforming growth factor-beta (TGF-beta)-induced epithelial-mesenchymal transition (EMT) of lung and colon cancer cell lines through the modulation of histone H3K27 methylation. Moreover, JARID2 is a part of GLP- and G9a-containing protein complex that promotes lysine 9 on histone H3 (H3K9) methylation on the cyclin D1 promoter and silences the expression of cyclin D1 and other cell cycle genes. It functions as a transcriptional repressor that plays critical roles in embryonic development including heart development in mice, and regulates cardiomyocyte proliferation via interaction with retinoblastoma protein (Rb), one of the master regulatory genes of the cell cycle. Furthermore, JARID2 acts as a transcriptional repressor of target genes, including Notch1. It directly binds to SETDB1 (SET domain, bifurcated 1) to form a complex that plays an important role in a novel process involving the modification of H3K9 methylation during heart development. Meanwhile, JARID2 is a key transcriptional repressor that plays a role in invariant natural killer T (iNKT) cell maturation. It regulates promyelocytic leukemia zinc finger (PLZF) expression by linking T-cell receptor (TCR) signaling to H3K9me3. JARID2 polymorphisms are associated with non-syndromic orofacial clefts (NSOC) susceptibility.


Pssm-ID: 350634  Cd Length: 112  Bit Score: 55.69  E-value: 4.47e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   19 FLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRY-- 96
Cdd:cd16870    8 KLACIKKHLESQGINLTPPPLIGGCELDLPRLYHLVQELGGMQQVTDKKKWNKVADHLNIPKTAQDRPSKLQDAYCKYll 87

                         90       100
                 ....*....|....*....|
gi 56549668   97 ----LEKYEKVHHFGEDDDE 112
Cdd:cd16870   88 sydtLSDEEKQKLEEEVRAE 107
ARID_ARID5A cd16884
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5A (ARID5A) ...
 18-101 7.94e-09

ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5A (ARID5A) and similar proteins; ARID5A, also called modulator recognition factor 1 (MRF-1), is an estrogen receptor alpha (ER alpha)-interacting protein that is expressed abundantly in cardiovascular tissues and suppresses ER alpha-induced transactivation. It also associates with thyroid receptor alpha (TR alpha) and retinoid X receptor alpha (RXR alpha) in a ligand-dependent manner, and with ER beta, androgen receptor (AR), and the retinoic acid receptor (RAR) in a ligand-independent manner. ARID5A functions as a negative regulator of RORgamma-induced Th17 cell differentiation and may be involved in the pathogenesis of rheumatoid arthritis (RA). Moreover, it is an important transcriptional partner of the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) in stimulation of chondrocyte-specific transcription. Meanwhile, ARID5A plays an important role in promotion of inflammatory processes and autoimmune diseases. It works as a unique RNA binding protein, which stabilizes interleukin-6 (IL-6) but not tumor necrosis factor-alpha (TNF-alpha) mRNA through binding to the 3' untranslated region (UTR) of IL-6 mRNA, and inhibits the destabilizing effect of regnase-1 on IL-6 mRNA. ARID5A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT).


Pssm-ID: 350648  Cd Length: 87  Bit Score: 54.24  E-value: 7.94e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   18 AFLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRYL 97
Cdd:cd16884    4 AFLVNLYKFMKERNTPIERIPHLGFKQINLWKIYKAVEKLGGYELVTARRLWKNVYDELGGSPGSTSAATCTRRHYERLV 83


                 ....
gi 56549668   98 EKYE 101
Cdd:cd16884   84 LPYV 87
SP2_N cd22540
N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins ...
 663-1152 4.19e-08

N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP2 contains the least conserved DNA-binding domain within the SP subfamily of proteins, and its DNA sequence specificity differs from the other SP proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate, or in some cases, repress expression from different promoters. The transcription factor SP2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. SP2 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP2.


Pssm-ID: 411776 [Multi-domain]  Cd Length: 511  Bit Score: 58.01  E-value: 4.19e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  663 TATQMSFPvQGVHTVAQTVSRIPQNP-----SPHTHQQQNAPVTVIQSKAPIPCEVVKAtvIQNSIPQTGVPVSIavggg 737
Cdd:cd22540   17 STTQDSQP-SPLALLAATCSKIGPPAveaavTPPAPPQPTPRKLVPIKPAPLPLGPGKN--SIGFLSAKGNIIQL----- 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  738 pPQSSVVQNHSTGPQPVTVVNSQTLLHHPSVIPQQSPLHTVVPG-QIPSGTPVTVIQQAVPqshmfGRVQNI---PACTS 813
Cdd:cd22540   89 -QGSQLSSSAPGGQQVFAIQNPTMIIKGSQTRSSTNQQYQISPQiQAAGQINNSGQIQIIP-----GTNQAIitpVQVLQ 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  814 TVSQGQQLITTSPQPVQTSsQQTSAGSQSQDTVIiappqyVTTSASNIVSATSVQNFQVA--TGQMVTIAGVPSPQASRV 891
Cdd:cd22540  163 QPQQAHKPVPIKPAPLQTS-NTNSASLQVPGNVI------KLQSGGNVALTLPVNNLVGTqdGATQLQLAAAPSKPSKKI 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  892 GFQ--NIAPKPLPSQQVSSTVVQQPIQQPQQPTQQSVVIVSQPaqqGQTYAPAIHQIVLANPAALPagQTVQLTGQPnit 969
Cdd:cd22540  236 RKKsaQAAQPAVTVAEQVETVLIETTADNIIQAGNNLLIVQSP---GTGQPAVLQQVQVLQPKQEQ--QVVQIPQQA--- 307

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  970 pSSSPSPVPATNNQVPTamSSSSTPQSQGPPPTVSQMLSVKRQ-----QQQQHSPAPPPQQVQVQVQQPQQVQmqvqpqq 1044
Cdd:cd22540  308 -LRVVQAASATLPTVPQ--KPLQNIQIQNSEPTPTQVYIKTPSgevqtVLLQEAPAATATPSSSTSTVQQQVT------- 377

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668 1045 SNAGVGQPASGeSSLIKQLLLPKRGPStpGGKLILPAPQIpppnnarAPSPQVVYQVASNqaaGFGVQGQTPAQQLLVGQ 1124
Cdd:cd22540  378 ANNGTGTSKPN-YNVRKERTLPKIAPA--GGIISLNAAQL-------AAAAQAIQTININ---GVQVQGVPVTITNAGGQ 444

                        490       500
                 ....*....|....*....|....*...
gi 56549668 1125 QNvqlvpsamppsGGVQTVPISNLQILP 1152
Cdd:cd22540  445 QQ-----------LTVQTVSSNNLTISG 461
ARID_ARID4A cd16882
ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) ...
 19-101 7.08e-08

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.


Pssm-ID: 350646  Cd Length: 87  Bit Score: 51.51  E-value: 7.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   19 FLDELRQFHHSRGSPFKKIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFALKQYYLRYLE 98
Cdd:cd16882    5 FLQQLYKFMEDRGTPINKPPVLGYKDLNLFKLFRLVYQQGGCDNIESGSVWKQIYMDLGIPILNSAASYNVKTAYRKYLY 84


                 ...
gi 56549668   99 KYE 101
Cdd:cd16882   85 GFE 87
ARID_KDM5A cd16873
ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A); KDM5A, also called ...
 14-101 1.13e-07

ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A); KDM5A, also called 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; 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 the 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, 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.


Pssm-ID: 350637  Cd Length: 92  Bit Score: 51.42  E-value: 1.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   14 RKGLAFLDELRQFHHSRGSPFKkIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFaLKQYY 93
Cdd:cd16873    2 RVKLDFLDQLAKFWELQGSTLK-IPVVERKILDLYALSKIVASEGGFEMVTKEKKWSKVGSRMGYLPGKGTGSL-LKSHY 79


                 ....*...
gi 56549668   94 LRYLEKYE 101
Cdd:cd16873   80 ERILYPYE 87
ARID_KDM5C_5D cd16875
ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D; This group ...
 14-101 8.62e-07

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.


Pssm-ID: 350639  Cd Length: 92  Bit Score: 48.77  E-value: 8.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   14 RKGLAFLDELRQFHHSRGSPFKkIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPrSCSNAAFALKQYY 93
Cdd:cd16875    2 RVKLNYLDQIAKFWEIQGSSLK-IPNVERRILDLYSLSKIVQEEGGYEAICKDRRWARVAQRLGYP-PGKNIGSLLRSHY 79


                 ....*...
gi 56549668   94 LRYLEKYE 101
Cdd:cd16875   80 ERIIYPYE 87
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 694-843 2.05e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.30  E-value: 2.05e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668    694 QQQNAPVTVIQSKAPIPCE--VVKATVIQNSIPQTGVPvSIAVGGGPPQSSVVQNHSTGPQPVTVVNSQTLLHHPSVIPQ 771
Cdd:pfam03154  167 LQTQPPVLQAQSGAASPPSppPPGTTQAATAGPTPSAP-SVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSP 245

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668    772 QSPLHTVVPGQIPSGTPVtviqQAVPQSHMFGRVQNIP-------------------ACTSTVSQGQQLITTSPQ-PVQT 831
Cdd:pfam03154  246 HPPLQPMTQPPPPSQVSP----QPLPQPSLHGQMPPMPhslqtgpshmqhpvppqpfPLTPQSSQSQVPPGPSPAaPGQS 321

                          170
                   ....*....|..
gi 56549668    832 SSQQTSAGSQSQ 843
Cdd:pfam03154  322 QQRIHTPPSQSQ 333
PHA03247 PHA03247
large tegument protein UL36; Provisional
 626-1097 3.55e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 45.70  E-value: 3.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   626 SVPDVSPAPSPAGIPHGSQtignhfQRTPVANQSSNLTATQM----SFPVQGVHTVAQTVSRIPQNPSPHTHQQQNAPVT 701
Cdd:PHA03247 2567 SVPPPRPAPRPSEPAVTSR------ARRPDAPPQSARPRAPVddrgDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDP 2640

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   702 VIQSKAPIPCEVVKATviqnSIPQTGVPVSIAVGGGPPQSSVVQNHSTGPQPVTVVNSQTLLHHPsviPQQSPLHTVVPG 781
Cdd:PHA03247 2641 HPPPTVPPPERPRDDP----APGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADP---PPPPPTPEPAPH 2713

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   782 QIPSGTPVTVIQQAVPQSHMFGRVQNIPACTSTVSQGQQLITTSPQPVQTSSQQTSAGSQSQdtviIAPPQYVTTSASNI 861
Cdd:PHA03247 2714 ALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAP----AAGPPRRLTRPAVA 2789

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   862 VSATSVQNFQVATGQMVTIAGVPSPQASRVGFQNIAP--KPLPSQQVSSTVVQQPIQQPQQPTQQSVVIVSQPAQQGQTY 939
Cdd:PHA03247 2790 SLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGplPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSR 2869

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   940 APAihqivlANPAAlPAGQTVQLTGQPNITPSSSPSPVPATNNQVPTAMSSSSTPQSQGPPPTVSQMLSVKRQQQQQHSP 1019
Cdd:PHA03247 2870 SPA------AKPAA-PARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPP 2942

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  1020 APPPQQVqvqvqqpqqvqmqvqpqqsnAGVGQPASGESSLIKQLLLPKRGPS----TPGGKLILPAPQIPPPNNARAPSP 1095
Cdd:PHA03247 2943 LAPTTDP--------------------AGAGEPSGAVPQPWLGALVPGRVAVprfrVPQPAPSREAPASSTPPLTGHSLS 3002


                  ..
gi 56549668  1096 QV 1097
Cdd:PHA03247 3003 RV 3004
ARID_KDM5B cd16874
ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B); KDM5B, also called ...
 12-100 5.41e-04

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.


Pssm-ID: 350638  Cd Length: 90  Bit Score: 40.69  E-value: 5.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668   12 ERRKGLAFLDELRQFHHSRGSPFKkIPAVGGKELDLHGLYTRVTTLGGFAKVSEKNQWGEIVEEFNFPRSCSNAAFaLKQ 91
Cdd:cd16874    3 QTRVKLNFLDQIAKFWELQGCTLK-IPHVERKILDLFQLNKLVAEEGGFDLVCKERKWTKIATKMGFAPGKAVGSH-IRA 80


                 ....*....
gi 56549668   92 YYLRYLEKY 100
Cdd:cd16874   81 HYERILYPY 89
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 628-764 3.45e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 42.33  E-value: 3.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668    628 PDVSPAPSPAGIPHGSQTIGNHFQRTPVANQSSNLTATQMSFPVQGVHTVaQTVSRiPQNPSPHTHQQQNAPVTVIQSKA 707
Cdd:pfam09770  214 PAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPV-TILQR-PQSPQPDPAQPSIQPQAQQFHQQ 291

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549668    708 PIPCEVVKATVIQN----SIPQTGVPV--SIAVGGGPPQSSVVQNHSTGPQPVTVVNSQTLLH 764
Cdd:pfam09770  292 PPPVPVQPTQILQNpnrlSAARVGYPQnpQPGVQPAPAHQAHRQQGSFGRQAPIITHPQQLAQ 354
SP4_N cd22536
N-terminal domain of transcription factor Specificity Protein (SP) 4; Specificity Proteins ...
 716-1227 5.99e-03

N-terminal domain of transcription factor Specificity Protein (SP) 4; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. Human SP4 is a risk gene of multiple psychiatric disorders including schizophrenia, bipolar disorder, and major depression. SP4 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP4.


Pssm-ID: 411773 [Multi-domain]  Cd Length: 623  Bit Score: 41.44  E-value: 5.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  716 ATVIQNSIPQTGVpvSIAVGGGPPQSSvvQNHSTGPQPVTVVNSqtllhhPSVIPQQSPLHTVVPGQIPSGTpvtviqqa 795
Cdd:cd22536   80 PTSKENNVAQQGV--SAATSSAAPSSS--NNGSTSPTKVKAGNS------NASAPGQFQVIQVQNMQNPSGS-------- 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  796 vpqshmfGRVQNIPACTSTVSQGQQLITTSPQPVQTSSQQTSAGSQSQDTVIIAPPQyvTTSASNIVSatsvqnfQVATG 875
Cdd:cd22536  142 -------VQYQVIPQIQTVEGQQIQISPANATALQDLQGQIQLIPAGNNQAILTTPN--RTASGNIIA-------QNLAN 205

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  876 QMVTIAGVPSpqasrVGFqniapkPLPSQQVSSTvvqqpiqqpqqptqqsvvivsqPAQQGQTYAPAIHQIVLANPA--- 952
Cdd:cd22536  206 QTVPVQIRPG-----VSI------PLQLQTIPGA----------------------QAQVVTTLPINIGGVTLALPVinn 252

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668  953 ALPAGQTVQLtGQPNITPSSSPSPVPATNnqvPTAMSSSSTPQSQGPP----------PTVSQMLSVKRQQQQQHSPAPP 1022
Cdd:cd22536  253 VAAGGGSGQL-VQPSDGGVSNGNQLVSTP---ITTASVSTMPESPSSSttctttastsLTSSDTLVSSAETGQYASTAAS 328

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668 1023 PQQVQVQVQQPQQVQMQVQPQQSNAGVGQPASGESSLIKQLLLPkrgpstpgGKLILPAPQIPPPnnarapsPQVVYQVA 1102
Cdd:cd22536  329 SERTEEEPQTSAAESEAQSSSQLQSNGLQNVQDQSNSLQQVQIV--------GQPILQQIQIQQP-------QQQIIQAI 393

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549668 1103 SNQAagFGVQ-GQTPAQQLLVGQQNVQLVPSAMP-----------PSGGV--QTVPISNLQILPGPLISNSPATifqgts 1168
Cdd:cd22536  394 QPQS--FQLQsGQTIQTIQQQPLQNVQLQAVQSPtqvliraptltPSGQIswQTVQVQNIQSLSNLQVQNAGLP------ 465

                        490       500       510       520       530       540       550
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549668 1169 gNQVTITVVPNTS-------FAPATVSQG----NATQLIAPAGITMS--GTQTGVGLPVQTLPATQASPAGQ 1227
Cdd:cd22536  466 -QQLTLTPVSSSAggttiaqIAPVAVAGTpitlNAAQLASVPNLQTVnvANLGAAGVQVQGVPVTITSVAGQ 536
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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