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Conserved domains on  [gi|1974213328|ref|XP_039209841|]
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protein polybromo-1 isoform X6 [Crotalus tigris]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 63-174 1.63e-67

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 222.59  E-value: 1.63e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   63 VDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNA 142
Cdd:cd05524      1 LDPIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNA 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1974213328  143 KSYYKPDSPEYKAACKLWDLYVRTKNEFVQKG 174
Cdd:cd05524     81 KAYYKPDSPEHKDACKLWELFLSARNEVLSGG 112
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 977-1094 3.22e-63

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


:

Pssm-ID: 240068  Cd Length: 121  Bit Score: 210.90  E-value: 3.22e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  977 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSNGEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVTVSKILGKCV 1056
Cdd:cd04717      3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGKCA 82

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1974213328 1057 VMFVKEYFKLCPENFRDEDVYVCESRYSAKTKSFKKIK 1094
Cdd:cd04717     83 VMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIK 120
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 541-642 5.63e-61

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 203.45  E-value: 5.63e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  541 QRMKILYNVVLEAREpGTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHY 620
Cdd:cd05518      3 KRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHY 81

                           90       100
                   ....*....|....*....|..
gi 1974213328  621 NEEGSQVYNDAHILEKILKEKR 642
Cdd:cd05518     82 NEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 403-504 6.12e-61

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99951  Cd Length: 103  Bit Score: 203.34  E-value: 6.12e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  403 SNPLYQLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRY 482
Cdd:cd05520      2 SNPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRY 81

                           90       100
                   ....*....|....*....|..
gi 1974213328  483 NVPNSAIYKRVLKMQQVMQAKK 504
Cdd:cd05520     82 NVPNSRIYKDAEKLQKLMQAKK 103
Bromo_polybromo_VI cd05526
Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ...
 795-902 5.25e-59

Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99956  Cd Length: 110  Bit Score: 198.36  E-value: 5.25e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  795 TLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIP--AVDPSFPSKPPLTFDIIRKNVENNRYRRLDLFQEHMFDVLERAR 872
Cdd:cd05526      1 QLLVQELLATLFVSVMNHQDEEGRCYSDSLAELPelAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1974213328  873 RMNRTDSEIYEDAVELQQFFIKIRDELCKN 902
Cdd:cd05526     81 RLSRTDSEIYEDAVELQQFFIKIRDELCKN 110
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 678-782 2.83e-58

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99946  Cd Length: 105  Bit Score: 195.99  E-value: 2.83e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  678 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 757
Cdd:cd05515      1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                           90       100
                   ....*....|....*....|....*
gi 1974213328  758 YNEPESLIYKDALVLHKVLLETRRD 782
Cdd:cd05515     81 YNEPDSQIYKDALTLQKVLLETKRE 105
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 1173-1291 3.76e-58

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


:

Pssm-ID: 240068  Cd Length: 121  Bit Score: 196.27  E-value: 3.76e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1173 DMWLKVGDCVFIKSHG-LVRARVGRIEKMWVR-DGAAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1250
Cdd:cd04717      1 GLQYRVGDCVYVANPEdPSKPIIFRIERLWKDeDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1974213328 1251 CAVLSFKDFLSCRPTEIHENDVLLCESRYNESDKQMKKFKG 1291
Cdd:cd04717     81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIKT 121
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 201-303 2.32e-55

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99948  Cd Length: 103  Bit Score: 187.65  E-value: 2.32e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKT 280
Cdd:cd05517      1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT 80

                           90       100
                   ....*....|....*....|...
gi 1974213328  281 YNEPGSQVFKDANAIKKIFNMKK 303
Cdd:cd05517     81 FNEPGSQVYKDANAIKKIFTAKK 103
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 1398-1453 4.06e-32

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


:

Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 119.65  E-value: 4.06e-32
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328 1398 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAKV 1453
Cdd:cd21984      1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQ 56
 
Name Accession Description Interval E-value
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 63-174 1.63e-67

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 222.59  E-value: 1.63e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   63 VDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNA 142
Cdd:cd05524      1 LDPIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNA 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1974213328  143 KSYYKPDSPEYKAACKLWDLYVRTKNEFVQKG 174
Cdd:cd05524     81 KAYYKPDSPEHKDACKLWELFLSARNEVLSGG 112
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 977-1094 3.22e-63

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 210.90  E-value: 3.22e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  977 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSNGEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVTVSKILGKCV 1056
Cdd:cd04717      3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGKCA 82

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1974213328 1057 VMFVKEYFKLCPENFRDEDVYVCESRYSAKTKSFKKIK 1094
Cdd:cd04717     83 VMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIK 120
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 541-642 5.63e-61

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 203.45  E-value: 5.63e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  541 QRMKILYNVVLEAREpGTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHY 620
Cdd:cd05518      3 KRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHY 81

                           90       100
                   ....*....|....*....|..
gi 1974213328  621 NEEGSQVYNDAHILEKILKEKR 642
Cdd:cd05518     82 NEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 403-504 6.12e-61

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 203.34  E-value: 6.12e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  403 SNPLYQLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRY 482
Cdd:cd05520      2 SNPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRY 81

                           90       100
                   ....*....|....*....|..
gi 1974213328  483 NVPNSAIYKRVLKMQQVMQAKK 504
Cdd:cd05520     82 NVPNSRIYKDAEKLQKLMQAKK 103
Bromo_polybromo_VI cd05526
Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ...
 795-902 5.25e-59

Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99956  Cd Length: 110  Bit Score: 198.36  E-value: 5.25e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  795 TLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIP--AVDPSFPSKPPLTFDIIRKNVENNRYRRLDLFQEHMFDVLERAR 872
Cdd:cd05526      1 QLLVQELLATLFVSVMNHQDEEGRCYSDSLAELPelAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1974213328  873 RMNRTDSEIYEDAVELQQFFIKIRDELCKN 902
Cdd:cd05526     81 RLSRTDSEIYEDAVELQQFFIKIRDELCKN 110
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 678-782 2.83e-58

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 195.99  E-value: 2.83e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  678 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 757
Cdd:cd05515      1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                           90       100
                   ....*....|....*....|....*
gi 1974213328  758 YNEPESLIYKDALVLHKVLLETRRD 782
Cdd:cd05515     81 YNEPDSQIYKDALTLQKVLLETKRE 105
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 1173-1291 3.76e-58

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 196.27  E-value: 3.76e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1173 DMWLKVGDCVFIKSHG-LVRARVGRIEKMWVR-DGAAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1250
Cdd:cd04717      1 GLQYRVGDCVYVANPEdPSKPIIFRIERLWKDeDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1974213328 1251 CAVLSFKDFLSCRPTEIHENDVLLCESRYNESDKQMKKFKG 1291
Cdd:cd04717     81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIKT 121
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 201-303 2.32e-55

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 187.65  E-value: 2.32e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKT 280
Cdd:cd05517      1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT 80

                           90       100
                   ....*....|....*....|...
gi 1974213328  281 YNEPGSQVFKDANAIKKIFNMKK 303
Cdd:cd05517     81 FNEPGSQVYKDANAIKKIFTAKK 103
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 976-1094 6.89e-41

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


Pssm-ID: 460207  Cd Length: 120  Bit Score: 146.68  E-value: 6.89e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  976 SMYHVGDYVYVEPAEANLQPHIVCIERLWEDS-NGEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVTVSKILGK 1054
Cdd:pfam01426    1 ETYSVGDFVLVEPDDADEPYYVARIEELFEDTkNGKKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1974213328 1055 CVVMFVKEYFKLCPENFRDEDVYVCESRYSAKTKSFKKIK 1094
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEPDDFFCELLYDPKTKSFKKLP 120
BAH smart00439
Bromo adjacent homology domain;
977-1094 5.55e-37

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 135.88  E-value: 5.55e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   977 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSNGE--KWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVTVSKILGK 1054
Cdd:smart00439    1 TISVGDFVLVEPDDADEPYYIGRIEEIFETKKNSesKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 1974213328  1055 CVVMFVKEYFKLCPENFRD-EDVYVCESRYSAKTKSFKKIK 1094
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSIGePDVFFCESAYDPEKGSFKKLP 121
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 1174-1290 8.04e-33

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


Pssm-ID: 460207  Cd Length: 120  Bit Score: 123.96  E-value: 8.04e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1174 MWLKVGDCVFIKSHG-LVRARVGRIEKMWVRDGA--AYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1250
Cdd:pfam01426    1 ETYSVGDFVLVEPDDaDEPYYVARIEELFEDTKNgkKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1974213328 1251 CAVLSFKDFLSCRPTEIHENDVLLCESRYNESDKQMKKFK 1290
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEPDDFFCELLYDPKTKSFKKLP 120
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 1398-1453 4.06e-32

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 119.65  E-value: 4.06e-32
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328 1398 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAKV 1453
Cdd:cd21984      1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQ 56
BROMO smart00297
bromo domain;
671-783 4.76e-30

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 115.45  E-value: 4.76e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   671 KSKYMTPMQQKLNEVYEAVKNYtdkrgrRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVM 750
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSH------PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNL 74

                            90       100       110
                    ....*....|....*....|....*....|...
gi 1974213328   751 MFNNACTYNEPESLIYKDALVLHKVLLETRRDI 783
Cdd:smart00297   75 MFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107
BAH smart00439
Bromo adjacent homology domain;
1175-1290 1.87e-29

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 114.31  E-value: 1.87e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  1175 WLKVGDCVFIKSH-GLVRARVGRIEKMWVRDG---AAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1250
Cdd:smart00439    1 TISVGDFVLVEPDdADEPYYIGRIEEIFETKKnseSKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 1974213328  1251 CAVLSFKDFLSCRPTEI-HENDVLLCESRYNESDKQMKKFK 1290
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSiGEPDVFFCESAYDPEKGSFKKLP 121
BROMO smart00297
bromo domain;
200-306 1.04e-28

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 111.60  E-value: 1.04e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   200 YLKEILEQLLEAVVVatnpsgHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAK 279
Cdd:smart00297    7 KLQELLKAVLDKLDS------HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*..
gi 1974213328   280 TYNEPGSQVFKDANAIKKIFNMKKAEI 306
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLREL 107
BROMO smart00297
bromo domain;
541-645 3.41e-27

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 107.36  E-value: 3.41e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   541 QRMKILYNVVLEAREpgtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHY 620
Cdd:smart00297    6 KKLQELLKAVLDKLD---SHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTY 82

                            90       100
                    ....*....|....*....|....*
gi 1974213328   621 NEEGSQVYNDAHILEKILKEKRKEL 645
Cdd:smart00297   83 NGPDSEVYKDAKKLEKFFEKKLREL 107
BROMO smart00297
bromo domain;
404-507 9.54e-27

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 105.82  E-value: 9.54e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   404 NPLYQLYDTVRNCRNNQgqLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYN 483
Cdd:smart00297    6 KKLQELLKAVLDKLDSH--PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|....
gi 1974213328   484 VPNSAIYKRVLKMQQVMQAKKKEL 507
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLREL 107
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 420-641 2.15e-25

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 110.28  E-value: 2.15e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  420 QGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQV 499
Cdd:COG5076    161 DGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKY 240

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  500 MqakKKELARRDEIEDGDSmissatsdagsskrkskknikKQRMKILYNVVLEAREPGTGRRLCEL-FMVKPSKKDYPDY 578
Cdd:COG5076    241 F---LKLIEEIPEEMLELS---------------------IKPGREEREERESVLITNSQAHVGAWpFLRPVSDEEVPDY 296

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1974213328  579 YKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEK 641
Cdd:COG5076    297 YKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANVLEDFVIKK 359
BROMO smart00297
bromo domain;
68-170 4.65e-25

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 101.20  E-value: 4.65e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328    68 VCHELYNTIRDYKDEqgRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYK 147
Cdd:smart00297    7 KLQELLKAVLDKLDS--HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84

                            90       100
                    ....*....|....*....|...
gi 1974213328   148 PDSPEYKAACKLWDLYVRTKNEF 170
Cdd:smart00297   85 PDSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 201-292 1.64e-21

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 90.07  E-value: 1.64e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEavvvatnpsgHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKT 280
Cdd:pfam00439    1 CLEILDKLME----------HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNART 70

                           90
                   ....*....|..
gi 1974213328  281 YNEPGSQVFKDA 292
Cdd:pfam00439   71 YNGPGSVIYKAA 82
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 73-158 1.10e-19

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 85.06  E-value: 1.10e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   73 YNTIRDYKDEQGRllCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPE 152
Cdd:pfam00439    1 CLEILDKLMEHPI--AAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVI 78


                   ....*.
gi 1974213328  153 YKAACK 158
Cdd:pfam00439   79 YKAAEK 84
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 208-334 2.95e-19

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 91.79  E-value: 2.95e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  208 LLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQ 287
Cdd:COG5076    150 IAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSS 229

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328  288 VFKDANAIKKIFNMK-----KAEIEHSELTKSSLR-----VRTGNLTASRLTSPSSQ 334
Cdd:COG5076    230 VYVDAKELEKYFLKLieeipEEMLELSIKPGREEReeresVLITNSQAHVGAWPFLR 286
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 422-491 5.34e-18

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 80.05  E-value: 5.34e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  422 QLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYK 491
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 560-633 2.54e-17

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 78.12  E-value: 2.54e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1974213328  560 RRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHI 633
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAEK 84
BROMO smart00297
bromo domain;
799-899 4.68e-15

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 72.70  E-value: 4.68e-15
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   799 QELIHNLFVSVMSHQDDegRCYSDSLAEIPAVD--PSFPS--KPPLTFDIIRKNVENNRYRRLDLFQEHMFDVLERARRM 874
Cdd:smart00297    5 QKKLQELLKAVLDKLDS--HPLSWPFLKPVSRKeaPDYYDiiKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTY 82

                            90       100
                    ....*....|....*....|....*
gi 1974213328   875 NRTDSEIYEDAVELQQFFIKIRDEL 899
Cdd:smart00297   83 NGPDSEVYKDAKKLEKFFEKKLREL 107
HMG smart00398
high mobility group;
1396-1452 5.56e-14

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 68.11  E-value: 5.56e-14
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328  1396 KRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:smart00398    1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKK 57
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 698-769 9.18e-14

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 68.11  E-value: 9.18e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328  698 RRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDA 769
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAA 82
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 809-887 3.33e-13

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 66.57  E-value: 3.33e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  809 VMSHQDDEGRCYSDSLAEIPAVDPSFPS--KPPLTFDIIRKNVENNRYRRLDLFQEHMFDVLERARRMNRTDSEIYEDAV 886
Cdd:pfam00439    4 ILDKLMEHPIAAPFLEPVDPDEYPDYYSviKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83


                   .
gi 1974213328  887 E 887
Cdd:pfam00439   84 K 84
HMG_box pfam00505
HMG (high mobility group) box;
1398-1452 1.07e-12

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 64.55  E-value: 1.07e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328 1398 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:pfam00505    2 KRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEK 56
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1359-1450 4.83e-08

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 55.25  E-value: 4.83e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1359 TIPQLQTPLSNELdIMPYTPPQS-TPKSIKGsvKKEGSKRkiNMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRN 1437
Cdd:COG5648     37 TLVELEKPLQQLL-TKPRKKTKSkRLVRKKK--DPNGPKR--PLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKE 111

                           90
                   ....*....|...
gi 1974213328 1438 LEASKKAEYEERA 1450
Cdd:COG5648    112 LTDEEKEPYYKEA 124
PTZ00199 PTZ00199
high mobility group protein; Provisional
 1391-1451 2.39e-03

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 39.07  E-value: 2.39e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1974213328 1391 KKEGSKRKINMSGYILFSSEMRAVIKAQHPDYS--FGELSRLVGTEWRNLEASKKAEYEERAA 1451
Cdd:PTZ00199    17 KKDPNAPKRALSAYMFFAKEKRAEIIAENPELAkdVAAVGKMVGEAWNKLSEEEKAPYEKKAQ 79
 
Name Accession Description Interval E-value
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 63-174 1.63e-67

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 222.59  E-value: 1.63e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   63 VDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNA 142
Cdd:cd05524      1 LDPIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNA 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1974213328  143 KSYYKPDSPEYKAACKLWDLYVRTKNEFVQKG 174
Cdd:cd05524     81 KAYYKPDSPEHKDACKLWELFLSARNEVLSGG 112
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 977-1094 3.22e-63

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 210.90  E-value: 3.22e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  977 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSNGEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVTVSKILGKCV 1056
Cdd:cd04717      3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGKCA 82

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1974213328 1057 VMFVKEYFKLCPENFRDEDVYVCESRYSAKTKSFKKIK 1094
Cdd:cd04717     83 VMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIK 120
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 541-642 5.63e-61

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 203.45  E-value: 5.63e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  541 QRMKILYNVVLEAREpGTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHY 620
Cdd:cd05518      3 KRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHY 81

                           90       100
                   ....*....|....*....|..
gi 1974213328  621 NEEGSQVYNDAHILEKILKEKR 642
Cdd:cd05518     82 NEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 403-504 6.12e-61

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 203.34  E-value: 6.12e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  403 SNPLYQLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRY 482
Cdd:cd05520      2 SNPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRY 81

                           90       100
                   ....*....|....*....|..
gi 1974213328  483 NVPNSAIYKRVLKMQQVMQAKK 504
Cdd:cd05520     82 NVPNSRIYKDAEKLQKLMQAKK 103
Bromo_polybromo_VI cd05526
Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ...
 795-902 5.25e-59

Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99956  Cd Length: 110  Bit Score: 198.36  E-value: 5.25e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  795 TLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIP--AVDPSFPSKPPLTFDIIRKNVENNRYRRLDLFQEHMFDVLERAR 872
Cdd:cd05526      1 QLLVQELLATLFVSVMNHQDEEGRCYSDSLAELPelAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1974213328  873 RMNRTDSEIYEDAVELQQFFIKIRDELCKN 902
Cdd:cd05526     81 RLSRTDSEIYEDAVELQQFFIKIRDELCKN 110
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 678-782 2.83e-58

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 195.99  E-value: 2.83e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  678 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 757
Cdd:cd05515      1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                           90       100
                   ....*....|....*....|....*
gi 1974213328  758 YNEPESLIYKDALVLHKVLLETRRD 782
Cdd:cd05515     81 YNEPDSQIYKDALTLQKVLLETKRE 105
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 1173-1291 3.76e-58

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 196.27  E-value: 3.76e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1173 DMWLKVGDCVFIKSHG-LVRARVGRIEKMWVR-DGAAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1250
Cdd:cd04717      1 GLQYRVGDCVYVANPEdPSKPIIFRIERLWKDeDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1974213328 1251 CAVLSFKDFLSCRPTEIHENDVLLCESRYNESDKQMKKFKG 1291
Cdd:cd04717     81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIKT 121
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 201-303 2.32e-55

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 187.65  E-value: 2.32e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKT 280
Cdd:cd05517      1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT 80

                           90       100
                   ....*....|....*....|...
gi 1974213328  281 YNEPGSQVFKDANAIKKIFNMKK 303
Cdd:cd05517     81 FNEPGSQVYKDANAIKKIFTAKK 103
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 976-1094 6.89e-41

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


Pssm-ID: 460207  Cd Length: 120  Bit Score: 146.68  E-value: 6.89e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  976 SMYHVGDYVYVEPAEANLQPHIVCIERLWEDS-NGEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVTVSKILGK 1054
Cdd:pfam01426    1 ETYSVGDFVLVEPDDADEPYYVARIEELFEDTkNGKKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1974213328 1055 CVVMFVKEYFKLCPENFRDEDVYVCESRYSAKTKSFKKIK 1094
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEPDDFFCELLYDPKTKSFKKLP 120
BAH smart00439
Bromo adjacent homology domain;
977-1094 5.55e-37

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 135.88  E-value: 5.55e-37
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   977 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSNGE--KWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVTVSKILGK 1054
Cdd:smart00439    1 TISVGDFVLVEPDDADEPYYIGRIEEIFETKKNSesKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 1974213328  1055 CVVMFVKEYFKLCPENFRD-EDVYVCESRYSAKTKSFKKIK 1094
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSIGePDVFFCESAYDPEKGSFKKLP 121
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 1174-1290 8.04e-33

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


Pssm-ID: 460207  Cd Length: 120  Bit Score: 123.96  E-value: 8.04e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1174 MWLKVGDCVFIKSHG-LVRARVGRIEKMWVRDGA--AYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1250
Cdd:pfam01426    1 ETYSVGDFVLVEPDDaDEPYYVARIEELFEDTKNgkKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1974213328 1251 CAVLSFKDFLSCRPTEIHENDVLLCESRYNESDKQMKKFK 1290
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEPDDFFCELLYDPKTKSFKKLP 120
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 543-641 9.25e-33

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 122.83  E-value: 9.25e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  543 MKILYNVVLEArEPGTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNE 622
Cdd:cd05519      5 MLEIYDAVLNC-EDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQ 83

                           90
                   ....*....|....*....
gi 1974213328  623 EGSQVYNDAHILEKILKEK 641
Cdd:cd05519     84 EGSIVYEDAVEMEKAFKKK 102
BAH cd04370
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). ...
 975-1094 3.08e-32

BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.


Pssm-ID: 239835 [Multi-domain]  Cd Length: 123  Bit Score: 122.12  E-value: 3.08e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  975 NSMYHVGDYVYVEPAE--ANLQPHIVCIERLWEDSNGEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVTVSKIL 1052
Cdd:cd04370      1 GITYEVGDSVYVEPDDsiKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESII 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1974213328 1053 GKCVVMFVKEYFKLC-PENFRDEDVYVCESRYSAKTKSFKKIK 1094
Cdd:cd04370     81 GKCKVLFVSEFEGLKqRPNKIDTDDFFCRLAYDPTTKEFKALE 123
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 1398-1453 4.06e-32

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 119.65  E-value: 4.06e-32
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328 1398 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAKV 1453
Cdd:cd21984      1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQ 56
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 541-644 2.66e-31

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 118.95  E-value: 2.66e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  541 QRMKILYNVVLEAREPGtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHY 620
Cdd:cd05515      3 QKLWELYNAVKNYTDGR-GRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKY 81

                           90       100
                   ....*....|....*....|....
gi 1974213328  621 NEEGSQVYNDAHILEKILKEKRKE 644
Cdd:cd05515     82 NEPDSQIYKDALTLQKVLLETKRE 105
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 678-779 2.82e-31

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 118.60  E-value: 2.82e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  678 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 757
Cdd:cd05519      1 LKAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANART 80

                           90       100
                   ....*....|....*....|..
gi 1974213328  758 YNEPESLIYKDALVLHKVLLET 779
Cdd:cd05519     81 YNQEGSIVYEDAVEMEKAFKKK 102
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 406-506 1.47e-30

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 116.64  E-value: 1.47e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  406 LYQLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVP 485
Cdd:cd05515      5 LWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEP 84

                           90       100
                   ....*....|....*....|.
gi 1974213328  486 NSAIYKRVLKMQQVMQAKKKE 506
Cdd:cd05515     85 DSQIYKDALTLQKVLLETKRE 105
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 201-305 1.96e-30

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 116.25  E-value: 1.96e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKT 280
Cdd:cd05515      1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                           90       100
                   ....*....|....*....|....*
gi 1974213328  281 YNEPGSQVFKDANAIKKIFNMKKAE 305
Cdd:cd05515     81 YNEPDSQIYKDALTLQKVLLETKRE 105
BROMO smart00297
bromo domain;
671-783 4.76e-30

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 115.45  E-value: 4.76e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   671 KSKYMTPMQQKLNEVYEAVKNYtdkrgrRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVM 750
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSH------PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNL 74

                            90       100       110
                    ....*....|....*....|....*....|...
gi 1974213328   751 MFNNACTYNEPESLIYKDALVLHKVLLETRRDI 783
Cdd:smart00297   75 MFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107
BAH smart00439
Bromo adjacent homology domain;
1175-1290 1.87e-29

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 114.31  E-value: 1.87e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  1175 WLKVGDCVFIKSH-GLVRARVGRIEKMWVRDG---AAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1250
Cdd:smart00439    1 TISVGDFVLVEPDdADEPYYIGRIEEIFETKKnseSKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 1974213328  1251 CAVLSFKDFLSCRPTEI-HENDVLLCESRYNESDKQMKKFK 1290
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSiGEPDVFFCESAYDPEKGSFKKLP 121
BROMO smart00297
bromo domain;
200-306 1.04e-28

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 111.60  E-value: 1.04e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   200 YLKEILEQLLEAVVVatnpsgHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAK 279
Cdd:smart00297    7 KLQELLKAVLDKLDS------HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*..
gi 1974213328   280 TYNEPGSQVFKDANAIKKIFNMKKAEI 306
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 680-783 1.20e-28

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 111.37  E-value: 1.20e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  680 QKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYN 759
Cdd:cd05516      4 KKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83

                           90       100
                   ....*....|....*....|....
gi 1974213328  760 EPESLIYKDALVLHKVLLETRRDI 783
Cdd:cd05516     84 LEGSLIYEDSIVLQSVFKSARQKI 107
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 200-302 6.25e-28

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 109.00  E-value: 6.25e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  200 YLKEILEQLLEAVvvatnpsgHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAK 279
Cdd:cd04369      4 KLRSLLDALKKLK--------RDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAK 75

                           90       100
                   ....*....|....*....|...
gi 1974213328  280 TYNEPGSQVFKDANAIKKIFNMK 302
Cdd:cd04369     76 TYNGPGSPIYKDAKKLEKLFEKL 98
BROMO smart00297
bromo domain;
541-645 3.41e-27

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 107.36  E-value: 3.41e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   541 QRMKILYNVVLEAREpgtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHY 620
Cdd:smart00297    6 KKLQELLKAVLDKLD---SHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTY 82

                            90       100
                    ....*....|....*....|....*
gi 1974213328   621 NEEGSQVYNDAHILEKILKEKRKEL 645
Cdd:smart00297   83 NGPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 69-169 8.01e-27

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 106.23  E-value: 8.01e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   69 CHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKP 148
Cdd:cd05515      5 LWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEP 84

                           90       100
                   ....*....|....*....|.
gi 1974213328  149 DSPEYKAACKLWDLYVRTKNE 169
Cdd:cd05515     85 DSQIYKDALTLQKVLLETKRE 105
BROMO smart00297
bromo domain;
404-507 9.54e-27

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 105.82  E-value: 9.54e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   404 NPLYQLYDTVRNCRNNQgqLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYN 483
Cdd:smart00297    6 KKLQELLKAVLDKLDSH--PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|....
gi 1974213328   484 VPNSAIYKRVLKMQQVMQAKKKEL 507
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 201-299 5.34e-26

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 104.05  E-value: 5.34e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKT 280
Cdd:cd05516      2 LTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQT 81

                           90
                   ....*....|....*....
gi 1974213328  281 YNEPGSQVFKDANAIKKIF 299
Cdd:cd05516     82 FNLEGSLIYEDSIVLQSVF 100
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 207-303 6.55e-26

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 103.57  E-value: 6.55e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  207 QLLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGS 286
Cdd:cd05520      7 QLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNS 86

                           90
                   ....*....|....*..
gi 1974213328  287 QVFKDANAIKKIFNMKK 303
Cdd:cd05520     87 RIYKDAEKLQKLMQAKK 103
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 201-303 7.24e-26

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 103.29  E-value: 7.24e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKT 280
Cdd:cd05518      1 RKKRMLALFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARH 80

                           90       100
                   ....*....|....*....|...
gi 1974213328  281 YNEPGSQVFKDANAIKKIFNMKK 303
Cdd:cd05518     81 YNEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 677-780 1.09e-25

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 102.80  E-value: 1.09e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  677 PMQQklneVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNAC 756
Cdd:cd05520      4 PLWQ----LYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAK 79

                           90       100
                   ....*....|....*....|....
gi 1974213328  757 TYNEPESLIYKDALVLHKVLLETR 780
Cdd:cd05520     80 RYNVPNSRIYKDAEKLQKLMQAKK 103
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 679-780 1.26e-25

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 102.52  E-value: 1.26e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  679 QQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTY 758
Cdd:cd05518      2 KKRMLALFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHY 81

                           90       100
                   ....*....|....*....|..
gi 1974213328  759 NEPESLIYKDALVLHKVLLETR 780
Cdd:cd05518     82 NEEGSQVYEDANILEKVLKEKR 103
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 560-641 1.56e-25

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 102.07  E-value: 1.56e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  560 RRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILK 639
Cdd:cd04369     17 RDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFE 96


                   ..
gi 1974213328  640 EK 641
Cdd:cd04369     97 KL 98
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 420-641 2.15e-25

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 110.28  E-value: 2.15e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  420 QGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQV 499
Cdd:COG5076    161 DGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKY 240

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  500 MqakKKELARRDEIEDGDSmissatsdagsskrkskknikKQRMKILYNVVLEAREPGTGRRLCEL-FMVKPSKKDYPDY 578
Cdd:COG5076    241 F---LKLIEEIPEEMLELS---------------------IKPGREEREERESVLITNSQAHVGAWpFLRPVSDEEVPDY 296

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1974213328  579 YKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEK 641
Cdd:COG5076    297 YKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANVLEDFVIKK 359
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 541-645 2.84e-25

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 101.74  E-value: 2.84e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  541 QRMKILYNVVLEAREPgTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHY 620
Cdd:cd05516      4 KKMNKIVDVVIKYKDS-DGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTF 82

                           90       100
                   ....*....|....*....|....*
gi 1974213328  621 NEEGSQVYNDAHILEKILKEKRKEL 645
Cdd:cd05516     83 NLEGSLIYEDSIVLQSVFKSARQKI 107
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 201-302 3.28e-25

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 101.26  E-value: 3.28e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKT 280
Cdd:cd05519      1 LKAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANART 80

                           90       100
                   ....*....|....*....|..
gi 1974213328  281 YNEPGSQVFKDANAIKKIFNMK 302
Cdd:cd05519     81 YNQEGSIVYEDAVEMEKAFKKK 102
BROMO smart00297
bromo domain;
68-170 4.65e-25

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 101.20  E-value: 4.65e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328    68 VCHELYNTIRDYKDEqgRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYK 147
Cdd:smart00297    7 KLQELLKAVLDKLDS--HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84

                            90       100
                    ....*....|....*....|...
gi 1974213328   148 PDSPEYKAACKLWDLYVRTKNEF 170
Cdd:smart00297   85 PDSEVYKDAKKLEKFFEKKLREL 107
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 70-162 8.19e-25

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 100.49  E-value: 8.19e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   70 HELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPD 149
Cdd:cd05520      6 WQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPN 85

                           90
                   ....*....|...
gi 1974213328  150 SPEYKAACKLWDL 162
Cdd:cd05520     86 SRIYKDAEKLQKL 98
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 541-642 1.27e-24

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 99.82  E-value: 1.27e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  541 QRMKILYNVVLEAREPGtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHY 620
Cdd:cd05517      3 QILEQLLEAVMTATDPS-GRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTF 81

                           90       100
                   ....*....|....*....|..
gi 1974213328  621 NEEGSQVYNDAHILEKILKEKR 642
Cdd:cd05517     82 NEPGSQVYKDANAIKKIFTAKK 103
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 428-786 1.57e-24

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 107.58  E-value: 1.57e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  428 FFHLPSKKKYPDYYQQiKMPISlqqIRTKLKNHEYET-----LDHLEcDLNLMFENAKRYNVPNSAIYKRV--LKMQQVM 500
Cdd:COG5076     39 APEEEGSKNLFQKQLK-RMPKE---YITSIVDDREPGsmanvNDDLE-NVGGITYSPFEKNRPESLRFDEIvfLAIESVT 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  501 QAKKKELARRDEIEDGDSMISSATsdagsskrKSKKNIKKQRMKILYNVVLEAREPGTGRRLceLFMVKPSKKDYPDYYK 580
Cdd:COG5076    114 PESGLGSLLMAHLKTSVKKRKTPK--------IEDELLYADNKAIAKFKKQLFLRDGRFLSS--IFLGLPSKREYPDYYE 183

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  581 IILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKekrKELGPLLEDDEVASPKLK 660
Cdd:COG5076    184 IIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFL---KLIEEIPEEMLELSIKPG 260

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  661 lsrktgispKKSKYMTPmqqklnevyeaVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQD 740
Cdd:COG5076    261 ---------REEREERE-----------SVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRP 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 1974213328  741 IDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDIEGD 786
Cdd:COG5076    321 EETFVRDAKLFFDNCVMYNGEVTDYYKNANVLEDFVIKKTRLIREY 366
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 408-507 2.37e-24

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 99.33  E-value: 2.37e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  408 QLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNS 487
Cdd:cd05524      9 ELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDS 88

                           90       100
                   ....*....|....*....|
gi 1974213328  488 AIYKRVLKMQQVMQAKKKEL 507
Cdd:cd05524     89 PEHKDACKLWELFLSARNEV 108
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 408-503 2.50e-24

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 98.95  E-value: 2.50e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  408 QLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNS 487
Cdd:cd05519      7 EIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGS 86

                           90
                   ....*....|....*.
gi 1974213328  488 AIYKRVLKMQQVMQAK 503
Cdd:cd05519     87 IVYEDAVEMEKAFKKK 102
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 413-498 2.71e-24

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 98.85  E-value: 2.71e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  413 VRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKR 492
Cdd:cd05522     13 LRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKD 92


                   ....*.
gi 1974213328  493 VLKMQQ 498
Cdd:cd05522     93 AVLLEK 98
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 406-503 4.00e-24

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 98.21  E-value: 4.00e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  406 LYQLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVP 485
Cdd:cd04369      1 LKKKLRSLLDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP 80

                           90
                   ....*....|....*...
gi 1974213328  486 NSAIYKRVLKMQQVMQAK 503
Cdd:cd04369     81 GSPIYKDAKKLEKLFEKL 98
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 678-778 5.05e-24

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 97.83  E-value: 5.05e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  678 MQQKLNEVYEAVKnytdKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 757
Cdd:cd04369      1 LKKKLRSLLDALK----KLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKT 76

                           90       100
                   ....*....|....*....|.
gi 1974213328  758 YNEPESLIYKDALVLHKVLLE 778
Cdd:cd04369     77 YNGPGSPIYKDAKKLEKLFEK 97
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 681-788 6.01e-24

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 98.17  E-value: 6.01e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  681 KLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNE 760
Cdd:cd05524      6 VCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYK 85

                           90       100
                   ....*....|....*....|....*...
gi 1974213328  761 PESLIYKDALVLHKVLLETRRDIEGDED 788
Cdd:cd05524     86 PDSPEHKDACKLWELFLSARNEVLSGGE 113
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 39-309 1.77e-23

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 104.50  E-value: 1.77e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   39 DDGHHSTNTPGPSRKRRRLSNLPTVDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQ 118
Cdd:COG5076    117 GLGSLLMAHLKTSVKKRKTPKIEDELLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQK 196

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  119 KLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYVRTKNEFVQKGEAeddeeedeghdnqgtiseiSSP 198
Cdd:COG5076    197 KLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLE-------------------LSI 257

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  199 GYLKEILEQLLEAVVvaTNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNA 278
Cdd:COG5076    258 KPGREEREERESVLI--TNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNC 335

                          250       260       270
                   ....*....|....*....|....*....|.
gi 1974213328  279 KTYNEPGSQVFKDANAIKKIFNMKKAEIEHS 309
Cdd:COG5076    336 VMYNGEVTDYYKNANVLEDFVIKKTRLIREY 366
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 543-642 1.47e-21

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 90.86  E-value: 1.47e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  543 MKILYNVVLEAREPgTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNE 622
Cdd:cd05520      5 LWQLYDTIRNARNN-QGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNV 83

                           90       100
                   ....*....|....*....|
gi 1974213328  623 EGSQVYNDAHILEKILKEKR 642
Cdd:cd05520     84 PNSRIYKDAEKLQKLMQAKK 103
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 201-292 1.64e-21

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 90.07  E-value: 1.64e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEavvvatnpsgHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKT 280
Cdd:pfam00439    1 CLEILDKLME----------HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNART 70

                           90
                   ....*....|..
gi 1974213328  281 YNEPGSQVFKDA 292
Cdd:pfam00439   71 YNGPGSVIYKAA 82
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 566-805 2.47e-21

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 97.95  E-value: 2.47e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  566 FMVKPSKKDYPDYYKIILEPMdlkiIEYNIRSDKYAGEEAmIEDMRLMF-----RNARHYNEEGSQVYNDAHIL-EKILK 639
Cdd:COG5076     39 APEEEGSKNLFQKQLKRMPKE----YITSIVDDREPGSMA-NVNDDLENvggitYSPFEKNRPESLRFDEIVFLaIESVT 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  640 EKRKELGPLLEDDEVASPKLKlsrktgiSPKKSKYMTPMQQKLneVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLT 719
Cdd:COG5076    114 PESGLGSLLMAHLKTSVKKRK-------TPKIEDELLYADNKA--IAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEI 184

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  720 IKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDIEGDEDSHVP-----NV 794
Cdd:COG5076    185 IKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLELSIkpgreER 264

                          250
                   ....*....|.
gi 1974213328  795 TLLIQELIHNL 805
Cdd:COG5076    265 EERESVLITNS 275
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 404-504 2.73e-21

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 90.19  E-value: 2.73e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  404 NPLYQLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYN 483
Cdd:cd05517      3 QILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82

                           90       100
                   ....*....|....*....|.
gi 1974213328  484 VPNSAIYKRVLKMQQVMQAKK 504
Cdd:cd05517     83 EPGSQVYKDANAIKKIFTAKK 103
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 66-165 2.86e-21

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 90.12  E-value: 2.86e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   66 IAVCHELYNTIRDYKdeqgRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSY 145
Cdd:cd04369      2 KKKLRSLLDALKKLK----RDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTY 77

                           90       100
                   ....*....|....*....|
gi 1974213328  146 YKPDSPEYKAACKLWDLYVR 165
Cdd:cd04369     78 NGPGSPIYKDAKKLEKLFEK 97
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 408-499 3.42e-21

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 90.18  E-value: 3.42e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  408 QLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNS 487
Cdd:cd05516      8 KIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGS 87

                           90
                   ....*....|..
gi 1974213328  488 AIYKRVLKMQQV 499
Cdd:cd05516     88 LIYEDSIVLQSV 99
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 216-301 2.37e-20

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 87.68  E-value: 2.37e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  216 TNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAI 295
Cdd:cd05522     17 RDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLL 96


                   ....*.
gi 1974213328  296 KKIFNM 301
Cdd:cd05522     97 EKEARL 102
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 677-774 3.17e-20

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 87.30  E-value: 3.17e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  677 PMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNAC 756
Cdd:cd05522      1 PYEARIKNILKGLRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAK 80

                           90
                   ....*....|....*...
gi 1974213328  757 TYNEPESLIYKDALVLHK 774
Cdd:cd05522     81 LYNENDSQEYKDAVLLEK 98
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 679-775 3.77e-20

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 87.11  E-value: 3.77e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  679 QQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTY 758
Cdd:cd05517      2 KQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTF 81

                           90
                   ....*....|....*..
gi 1974213328  759 NEPESLIYKDALVLHKV 775
Cdd:cd05517     82 NEPGSQVYKDANAIKKI 98
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 73-158 1.10e-19

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 85.06  E-value: 1.10e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   73 YNTIRDYKDEQGRllCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPE 152
Cdd:pfam00439    1 CLEILDKLMEHPI--AAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVI 78


                   ....*.
gi 1974213328  153 YKAACK 158
Cdd:pfam00439   79 YKAAEK 84
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 67-167 1.34e-19

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 85.52  E-value: 1.34e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   67 AVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYY 146
Cdd:cd05525      5 QVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYY 84

                           90       100
                   ....*....|....*....|.
gi 1974213328  147 KPDSPEYKAACKLWDLYVRTK 167
Cdd:cd05525     85 GRKSPIGRDVCRLRKAYYQAK 105
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 208-334 2.95e-19

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 91.79  E-value: 2.95e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  208 LLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQ 287
Cdd:COG5076    150 IAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSS 229

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328  288 VFKDANAIKKIFNMK-----KAEIEHSELTKSSLR-----VRTGNLTASRLTSPSSQ 334
Cdd:COG5076    230 VYVDAKELEKYFLKLieeipEEMLELSIKPGREEReeresVLITNSQAHVGAWPFLR 286
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 566-645 6.34e-19

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 83.37  E-value: 6.34e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  566 FMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEKRKEL 645
Cdd:cd05509     22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKEL 101
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 72-159 8.26e-19

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 83.26  E-value: 8.26e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   72 LYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSP 151
Cdd:cd05518      8 LFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQ 87


                   ....*...
gi 1974213328  152 EYKAACKL 159
Cdd:cd05518     88 VYEDANIL 95
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 76-159 8.73e-19

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 83.06  E-value: 8.73e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   76 IRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKA 155
Cdd:cd05522     13 LRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKD 92


                   ....
gi 1974213328  156 ACKL 159
Cdd:cd05522     93 AVLL 96
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 67-166 8.98e-19

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 83.16  E-value: 8.98e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   67 AVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYY 146
Cdd:cd05519      3 AAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYN 82

                           90       100
                   ....*....|....*....|
gi 1974213328  147 KPDSPEYKAACKLWDLYVRT 166
Cdd:cd05519     83 QEGSIVYEDAVEMEKAFKKK 102
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 422-491 5.34e-18

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 80.05  E-value: 5.34e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  422 QLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYK 491
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 541-636 7.93e-18

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 80.36  E-value: 7.93e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  541 QRMKILYNVVLEAREPGtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHY 620
Cdd:cd05522      4 ARIKNILKGLRKERDEN-GRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLY 82

                           90
                   ....*....|....*.
gi 1974213328  621 NEEGSQVYNDAHILEK 636
Cdd:cd05522     83 NENDSQEYKDAVLLEK 98
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 201-300 8.17e-18

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 80.44  E-value: 8.17e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNgsYKSIHAMTKDIDLLVKNAKT 280
Cdd:cd05521      2 LSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARL 79

                           90       100
                   ....*....|....*....|
gi 1974213328  281 YNEPGSQVFKDANAIKKIFN 300
Cdd:cd05521     80 YNTKGSVIYKYALILEKYIN 99
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 70-145 1.17e-17

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 80.16  E-value: 1.17e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328   70 HELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSY 145
Cdd:cd05516      7 NKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTF 82
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 560-633 2.54e-17

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 78.12  E-value: 2.54e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1974213328  560 RRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHI 633
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAEK 84
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 677-779 4.94e-17

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 78.13  E-value: 4.94e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  677 PMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMmaNKYQDIDSMVEDFVMMFNNAC 756
Cdd:cd05521      1 KLSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRL--PHYTNAQEFVNDLAQIPWNAR 78

                           90       100
                   ....*....|....*....|...
gi 1974213328  757 TYNEPESLIYKDALVLHKVLLET 779
Cdd:cd05521     79 LYNTKGSVIYKYALILEKYINDV 101
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 406-508 5.14e-17

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 78.59  E-value: 5.14e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  406 LYQLYDTVRNCRNnqgqliSEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVP 485
Cdd:cd05504     17 LEQLLVEIVKHKD------SWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPE 90

                           90       100
                   ....*....|....*....|...
gi 1974213328  486 NSAIYKRVLKMQQVMQAKKKELA 508
Cdd:cd05504     91 HTSVYKAGTRLQRFFIKRCRKLG 113
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 237-302 1.37e-16

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 76.82  E-value: 1.37e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328  237 PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAIKKIFNMK 302
Cdd:cd05509     32 PDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKK 97
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 402-498 9.12e-16

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 74.67  E-value: 9.12e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  402 ISNPLYQLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNheYETLDHLECDLNLMFENAKR 481
Cdd:cd05521      2 LSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARL 79

                           90
                   ....*....|....*..
gi 1974213328  482 YNVPNSAIYKRVLKMQQ 498
Cdd:cd05521     80 YNTKGSVIYKYALILEK 96
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 566-647 1.36e-15

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 74.35  E-value: 1.36e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  566 FMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEKRKEL 645
Cdd:cd05504     33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKL 112


                   ..
gi 1974213328  646 GP 647
Cdd:cd05504    113 GL 114
BAH_BAHCC1 cd04714
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. ...
 980-1087 2.97e-15

BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240065  Cd Length: 121  Bit Score: 73.59  E-value: 2.97e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  980 VGDYVYVEPAEANLQPHIVCIERLWEDSNGEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVTVSKILGKCVVMF 1059
Cdd:cd04714      6 VGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHKCYVLT 85

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1974213328 1060 VKEYFKL---CPENFRDEDVYVCESRYSAKT 1087
Cdd:cd04714     86 FAEYERLarvKKKPQDGVDFYYCAGTYNPDT 116
BROMO smart00297
bromo domain;
799-899 4.68e-15

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 72.70  E-value: 4.68e-15
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   799 QELIHNLFVSVMSHQDDegRCYSDSLAEIPAVD--PSFPS--KPPLTFDIIRKNVENNRYRRLDLFQEHMFDVLERARRM 874
Cdd:smart00297    5 QKKLQELLKAVLDKLDS--HPLSWPFLKPVSRKeaPDYYDiiKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTY 82

                            90       100
                    ....*....|....*....|....*
gi 1974213328   875 NRTDSEIYEDAVELQQFFIKIRDEL 899
Cdd:smart00297   83 NGPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 427-507 4.69e-15

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 72.59  E-value: 4.69e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  427 PFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQVMQAKKKE 506
Cdd:cd05509     21 PFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKE 100


                   .
gi 1974213328  507 L 507
Cdd:cd05509    101 L 101
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 407-512 4.70e-15

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 72.68  E-value: 4.70e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  407 YQLYDTVRNCRNNQGqliSEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPN 486
Cdd:cd05511      3 FILDEIVNELKNLPD---SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPD 79

                           90       100
                   ....*....|....*....|....*.
gi 1974213328  487 SAIYKrvlKMQQVMQAKKKELARRDE 512
Cdd:cd05511     80 SVYTK---KAKEMLELAEELLAEREE 102
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 237-302 1.06e-14

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 71.55  E-value: 1.06e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328  237 PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAIKKIFNMK 302
Cdd:cd05499     36 PNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 570-647 1.20e-14

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 71.55  E-value: 1.20e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  570 PSKKDYPDYYKIILEPMDLKIIEYNIR---SDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEKRKELG 646
Cdd:cd05502     28 PVSPSVPNYYKIIKTPMDLSLIRKKLQpksPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLKEIL 107


                   .
gi 1974213328  647 P 647
Cdd:cd05502    108 P 108
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 546-646 3.75e-14

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 70.44  E-value: 3.75e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  546 LYNVVLEAREPGtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGS 625
Cdd:cd05524     10 LYDTIRNYKSED-GRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDS 88

                           90       100
                   ....*....|....*....|.
gi 1974213328  626 QVYNDAHILEKILKEKRKELG 646
Cdd:cd05524     89 PEHKDACKLWELFLSARNEVL 109
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 563-648 4.02e-14

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 69.99  E-value: 4.02e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  563 CELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDA-HIL---EKIL 638
Cdd:cd05511     18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAkEMLelaEELL 97

                           90
                   ....*....|
gi 1974213328  639 KEKRKELGPL 648
Cdd:cd05511     98 AEREEKLTQL 107
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 231-302 4.26e-14

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 69.67  E-value: 4.26e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328  231 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAIKKIFNMK 302
Cdd:cd05506     27 VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIFETR 98
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 1387-1452 4.75e-14

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal proteins NHP6A, NHP6B and similar proteins; This subfamily includes Saccharomyces cerevisiae high-mobility-group proteins NHP6A and its closely related paralog NHP6B. NHP6A and NHP6B seem to be functionally redundant. They are DNA-binding proteins that induce severe bending of DNA and are required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. They augment the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex. They may also play essential roles in transcriptional initiation fidelity of some but not all tRNA genes.


Pssm-ID: 438792 [Multi-domain]  Cd Length: 81  Bit Score: 68.93  E-value: 4.75e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328 1387 KGSVKKEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd01390      4 KGRKKKDPNAPKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAK 69
HMG smart00398
high mobility group;
1396-1452 5.56e-14

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 68.11  E-value: 5.56e-14
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328  1396 KRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:smart00398    1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKK 57
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1401-1452 6.70e-14

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 67.54  E-value: 6.70e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd00084      3 LSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKE 54
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 698-769 9.18e-14

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 68.11  E-value: 9.18e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328  698 RRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDA 769
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAA 82
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 406-499 1.13e-13

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 68.57  E-value: 1.13e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  406 LYQLYDTVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVP 485
Cdd:cd05525      7 LKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGR 86

                           90
                   ....*....|....
gi 1974213328  486 NSAIYKRVLKMQQV 499
Cdd:cd05525     87 KSPIGRDVCRLRKA 100
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 101-159 1.88e-13

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 67.96  E-value: 1.88e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  101 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKL 159
Cdd:cd05509     32 PDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKL 90
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 809-887 3.33e-13

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


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 66.57  E-value: 3.33e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  809 VMSHQDDEGRCYSDSLAEIPAVDPSFPS--KPPLTFDIIRKNVENNRYRRLDLFQEHMFDVLERARRMNRTDSEIYEDAV 886
Cdd:pfam00439    4 ILDKLMEHPIAAPFLEPVDPDEYPDYYSviKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83


                   .
gi 1974213328  887 E 887
Cdd:pfam00439   84 K 84
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 568-641 3.74e-13

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 66.97  E-value: 3.74e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1974213328  568 VKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEK 641
Cdd:cd05506     25 VDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIFETR 98
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 231-299 3.95e-13

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 66.95  E-value: 3.95e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  231 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAIKKIF 299
Cdd:cd05500     31 PVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAF 99
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 228-300 4.10e-13

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 67.75  E-value: 4.10e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1974213328  228 QKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVfkdANAIKKIFN 300
Cdd:cd05529     50 YPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEI---AKKAKRLSD 119
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 205-290 5.44e-13

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 67.04  E-value: 5.44e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  205 LEQLLEAVVvatnpsGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEP 284
Cdd:cd05504     17 LEQLLVEIV------KHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPE 90


                   ....*.
gi 1974213328  285 GSQVFK 290
Cdd:cd05504     91 HTSVYK 96
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 542-641 5.99e-13

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 66.58  E-value: 5.99e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  542 RMKILYNVVLEAREPgTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRsdKYAGEEAMIEDMRLMFRNARHYN 621
Cdd:cd05521      5 KLKPLYDGIYTLKEE-NGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYN 81

                           90       100
                   ....*....|....*....|
gi 1974213328  622 EEGSQVYNDAHILEKILKEK 641
Cdd:cd05521     82 TKGSVIYKYALILEKYINDV 101
HMG_box pfam00505
HMG (high mobility group) box;
1398-1452 1.07e-12

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 64.55  E-value: 1.07e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328 1398 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:pfam00505    2 KRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEK 56
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 227-306 1.74e-12

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 65.39  E-value: 1.74e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  227 FQKlPSKVQYPDYYAIIKEPIDLKTIAQRIQNGS---YKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAIKKIFNMKK 303
Cdd:cd05502     25 FHE-PVSPSVPNYYKIIKTPMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQL 103


                   ...
gi 1974213328  304 AEI 306
Cdd:cd05502    104 KEI 106
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 201-299 2.00e-12

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 65.10  E-value: 2.00e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  201 LKEILEQLLEAVVVATNPSGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKT 280
Cdd:cd05525      3 LAQVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEK 82

                           90
                   ....*....|....*....
gi 1974213328  281 YNEPGSQVFKDANAIKKIF 299
Cdd:cd05525     83 YYGRKSPIGRDVCRLRKAY 101
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 224-310 2.20e-12

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 65.36  E-value: 2.20e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  224 SELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDAnaiKKIFNMKK 303
Cdd:cd05511     18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKA---KEMLELAE 94


                   ....*..
gi 1974213328  304 AEIEHSE 310
Cdd:cd05511     95 ELLAERE 101
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 568-645 2.45e-12

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 64.75  E-value: 2.45e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1974213328  568 VKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEKRKEL 645
Cdd:cd05497     30 VDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLAQM 107
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 704-783 2.52e-12

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 65.11  E-value: 2.52e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  704 FLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDI 783
Cdd:cd05504     33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKL 112
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 221-305 3.21e-12

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 64.75  E-value: 3.21e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  221 HLISELFQKL--PSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAIKKI 298
Cdd:cd05497     20 HKFAWPFQQPvdAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKL 99


                   ....*..
gi 1974213328  299 FNMKKAE 305
Cdd:cd05497    100 FLQKLAQ 106
BAH cd04370
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). ...
 1178-1290 3.98e-12

BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.


Pssm-ID: 239835 [Multi-domain]  Cd Length: 123  Bit Score: 64.72  E-value: 3.98e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1178 VGDCVFIKSHGLVRA---RVGRIEKMWVR-DGAAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGKCAV 1253
Cdd:cd04370      6 VGDSVYVEPDDSIKSdppYIARIEELWEDtNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESIIGKCKV 85

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1974213328 1254 LSFKDFLSCRPTEIHE-NDVLLCESRYNESDKQMKKFK 1290
Cdd:cd04370     86 LFVSEFEGLKQRPNKIdTDDFFCRLAYDPTTKEFKALE 123
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 576-641 4.37e-12

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 63.84  E-value: 4.37e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328  576 PDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEK 641
Cdd:cd05499     36 PNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 566-642 5.72e-12

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 63.55  E-value: 5.72e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328  566 FMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILkEKR 642
Cdd:cd05503     21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFF-EKR 96
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 203-297 9.49e-12

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 63.23  E-value: 9.49e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  203 EILEQLLEAVVVATNPSGHliSELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYN 282
Cdd:cd05510      7 EFYESLDKVLNELKTYTEH--STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYN 84

                           90
                   ....*....|....*.
gi 1974213328  283 EPGSQVFKD-ANAIKK 297
Cdd:cd05510     85 SDPSHPLRRhANFMKK 100
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 235-282 1.39e-11

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 62.76  E-value: 1.39e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1974213328  235 QYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYN 282
Cdd:cd05528     32 EVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 568-641 1.64e-11

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 62.30  E-value: 1.64e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1974213328  568 VKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEK 641
Cdd:cd05498     28 VDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 708-775 1.84e-11

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 62.30  E-value: 1.84e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1974213328  708 PSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKV 775
Cdd:cd05498     30 PEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDV 97
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 231-302 3.14e-11

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 61.53  E-value: 3.14e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328  231 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAIKKIFNMK 302
Cdd:cd05498     30 PEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 675-775 3.24e-11

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 61.56  E-value: 3.24e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  675 MTPMQQKLneVYEAVKNYtdKRGRrlSAIFLRLPS---RSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMM 751
Cdd:cd05500      1 MTKHQHKF--LLSSIRSL--KRLK--DARPFLVPVdpvKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLM 74

                           90       100
                   ....*....|....*....|....
gi 1974213328  752 FNNACTYNEPESLIYKDALVLHKV 775
Cdd:cd05500     75 VDNCLTFNGPEHPVSQMGKRLQAA 98
BAH_BAHCC1 cd04714
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. ...
 1176-1280 4.59e-11

BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240065  Cd Length: 121  Bit Score: 61.65  E-value: 4.59e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1176 LKVGDCVFIKSHGLVRAR-VGRIEKMWVRDGAA------YFFgpifiHPEETEHEPTKMFYKKEVFLSNLEETCPMTCIL 1248
Cdd:cd04714      4 IRVGDCVLFKSPGRPSLPyVARIESLWEDPEGNmvvrvkWYY-----RPEETKGGRKPNHGEKELFASDHQDENSVQTIE 78

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1974213328 1249 GKCAVLSFKDF---LSCRPTEIHENDVLLCESRYN 1280
Cdd:cd04714     79 HKCYVLTFAEYerlARVKKKPQDGVDFYYCAGTYN 113
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 1401-1452 5.64e-11

high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; The HMG20 subfamily includes HMG20A and HMG20B. HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1, HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B. HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2, HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. Both HMG20A and HMG20B contain one HMG-box.


Pssm-ID: 438796 [Multi-domain]  Cd Length: 81  Bit Score: 60.25  E-value: 5.64e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd21980      6 LTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEK 57
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 568-636 7.41e-11

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 60.40  E-value: 7.41e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  568 VKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEK 636
Cdd:cd05500     29 VDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQA 97
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 432-503 8.47e-11

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 60.37  E-value: 8.47e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328  432 PSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQVMQAK 503
Cdd:cd05498     30 PEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 432-499 1.55e-10

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 59.63  E-value: 1.55e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1974213328  432 PSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQV 499
Cdd:cd05500     31 PVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAA 98
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 708-778 1.79e-10

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 59.76  E-value: 1.79e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1974213328  708 PSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLE 778
Cdd:cd05495     31 PKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 712-778 1.91e-10

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 59.36  E-value: 1.91e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328  712 ELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLE 778
Cdd:cd05497     36 NLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQ 102
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 704-775 2.09e-10

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 59.11  E-value: 2.09e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328  704 FLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKV 775
Cdd:cd05509     22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKF 93
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 678-780 2.24e-10

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 59.33  E-value: 2.24e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  678 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACT 757
Cdd:cd05525      3 LAQVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEK 82

                           90       100
                   ....*....|....*....|...
gi 1974213328  758 YNEPESLIYKDALVLHKVLLETR 780
Cdd:cd05525     83 YYGRKSPIGRDVCRLRKAYYQAK 105
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 95-159 3.25e-10

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 58.86  E-value: 3.25e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328   95 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKL 159
Cdd:cd05500     31 PVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRL 95
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 425-509 3.33e-10

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 58.99  E-value: 3.33e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  425 SEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRvlkMQQVMQAKK 504
Cdd:cd05510     26 STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPLRR---HANFMKKKA 102


                   ....*
gi 1974213328  505 KELAR 509
Cdd:cd05510    103 EHLLK 107
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 231-299 3.39e-10

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 58.99  E-value: 3.39e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  231 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAIKKIF 299
Cdd:cd05495     31 PKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVF 99
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 419-497 3.81e-10

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


Pssm-ID: 99944  Cd Length: 98  Bit Score: 58.18  E-value: 3.81e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  419 NQGQLISEPFfhlpSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQ 497
Cdd:cd05512     17 DTAEIFSEPV----DLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLR 91
HMG-box_AtSSRP1 cd22013
high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and ...
 1391-1452 4.12e-10

high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and similar proteins; SSRP1, also called facilitates chromatin transcription complex subunit SSRP1, high mobility group B protein 8, nucleosome/chromatin assembly factor group D 08 (or D 8), protein NUCLEAR FUSION DEFECTIVE 8, or recombination signal sequence recognition protein 1, is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair. SSRP1 may bind specifically to double-stranded DNA. It is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. SSRP1 contains only one HMG-box domain.


Pssm-ID: 438829 [Multi-domain]  Cd Length: 80  Bit Score: 57.56  E-value: 4.12e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328 1391 KKEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd22013      3 KKDPNAPKRALSGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAKAQV 64
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 541-637 4.18e-10

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 58.56  E-value: 4.18e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  541 QRMKILYNVVLEAREPgTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHY 620
Cdd:cd05525      5 QVLKEICDAIITYKDS-NGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKY 83

                           90
                   ....*....|....*..
gi 1974213328  621 NEEGSQVYNDAHILEKI 637
Cdd:cd05525     84 YGRKSPIGRDVCRLRKA 100
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 101-162 4.20e-10

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


Pssm-ID: 99944  Cd Length: 98  Bit Score: 58.18  E-value: 4.20e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328  101 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDL 162
Cdd:cd05512     32 PDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLRDQ 93
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 438-503 6.08e-10

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 58.07  E-value: 6.08e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328  438 PDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQVMQAK 503
Cdd:cd05499     36 PNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 95-165 6.51e-10

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 57.84  E-value: 6.51e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1974213328   95 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYVR 165
Cdd:cd05495     31 PKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 1401-1452 8.61e-10

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 56.15  E-value: 8.61e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd21994      3 MSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEK 54
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 424-491 9.41e-10

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 58.12  E-value: 9.41e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  424 ISEPFFH-LPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYK 491
Cdd:cd05529     44 IAEYFEYpVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAK 112
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 91-159 9.52e-10

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 57.79  E-value: 9.52e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328   91 FIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKL 159
Cdd:cd05504     33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRL 101
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 1402-1452 1.23e-09

second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438795 [Multi-domain]  Cd Length: 71  Bit Score: 55.88  E-value: 1.23e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1974213328 1402 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd21979      8 SAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAK 58
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 235-299 1.45e-09

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 56.61  E-value: 1.45e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328  235 QYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAIKKIF 299
Cdd:cd05503     29 LVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFF 93
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 546-651 1.47e-09

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 57.07  E-value: 1.47e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  546 LYNVVLEARepgTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGS 625
Cdd:cd05510     12 LDKVLNELK---TYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPS 88

                           90       100
                   ....*....|....*....|....*.
gi 1974213328  626 QVYNDAHILekiLKEKRKELGPLLED 651
Cdd:cd05510     89 HPLRRHANF---MKKKAEHLLKLIPD 111
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 568-628 2.57e-09

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 56.30  E-value: 2.57e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1974213328  568 VKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVY 628
Cdd:cd05495     29 VDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVY 89
HMG-box_ROX1-like cd01389
high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar ...
 1404-1453 4.50e-09

high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar proteins; This family includes class I members of the HMG-box superfamily of DNA-binding proteins, including Saccharomyces cerevisiae repressor ROX1, Schizosaccharomyces pombe mating-type M-specific polypeptide Mc (mat-Mc), Schizosaccharomyces pombe transcription factor ste11, Podospora anserina MAT+ sexual cell fertilization-promoting factor (FPR1), Podospora anserina sporulation minus regulator 2 (SMR2) and Candida albicans repressor of filamentous growth 1 (RFG1). These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. ROX1, also called heme-dependent repression factor, or hypoxic function repressor, is a transcription factor that represses the expression of HEM13, COX5B, ANB1, CYC7 or AAC3. It binds to the DNA sequence 5'-RRRTAACAAGAG-3'. mat-Mc belongs to the mating type protein family, which contains sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. mat-Mc is a positive regulator of MFM genes and is required for conjugation and efficient meiosis. Its HMG box recognizes the DNA sequence 5'-AACAAAG-3'. Ste11 is a key transcription factor for sexual development. It activates the transcription of the matp, matm, mei2, mfm, ste6 and rgs1 genes. It binds specifically to a DNA fragment carrying a 10-base motif 5'-TTCTTTGTTY-3'. FPR1 controls fertilization, probably by determining the mating type. SMR2 is a transcription factor that is required for post-fertilization events. It is required for the developmental events that occur in the female organ after fertilization. RFG1 is a transcription regulator that functions in both the positive and negative regulation of filamentous growth, depending upon environmental conditions.


Pssm-ID: 438791 [Multi-domain]  Cd Length: 72  Bit Score: 54.51  E-value: 4.50e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1404 YILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAKV 1453
Cdd:cd01389      8 FILFRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEEE 57
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 101-163 5.15e-09

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 55.36  E-value: 5.15e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1974213328  101 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLY 163
Cdd:cd05498     36 HDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVF 98
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 714-783 5.25e-09

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 55.11  E-value: 5.25e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  714 PDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDAlvlhKVLLETRRDI 783
Cdd:cd05513     32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAA----KKLLHSGMKI 97
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 101-159 6.01e-09

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 55.11  E-value: 6.01e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  101 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKL 159
Cdd:cd05513     32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 425-502 6.59e-09

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 55.14  E-value: 6.59e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  425 SEPFFHL--PSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQVMQA 502
Cdd:cd05495     22 SLPFRQPvdPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 713-769 8.10e-09

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 54.96  E-value: 8.10e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328  713 LPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDA 769
Cdd:cd05511     30 VPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKA 86
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 72-167 8.51e-09

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 54.64  E-value: 8.51e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   72 LYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKmeEYDDVNVLTADFQLLFNNAKSYYKPDSP 151
Cdd:cd05521      9 LYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYNTKGSV 86

                           90
                   ....*....|....*.
gi 1974213328  152 EYKAACKLwDLYVRTK 167
Cdd:cd05521     87 IYKYALIL-EKYINDV 101
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 429-483 1.89e-08

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 53.90  E-value: 1.89e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328  429 FHLP-SKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYN 483
Cdd:cd05528     24 FTKPvDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 570-627 2.84e-08

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 52.92  E-value: 2.84e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1974213328  570 PSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQV 627
Cdd:cd05505     25 VTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV 82
HMG-box_HMG20B cd22018
high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar ...
 1398-1452 2.87e-08

high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar proteins; HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2 (HMGXB2), HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex.


Pssm-ID: 438834 [Multi-domain]  Cd Length: 85  Bit Score: 52.67  E-value: 2.87e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328 1398 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd22018      3 KAPVTGYVRFLNERREQIRTQHPDLPFPEITKMLGAEWSKLQPHEKQRYLDEAER 57
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 700-774 2.99e-08

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 53.45  E-value: 2.99e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1974213328  700 LSAIFLRlPSRSELPDYYLTIKKPVDMEKIRSHM---MANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHK 774
Cdd:cd05502     21 LSLPFHE-PVSPSVPNYYKIIKTPMDLSLIRKKLqpkSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELEL 97
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 711-772 3.33e-08

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


Pssm-ID: 99944  Cd Length: 98  Bit Score: 52.79  E-value: 3.33e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328  711 SELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVL 772
Cdd:cd05512     29 SEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRL 90
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 220-300 3.41e-08

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 52.80  E-value: 3.41e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  220 GHLISELFQKLPSKVQY--------PDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKD 291
Cdd:cd05513      7 EQLIRQLQRKDPHGFFAfpvtdfiaPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKA 86


                   ....*....
gi 1974213328  292 AnaiKKIFN 300
Cdd:cd05513     87 A---KKLLH 92
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 85-159 3.66e-08

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 53.06  E-value: 3.66e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   85 RLLCELFIRAPKRRNQ-------PDYYEVVSQPIDLMKIQQKLKMEE---YDDVNVLTADFQLLFNNAKSYYKPDSPEYK 154
Cdd:cd05502     11 RLLLELYCHELSLPFHepvspsvPNYYKIIKTPMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYKFNEEDSEVAQ 90


                   ....*
gi 1974213328  155 AACKL 159
Cdd:cd05502     91 AGKEL 95
HMG-box_HMG20A cd22017
high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar ...
 1392-1452 4.04e-08

high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar proteins; HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1 (HMGXB1), HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B.


Pssm-ID: 438833 [Multi-domain]  Cd Length: 104  Bit Score: 52.64  E-value: 4.04e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1974213328 1392 KEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd22017     16 RDSNAPKAPLTGYVRFMNERREQLRAERPDVPFPEITRMLGNEWSKLPAEEKQRYLDEAEK 76
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 708-775 4.45e-08

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 52.67  E-value: 4.45e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1974213328  708 PSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKV 775
Cdd:cd05499     30 PVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEV 97
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 425-498 4.67e-08

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 52.54  E-value: 4.67e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1974213328  425 SEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQ 498
Cdd:cd05505     18 SWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYVLSCMRKTEQ 91
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1359-1450 4.83e-08

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 55.25  E-value: 4.83e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1359 TIPQLQTPLSNELdIMPYTPPQS-TPKSIKGsvKKEGSKRkiNMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRN 1437
Cdd:COG5648     37 TLVELEKPLQQLL-TKPRKKTKSkRLVRKKK--DPNGPKR--PLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKE 111

                           90
                   ....*....|...
gi 1974213328 1438 LEASKKAEYEERA 1450
Cdd:COG5648    112 LTDEEKEPYYKEA 124
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 712-780 5.22e-08

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 52.38  E-value: 5.22e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  712 ELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKvLLETR 780
Cdd:cd05503     29 LVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRK-FFEKR 96
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 429-491 5.30e-08

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 52.68  E-value: 5.30e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328  429 FHLPSKKKYPDYYQQIKMPISLQQIRTKLK----NHeYETLDHLECDLNLMFENAKRYNVPNSAIYK 491
Cdd:cd05502     25 FHEPVSPSVPNYYKIIKTPMDLSLIRKKLQpkspQH-YSSPEEFVADVRLMFKNCYKFNEEDSEVAQ 90
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 575-638 5.47e-08

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 53.11  E-value: 5.47e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1974213328  575 YPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKIL 638
Cdd:cd05529     58 YPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWL 121
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 224-282 5.54e-08

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 52.85  E-value: 5.54e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  224 SELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYN 282
Cdd:cd05496     23 SEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT 81
HMG-box_TOX-like cd21995
high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family ...
 1402-1452 6.48e-08

high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family includes four members: TOX, TOX2, TOX3 and TOX4. TOX, also called thymus high mobility group box protein TOX, is a transcriptional regulator with a major role in neural stem cell commitment and corticogenesis as well as in lymphoid cell development and lymphoid tissue organogenesis. It binds to GC-rich DNA sequences in the proximity of transcription start sites and may alter chromatin structure, modifying access of transcription factors to DNA. TOX2, also called granulosa cell HMG box protein 1 (GCX-1), is a putative transcriptional activator involved in the hypothalamic-pituitary-gonadal system. TOX3, also called CAG trinucleotide repeat-containing gene F9 protein (CAGF9), or trinucleotide repeat-containing gene 9 protein (TNRC9), is a transcriptional coactivator of the p300/CBP-mediated transcription complex. It activates transactivation through cAMP response element (CRE) sites. It protects against cell death by inducing anti-apoptotic and repressing pro-apoptotic transcripts. TOX4, also called epidermal Langerhans cell protein LCP1, is a component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. All family members contain one HMG-box domain.


Pssm-ID: 438811 [Multi-domain]  Cd Length: 70  Bit Score: 50.94  E-value: 6.48e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1974213328 1402 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEER--AAK 1452
Cdd:cd21995      5 SAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLDEEQKQVYKKKteAAK 57
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 708-761 9.24e-08

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 51.56  E-value: 9.24e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1974213328  708 PSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEP 761
Cdd:cd05506     27 VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPP 80
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 227-288 1.02e-07

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 51.38  E-value: 1.02e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328  227 FQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQV 288
Cdd:cd05505     21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV 82
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
 1196-1288 1.18e-07

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 52.59  E-value: 1.18e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1196 RIEKMWVRDGAAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGKCAVLSFKDFlscRPTEIHENDVLLC 1275
Cdd:cd04718     57 RIEKLWEENGTYWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVKCPKEF---RDASNDGDDVFLC 133

                           90
                   ....*....|...
gi 1974213328 1276 ESRYNESDKQMKK 1288
Cdd:cd04718    134 EYEYDVHWQSFKR 146
BAH_Orc1p_like cd04715
BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of ...
 1165-1266 1.33e-07

BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240066  Cd Length: 159  Bit Score: 52.89  E-value: 1.33e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1165 YYEQLCYNDMWLKVGDCVFIKsHGLVRARVGRIEKMW---VRDGAAY-----FFGPIFIHPEeteHEPTKMFYKKEVFLS 1236
Cdd:cd04715     19 FYRSFTYDGVEYRLYDDVYVH-NGDSEPYIGKIIKIYetaIDSGKKKvkviwFFRPSEIRME---LKGEPKRHINEVFLA 94

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1974213328 1237 -----NLEETCPMTCILGKCAVLSF-KDFLSCRPTE 1266
Cdd:cd04715     95 cgrgeGLANINLLESIIGKCNVVCIsEDFRNPQPSD 130
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 95-163 1.35e-07

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 51.13  E-value: 1.35e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328   95 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLY 163
Cdd:cd05499     30 PVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVF 98
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 429-507 1.85e-07

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 50.88  E-value: 1.85e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  429 FHLP---SKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDhlEC--DLNLMFENAKRYNVPNSAIYKRVLKMQQVMQAK 503
Cdd:cd05497     26 FQQPvdaVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSAS--ECiqDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQK 103


                   ....
gi 1974213328  504 KKEL 507
Cdd:cd05497    104 LAQM 107
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 438-499 2.03e-07

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 50.49  E-value: 2.03e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1974213328  438 PDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQV 499
Cdd:cd05513     32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKLLHS 93
HMG-box_AtHMGB6-like_rpt2 cd22007
second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1401-1452 2.10e-07

second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438823 [Multi-domain]  Cd Length: 68  Bit Score: 49.56  E-value: 2.10e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd22007      5 QSAYFLYANDRRAALKEENKNVKITEIAKMLGAEWKNLSDAKKKPYEEKAKK 56
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 427-489 2.58e-07

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 50.45  E-value: 2.58e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1974213328  427 PFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAI 489
Cdd:cd05503     20 PFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEV 82
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 224-298 3.07e-07

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 50.07  E-value: 3.07e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328  224 SELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAIKKI 298
Cdd:cd05508     20 AEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKI 94
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 204-282 3.10e-07

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


Pssm-ID: 99944  Cd Length: 98  Bit Score: 50.09  E-value: 3.10e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  204 ILEQLLEAVvvATNPSGHLISElfqKLPSKvQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYN 282
Cdd:cd05512      5 LLRKTLDQL--QEKDTAEIFSE---PVDLS-EVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN 77
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 1396-1450 4.90e-07

HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 48.56  E-value: 4.90e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328 1396 KRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERA 1450
Cdd:pfam09011    3 KPKRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMA 57
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 101-161 5.95e-07

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 49.66  E-value: 5.95e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328  101 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKA----ACKLWD 161
Cdd:cd05528     34 PDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDPADKLirsrACELRD 98
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
 1000-1093 6.05e-07

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 50.66  E-value: 6.05e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1000 IERLWEDsNGEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKVTVSKILGKCVVMfvkeyfklCPENFRDE----- 1074
Cdd:cd04718     58 IEKLWEE-NGTYWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVK--------CPKEFRDAsndgd 128

                           90
                   ....*....|....*....
gi 1974213328 1075 DVYVCESRYSAKTKSFKKI 1093
Cdd:cd04718    129 DVFLCEYEYDVHWQSFKRL 147
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 69-150 6.75e-07

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 49.07  E-value: 6.75e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328   69 CHELYNTIRDYKDEQGrllcelFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKP 148
Cdd:cd05505      5 CEEILSKILKYRFSWP------FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYEN 78


                   ..
gi 1974213328  149 DS 150
Cdd:cd05505     79 GS 80
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 574-645 6.82e-07

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 49.76  E-value: 6.82e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1974213328  574 DYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYN-EEGSQVYNDAHILEKILKEKRKEL 645
Cdd:cd05496     34 KYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTpNKRSRIYSMTLRLSALFEEHIKKI 106
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 802-892 9.14e-07

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 48.78  E-value: 9.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  802 IHNLFVSVMSHQDDEGRCYSDSLAEIP--AVDPSFPS--KPPLTFDIIRKNVENNRYRRLDLFQEHMFDVLERARRMNRT 877
Cdd:cd05522      6 IKNILKGLRKERDENGRLLTLHFEKLPdkAREPEYYQeiSNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNEN 85

                           90
                   ....*....|....*
gi 1974213328  878 DSEIYEDAVELQQFF 892
Cdd:cd05522     86 DSQEYKDAVLLEKEA 100
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 1401-1449 1.01e-06

second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2), intrastrand cross-link recognition protein (Ixr1) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Both ABF2 and Ixr1 contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438828 [Multi-domain]  Cd Length: 64  Bit Score: 47.67  E-value: 1.01e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEER 1449
Cdd:cd22012      6 ASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQEE 54
HMG-box_HMGXB4 cd21982
high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar ...
 1397-1450 1.11e-06

high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar proteins; HMGXB4, also called HMG box-containing protein 4, high mobility group protein 2-like 1 (HMG2L1), or protein HMGBCG, is a non-histone chromosomal protein that negatively regulates Wnt/beta-catenin signaling during development. It plays a role in the hematopoietic system.


Pssm-ID: 438798 [Multi-domain]  Cd Length: 61  Bit Score: 47.27  E-value: 1.11e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1974213328 1397 RKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERA 1450
Cdd:cd21982      1 KKKNMSAYQVFCKEYRVSIVAEHPGIDFGELSKKLAEVWKQLPEKDKLVWKQKA 54
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 564-639 1.20e-06

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 48.53  E-value: 1.20e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328  564 ELFMVKPSKKDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILK 639
Cdd:cd05508     21 EPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKICE 96
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 425-507 1.22e-06

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 48.99  E-value: 1.22e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  425 SEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNvPN--SAIYKRVLKMQQVMQA 502
Cdd:cd05496     23 SEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT-PNkrSRIYSMTLRLSALFEE 101


                   ....*
gi 1974213328  503 KKKEL 507
Cdd:cd05496    102 HIKKI 106
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 1401-1450 1.78e-06

high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family transcription factors; The SOX gene family of transcription factors are characterized by the evolutionarily conserved SRY-type HMG box, which is a DNA binding domain that binds the minor groove of DNA on a common consensus site, (A/T)(A/T)CAA(A/T)G but with different levels of efficiency. Members include SRY and its homologs identified in mammals that can be subdivided into 8 groups (A, B1, B2, C, D, E, F, G, H). They are involved in embryonic development, regulating processes such as cell differentiation, maintenance of stemness, sex determination, and development of the central nervous, haematopoietic and other organ systems. The SOX gene family has a crucial role in carcinogenesis and cancer progression.


Pssm-ID: 438820 [Multi-domain]  Cd Length: 75  Bit Score: 47.15  E-value: 1.78e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERA 1450
Cdd:cd22004      6 MNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEA 55
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 677-763 1.82e-06

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 48.21  E-value: 1.82e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  677 PMQQKLNEVYEAVKNYTDKrgrrlSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNAC 756
Cdd:cd05510      7 EFYESLDKVLNELKTYTEH-----STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCL 81


                   ....*..
gi 1974213328  757 TYNEPES 763
Cdd:cd05510     82 LYNSDPS 88
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 95-159 2.03e-06

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 47.71  E-value: 2.03e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328   95 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKL 159
Cdd:cd05506     27 VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKEL 91
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 101-173 2.75e-06

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 47.64  E-value: 2.75e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1974213328  101 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYVRTKNEFVQK 173
Cdd:cd05511     31 PDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAEELLAEREEK 103
HMG-box_AtHMGB9-like cd22009
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 ...
 1398-1452 3.22e-06

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 (HMGB9) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB9, 10, 11, and 15. They are DNA-binding proteins containing both HMG-box and AT-rich interaction domains. They bind preferentially to DNA with A/T-rich content. HMGB9 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily have only one HMG-box domain.


Pssm-ID: 438825 [Multi-domain]  Cd Length: 67  Bit Score: 46.30  E-value: 3.22e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328 1398 KINMSGYILFSSEMRAVIKAQHPDYSfGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd22009      2 KPNRSGYNFFFAEQHARLKALYPGKD-REISKMIGEMWSNLTEEEKEVYQDKGVE 55
BAH_Dnmt1_I cd04760
BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5) ...
 980-1057 6.16e-06

BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240107  Cd Length: 124  Bit Score: 47.07  E-value: 6.16e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1974213328  980 VGDYVYVEPAEANLQPHIVCIERLWEDSNGEKWLYGCWFYRPNETFHLATRKflEKEVFKSDYYNKVTVSKILGKCVV 1057
Cdd:cd04760      6 AGDCVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVLGETSD--PLELFLVDECEDMALSSIHGKVNV 81
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 410-501 6.23e-06

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 46.59  E-value: 6.23e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  410 YDTVRNCRNnqgqliSEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAI 489
Cdd:cd05507     12 YRTLASHRY------ASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDV 85

                           90
                   ....*....|...
gi 1974213328  490 YKRVLKMQQ-VMQ 501
Cdd:cd05507     86 YLMAVEMQReVMS 98
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 699-765 8.59e-06

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 45.99  E-value: 8.59e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328  699 RLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLI 765
Cdd:cd05505     16 RFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV 82
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 425-483 9.14e-06

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 45.88  E-value: 9.14e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328  425 SEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYN 483
Cdd:cd05501     18 SKSGFFISKPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFY 76
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 221-295 9.84e-06

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 45.82  E-value: 9.84e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328  221 HLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMTKDIDLLVKNAKTYNEPGSQVFKDANAI 295
Cdd:cd05507     18 HRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEM 92
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 69-145 1.01e-05

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 46.28  E-value: 1.01e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328   69 CHELYNTIRDYKDEQgrllcELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSY 145
Cdd:cd05510     12 LDKVLNELKTYTEHS-----TPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLY 83
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 1401-1452 1.29e-05

fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins; UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the fourth one.


Pssm-ID: 438817 [Multi-domain]  Cd Length: 66  Bit Score: 44.60  E-value: 1.29e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd22001      7 ISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEAL 58
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 95-148 1.54e-05

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 45.49  E-value: 1.54e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1974213328   95 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKP 148
Cdd:cd05497     32 AVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKP 85
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 438-490 1.85e-05

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 45.01  E-value: 1.85e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1974213328  438 PDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIY 490
Cdd:cd05506     33 PDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVH 85
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 69-145 1.92e-05

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 45.53  E-value: 1.92e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328   69 CHELYNTIRDYKDEqgrllcELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSY 145
Cdd:cd05496     10 CKELVNLMWDCEDS------EPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSY 80
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1392-1452 2.35e-05

third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the third one.


Pssm-ID: 438824 [Multi-domain]  Cd Length: 78  Bit Score: 44.17  E-value: 2.35e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1974213328 1392 KEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd22008      5 VDPNKPKKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAV 65
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 576-631 2.63e-05

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 44.66  E-value: 2.63e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328  576 PDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVYNDA 631
Cdd:cd05507     34 PGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMA 89
HMG-box_AtHMGB1-like cd22005
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 ...
 1402-1452 3.37e-05

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 (HMGB1) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB1, 2, 3, 4, 5, 7, 12 and 14. They bind preferentially to double-stranded DNA. HMGB1 modulates general plant growth and stress tolerance and confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. HMGB2 and HMGB5 confer sensitivity to salt and drought stresses. HMGB7 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily contain only one HMG-box domain.


Pssm-ID: 438821 [Multi-domain]  Cd Length: 60  Bit Score: 43.07  E-value: 3.37e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1974213328 1402 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd22005      5 TAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAEK 55
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 576-631 3.55e-05

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 44.32  E-value: 3.55e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328  576 PDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSqVYNDA 631
Cdd:cd05513     32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDT-IYYKA 86
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 1395-1452 4.10e-05

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.


Pssm-ID: 438809 [Multi-domain]  Cd Length: 62  Bit Score: 43.02  E-value: 4.10e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1974213328 1395 SKRKInmSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd21993      2 NKKKK--SGFQLWLEENRSSIEEENPELSEAEIIKLAMQRFRALPKEEKQKWNEKAKG 57
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 577-644 5.81e-05

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 43.57  E-value: 5.81e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1974213328  577 DYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYNEEGSQVyNDAHILEKILKEKRKE 644
Cdd:cd05501     32 DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDDDFG-QVGITLEKKFEKNFKE 98
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1402-1449 7.70e-05

first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438822 [Multi-domain]  Cd Length: 68  Bit Score: 42.44  E-value: 7.70e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1974213328 1402 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEER 1449
Cdd:cd22006      5 TAYFLWCKDQREEVKKENPNADFSEVSKILGAKWKNLSEEEKKPYEEK 52
HMG-box_SMARCE1 cd21983
high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent ...
 1404-1448 1.02e-04

high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1) and similar proteins; SMARCE1, also called BRG1-associated factor 57 (BAF57), is a ubiquitously expressed protein involved in transcriptional activation and repression of select genes by chromatin remodeling. It is a component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. SMARCE1 has a single HMG domain that displays non-specific DNA-binding characteristics. It also contains a kinesin-like coiled-coil (KLCC) domain.


Pssm-ID: 438799 [Multi-domain]  Cd Length: 73  Bit Score: 42.28  E-value: 1.02e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1974213328 1404 YILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEE 1448
Cdd:cd21983     12 YMRYSRKVWDQVKASNPDLKLWEIGKIIGQMWRELSDEEKQEYIE 56
HMG-box_BHMG1 cd21977
high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing ...
 1397-1451 1.13e-04

high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing protein 1 (BHMG1) and similar proteins; BHMG1 is an uncharacterized HMG-box containing protein that contains a degenerate basic motif not likely to bind DNA.


Pssm-ID: 438793 [Multi-domain]  Cd Length: 66  Bit Score: 41.92  E-value: 1.13e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328 1397 RKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAA 1451
Cdd:cd21977      1 KKKWVNGFIMFCRLNRKNYIDKHPGLASTELTKELGQLWRELSAEEKKPYCVRAR 55
BAH_plant_3 cd04713
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
 958-1096 1.19e-04

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240064  Cd Length: 146  Bit Score: 43.99  E-value: 1.19e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  958 SGLSNLHRTYSQDCSFKNSMYHVGDYVYVEPaEANLQPHIVCIERLWEDSNGEKWLYGCWFYRPNEtfhLATRKFLE--- 1034
Cdd:cd04713      1 TGKGKKKKCHYTSFEKDGNKYRLEDCVLLVP-EDDQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEE---IEKKKGGNwka 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328 1035 ---KEVFKSDYYNKVTVSKILGKCVVMFVKEYFKLcpENFRDEDVYVCESRYSAKTKsfkkiKLW 1096
Cdd:cd04713     77 edpRELFYSFHRDEVPAESVLHPCKVAFVPKGKQI--PLRKGHSGFIVRRVYDNVNK-----KLW 134
BAH_MTA cd04709
BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The ...
 975-1066 1.54e-04

BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240060  Cd Length: 164  Bit Score: 43.92  E-value: 1.54e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  975 NSMYHVGDYVYVEPAEANlqPHIVC-IERLWEDSNGEKWLYGCWFYR----PNETFHLAT--RKFLE------------- 1034
Cdd:cd04709      1 ANMYRVGDYVYFESSPNN--PYLIRrIEELNKTARGHVEAKVVCYYRrrdiPDSLYQLADqhRRELEeksddltpkqrhq 78

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1974213328 1035 ---KEVFKSDYYNKVTVSKILGKCVVMFVKEYFKL 1066
Cdd:cd04709     79 lrhRELFLSRQVETLPATHIRGKCSVTLLNDTESA 113
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 574-621 1.61e-04

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 42.73  E-value: 1.61e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1974213328  574 DYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYN 621
Cdd:cd05528     32 EVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
BAH_Orc1p_animal cd04719
BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces ...
 980-1061 1.77e-04

BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240070  Cd Length: 128  Bit Score: 43.13  E-value: 1.77e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  980 VGDYVYVEPAEANlQPHIVCIERLWEDSNGE---KWLYGCWFYRPNET----FHLATRKFLEKEVFKSDYY---NKVTVS 1049
Cdd:cd04719      6 VGDFVLIEGEDAD-GPDVARILHLYEDGNEDddpKRAIVQWFSRPSEVpknkRKLLGREPHSQEVFFYSRSscdNDIDAE 84

                           90
                   ....*....|..
gi 1974213328 1050 KILGKCVVMFVK 1061
Cdd:cd04719     85 TIIGKVRVEPVE 96
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 1401-1452 2.42e-04

high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; PMS1, also called DNA mismatch repair protein PMS1, is probably involved in the repair of mismatches in DNA.


Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 40.99  E-value: 2.42e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd21985      6 MSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAAK 57
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 1402-1452 2.60e-04

first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. ABF2 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438826 [Multi-domain]  Cd Length: 68  Bit Score: 40.98  E-value: 2.60e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1974213328 1402 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd22010      6 SAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLSADDKKKYEDDFQR 56
HMG-box_CIC-like cd21990
high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a ...
 1401-1453 3.16e-04

high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a transcriptional repressor which plays a role in the development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, CIC is involved in brain development.


Pssm-ID: 438806 [Multi-domain]  Cd Length: 78  Bit Score: 40.90  E-value: 3.16e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAKV 1453
Cdd:cd21990      6 MNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPEEKQKYHDLAFQV 58
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 707-782 3.56e-04

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 42.32  E-value: 3.56e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1974213328  707 LPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRD 782
Cdd:cd05529     52 VDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLRILSS 127
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 1402-1448 3.83e-04

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438827 [Multi-domain]  Cd Length: 75  Bit Score: 40.60  E-value: 3.83e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1974213328 1402 SGYILFSSEMRAVIKAQ-HPDYSFGELSRLVGTEWRNL-EASKKAEYEE 1448
Cdd:cd22011      6 SAYFLFSQEIRKNLKSQgSPEEKVPELSKRAAEQWRSLtLAEKQPYYDE 54
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 91-149 4.62e-04

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 41.26  E-value: 4.62e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328   91 FIRAPKRRNqpDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPD 149
Cdd:cd05501     23 FISKPYYIR--DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD 79
BAH_plant_1 cd04721
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
 980-1084 5.36e-04

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240072  Cd Length: 130  Bit Score: 41.66  E-value: 5.36e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  980 VGDYVYVEPAEANLqpHIVCIERLWEDSNGEKWLYGCWFYRPNET-FHLATRKFLEKEVFKSDYYNKVTVSKILGKCVVM 1058
Cdd:cd04721     10 VHDFVYVLSEEEDR--YVAYIEDLYEDKKGSKMVKVRWFHTTDEVgAALSPDSVNPREIFLSPNLQVISVECIDGLATVL 87

                           90       100
                   ....*....|....*....|....*....
gi 1974213328 1059 fVKEYFKLC---PENFRDEDVYVCESRYS 1084
Cdd:cd04721     88 -TREHYEKFqsvPKNSSELQAYFCYRQID 115
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 712-759 6.49e-04

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 41.19  E-value: 6.49e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1974213328  712 ELPDYYLTIKKPVDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYN 759
Cdd:cd05528     32 EVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 573-621 6.85e-04

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


Pssm-ID: 99944  Cd Length: 98  Bit Score: 40.46  E-value: 6.85e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1974213328  573 KDYPDYYKIILEPMDLKIIEYNIRSDKYAGEEAMIEDMRLMFRNARHYN 621
Cdd:cd05512     29 SEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN 77
HMG-box_SoxF_SOX7 cd22046
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar ...
 1389-1453 1.06e-03

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar proteins; SOX-7 is an endothelial-associated transcription factor that acts as a tumor suppressor in a number of cancer types. It binds the DNA sequence 5'-AACAAT-3'. SOX-7 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438849 [Multi-domain]  Cd Length: 88  Bit Score: 39.67  E-value: 1.06e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1974213328 1389 SVKKEGSKRKIN--MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAKV 1453
Cdd:cd22046      2 SPGEKGSEPRIRrpMNAFMVWAKDERKRLAVQNPDLHNAELSKMLGKSWKALTPSQKRPYVEEAERL 68
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 101-170 1.20e-03

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 40.78  E-value: 1.20e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  101 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYVRTKNEF 170
Cdd:cd05529     59 PDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLRILSSL 128
HMG-box_HMGB_rpt1 cd21978
first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 1396-1452 1.39e-03

first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian cells. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of the HMGB family that functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory responses. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. This family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa, is a tumor suppressor that is a major constituent of promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomere lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, binds preferentially to single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438794 [Multi-domain]  Cd Length: 69  Bit Score: 38.82  E-value: 1.39e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1974213328 1396 KRKINMSGYILFSSEMRAVIKAQHPDYS--FGELSRLVGTEWRNLEASKKAEYEERAAK 1452
Cdd:cd21978      1 KPRGKMSSYAFFVQTCREEHKKKHPNESvnFSEFSKKCSERWKTMSAKEKKKFEDMAKK 59
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 781-895 2.30e-03

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 40.01  E-value: 2.30e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  781 RDIEGDEDSHVPNVTLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVDPSFPSkpPLTFDIIRKNVENNRYRRLDLF 860
Cdd:cd05529     12 FDPGWEQPHIRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRAWYPDYWNRVPV--PMDLETIRSRLENRYYRSLEAL 89

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1974213328  861 QehmFDV--LER-ARRMNRTDSEIYEDAVELQQFFIKI 895
Cdd:cd05529     90 R---HDVrlILSnAETFNEPNSEIAKKAKRLSDWLLRI 124
PTZ00199 PTZ00199
high mobility group protein; Provisional
 1391-1451 2.39e-03

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 39.07  E-value: 2.39e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1974213328 1391 KKEGSKRKINMSGYILFSSEMRAVIKAQHPDYS--FGELSRLVGTEWRNLEASKKAEYEERAA 1451
Cdd:PTZ00199    17 KKDPNAPKRALSAYMFFAKEKRAEIIAENPELAkdVAAVGKMVGEAWNKLSEEEKAPYEKKAQ 79
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 101-155 2.44e-03

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 38.89  E-value: 2.44e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1974213328  101 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKA 155
Cdd:cd05503     31 PGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRA 85
BAH_Orc1p_like cd04715
BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of ...
 957-1065 4.56e-03

BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240066  Cd Length: 159  Bit Score: 39.80  E-value: 4.56e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1974213328  957 GSGLSNLHRTYSQDCSFKNSMYHVGDYVYVEPAEAnlQPHIVCIERLWEDSN--GEKWLYGCWFYRPNET--FHLATRKF 1032
Cdd:cd04715      9 GEGGKKKDGQFYRSFTYDGVEYRLYDDVYVHNGDS--EPYIGKIIKIYETAIdsGKKKVKVIWFFRPSEIrmELKGEPKR 86

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1974213328 1033 LEKEVFKS-----DYYNKVTVSKILGKCVVMFVKEYFK 1065
Cdd:cd04715     87 HINEVFLAcgrgeGLANINLLESIIGKCNVVCISEDFR 124
HMG-box_SoxF_SOX17 cd22047
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and ...
 1401-1453 5.27e-03

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and similar proteins; SOX-17 is a developmental transcription regulator involved in endoderm formation, angiogenesis, and carcinogenesis. It acts as a tumor suppressor and modulates WNT signaling. SOX-17 binds target promoter DNA and bends the DNA. It binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. SOX-17 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438850 [Multi-domain]  Cd Length: 81  Bit Score: 37.76  E-value: 5.27e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERAAKV 1453
Cdd:cd22047     11 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERL 63
HMG-box_HBP2 cd21989
high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar ...
 1401-1450 5.63e-03

high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar proteins; HBP2, also called HMG box transcription factor BBX, or Bobby sox homolog, is a transcription factor that is necessary for cell cycle progression from the G1 to S phase.


Pssm-ID: 438805 [Multi-domain]  Cd Length: 69  Bit Score: 37.00  E-value: 5.63e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1974213328 1401 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEASKKAEYEERA 1450
Cdd:cd21989      4 MNAFLLFCKRHRSLVRERHPRLDNRGITKILGDWWAVLDPDEKQKYTDLA 53
 
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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