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Conserved domains on  [gi|20137608|sp|Q9Z330|]
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RecName: Full=DNA (cytosine-5)-methyltransferase 1; Short=Dnmt1; AltName: Full=DNA MTase RnoIP; Short=M.RnoIP; AltName: Full=DNA methyltransferase I; AltName: Full=MCMT

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
BAH_Dnmt1_II cd04711
BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5) ...
 978-1106 4.65e-79

BAH, or Bromo Adjacent Homology domain, second 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: 240062  Cd Length: 137  Bit Score: 256.65  E-value: 4.65e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  978 YRKYSDYIKGSNLDAPEPYRIGRIKEIYCGKKKGGKVNEADIKIRLYKFYRPENTHKSIQATYHADINLLYWSDEEAVVD 1057
Cdd:cd04711    9 YRKSSDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKATYHADINMLYWSDEEATVD 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 20137608 1058 FSDVQGRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYNSKTKSFEDPPN 1106
Cdd:cd04711   89 FSAVQGRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFEDPPN 137
BAH_Dnmt1_I cd04760
BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5) ...
 759-881 8.81e-64

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: 212.32  E-value: 8.81e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  759 ETLEVGDCVSVIPDDPSKPLYLARVTALWEDKN-GQMFHAHWFCAGTDTVLGATSDPLELFLVGECENMQLSYIHSKVKV 837
Cdd:cd04760    2 EELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIgGKMFHAHWFCRGSDTVLGETSDPLELFLVDECEDMALSSIHGKVNV 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 20137608  838 IYRGPSPNWAMEGGMDPEaMLPGAEDGKTYFYQFWYSQDYARFE 881
Cdd:cd04760   82 IYKAPSENWSMEGGMDEE-DEIFEDDGKTFFYQKWYDPECARFE 124
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
1142-1600 3.29e-62

DNA-cytosine methylase [Replication, recombination and repair];


:

Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 214.29  E-value: 3.29e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1142 PKLRTLDVFSGCGGLTEGFHQAGIsETLWAIEMWEPAAQAFRLNNPGTTVFTEDcnvlLKLVMAGEVtnslgqrlpqKGD 1221
Cdd:COG0270    2 KKLTVIDLFAGAGGLSLGFEKAGF-EVVFAVEIDPDACETYRANFPEAKVIEGD----IRDIDPEEL----------IPD 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1222 VEMLCGGPPCQGFSGMNRfnSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFRRSMVLKLTLRCLVRMGYQCTF 1301
Cdd:COG0270   67 VDLLIGGPPCQPFSVAGK--RKGLEDPRGTLFFEFIRIVEELRPKAFVLENVPGLLSSDKGKTFEEILKELEELGYRVDY 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1302 GVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHvfapracqlsvvvddkkfvsnitrlssgPFRTITMRDTMSDLPE 1381
Cdd:COG0270  145 KVLNAADYGVPQNRERVFIVGFRKDLDLFEFPEPTH----------------------------LKPYVTVGDALEDLPD 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1382 iqngasapeisykwratvlvpeaaarvalpahpqgpypqvheraggcrmrhiplspgsdwrdlpniqvrlrdgvitnklr 1461
Cdd:COG0270      --------------------------------------------------------------------------------

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1462 ytfhdtkngcsstgalrgvcscaegktcdpasrqfntlipwclPHTGNRHnhwaglygrlewdgffSTTVTNpePMGKQG 1541
Cdd:COG0270  197 -------------------------------------------AHEARYL----------------SETITA--GYGGGG 215

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 20137608 1542 RVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDRHRQVGNAVPPPLAKAIGLEIKLCL 1600
Cdd:COG0270  216 RFLHPGEPRRLTVREAARLQGFPDDFKFPGSKTQAYRQIGNAVPPPLAEAIAKAILKAL 274
DNMT1-RFD pfam12047
Cytosine specific DNA methyltransferase replication foci domain; This domain is part of a ...
 405-540 1.57e-51

Cytosine specific DNA methyltransferase replication foci domain; This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties.


:

Pssm-ID: 463444  Cd Length: 143  Bit Score: 178.30  E-value: 1.57e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    405 YDSSPMHKFTFFSVYCSRGHLCPVDTGLIEKNVELYFSGVAKAIHEENPSVEG-GVNGKN----LGPINQWWISGFDGGE 479
Cdd:pfam12047    1 EEDRPQRKLTDFELYDKDGHLCPFDVLLIEKNVDIFISGIVKPIDEDEPSLDGkGIEDKGmqikLGPIKEWTISGFDGGE 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 20137608    480 KALIGFSTAFAEYFLMEPSPEYAPIFGLMQEKIYISKIVVEFLQSNP--DAVYEDLINKIETT 540
Cdd:pfam12047   81 KALIWLSTEFAWYKLLKPSAEYAPIYELVYEKARLSVEVVEFLQRSPgsELSYEDLINRVLTS 143
DMAP_binding pfam06464
DMAP1-binding Domain; This domain binds DMAP1, a transcriptional co-repressor.
 16-106 4.54e-24

DMAP1-binding Domain; This domain binds DMAP1, a transcriptional co-repressor.


:

Pssm-ID: 368923 [Multi-domain]  Cd Length: 104  Bit Score: 98.26  E-value: 4.54e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608     16 PAGSLPDHVRRRLKDLERDG----LTEKECVKEKLNLLHEFL---------QTEIKSQLCDLETKLHKEELSEEGYLAKV 82
Cdd:pfam06464    1 NPPSLPDDVRERLSELDLDLsegdITEKGYEKKKLKLLRKFLlhpetptklSAEAQNQLASLETKLRDEELSEEVYLEKV 80

                           90       100
                   ....*....|....*....|....
gi 20137608     83 KTLLNKDLCLENGTLSLTQKANGC 106
Cdd:pfam06464   81 KALLAKELERENGLNAPTKEQSGL 104
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 649-695 6.20e-19

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


:

Pssm-ID: 366873  Cd Length: 48  Bit Score: 81.63  E-value: 6.20e-19
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 20137608    649 ENTMKRRRCGVCEVCQQPE-CGKCKACKDMVKFGGTGRSKQACLKRRC 695
Cdd:pfam02008    1 RNRRKRRRCGVCEGCQRPEdCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 109-327 7.21e-06

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 50.67  E-value: 7.21e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   109 NGSRPTWKAEMADSNRSPRSRPKPRGPRRSKSDSETMIEASSSSVATRRTTRQTTITSHFKGPAKRKPKEDSEKGnanes 188
Cdd:PRK12678   60 GGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERG----- 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   189 AAEERDQDKKRRVAGTESRASRAGESVEKPERVRPGtqlcQEEQGEQEDDRRPRRQTRELASRRKSREDPDREARPGTHL 268
Cdd:PRK12678  135 EAARRGAARKAGEGGEQPATEARADAAERTEEEERD----ERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRRE 210

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 20137608   269 DVDDDDEKDKRSSRPRSQPRDLATKRRPKEEVEQITPEPPEGKDEDEREEKRRKTTRKK 327
Cdd:PRK12678  211 QGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDR 269
 
Name Accession Description Interval E-value
BAH_Dnmt1_II cd04711
BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5) ...
 978-1106 4.65e-79

BAH, or Bromo Adjacent Homology domain, second 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: 240062  Cd Length: 137  Bit Score: 256.65  E-value: 4.65e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  978 YRKYSDYIKGSNLDAPEPYRIGRIKEIYCGKKKGGKVNEADIKIRLYKFYRPENTHKSIQATYHADINLLYWSDEEAVVD 1057
Cdd:cd04711    9 YRKSSDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKATYHADINMLYWSDEEATVD 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 20137608 1058 FSDVQGRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYNSKTKSFEDPPN 1106
Cdd:cd04711   89 FSAVQGRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFEDPPN 137
BAH_Dnmt1_I cd04760
BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5) ...
 759-881 8.81e-64

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: 212.32  E-value: 8.81e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  759 ETLEVGDCVSVIPDDPSKPLYLARVTALWEDKN-GQMFHAHWFCAGTDTVLGATSDPLELFLVGECENMQLSYIHSKVKV 837
Cdd:cd04760    2 EELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIgGKMFHAHWFCRGSDTVLGETSDPLELFLVDECEDMALSSIHGKVNV 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 20137608  838 IYRGPSPNWAMEGGMDPEaMLPGAEDGKTYFYQFWYSQDYARFE 881
Cdd:cd04760   82 IYKAPSENWSMEGGMDEE-DEIFEDDGKTFFYQKWYDPECARFE 124
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
1142-1600 3.29e-62

DNA-cytosine methylase [Replication, recombination and repair];


Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 214.29  E-value: 3.29e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1142 PKLRTLDVFSGCGGLTEGFHQAGIsETLWAIEMWEPAAQAFRLNNPGTTVFTEDcnvlLKLVMAGEVtnslgqrlpqKGD 1221
Cdd:COG0270    2 KKLTVIDLFAGAGGLSLGFEKAGF-EVVFAVEIDPDACETYRANFPEAKVIEGD----IRDIDPEEL----------IPD 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1222 VEMLCGGPPCQGFSGMNRfnSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFRRSMVLKLTLRCLVRMGYQCTF 1301
Cdd:COG0270   67 VDLLIGGPPCQPFSVAGK--RKGLEDPRGTLFFEFIRIVEELRPKAFVLENVPGLLSSDKGKTFEEILKELEELGYRVDY 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1302 GVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHvfapracqlsvvvddkkfvsnitrlssgPFRTITMRDTMSDLPE 1381
Cdd:COG0270  145 KVLNAADYGVPQNRERVFIVGFRKDLDLFEFPEPTH----------------------------LKPYVTVGDALEDLPD 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1382 iqngasapeisykwratvlvpeaaarvalpahpqgpypqvheraggcrmrhiplspgsdwrdlpniqvrlrdgvitnklr 1461
Cdd:COG0270      --------------------------------------------------------------------------------

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1462 ytfhdtkngcsstgalrgvcscaegktcdpasrqfntlipwclPHTGNRHnhwaglygrlewdgffSTTVTNpePMGKQG 1541
Cdd:COG0270  197 -------------------------------------------AHEARYL----------------SETITA--GYGGGG 215

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 20137608 1542 RVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDRHRQVGNAVPPPLAKAIGLEIKLCL 1600
Cdd:COG0270  216 RFLHPGEPRRLTVREAARLQGFPDDFKFPGSKTQAYRQIGNAVPPPLAEAIAKAILKAL 274
DNMT1-RFD pfam12047
Cytosine specific DNA methyltransferase replication foci domain; This domain is part of a ...
 405-540 1.57e-51

Cytosine specific DNA methyltransferase replication foci domain; This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties.


Pssm-ID: 463444  Cd Length: 143  Bit Score: 178.30  E-value: 1.57e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    405 YDSSPMHKFTFFSVYCSRGHLCPVDTGLIEKNVELYFSGVAKAIHEENPSVEG-GVNGKN----LGPINQWWISGFDGGE 479
Cdd:pfam12047    1 EEDRPQRKLTDFELYDKDGHLCPFDVLLIEKNVDIFISGIVKPIDEDEPSLDGkGIEDKGmqikLGPIKEWTISGFDGGE 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 20137608    480 KALIGFSTAFAEYFLMEPSPEYAPIFGLMQEKIYISKIVVEFLQSNP--DAVYEDLINKIETT 540
Cdd:pfam12047   81 KALIWLSTEFAWYKLLKPSAEYAPIYELVYEKARLSVEVVEFLQRSPgsELSYEDLINRVLTS 143
DNA_methylase pfam00145
C-5 cytosine-specific DNA methylase;
1144-1597 3.02e-39

C-5 cytosine-specific DNA methylase;


Pssm-ID: 395093 [Multi-domain]  Cd Length: 324  Bit Score: 149.39  E-value: 3.02e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1144 LRTLDVFSGCGGLTEGFHQAGIsETLWAIEMWEPAAQAFRLNNPgTTVFtedcnvllklvmaGEVTNSLGQRLPqkgDVE 1223
Cdd:pfam00145    1 FKFIDLFAGIGGFRLGLEQAGF-ECVAANEIDKSAAKTYEANFP-KVPI-------------GDITLIDIKDIP---DID 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1224 MLCGGPPCQGFS--GMNRFNSRTYskfkNSLVVSFLSYCDYYRPRFFLLENVRNFVSFRRSMVLKLTLRCLVRMGYQCTF 1301
Cdd:pfam00145   63 ILTGGFPCQDFSiaGKQKGFEDTR----GTLFFEIIRIIKEKKPKAFLLENVKGLLSHDNGNTLNVILETLEELGYHVSW 138

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1302 GVLQAGQYGVAQTRRRAIILAAAPG-EKLPLFPEPlhvfapracqlsvvvddkkfvsnitrlssgPFRTITMRDTMSDLP 1380
Cdd:pfam00145  139 KVLNASDYGVPQNRERVFIVGIRKDlNLNVLVPVP------------------------------EFDFPKPKDLTGTIR 188

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1381 EIQNGASAPEISYKWrATVLVPEAAARVALPAHPQGPYPQVheraggcrmrhiplspgsdwrdlpNIQVRLRDGVITNKL 1460
Cdd:pfam00145  189 DLLEEPSLDENKYNL-SDKFVENHERRKPTTKAPGGGYPTY------------------------LLRNRIDKVEEGKGP 243

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1461 RYTFHDtkngcsstgalrgvcscaegktcdpasrqfntlipwclphtgnrhnhwaglYGRLEwdgffsttVTNPEPMGKQ 1540
Cdd:pfam00145  244 SFTYRK---------------------------------------------------SGRPE--------APKTGILGKN 264

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 20137608   1541 GR--VLHPEQHRVVSVRECARSQGFPDTYRLFGNILDRHRQVGNAVPPPLAKAIGLEIK 1597
Cdd:pfam00145  265 GErfRGHPKNIRRLTPRECARLQGFPDDFIFPGSKTQLYKQIGNAVPVPVAEAIAKAIK 323
BAH smart00439
Bromo adjacent homology domain;
983-1105 5.32e-34

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 127.02  E-value: 5.32e-34
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608     983 DYIKGSNLDAPEPYRIGRIKEIYCGKKkggkvNEADIKIRLYKFYRPENTHKSiqATYHADINLLYWSDEEAVVDFSDVQ 1062
Cdd:smart00439    6 DFVLVEPDDADEPYYIGRIEEIFETKK-----NSESKMVRVRWFYRPEETVLE--KAALFDKNEVFLSDEYDTVPLSDII 78

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|...
gi 20137608    1063 GRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYNSKTKSFEDPP 1105
Cdd:smart00439   79 GKCNVLYKSDYPGLRPEGSIGEPDVFFCESAYDPEKGSFKKLP 121
Cyt_C5_DNA_methylase cd00315
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
 1144-1597 1.75e-33

Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or 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.


Pssm-ID: 238192 [Multi-domain]  Cd Length: 275  Bit Score: 131.20  E-value: 1.75e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1144 LRTLDVFSGCGGLTEGFHQAGiSETLWAIEMWEPAAQAFRLNNPGTTVFtedcnvllklvmaGEVTNSLGQRLPqkGDVE 1223
Cdd:cd00315    1 LRVIDLFAGIGGFRLGLEKAG-FEIVAANEIDKSAAETYEANFPNKLIE-------------GDITKIDEKDFI--PDID 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1224 MLCGGPPCQGFS--GMNRFNSRTYSKfknslvvSFLSYCDY---YRPRFFLLENVRNFVSFRRSMVLKLTLRCLVRMGYQ 1298
Cdd:cd00315   65 LLTGGFPCQPFSiaGKRKGFEDTRGT-------LFFEIIRIlkeKKPKYFLLENVKGLLTHDNGNTLKVILNTLEELGYN 137

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1299 CTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFapracqlsvvvDDKKFVSNITRLSSGPFRTITMrdtmsd 1378
Cdd:cd00315  138 VYWKLLNASDYGVPQNRERVFIIGIRKDLILNFFSPFPKPS-----------EKKKTLKDILRIRDPDEPSPTL------ 200

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1379 lpeiqngasapeisykwratvlvpeaaarvalpahpqgpypqvheraggcrmrhiplspgsdwrdlpniqvrlrdgvitn 1458
Cdd:cd00315      --------------------------------------------------------------------------------

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1459 klrytfhdtkngcsstgalrgvcscaegktcdpasrqfntlipwclphTGNRHNHWAGLYgrlewdgffsttvtnpepMG 1538
Cdd:cd00315  201 ------------------------------------------------TASYGKGTGSVH------------------PT 214

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1539 KQGRVLHPEQHRVVSVRECARSQGFPDTYRLFG-NILDRHRQVGNAVPPPLAKAIGLEIK 1597
Cdd:cd00315  215 APDMIGKESNIRRLTPRECARLQGFPDDFEFPGkSVTQAYRQIGNSVPVPVAEAIAKAIK 274
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 983-1105 1.40e-30

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: 117.41  E-value: 1.40e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    983 DYIKGSNLDAPEPYRIGRIKEIYCGKKKGgkvneaDIKIRLYKFYRPENTHKSIQATYHADinLLYWSDEEAVVDFSDVQ 1062
Cdd:pfam01426    7 DFVLVEPDDADEPYYVARIEELFEDTKNG------KKMVRVQWFYRPEETVHRAGKAFNKD--ELFLSDEEDDVPLSAII 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 20137608   1063 GRCTVEYGEDLLESIQDYSqGGPDRFYFLEAYNSKTKSFEDPP 1105
Cdd:pfam01426   79 GKCSVLHKSDLESLDPYKI-KEPDDFFCELLYDPKTKSFKKLP 120
dcm TIGR00675
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
 1148-1596 2.06e-29

DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273211 [Multi-domain]  Cd Length: 315  Bit Score: 120.51  E-value: 2.06e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1148 DVFSGCGGLTEGFHQAGIsETLWAIEMWEPAAQAFRLNNPGTTVFtedcnvllklvmaGEVTNSLGQRLPqkgDVEMLCG 1227
Cdd:TIGR00675    3 DLFAGIGGIRLGFEQAGF-KCVFASEIDKYAQKTYEANFGNKVPF-------------GDITKISPSDIP---DFDILLG 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1228 GPPCQGFSgMNRFNsRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFRRSMVLKLTLRCLVRMGYQCTFGVLQAG 1307
Cdd:TIGR00675   66 GFPCQPFS-IAGKR-KGFEDTRGTLFFEIVRILKEKKPKFFLLENVKGLVSHDKGRTFKVIIETLEELGYKVYYKVLNAK 143

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1308 QYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKfvsnitRLSSGPFRTITMRDTMSDLPEiqNGAS 1387
Cdd:TIGR00675  144 DFGVPQNRERIYIVGFRDFDDKLNFEFPKPIYVAKKKRIGDLLDLSV------DLEEKYYLSEEKKNGLLLLLE--NMRK 215

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1388 APEISYKWRatvlvpeaaarvalpahpqgpypqvheraggcrmrhiPLSPGSDWrdlpniqvrlrdgvitnklrytfhdt 1467
Cdd:TIGR00675  216 KEGTGEQIG-------------------------------------SFYNRESK-------------------------- 232

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1468 kngcsstgalrgvcscaegktcdpaSRQFNTLipwclphTGNRHNHWAGlygrlewdgffstTVTNPEPMGKQGRVlHPE 1547
Cdd:TIGR00675  233 -------------------------SSIIRTL-------SARGYTFVKG-------------GKSVLIVPHKSTVV-HPG 266

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*....
gi 20137608   1548 QHRVVSVRECARSQGFPDTYRLFGNILDRHRQVGNAVPPPLAKAIGLEI 1596
Cdd:TIGR00675  267 RIRRLTPRECARLQGFPDDFKFPVSDSQLYKQAGNAVVVPVIEAIAKQI 315
BAH smart00439
Bromo adjacent homology domain;
760-884 3.59e-26

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 104.68  E-value: 3.59e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608     760 TLEVGDCVSVIPDDPSKPLYLARVTALWEDKNGQ---MFHAHWFCAGTDTVLGAT--SDPLELFLVGECENMQLSYIHSK 834
Cdd:smart00439    1 TISVGDFVLVEPDDADEPYYIGRIEEIFETKKNSeskMVRVRWFYRPEETVLEKAalFDKNEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|
gi 20137608     835 VKVIYRGPSPNWAMEGGMDPEamlpgaedgKTYFYQFWYSQDYARFESPP 884
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSIGEP---------DVFFCESAYDPEKGSFKKLP 121
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 759-884 4.75e-26

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: 104.31  E-value: 4.75e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    759 ETLEVGDCVSVIPDDPSKPLYLARVTALWEDKNG--QMFHAHWFCAGTDTV--LGATSDPLELFLVGECENMQLSYIHSK 834
Cdd:pfam01426    1 ETYSVGDFVLVEPDDADEPYYVARIEELFEDTKNgkKMVRVQWFYRPEETVhrAGKAFNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 20137608    835 VKVIYRGPSPNWAMEGGMDPeamlpgaedgKTYFYQFWYSQDYARFESPP 884
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEP----------DDFFCELLYDPKTKSFKKLP 120
DMAP_binding pfam06464
DMAP1-binding Domain; This domain binds DMAP1, a transcriptional co-repressor.
 16-106 4.54e-24

DMAP1-binding Domain; This domain binds DMAP1, a transcriptional co-repressor.


Pssm-ID: 368923 [Multi-domain]  Cd Length: 104  Bit Score: 98.26  E-value: 4.54e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608     16 PAGSLPDHVRRRLKDLERDG----LTEKECVKEKLNLLHEFL---------QTEIKSQLCDLETKLHKEELSEEGYLAKV 82
Cdd:pfam06464    1 NPPSLPDDVRERLSELDLDLsegdITEKGYEKKKLKLLRKFLlhpetptklSAEAQNQLASLETKLRDEELSEEVYLEKV 80

                           90       100
                   ....*....|....*....|....
gi 20137608     83 KTLLNKDLCLENGTLSLTQKANGC 106
Cdd:pfam06464   81 KALLAKELERENGLNAPTKEQSGL 104
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 649-695 6.20e-19

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


Pssm-ID: 366873  Cd Length: 48  Bit Score: 81.63  E-value: 6.20e-19
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 20137608    649 ENTMKRRRCGVCEVCQQPE-CGKCKACKDMVKFGGTGRSKQACLKRRC 695
Cdd:pfam02008    1 RNRRKRRRCGVCEGCQRPEdCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 109-327 7.21e-06

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 50.67  E-value: 7.21e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   109 NGSRPTWKAEMADSNRSPRSRPKPRGPRRSKSDSETMIEASSSSVATRRTTRQTTITSHFKGPAKRKPKEDSEKGnanes 188
Cdd:PRK12678   60 GGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERG----- 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   189 AAEERDQDKKRRVAGTESRASRAGESVEKPERVRPGtqlcQEEQGEQEDDRRPRRQTRELASRRKSREDPDREARPGTHL 268
Cdd:PRK12678  135 EAARRGAARKAGEGGEQPATEARADAAERTEEEERD----ERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRRE 210

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 20137608   269 DVDDDDEKDKRSSRPRSQPRDLATKRRPKEEVEQITPEPPEGKDEDEREEKRRKTTRKK 327
Cdd:PRK12678  211 QGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDR 269
Caldesmon pfam02029
Caldesmon;
173-353 5.08e-03

Caldesmon;


Pssm-ID: 460421 [Multi-domain]  Cd Length: 495  Bit Score: 41.39  E-value: 5.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    173 KRKPKEDSEKGNANESAAEERDQDKKrrvagTESRASRAGESVEKPERvRPGTQlcqEEQG--EQEDDRRPRRQTR--EL 248
Cdd:pfam02029   12 RRRAREERRRQKEEEEPSGQVTESVE-----PNEHNSYEEDSELKPSG-QGGLD---EEEAflDRTAKREERRQKRlqEA 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    249 ASRRKSREDPDREARPGTHLDVDDDDEKDKRSSRPRSQPRDL-------ATKRRPKEEVEQITP-EPPEGKDEDEREEKR 320
Cdd:pfam02029   83 LERQKEFDPTIADEKESVAERKENNEEEENSSWEKEEKRDSRlgrykeeETEIREKEYQENKWStEVRQAEEEGEEEEDK 162

                          170       180       190
                   ....*....|....*....|....*....|...
gi 20137608    321 RKTTRKKPEPLSIPVQSRVERKASQGKASAIPK 353
Cdd:pfam02029  163 SEEAEEVPTENFAKEEVKDEKIKKEKKVKYESK 195
 
Name Accession Description Interval E-value
BAH_Dnmt1_II cd04711
BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5) ...
 978-1106 4.65e-79

BAH, or Bromo Adjacent Homology domain, second 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: 240062  Cd Length: 137  Bit Score: 256.65  E-value: 4.65e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  978 YRKYSDYIKGSNLDAPEPYRIGRIKEIYCGKKKGGKVNEADIKIRLYKFYRPENTHKSIQATYHADINLLYWSDEEAVVD 1057
Cdd:cd04711    9 YRKSSDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKATYHADINMLYWSDEEATVD 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 20137608 1058 FSDVQGRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYNSKTKSFEDPPN 1106
Cdd:cd04711   89 FSAVQGRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFEDPPN 137
BAH_Dnmt1_I cd04760
BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5) ...
 759-881 8.81e-64

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: 212.32  E-value: 8.81e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  759 ETLEVGDCVSVIPDDPSKPLYLARVTALWEDKN-GQMFHAHWFCAGTDTVLGATSDPLELFLVGECENMQLSYIHSKVKV 837
Cdd:cd04760    2 EELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIgGKMFHAHWFCRGSDTVLGETSDPLELFLVDECEDMALSSIHGKVNV 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 20137608  838 IYRGPSPNWAMEGGMDPEaMLPGAEDGKTYFYQFWYSQDYARFE 881
Cdd:cd04760   82 IYKAPSENWSMEGGMDEE-DEIFEDDGKTFFYQKWYDPECARFE 124
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
1142-1600 3.29e-62

DNA-cytosine methylase [Replication, recombination and repair];


Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 214.29  E-value: 3.29e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1142 PKLRTLDVFSGCGGLTEGFHQAGIsETLWAIEMWEPAAQAFRLNNPGTTVFTEDcnvlLKLVMAGEVtnslgqrlpqKGD 1221
Cdd:COG0270    2 KKLTVIDLFAGAGGLSLGFEKAGF-EVVFAVEIDPDACETYRANFPEAKVIEGD----IRDIDPEEL----------IPD 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1222 VEMLCGGPPCQGFSGMNRfnSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFRRSMVLKLTLRCLVRMGYQCTF 1301
Cdd:COG0270   67 VDLLIGGPPCQPFSVAGK--RKGLEDPRGTLFFEFIRIVEELRPKAFVLENVPGLLSSDKGKTFEEILKELEELGYRVDY 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1302 GVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHvfapracqlsvvvddkkfvsnitrlssgPFRTITMRDTMSDLPE 1381
Cdd:COG0270  145 KVLNAADYGVPQNRERVFIVGFRKDLDLFEFPEPTH----------------------------LKPYVTVGDALEDLPD 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1382 iqngasapeisykwratvlvpeaaarvalpahpqgpypqvheraggcrmrhiplspgsdwrdlpniqvrlrdgvitnklr 1461
Cdd:COG0270      --------------------------------------------------------------------------------

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1462 ytfhdtkngcsstgalrgvcscaegktcdpasrqfntlipwclPHTGNRHnhwaglygrlewdgffSTTVTNpePMGKQG 1541
Cdd:COG0270  197 -------------------------------------------AHEARYL----------------SETITA--GYGGGG 215

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 20137608 1542 RVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDRHRQVGNAVPPPLAKAIGLEIKLCL 1600
Cdd:COG0270  216 RFLHPGEPRRLTVREAARLQGFPDDFKFPGSKTQAYRQIGNAVPPPLAEAIAKAILKAL 274
DNMT1-RFD pfam12047
Cytosine specific DNA methyltransferase replication foci domain; This domain is part of a ...
 405-540 1.57e-51

Cytosine specific DNA methyltransferase replication foci domain; This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties.


Pssm-ID: 463444  Cd Length: 143  Bit Score: 178.30  E-value: 1.57e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    405 YDSSPMHKFTFFSVYCSRGHLCPVDTGLIEKNVELYFSGVAKAIHEENPSVEG-GVNGKN----LGPINQWWISGFDGGE 479
Cdd:pfam12047    1 EEDRPQRKLTDFELYDKDGHLCPFDVLLIEKNVDIFISGIVKPIDEDEPSLDGkGIEDKGmqikLGPIKEWTISGFDGGE 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 20137608    480 KALIGFSTAFAEYFLMEPSPEYAPIFGLMQEKIYISKIVVEFLQSNP--DAVYEDLINKIETT 540
Cdd:pfam12047   81 KALIWLSTEFAWYKLLKPSAEYAPIYELVYEKARLSVEVVEFLQRSPgsELSYEDLINRVLTS 143
DNA_methylase pfam00145
C-5 cytosine-specific DNA methylase;
1144-1597 3.02e-39

C-5 cytosine-specific DNA methylase;


Pssm-ID: 395093 [Multi-domain]  Cd Length: 324  Bit Score: 149.39  E-value: 3.02e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1144 LRTLDVFSGCGGLTEGFHQAGIsETLWAIEMWEPAAQAFRLNNPgTTVFtedcnvllklvmaGEVTNSLGQRLPqkgDVE 1223
Cdd:pfam00145    1 FKFIDLFAGIGGFRLGLEQAGF-ECVAANEIDKSAAKTYEANFP-KVPI-------------GDITLIDIKDIP---DID 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1224 MLCGGPPCQGFS--GMNRFNSRTYskfkNSLVVSFLSYCDYYRPRFFLLENVRNFVSFRRSMVLKLTLRCLVRMGYQCTF 1301
Cdd:pfam00145   63 ILTGGFPCQDFSiaGKQKGFEDTR----GTLFFEIIRIIKEKKPKAFLLENVKGLLSHDNGNTLNVILETLEELGYHVSW 138

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1302 GVLQAGQYGVAQTRRRAIILAAAPG-EKLPLFPEPlhvfapracqlsvvvddkkfvsnitrlssgPFRTITMRDTMSDLP 1380
Cdd:pfam00145  139 KVLNASDYGVPQNRERVFIVGIRKDlNLNVLVPVP------------------------------EFDFPKPKDLTGTIR 188

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1381 EIQNGASAPEISYKWrATVLVPEAAARVALPAHPQGPYPQVheraggcrmrhiplspgsdwrdlpNIQVRLRDGVITNKL 1460
Cdd:pfam00145  189 DLLEEPSLDENKYNL-SDKFVENHERRKPTTKAPGGGYPTY------------------------LLRNRIDKVEEGKGP 243

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1461 RYTFHDtkngcsstgalrgvcscaegktcdpasrqfntlipwclphtgnrhnhwaglYGRLEwdgffsttVTNPEPMGKQ 1540
Cdd:pfam00145  244 SFTYRK---------------------------------------------------SGRPE--------APKTGILGKN 264

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 20137608   1541 GR--VLHPEQHRVVSVRECARSQGFPDTYRLFGNILDRHRQVGNAVPPPLAKAIGLEIK 1597
Cdd:pfam00145  265 GErfRGHPKNIRRLTPRECARLQGFPDDFIFPGSKTQLYKQIGNAVPVPVAEAIAKAIK 323
BAH smart00439
Bromo adjacent homology domain;
983-1105 5.32e-34

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 127.02  E-value: 5.32e-34
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608     983 DYIKGSNLDAPEPYRIGRIKEIYCGKKkggkvNEADIKIRLYKFYRPENTHKSiqATYHADINLLYWSDEEAVVDFSDVQ 1062
Cdd:smart00439    6 DFVLVEPDDADEPYYIGRIEEIFETKK-----NSESKMVRVRWFYRPEETVLE--KAALFDKNEVFLSDEYDTVPLSDII 78

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|...
gi 20137608    1063 GRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYNSKTKSFEDPP 1105
Cdd:smart00439   79 GKCNVLYKSDYPGLRPEGSIGEPDVFFCESAYDPEKGSFKKLP 121
Cyt_C5_DNA_methylase cd00315
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
 1144-1597 1.75e-33

Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or 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.


Pssm-ID: 238192 [Multi-domain]  Cd Length: 275  Bit Score: 131.20  E-value: 1.75e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1144 LRTLDVFSGCGGLTEGFHQAGiSETLWAIEMWEPAAQAFRLNNPGTTVFtedcnvllklvmaGEVTNSLGQRLPqkGDVE 1223
Cdd:cd00315    1 LRVIDLFAGIGGFRLGLEKAG-FEIVAANEIDKSAAETYEANFPNKLIE-------------GDITKIDEKDFI--PDID 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1224 MLCGGPPCQGFS--GMNRFNSRTYSKfknslvvSFLSYCDY---YRPRFFLLENVRNFVSFRRSMVLKLTLRCLVRMGYQ 1298
Cdd:cd00315   65 LLTGGFPCQPFSiaGKRKGFEDTRGT-------LFFEIIRIlkeKKPKYFLLENVKGLLTHDNGNTLKVILNTLEELGYN 137

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1299 CTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFapracqlsvvvDDKKFVSNITRLSSGPFRTITMrdtmsd 1378
Cdd:cd00315  138 VYWKLLNASDYGVPQNRERVFIIGIRKDLILNFFSPFPKPS-----------EKKKTLKDILRIRDPDEPSPTL------ 200

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1379 lpeiqngasapeisykwratvlvpeaaarvalpahpqgpypqvheraggcrmrhiplspgsdwrdlpniqvrlrdgvitn 1458
Cdd:cd00315      --------------------------------------------------------------------------------

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1459 klrytfhdtkngcsstgalrgvcscaegktcdpasrqfntlipwclphTGNRHNHWAGLYgrlewdgffsttvtnpepMG 1538
Cdd:cd00315  201 ------------------------------------------------TASYGKGTGSVH------------------PT 214

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1539 KQGRVLHPEQHRVVSVRECARSQGFPDTYRLFG-NILDRHRQVGNAVPPPLAKAIGLEIK 1597
Cdd:cd00315  215 APDMIGKESNIRRLTPRECARLQGFPDDFEFPGkSVTQAYRQIGNSVPVPVAEAIAKAIK 274
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 983-1105 1.40e-30

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: 117.41  E-value: 1.40e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    983 DYIKGSNLDAPEPYRIGRIKEIYCGKKKGgkvneaDIKIRLYKFYRPENTHKSIQATYHADinLLYWSDEEAVVDFSDVQ 1062
Cdd:pfam01426    7 DFVLVEPDDADEPYYVARIEELFEDTKNG------KKMVRVQWFYRPEETVHRAGKAFNKD--ELFLSDEEDDVPLSAII 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 20137608   1063 GRCTVEYGEDLLESIQDYSqGGPDRFYFLEAYNSKTKSFEDPP 1105
Cdd:pfam01426   79 GKCSVLHKSDLESLDPYKI-KEPDDFFCELLYDPKTKSFKKLP 120
dcm TIGR00675
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
 1148-1596 2.06e-29

DNA-methyltransferase (dcm); All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273211 [Multi-domain]  Cd Length: 315  Bit Score: 120.51  E-value: 2.06e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1148 DVFSGCGGLTEGFHQAGIsETLWAIEMWEPAAQAFRLNNPGTTVFtedcnvllklvmaGEVTNSLGQRLPqkgDVEMLCG 1227
Cdd:TIGR00675    3 DLFAGIGGIRLGFEQAGF-KCVFASEIDKYAQKTYEANFGNKVPF-------------GDITKISPSDIP---DFDILLG 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1228 GPPCQGFSgMNRFNsRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFRRSMVLKLTLRCLVRMGYQCTFGVLQAG 1307
Cdd:TIGR00675   66 GFPCQPFS-IAGKR-KGFEDTRGTLFFEIVRILKEKKPKFFLLENVKGLVSHDKGRTFKVIIETLEELGYKVYYKVLNAK 143

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1308 QYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKfvsnitRLSSGPFRTITMRDTMSDLPEiqNGAS 1387
Cdd:TIGR00675  144 DFGVPQNRERIYIVGFRDFDDKLNFEFPKPIYVAKKKRIGDLLDLSV------DLEEKYYLSEEKKNGLLLLLE--NMRK 215

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1388 APEISYKWRatvlvpeaaarvalpahpqgpypqvheraggcrmrhiPLSPGSDWrdlpniqvrlrdgvitnklrytfhdt 1467
Cdd:TIGR00675  216 KEGTGEQIG-------------------------------------SFYNRESK-------------------------- 232

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   1468 kngcsstgalrgvcscaegktcdpaSRQFNTLipwclphTGNRHNHWAGlygrlewdgffstTVTNPEPMGKQGRVlHPE 1547
Cdd:TIGR00675  233 -------------------------SSIIRTL-------SARGYTFVKG-------------GKSVLIVPHKSTVV-HPG 266

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*....
gi 20137608   1548 QHRVVSVRECARSQGFPDTYRLFGNILDRHRQVGNAVPPPLAKAIGLEI 1596
Cdd:TIGR00675  267 RIRRLTPRECARLQGFPDDFKFPVSDSQLYKQAGNAVVVPVIEAIAKQI 315
BAH smart00439
Bromo adjacent homology domain;
760-884 3.59e-26

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 104.68  E-value: 3.59e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608     760 TLEVGDCVSVIPDDPSKPLYLARVTALWEDKNGQ---MFHAHWFCAGTDTVLGAT--SDPLELFLVGECENMQLSYIHSK 834
Cdd:smart00439    1 TISVGDFVLVEPDDADEPYYIGRIEEIFETKKNSeskMVRVRWFYRPEETVLEKAalFDKNEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|
gi 20137608     835 VKVIYRGPSPNWAMEGGMDPEamlpgaedgKTYFYQFWYSQDYARFESPP 884
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSIGEP---------DVFFCESAYDPEKGSFKKLP 121
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 759-884 4.75e-26

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: 104.31  E-value: 4.75e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    759 ETLEVGDCVSVIPDDPSKPLYLARVTALWEDKNG--QMFHAHWFCAGTDTV--LGATSDPLELFLVGECENMQLSYIHSK 834
Cdd:pfam01426    1 ETYSVGDFVLVEPDDADEPYYVARIEELFEDTKNgkKMVRVQWFYRPEETVhrAGKAFNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 20137608    835 VKVIYRGPSPNWAMEGGMDPeamlpgaedgKTYFYQFWYSQDYARFESPP 884
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEP----------DDFFCELLYDPKTKSFKKLP 120
DMAP_binding pfam06464
DMAP1-binding Domain; This domain binds DMAP1, a transcriptional co-repressor.
 16-106 4.54e-24

DMAP1-binding Domain; This domain binds DMAP1, a transcriptional co-repressor.


Pssm-ID: 368923 [Multi-domain]  Cd Length: 104  Bit Score: 98.26  E-value: 4.54e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608     16 PAGSLPDHVRRRLKDLERDG----LTEKECVKEKLNLLHEFL---------QTEIKSQLCDLETKLHKEELSEEGYLAKV 82
Cdd:pfam06464    1 NPPSLPDDVRERLSELDLDLsegdITEKGYEKKKLKLLRKFLlhpetptklSAEAQNQLASLETKLRDEELSEEVYLEKV 80

                           90       100
                   ....*....|....*....|....
gi 20137608     83 KTLLNKDLCLENGTLSLTQKANGC 106
Cdd:pfam06464   81 KALLAKELERENGLNAPTKEQSGL 104
BAH cd04370
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). ...
 977-1101 1.35e-19

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: 86.29  E-value: 1.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  977 TYRKY-SDYIKGSNLDAPEPYRIGRIKEIYCGKkkggkvnEADIKIRLYKFYRPENTHKSiqATYHADINLLYWSDEEAV 1055
Cdd:cd04370    3 TYEVGdSVYVEPDDSIKSDPPYIARIEELWEDT-------NGSKQVKVRWFYRPEETPKG--LSPFALRRELFLSDHLDE 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 20137608 1056 VDFSDVQGRCTVEYGEDLLESIQDYSQGGPDRFYFLEAYNSKTKSF 1101
Cdd:cd04370   74 IPVESIIGKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEF 119
zf-CXXC pfam02008
CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to ...
 649-695 6.20e-19

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.


Pssm-ID: 366873  Cd Length: 48  Bit Score: 81.63  E-value: 6.20e-19
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 20137608    649 ENTMKRRRCGVCEVCQQPE-CGKCKACKDMVKFGGTGRSKQACLKRRC 695
Cdd:pfam02008    1 RNRRKRRRCGVCEGCQRPEdCGQCSFCLDMPKFGGPGKKKQKCRLRRC 48
BAH cd04370
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). ...
 758-882 1.81e-17

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: 80.13  E-value: 1.81e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  758 EETLEVGDCVSVIPDD--PSKPLYLARVTALWEDKNG-QMFHAHWFCAGTDTVLGATS--DPLELFLVGECENMQLSYIH 832
Cdd:cd04370    1 GITYEVGDSVYVEPDDsiKSDPPYIARIEELWEDTNGsKQVKVRWFYRPEETPKGLSPfaLRRELFLSDHLDEIPVESII 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 20137608  833 SKVKVIYrgPSPNWameggmdPEAMLPGAEDGKTYFYQFWYSQDYARFES 882
Cdd:cd04370   81 GKCKVLF--VSEFE-------GLKQRPNKIDTDDFFCRLAYDPTTKEFKA 121
BAH_plantDCM_II cd04708
BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5) ...
 931-1156 1.73e-14

BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. 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: 240059  Cd Length: 202  Bit Score: 74.03  E-value: 1.73e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  931 TKNGVVYRLGDSVYLPPEAFtfnikmaspmkrskrdpvNENPVPRDTYRKysdyikGSNLDAPePYRIGRIKEIYCGKK- 1009
Cdd:cd04708    2 VYDGVTYSVGDFLYVSPDAF------------------AEEERERATFKA------GRNVGLK-AFVVCQVLEIVVEKEs 56

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608 1010 KGGKVNEADIKIRlyKFYRPENThkSIQATYHADINLLYWSDEEAVVDFSDVQGRCTVEYGEDLLESiQDYSQGGPdRFY 1089
Cdd:cd04708   57 KQADVASTQVKVR--RFYRPEDV--SPEKAYASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDS-DAPVIFEH-VFF 130

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 20137608 1090 FLEAYNSKTKSFEDPPNHARSPGNKGKGKGKGKGK-----GKPQVSEPKEPEAAIKLPKLRTLDVFSGCGGL 1156
Cdd:cd04708  131 CELLYDPAKGSLKQLPPNIKEEAYSTGASDSALRKrkgkgKGDSESDSEAPVKAPKENRLATLDIFAGCGGL 202
BAH_fungalPHD cd04710
BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. ...
 994-1103 3.48e-08

BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. 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: 240061  Cd Length: 135  Bit Score: 53.91  E-value: 3.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  994 EPYRIGRIKEiYCGKKKGGKVNEADIK------IRLYKFYRPenthKSIQATYHADINLLYWSDEEAVVDFSDVQGRCTV 1067
Cdd:cd04710   27 EPYYIGRIME-FVPKHEFPSGIHARVFpasyfqVRLNWYYRP----RDISRRVVADSRLLYASMHSDICPIGSVRGKCTV 101

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 20137608 1068 EYgEDLLESIQDYSQgGPDRFYFLEAYNSKTKSFED 1103
Cdd:cd04710  102 RH-RDQIPDLEEYKK-RPNHFYFDQLFDRYILRYYD 135
BAH_DCM_I cd04712
BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) ...
 756-839 1.44e-06

BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. 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: 240063  Cd Length: 130  Bit Score: 48.94  E-value: 1.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608  756 IDEETLEVGDCVSVIPDDPSKPLYLA----------RVTALWEDKNG-QMFHAHWFCAGTDTVLGATSDPLELFLVGECE 824
Cdd:cd04712    1 IHGLTIRVGDVVSVERDDADSTTKWNddhrwlplvqFVEYMKKGSDGsKMFHGRWLYRGCDTVLGNYANERELFLTNECT 80

                         90
                 ....*....|....*
gi 20137608  825 NMQLSYIHSKVKVIY 839
Cdd:cd04712   81 CLELDLLSTEIKGVH 95
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 109-327 7.21e-06

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 50.67  E-value: 7.21e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   109 NGSRPTWKAEMADSNRSPRSRPKPRGPRRSKSDSETMIEASSSSVATRRTTRQTTITSHFKGPAKRKPKEDSEKGnanes 188
Cdd:PRK12678   60 GGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERG----- 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   189 AAEERDQDKKRRVAGTESRASRAGESVEKPERVRPGtqlcQEEQGEQEDDRRPRRQTRELASRRKSREDPDREARPGTHL 268
Cdd:PRK12678  135 EAARRGAARKAGEGGEQPATEARADAAERTEEEERD----ERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRRE 210

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 20137608   269 DVDDDDEKDKRSSRPRSQPRDLATKRRPKEEVEQITPEPPEGKDEDEREEKRRKTTRKK 327
Cdd:PRK12678  211 QGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDR 269
PTZ00121 PTZ00121
MAEBL; Provisional
 172-350 2.43e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 49.37  E-value: 2.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   172 AKRKPKEDSEKGNANESAAEERDQDKKRRV----AGTESRAS---RAGESVEKPERVRPGTQLCQEEQGEQEDDRRPRRQ 244
Cdd:PTZ00121 1495 AKKKADEAKKAAEAKKKADEAKKAEEAKKAdeakKAEEAKKAdeaKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEE 1574

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   245 TRELASRRKSREDPDREARPGTHLDVDDDDEKDK-RSSRPRSQPRDLATKRRPKEEVEQitpePPEGKDEDEREEKRRKT 323
Cdd:PTZ00121 1575 DKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKaEEAKKAEEAKIKAEELKKAEEEKK----KVEQLKKKEAEEKKKAE 1650

                         170       180
                  ....*....|....*....|....*..
gi 20137608   324 TRKKPEPLSIPVQSRVERKASQGKASA 350
Cdd:PTZ00121 1651 ELKKAEEENKIKAAEEAKKAEEDKKKA 1677
rne PRK10811
ribonuclease E; Reviewed
 168-357 2.46e-05

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 49.27  E-value: 2.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   168 FKGPAKRKPKEDSEKGNANEsaaEERDQDkkRRVAGTESRASRAGESVEKPERVRpgtqlcqEEQGEQ-EDDRRPRRQTR 246
Cdd:PRK10811  580 FSGGEETKPQEQPAPKAEAK---PERQQD--RRKPRQNNRRDRNERRDTRDNRTR-------REGRENrEENRRNRRQAQ 647

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   247 ElasrrksREDPDREARPGTHLDVDDDDEKDKRSSRPRSQPRDLATKRRPKEEVEQITPEPPEGKDEDEREEKRRKTTRK 326
Cdd:PRK10811  648 Q-------QTAETRESQQAEVTEKARTQDEQQQAPRRERQRRRNDEKRQAQQEAKALNVEEQSVQETEQEERVQQVQPRR 720

                         170       180       190
                  ....*....|....*....|....*....|...
gi 20137608   327 KPEPLS--IPVQSRVERKASQGKASAIPKLNPP 357
Cdd:PRK10811  721 KQRQLNqkVRIEQSVAEEAVAPVVEETVAAEPV 753
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 761-800 2.80e-05

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: 45.27  E-value: 2.80e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 20137608  761 LEVGDCVSVIPDDPSKPLYLARVTALWEDKNGQ-MFHAHWF 800
Cdd:cd04717    4 YRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEkFFFGCWF 44
BAH_BAHCC1 cd04714
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. ...
 758-800 6.16e-05

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: 44.31  E-value: 6.16e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 20137608  758 EETLEVGDCVSVIPDDPSKPLYLARVTALWEDKNGQM-FHAHWF 800
Cdd:cd04714    1 KEIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMvVRVKWY 44
PTZ00121 PTZ00121
MAEBL; Provisional
 169-329 9.90e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.44  E-value: 9.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   169 KGPAKRKPKEDSEKGNANESAAEERDQDKKRRVAGTESRASRAGESVEKPERvRPGTQLCQEEQGEQEDDRRPRRQTREL 248
Cdd:PTZ00121 1606 KMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEE-ENKIKAAEEAKKAEEDKKKAEEAKKAE 1684

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   249 ASRRKSREDPDREARpgthldvddDDEKDKRSSRPRSQPRDLATKRRPKEEVEQITPEppEGKDEDEREEKRRKTTRKKP 328
Cdd:PTZ00121 1685 EDEKKAAEALKKEAE---------EAKKAEELKKKEAEEKKKAEELKKAEEENKIKAE--EAKKEAEEDKKKAEEAKKDE 1753


                  .
gi 20137608   329 E 329
Cdd:PTZ00121 1754 E 1754
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 107-321 4.24e-04

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 44.89  E-value: 4.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   107 PANGSRPTWKAEMADSNRSPRSRPKPRGPRRSKSDSETMIEASSSSVATRRTTRQTTITSHfkgPAKRKPKEDSEKGNAN 186
Cdd:PRK12678   75 AAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGE---AARRGAARKAGEGGEQ 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   187 ESAAEERDQDKKRRVAGTESRASRAGESVEKPERVRPGTQLCQEEQ--GEQEDDRRPRRQTRElASRRKSREDPDREARP 264
Cdd:PRK12678  152 PATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGrdGDDRDRRDRREQGDR-REERGRRDGGDRRGRR 230

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 20137608   265 GthldvddddekdkRSSRPRSQPRDLATKRRPKEEVEQITPEPPEGKDEDEREEKRR 321
Cdd:PRK12678  231 R-------------RRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGR 274
Caldesmon pfam02029
Caldesmon;
173-353 5.08e-03

Caldesmon;


Pssm-ID: 460421 [Multi-domain]  Cd Length: 495  Bit Score: 41.39  E-value: 5.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    173 KRKPKEDSEKGNANESAAEERDQDKKrrvagTESRASRAGESVEKPERvRPGTQlcqEEQG--EQEDDRRPRRQTR--EL 248
Cdd:pfam02029   12 RRRAREERRRQKEEEEPSGQVTESVE-----PNEHNSYEEDSELKPSG-QGGLD---EEEAflDRTAKREERRQKRlqEA 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608    249 ASRRKSREDPDREARPGTHLDVDDDDEKDKRSSRPRSQPRDL-------ATKRRPKEEVEQITP-EPPEGKDEDEREEKR 320
Cdd:pfam02029   83 LERQKEFDPTIADEKESVAERKENNEEEENSSWEKEEKRDSRlgrykeeETEIREKEYQENKWStEVRQAEEEGEEEEDK 162

                          170       180       190
                   ....*....|....*....|....*....|...
gi 20137608    321 RKTTRKKPEPLSIPVQSRVERKASQGKASAIPK 353
Cdd:pfam02029  163 SEEAEEVPTENFAKEEVKDEKIKKEKKVKYESK 195
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 100-263 5.43e-03

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 41.43  E-value: 5.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   100 TQKANGCPANGSRPTWKAEMADSNRSPRSRPKPRGPRRSKSDSETMIEASSSSVATRRTTRQTTITSHFKGPAKRKPKED 179
Cdd:PRK12678   76 AARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATE 155

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 20137608   180 SEKGNANESAAEERDQDKKRRVAGTESRASRAGESVEKPERVRPGTQLCQE---EQGEQEDDR--RPRRQTRELASRRKS 254
Cdd:PRK12678  156 ARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRdrrEQGDRREERgrRDGGDRRGRRRRRDR 235


                  ....*....
gi 20137608   255 REDPDREAR 263
Cdd:PRK12678  236 RDARGDDNR 244
 
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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