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Conserved domains on  [gi|970318137|ref|WP_058685590|]
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MULTISPECIES: DNA (cytosine-5-)-methyltransferase [Enterobacteriaceae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
71-407 7.91e-125

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


:

Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 361.82  E-value: 7.91e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  71 NNIYTVLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNRPEWNVVEGDVSKVDFTPYRDTVDVLAGGFPCQAFS 150
Cdd:COG0270    1 SKKLTVIDLFAGAGGLSLGFEKAGFEVVFAVEIDPDACETYRANFPEAKVIEGDIRDIDPEELIPDVDLLIGGPPCQPFS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 151 YAGKKLGFEDTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTlFEPRVLKAIFYKVPQKRE 230
Cdd:COG0270   81 VAGKRKGLEDPRGTLFFEFIRIVEELRPKAFVLENVPGLLSSDKGKTFEEILKELEELGYR-VDYKVLNAADYGVPQNRE 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 231 RLIIVAVRNDLaNGIDYEWPSSYNKILTLKDALKkgelydsdvpesegqkypkrkaeilsmvppggywrDLPEDIQKEYM 310
Cdd:COG0270  160 RVFIVGFRKDL-DLFEFPEPTHLKPYVTVGDALE-----------------------------------DLPDAHEARYL 203

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 311 lksfylgggktgmarrlswdepSLTLTCAPAqKQTERCHPEETRPLTVREYARIQTFPDDWVFEGPMSAKYKQIGNAVPV 390
Cdd:COG0270  204 ----------------------SETITAGYG-GGGRFLHPGEPRRLTVREAARLQGFPDDFKFPGSKTQAYRQIGNAVPP 260

                        330
                 ....*....|....*..
gi 970318137 391 NLSFAVGKSVVHLLEKI 407
Cdd:COG0270  261 PLAEAIAKAILKALEKL 277
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 6-52 1.55e-11

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


:

Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 58.75  E-value: 1.55e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNdENNYRFYRKDQLKHF 52
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRT-PGGHRRFPEEDLERL 46
 
Name Accession Description Interval E-value
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
71-407 7.91e-125

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


Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 361.82  E-value: 7.91e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  71 NNIYTVLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNRPEWNVVEGDVSKVDFTPYRDTVDVLAGGFPCQAFS 150
Cdd:COG0270    1 SKKLTVIDLFAGAGGLSLGFEKAGFEVVFAVEIDPDACETYRANFPEAKVIEGDIRDIDPEELIPDVDLLIGGPPCQPFS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 151 YAGKKLGFEDTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTlFEPRVLKAIFYKVPQKRE 230
Cdd:COG0270   81 VAGKRKGLEDPRGTLFFEFIRIVEELRPKAFVLENVPGLLSSDKGKTFEEILKELEELGYR-VDYKVLNAADYGVPQNRE 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 231 RLIIVAVRNDLaNGIDYEWPSSYNKILTLKDALKkgelydsdvpesegqkypkrkaeilsmvppggywrDLPEDIQKEYM 310
Cdd:COG0270  160 RVFIVGFRKDL-DLFEFPEPTHLKPYVTVGDALE-----------------------------------DLPDAHEARYL 203

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 311 lksfylgggktgmarrlswdepSLTLTCAPAqKQTERCHPEETRPLTVREYARIQTFPDDWVFEGPMSAKYKQIGNAVPV 390
Cdd:COG0270  204 ----------------------SETITAGYG-GGGRFLHPGEPRRLTVREAARLQGFPDDFKFPGSKTQAYRQIGNAVPP 260

                        330
                 ....*....|....*..
gi 970318137 391 NLSFAVGKSVVHLLEKI 407
Cdd:COG0270  261 PLAEAIAKAILKALEKL 277
dcm TIGR00675
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
 76-400 5.72e-115

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: 338.53  E-value: 5.72e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137   76 VLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNRPEwNVVEGDVSKVDFTPYRDtVDVLAGGFPCQAFSYAGKK 155
Cdd:TIGR00675   1 FIDLFAGIGGIRLGFEQAGFKCVFASEIDKYAQKTYEANFGN-KVPFGDITKISPSDIPD-FDILLGGFPCQPFSIAGKR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  156 LGFEDTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTLFEpRVLKAIFYKVPQKRERLIIV 235
Cdd:TIGR00675  79 KGFEDTRGTLFFEIVRILKEKKPKFFLLENVKGLVSHDKGRTFKVIIETLEELGYKVYY-KVLNAKDFGVPQNRERIYIV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  236 AVRNDLANgIDYEWPSSYNkiltLKDALKKGELYDSDVPESEGQKYPKRKAEILSMVPPGGYWRDLpediqKEYMLKSFY 315
Cdd:TIGR00675 158 GFRDFDDK-LNFEFPKPIY----VAKKKRIGDLLDLSVDLEEKYYLSEEKKNGLLLLLENMRKKEG-----TGEQIGSFY 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  316 LGGGKTGMARRLSWD-----EPSLTLTCAPAQKQteRCHPEETRPLTVREYARIQTFPDDWVFEGPMSAKYKQIGNAVPV 390
Cdd:TIGR00675 228 NRESKSSIIRTLSARgytfvKGGKSVLIVPHKST--VVHPGRIRRLTPRECARLQGFPDDFKFPVSDSQLYKQAGNAVVV 305

                         330
                  ....*....|
gi 970318137  391 NLSFAVGKSV 400
Cdd:TIGR00675 306 PVIEAIAKQI 315
DNA_methylase pfam00145
C-5 cytosine-specific DNA methylase;
74-402 5.35e-101

C-5 cytosine-specific DNA methylase;


Pssm-ID: 395093 [Multi-domain]  Cd Length: 324  Bit Score: 303.08  E-value: 5.35e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137   74 YTVLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNRPEwnVVEGDVSKVDFTPYRDtVDVLAGGFPCQAFSYAG 153
Cdd:pfam00145   1 FKFIDLFAGIGGFRLGLEQAGFECVAANEIDKSAAKTYEANFPK--VPIGDITLIDIKDIPD-IDILTGGFPCQDFSIAG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  154 KKLGFEDTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTLFePRVLKAIFYKVPQKRERLI 233
Cdd:pfam00145  78 KQKGFEDTRGTLFFEIIRIIKEKKPKAFLLENVKGLLSHDNGNTLNVILETLEELGYHVS-WKVLNASDYGVPQNRERVF 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  234 IVAVRNDL-----ANGIDYEWPSSYNKILTLKDaLKKGELYDSDVPESEGQKYPKRKAEILSMVPPGGYWRDLpedIQKE 308
Cdd:pfam00145 157 IVGIRKDLnlnvlVPVPEFDFPKPKDLTGTIRD-LLEEPSLDENKYNLSDKFVENHERRKPTTKAPGGGYPTY---LLRN 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  309 yMLKSFYLGGGKTGMARRLSWDEPSLTLtcaPAQKQTER--CHPEETRPLTVREYARIQTFPDDWVFEGPMSAKYKQIGN 386
Cdd:pfam00145 233 -RIDKVEEGKGPSFTYRKSGRPEAPKTG---ILGKNGERfrGHPKNIRRLTPRECARLQGFPDDFIFPGSKTQLYKQIGN 308

                         330
                  ....*....|....*.
gi 970318137  387 AVPVNLSFAVGKSVVH 402
Cdd:pfam00145 309 AVPVPVAEAIAKAIKK 324
Cyt_C5_DNA_methylase cd00315
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
 74-402 1.70e-97

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: 292.22  E-value: 1.70e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  74 YTVLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNRPEWnVVEGDVSKVDFTPYRDTVDVLAGGFPCQAFSYAG 153
Cdd:cd00315    1 LRVIDLFAGIGGFRLGLEKAGFEIVAANEIDKSAAETYEANFPNK-LIEGDITKIDEKDFIPDIDLLTGGFPCQPFSIAG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 154 KKLGFEDTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTLFePRVLKAIFYKVPQKRERLI 233
Cdd:cd00315   80 KRKGFEDTRGTLFFEIIRILKEKKPKYFLLENVKGLLTHDNGNTLKVILNTLEELGYNVY-WKLLNASDYGVPQNRERVF 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 234 IVAVRNDLANGIDYEWPSSYNKILTLKDALkkgelydsdvpesegqkypkrkaeilsmvppggywrdlpediqkeymlks 313
Cdd:cd00315  159 IIGIRKDLILNFFSPFPKPSEKKKTLKDIL-------------------------------------------------- 188

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 314 fylgggktgmaRRLSWDEPSLTLTC--APAQKQTERC------HPEETRPLTVREYARIQTFPDDWVF-EGPMSAKYKQI 384
Cdd:cd00315  189 -----------RIRDPDEPSPTLTAsyGKGTGSVHPTapdmigKESNIRRLTPRECARLQGFPDDFEFpGKSVTQAYRQI 257

                        330
                 ....*....|....*...
gi 970318137 385 GNAVPVNLSFAVGKSVVH 402
Cdd:cd00315  258 GNSVPVPVAEAIAKAIKE 275
PRK10458 PRK10458
DNA cytosine methylase; Provisional
 18-398 1.12e-29

DNA cytosine methylase; Provisional


Pssm-ID: 236696 [Multi-domain]  Cd Length: 467  Bit Score: 119.78  E-value: 1.12e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  18 SKETLRRWdTAGKLVSQRNDENNYRFYRK---DQLKHFEQAQFLFksqwsdesktcnniytvLELFAGAGGMALGLEKAG 94
Cdd:PRK10458  48 SRAILKRW-LAGKSAWHRLSEAEFAHLQTllpKPPAHHPHYAFRF-----------------IDLFAGIGGIRRGFEAIG 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  95 LKSVLLNEIDSHACKTLRKN---RPEWNVVEGDVSKVDFTpYRDTV----------------DVLAGGFPCQAFSYAG-- 153
Cdd:PRK10458 110 GQCVFTSEWNKHAVRTYKANwycDPATHRFNEDIRDITLS-HKEGVsdeeaaehirqhipdhDVLLAGFPCQPFSLAGvs 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 154 KK------LGFE-DTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTLF--------EPRVL 218
Cdd:PRK10458 189 KKnslgraHGFEcETQGTLFFDVARIIDAKRPAIFVLENVKNLKSHDKGKTFRIIMQTLDELGYDVAdaedngpdDPKII 268

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 219 KAIFYkVPQKRERLIIVAVRNDLANGIDYewpssynkilTLKDALKK--------GELYDSDVPEsegqKYpkrkaeILS 290
Cdd:PRK10458 269 DGKHF-LPQHRERIVLVGFRRDLNLKADF----------TLRDISECypaqrptlAELLDPVVDA----KY------ILT 327

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 291 MVppggYWRDLpEDIQKEYMLKSFYLGGG------KTGMARRLS---------------WDEPSLTLTCAPAQKQTERch 349
Cdd:PRK10458 328 PV----LWKYL-YRYAKKHQAKGNGFGYGlvypnnPQSVTRTLSaryykdgseilidrgWDMALGEKDFDDPENQQHR-- 400

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970318137 350 peeTRPLTVREYARIQTF--PDDWVFEGPMS--AKYKQIGNAVPVNLSFAVGK 398
Cdd:PRK10458 401 ---PRRLTPRECARLMGFeaPGEAKFRIPVSdtQAYRQFGNSVVVPVFAAVAK 450
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 6-52 1.55e-11

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 58.75  E-value: 1.55e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNdENNYRFYRKDQLKHF 52
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRT-PGGHRRFPEEDLERL 46
MerR pfam00376
MerR family regulatory protein;
9-44 3.39e-09

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 52.03  E-value: 3.39e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 970318137    9 SEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFY 44
Cdd:pfam00376   3 GEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
7-53 8.69e-08

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 51.92  E-value: 8.69e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 970318137   7 SLSEVADILGVSKETLRRWDTAGKLVSQRnDENNYRFYRKDQLKHFE 53
Cdd:COG2452    2 TPGEAAELLGVSPKTLRRWEKEGKLPAIR-TPGGHRRYPESEVERLE 47
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
6-59 1.45e-06

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 45.59  E-value: 1.45e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 970318137     6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQLKHFEQAQFLF 59
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLK 54
rADc smart00650
Ribosomal RNA adenine dimethylases;
75-130 4.66e-03

Ribosomal RNA adenine dimethylases;


Pssm-ID: 128898  Cd Length: 169  Bit Score: 37.49  E-value: 4.66e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137    75 TVLELFAGAGGMALGLEKAGlKSVLLNEIDSHACKTLRKnRPEW----NVVEGDVSKVDF 130
Cdd:smart00650  16 TVLEIGPGKGALTEELLERA-KRVTAIEIDPRLAPRLRE-KFAAadnlTVIHGDALKFDL 73
 
Name Accession Description Interval E-value
Dcm COG0270
DNA-cytosine methylase [Replication, recombination and repair];
71-407 7.91e-125

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


Pssm-ID: 440040 [Multi-domain]  Cd Length: 277  Bit Score: 361.82  E-value: 7.91e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  71 NNIYTVLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNRPEWNVVEGDVSKVDFTPYRDTVDVLAGGFPCQAFS 150
Cdd:COG0270    1 SKKLTVIDLFAGAGGLSLGFEKAGFEVVFAVEIDPDACETYRANFPEAKVIEGDIRDIDPEELIPDVDLLIGGPPCQPFS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 151 YAGKKLGFEDTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTlFEPRVLKAIFYKVPQKRE 230
Cdd:COG0270   81 VAGKRKGLEDPRGTLFFEFIRIVEELRPKAFVLENVPGLLSSDKGKTFEEILKELEELGYR-VDYKVLNAADYGVPQNRE 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 231 RLIIVAVRNDLaNGIDYEWPSSYNKILTLKDALKkgelydsdvpesegqkypkrkaeilsmvppggywrDLPEDIQKEYM 310
Cdd:COG0270  160 RVFIVGFRKDL-DLFEFPEPTHLKPYVTVGDALE-----------------------------------DLPDAHEARYL 203

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 311 lksfylgggktgmarrlswdepSLTLTCAPAqKQTERCHPEETRPLTVREYARIQTFPDDWVFEGPMSAKYKQIGNAVPV 390
Cdd:COG0270  204 ----------------------SETITAGYG-GGGRFLHPGEPRRLTVREAARLQGFPDDFKFPGSKTQAYRQIGNAVPP 260

                        330
                 ....*....|....*..
gi 970318137 391 NLSFAVGKSVVHLLEKI 407
Cdd:COG0270  261 PLAEAIAKAILKALEKL 277
dcm TIGR00675
DNA-methyltransferase (dcm); All proteins in this family for which functions are known are ...
 76-400 5.72e-115

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: 338.53  E-value: 5.72e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137   76 VLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNRPEwNVVEGDVSKVDFTPYRDtVDVLAGGFPCQAFSYAGKK 155
Cdd:TIGR00675   1 FIDLFAGIGGIRLGFEQAGFKCVFASEIDKYAQKTYEANFGN-KVPFGDITKISPSDIPD-FDILLGGFPCQPFSIAGKR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  156 LGFEDTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTLFEpRVLKAIFYKVPQKRERLIIV 235
Cdd:TIGR00675  79 KGFEDTRGTLFFEIVRILKEKKPKFFLLENVKGLVSHDKGRTFKVIIETLEELGYKVYY-KVLNAKDFGVPQNRERIYIV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  236 AVRNDLANgIDYEWPSSYNkiltLKDALKKGELYDSDVPESEGQKYPKRKAEILSMVPPGGYWRDLpediqKEYMLKSFY 315
Cdd:TIGR00675 158 GFRDFDDK-LNFEFPKPIY----VAKKKRIGDLLDLSVDLEEKYYLSEEKKNGLLLLLENMRKKEG-----TGEQIGSFY 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  316 LGGGKTGMARRLSWD-----EPSLTLTCAPAQKQteRCHPEETRPLTVREYARIQTFPDDWVFEGPMSAKYKQIGNAVPV 390
Cdd:TIGR00675 228 NRESKSSIIRTLSARgytfvKGGKSVLIVPHKST--VVHPGRIRRLTPRECARLQGFPDDFKFPVSDSQLYKQAGNAVVV 305

                         330
                  ....*....|
gi 970318137  391 NLSFAVGKSV 400
Cdd:TIGR00675 306 PVIEAIAKQI 315
DNA_methylase pfam00145
C-5 cytosine-specific DNA methylase;
74-402 5.35e-101

C-5 cytosine-specific DNA methylase;


Pssm-ID: 395093 [Multi-domain]  Cd Length: 324  Bit Score: 303.08  E-value: 5.35e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137   74 YTVLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNRPEwnVVEGDVSKVDFTPYRDtVDVLAGGFPCQAFSYAG 153
Cdd:pfam00145   1 FKFIDLFAGIGGFRLGLEQAGFECVAANEIDKSAAKTYEANFPK--VPIGDITLIDIKDIPD-IDILTGGFPCQDFSIAG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  154 KKLGFEDTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTLFePRVLKAIFYKVPQKRERLI 233
Cdd:pfam00145  78 KQKGFEDTRGTLFFEIIRIIKEKKPKAFLLENVKGLLSHDNGNTLNVILETLEELGYHVS-WKVLNASDYGVPQNRERVF 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  234 IVAVRNDL-----ANGIDYEWPSSYNKILTLKDaLKKGELYDSDVPESEGQKYPKRKAEILSMVPPGGYWRDLpedIQKE 308
Cdd:pfam00145 157 IVGIRKDLnlnvlVPVPEFDFPKPKDLTGTIRD-LLEEPSLDENKYNLSDKFVENHERRKPTTKAPGGGYPTY---LLRN 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  309 yMLKSFYLGGGKTGMARRLSWDEPSLTLtcaPAQKQTER--CHPEETRPLTVREYARIQTFPDDWVFEGPMSAKYKQIGN 386
Cdd:pfam00145 233 -RIDKVEEGKGPSFTYRKSGRPEAPKTG---ILGKNGERfrGHPKNIRRLTPRECARLQGFPDDFIFPGSKTQLYKQIGN 308

                         330
                  ....*....|....*.
gi 970318137  387 AVPVNLSFAVGKSVVH 402
Cdd:pfam00145 309 AVPVPVAEAIAKAIKK 324
Cyt_C5_DNA_methylase cd00315
Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many ...
 74-402 1.70e-97

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: 292.22  E-value: 1.70e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  74 YTVLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNRPEWnVVEGDVSKVDFTPYRDTVDVLAGGFPCQAFSYAG 153
Cdd:cd00315    1 LRVIDLFAGIGGFRLGLEKAGFEIVAANEIDKSAAETYEANFPNK-LIEGDITKIDEKDFIPDIDLLTGGFPCQPFSIAG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 154 KKLGFEDTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTLFePRVLKAIFYKVPQKRERLI 233
Cdd:cd00315   80 KRKGFEDTRGTLFFEIIRILKEKKPKYFLLENVKGLLTHDNGNTLKVILNTLEELGYNVY-WKLLNASDYGVPQNRERVF 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 234 IVAVRNDLANGIDYEWPSSYNKILTLKDALkkgelydsdvpesegqkypkrkaeilsmvppggywrdlpediqkeymlks 313
Cdd:cd00315  159 IIGIRKDLILNFFSPFPKPSEKKKTLKDIL-------------------------------------------------- 188

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 314 fylgggktgmaRRLSWDEPSLTLTC--APAQKQTERC------HPEETRPLTVREYARIQTFPDDWVF-EGPMSAKYKQI 384
Cdd:cd00315  189 -----------RIRDPDEPSPTLTAsyGKGTGSVHPTapdmigKESNIRRLTPRECARLQGFPDDFEFpGKSVTQAYRQI 257

                        330
                 ....*....|....*...
gi 970318137 385 GNAVPVNLSFAVGKSVVH 402
Cdd:cd00315  258 GNSVPVPVAEAIAKAIKE 275
PRK10458 PRK10458
DNA cytosine methylase; Provisional
 18-398 1.12e-29

DNA cytosine methylase; Provisional


Pssm-ID: 236696 [Multi-domain]  Cd Length: 467  Bit Score: 119.78  E-value: 1.12e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  18 SKETLRRWdTAGKLVSQRNDENNYRFYRK---DQLKHFEQAQFLFksqwsdesktcnniytvLELFAGAGGMALGLEKAG 94
Cdd:PRK10458  48 SRAILKRW-LAGKSAWHRLSEAEFAHLQTllpKPPAHHPHYAFRF-----------------IDLFAGIGGIRRGFEAIG 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  95 LKSVLLNEIDSHACKTLRKN---RPEWNVVEGDVSKVDFTpYRDTV----------------DVLAGGFPCQAFSYAG-- 153
Cdd:PRK10458 110 GQCVFTSEWNKHAVRTYKANwycDPATHRFNEDIRDITLS-HKEGVsdeeaaehirqhipdhDVLLAGFPCQPFSLAGvs 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 154 KK------LGFE-DTRGTLFFEFARAVKEINPKVLLAENVRGLLNHDDGRTLETIKNIITDLGYTLF--------EPRVL 218
Cdd:PRK10458 189 KKnslgraHGFEcETQGTLFFDVARIIDAKRPAIFVLENVKNLKSHDKGKTFRIIMQTLDELGYDVAdaedngpdDPKII 268

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 219 KAIFYkVPQKRERLIIVAVRNDLANGIDYewpssynkilTLKDALKK--------GELYDSDVPEsegqKYpkrkaeILS 290
Cdd:PRK10458 269 DGKHF-LPQHRERIVLVGFRRDLNLKADF----------TLRDISECypaqrptlAELLDPVVDA----KY------ILT 327

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 291 MVppggYWRDLpEDIQKEYMLKSFYLGGG------KTGMARRLS---------------WDEPSLTLTCAPAQKQTERch 349
Cdd:PRK10458 328 PV----LWKYL-YRYAKKHQAKGNGFGYGlvypnnPQSVTRTLSaryykdgseilidrgWDMALGEKDFDDPENQQHR-- 400

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970318137 350 peeTRPLTVREYARIQTF--PDDWVFEGPMS--AKYKQIGNAVPVNLSFAVGK 398
Cdd:PRK10458 401 ---PRRLTPRECARLMGFeaPGEAKFRIPVSdtQAYRQFGNSVVVPVFAAVAK 450
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 6-52 1.55e-11

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 58.75  E-value: 1.55e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNdENNYRFYRKDQLKHF 52
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRT-PGGHRRFPEEDLERL 46
MerR pfam00376
MerR family regulatory protein;
9-44 3.39e-09

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 52.03  E-value: 3.39e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 970318137    9 SEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFY 44
Cdd:pfam00376   3 GEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38
HTH_MerR-SF cd04761
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 6-54 4.59e-09

Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133389 [Multi-domain]  Cd Length: 49  Bit Score: 51.82  E-value: 4.59e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNdENNYRFYRKDQLKHFEQ 54
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPART-EGGYRLYSDADLERLRL 48
MerR_1 pfam13411
MerR HTH family regulatory protein;
6-60 1.42e-08

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 51.02  E-value: 1.42e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 970318137    6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNdENNYRFYRKDQLKHFEQAQFLFK 60
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRT-ERGRRYYTDEDVERLRLIKALLE 54
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 6-58 4.88e-08

Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein.


Pssm-ID: 133381 [Multi-domain]  Cd Length: 103  Bit Score: 50.56  E-value: 4.88e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQLKHFEQAQFL 58
Cdd:cd01106    1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFL 53
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 6-58 7.60e-08

Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133378 [Multi-domain]  Cd Length: 100  Bit Score: 49.94  E-value: 7.60e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRnDENNYRFYRKDQLKHFEQAQFL 58
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPER-SENGYRLYSEEDLERLRLIRRL 52
HTH_BmrR-like cd04768
Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix ...
 6-58 7.87e-08

Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133396 [Multi-domain]  Cd Length: 96  Bit Score: 49.66  E-value: 7.87e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQLKHFEQAQFL 58
Cdd:cd04768    1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFL 53
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
7-53 8.69e-08

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 51.92  E-value: 8.69e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 970318137   7 SLSEVADILGVSKETLRRWDTAGKLVSQRnDENNYRFYRKDQLKHFE 53
Cdd:COG2452    2 TPGEAAELLGVSPKTLRRWEKEGKLPAIR-TPGGHRRYPESEVERLE 47
HTH_BltR cd04782
Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) ...
 6-58 9.57e-08

Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133409 [Multi-domain]  Cd Length: 97  Bit Score: 49.54  E-value: 9.57e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQLKHFEQAQFL 58
Cdd:cd04782    1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLL 53
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
9-58 2.62e-07

DNA-binding transcriptional regulator, MerR family [Transcription];


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 48.36  E-value: 2.62e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 970318137   9 SEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQLKHFEQAQFL 58
Cdd:COG0789    2 GEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRL 51
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 75-149 4.57e-07

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 47.81  E-value: 4.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  75 TVLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNR-----PEWNVVEGDVSKVDFTPYRdTVDVLAGGFPCQAF 149
Cdd:cd02440    1 RVLDLGCGTGALALALASGPGARVTGVDISPVALELARKAAaallaDNVEVLKGDAEELPPEADE-SFDVIISDPPLHHL 79
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 7-85 9.05e-07

Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.


Pssm-ID: 133400  Cd Length: 108  Bit Score: 46.97  E-value: 9.05e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 970318137   7 SLSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQLKHFEQAQFLFKSQWSDEsktcnNIYTVLELFAGAGG 85
Cdd:cd04773    2 TIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLE-----QIATVVEQLRHAGG 75
HTH_MERR smart00422
helix_turn_helix, mercury resistance;
6-59 1.45e-06

helix_turn_helix, mercury resistance;


Pssm-ID: 197716  Cd Length: 70  Bit Score: 45.59  E-value: 1.45e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 970318137     6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQLKHFEQAQFLF 59
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLK 54
RsmD COG0742
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 75-128 5.38e-06

16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA G966 N2-methylase RsmD is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440505 [Multi-domain]  Cd Length: 183  Bit Score: 46.61  E-value: 5.38e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 970318137  75 TVLELFAGAGgmALGLEKA--GLKSVLLNEIDSHACKTLRKN------RPEWNVVEGDVSKV 128
Cdd:COG0742   44 RVLDLFAGSG--ALGLEALsrGAASVVFVEKDRKAAAVIRKNleklglEDRARVIRGDALRF 103
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
75-137 2.06e-05

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 45.28  E-value: 2.06e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 970318137  75 TVLELFAGAGGMALGLEKAGLKSVLLNEIDSHACKTLRKNRPEWN----VVEGDVSKVDFTPYRDTV 137
Cdd:COG2263   48 TVLDLGCGTGMLAIGAALLGAKKVVGVDIDPEALEIARENAERLGvrvdFIRADVTRIPLGGSVDTV 114
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 6-49 4.43e-05

Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133382 [Multi-domain]  Cd Length: 108  Bit Score: 42.12  E-value: 4.43e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDE-NNYRFYRKDQL 49
Cdd:cd01107    1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPdTGYRYYSAEQL 45
HTH_Cfa-like cd04775
Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative ...
 6-58 1.02e-04

Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133402 [Multi-domain]  Cd Length: 102  Bit Score: 40.98  E-value: 1.02e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNdENNYRFYRKDQLKHFEQAQFL 58
Cdd:cd04775    2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARS-EANYRLYSEADLSRLEKIVFL 53
Cons_hypoth95 pfam03602
Conserved hypothetical protein 95;
75-114 1.75e-04

Conserved hypothetical protein 95;


Pssm-ID: 427391 [Multi-domain]  Cd Length: 179  Bit Score: 42.23  E-value: 1.75e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 970318137   75 TVLELFAGAGgmALGLEKA--GLKSVLLNEIDSHACKTLRKN 114
Cdd:pfam03602  44 RVLDLFAGSG--ALGLEALsrGAKRVTLVEKDKRAVQILKEN 83
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 6-58 2.05e-04

Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.


Pssm-ID: 133379  Cd Length: 68  Bit Score: 39.15  E-value: 2.05e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQLKHFEQAQFL 58
Cdd:cd01104    1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRL 53
HTH_GlnR-like cd01105
Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix ...
 6-49 2.33e-04

Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133380  Cd Length: 88  Bit Score: 39.91  E-value: 2.33e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQL 49
Cdd:cd01105    2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADV 45
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 6-56 3.59e-04

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 38.21  E-value: 3.59e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 970318137    6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNdeNNYRFYRKDQLKHFEQAQ 56
Cdd:pfam12728   2 LTVEEAAELLGVSRRTVYRLIRSGELPAAKI--GRRWRIRKSDLEEWLERR 50
HTH_MlrA-like_sg2 cd04765
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 6-50 1.61e-03

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133393  Cd Length: 99  Bit Score: 37.62  E-value: 1.61e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQLK 50
Cdd:cd04765    1 FSIGEVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVE 45
HTH_HMRTR_unk cd04787
Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription ...
 8-49 2.10e-03

Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators; Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the conserved, metal-binding cysteines seen in the MerR1 group.


Pssm-ID: 133414 [Multi-domain]  Cd Length: 133  Bit Score: 38.05  E-value: 2.10e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 970318137   8 LSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQL 49
Cdd:cd04787    3 VKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDL 44
HTH_YyaN cd01109
Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; ...
 6-50 2.20e-03

Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133384 [Multi-domain]  Cd Length: 113  Bit Score: 37.44  E-value: 2.20e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVS-QRnDENNYRFYRKDQLK 50
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPvKR-DENGIRDFTEEDLE 45
HTH_Cfa cd04789
Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative ...
 6-56 3.29e-03

Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133416  Cd Length: 102  Bit Score: 36.70  E-value: 3.29e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDeNNYRFYRK---DQLKHFEQAQ 56
Cdd:cd04789    2 YTISELAEKAGISRSTLLYYEKLGLITGTRNA-NGYRLYPDsdlQRLLLIQQLQ 54
rADc smart00650
Ribosomal RNA adenine dimethylases;
75-130 4.66e-03

Ribosomal RNA adenine dimethylases;


Pssm-ID: 128898  Cd Length: 169  Bit Score: 37.49  E-value: 4.66e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137    75 TVLELFAGAGGMALGLEKAGlKSVLLNEIDSHACKTLRKnRPEW----NVVEGDVSKVDF 130
Cdd:smart00650  16 TVLEIGPGKGALTEELLERA-KRVTAIEIDPRLAPRLRE-KFAAadnlTVIHGDALKFDL 73
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 75-236 5.45e-03

tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440663 [Multi-domain]  Cd Length: 172  Bit Score: 37.62  E-value: 5.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137  75 TVLELFAGAGGMALGLEKAGLKsVLLNEIDSHACKTLRKN-----RPEWNVVEGDVSKVDFTpyRDTVDVLAGGFPcqaf 149
Cdd:COG1041   29 TVLDPFCGTGTILIEAGLLGRR-VIGSDIDPKMVEGARENlehygYEDADVIRGDARDLPLA--DESVDAIVTDPP---- 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970318137 150 sYAgkkLGFEDTRGTLFFEFARAVKEInPKVLlaenvrgllnHDDGR----TLETIKNIITDLGYTlfeprVLKAIFYKV 225
Cdd:COG1041  102 -YG---RSSKISGEELLELYEKALEEA-ARVL----------KPGGRvvivTPRDIDELLEEAGFK-----VLERHEQRV 161

                        170
                 ....*....|.
gi 970318137 226 PQKRERLIIVA 236
Cdd:COG1041  162 HKSLTRYILVL 172
HTH_YfmP cd04774
Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) ...
 6-54 7.88e-03

Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133401 [Multi-domain]  Cd Length: 96  Bit Score: 35.57  E-value: 7.88e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGkLVSQRNDENNYRFYRKDQLKHFEQ 54
Cdd:cd04774    1 YKVDEVAKRLGLTKRTLKYYEEIG-LVSPERSEGRYRLYSEEDLKRLER 48
HTH_MlrA-like_sg1 cd04764
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 6-52 8.22e-03

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.


Pssm-ID: 133392  Cd Length: 67  Bit Score: 34.61  E-value: 8.22e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNdENNYRFYRKDQLKHF 52
Cdd:cd04764    1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPRT-ENGRRYYTDEDIELL 46
HTH_Cfa-like_unk cd04790
Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative ...
 6-54 9.81e-03

Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133417 [Multi-domain]  Cd Length: 172  Bit Score: 36.64  E-value: 9.81e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 970318137   6 FSLSEVADILGVSKETLRRWDTAGKLVSQRNDENNYRFYRKDQLKHFEQ 54
Cdd:cd04790    2 LTISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQ 50
 
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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