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Conserved domains on  [gi|1550318548|gb|RVP85738|]
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methylated-DNA--[protein]-cysteine S-methyltransferase [Sinorhizobium meliloti]

Protein Classification

HTH_18 and ATase domain-containing protein( domain architecture ID 12122940)

HTH_18 and ATase domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AdaB COG0350
DNA repair enzyme Ada (O6-methylguanine-DNA--protein-cysteine methyltransferase) [Replication, ...
 125-290 9.88e-62

DNA repair enzyme Ada (O6-methylguanine-DNA--protein-cysteine methyltransferase) [Replication, recombination and repair];


:

Pssm-ID: 440119 [Multi-domain]  Cd Length: 163  Bit Score: 192.78  E-value: 9.88e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 125 TIRYGFHPSPFGTALVMVTDRGLAGLAFADSGEERAsfedmAARWPNAtYVEDSAATARYAARI---FDPDRWCAEEPLR 201
Cdd:COG0350     1 TIRYAIFDTPLGPLLIAATDRGLCALSFGDDREEAL-----LARFPAA-LREDPPLLAEAARQLdayFAGERKDFDLPLD 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 202 ifLIGSDFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRA 281
Cdd:COG0350    75 --LRGTPFQRRVWEALRKIPYGETVTYGELARAIGRPKAARAVGSACGANPIPIIIPCHRVIGADGSLGGYAGGLERKRA 152


                  ....*....
gi 1550318548 282 ILGWEAGKA 290
Cdd:COG0350   153 LLELEGALA 161
HTH_18 pfam12833
Helix-turn-helix domain;
41-120 3.12e-20

Helix-turn-helix domain;


:

Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 82.64  E-value: 3.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  41 LARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQE-DMPLLETSIEVGLSGPSRLHDLFVTHEAMSPGEWKA 119
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 1550318548 120 R 120
Cdd:pfam12833  81 R 81
 
Name Accession Description Interval E-value
AdaB COG0350
DNA repair enzyme Ada (O6-methylguanine-DNA--protein-cysteine methyltransferase) [Replication, ...
 125-290 9.88e-62

DNA repair enzyme Ada (O6-methylguanine-DNA--protein-cysteine methyltransferase) [Replication, recombination and repair];


Pssm-ID: 440119 [Multi-domain]  Cd Length: 163  Bit Score: 192.78  E-value: 9.88e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 125 TIRYGFHPSPFGTALVMVTDRGLAGLAFADSGEERAsfedmAARWPNAtYVEDSAATARYAARI---FDPDRWCAEEPLR 201
Cdd:COG0350     1 TIRYAIFDTPLGPLLIAATDRGLCALSFGDDREEAL-----LARFPAA-LREDPPLLAEAARQLdayFAGERKDFDLPLD 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 202 ifLIGSDFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRA 281
Cdd:COG0350    75 --LRGTPFQRRVWEALRKIPYGETVTYGELARAIGRPKAARAVGSACGANPIPIIIPCHRVIGADGSLGGYAGGLERKRA 152


                  ....*....
gi 1550318548 282 ILGWEAGKA 290
Cdd:COG0350   153 LLELEGALA 161
DNA_binding_1 pfam01035
6-O-methylguanine DNA methyltransferase, DNA binding domain; This is the C-terminal ...
 208-287 4.77e-38

6-O-methylguanine DNA methyltransferase, DNA binding domain; This is the C-terminal DNA-binding domain of 6-O-methylguanine-DNA methyltransferases.


Pssm-ID: 460036  Cd Length: 81  Bit Score: 129.02  E-value: 4.77e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 208 DFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRAILGWEA 287
Cdd:pfam01035   1 PFQRRVWEALRQIPYGKTTTYGEIAKLLGRPKAARAVGNALGANPIPIIVPCHRVVGSDGSLGGYAGGLERKRALLELEG 80
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
8-287 1.38e-36

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 133.38  E-value: 1.38e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548   8 PTDITPEGTDYDTVRRVIAMLTEDyreQP-SLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVtldHAKRL---LRQe 83
Cdd:PRK15435   74 PDKANPQQHRLDKITHACRLLEQE---TPvTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAW---RARRLreaLAK- 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  84 DMPLLETSIEVGLSGPSRLHDLFVTHEAMSPGEWKARGAGLTIRYGFHPSPFGTALVMVTDRGLAGLAFADSgeERASFE 163
Cdd:PRK15435  147 GESVTTSILNAGFPDSSSYYRKADETLGMTAKQFRHGGENLAVRYALADCELGRCLVAESERGICAILLGDD--DAALIS 224

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 164 DMAARWPNAtyvEDSAATARYAARIFDPDRWC--AEEPLRIFL--IGSDFQIRVWQTLLQIPLGKATTYSRIAENLGQPT 239
Cdd:PRK15435  225 ELQQMFPAA---DNAPADLTFQQHVREVIASLnqRDTPLTLPLdiRGTAFQQQVWQALRTIPCGETVSYQQLANAIGKPK 301

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1550318548 240 ASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRAILGWEA 287
Cdd:PRK15435  302 AVRAVASACAANKLAIVIPCHRVVRGDGALSGYRWGVSRKAQLLRREA 349
ATase cd06445
The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT ...
 209-286 2.17e-35

The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of the C-terminal domain, suggesting an important structural role for the N-terminal domain in orienting the C-terminal domain for proper catalysis. Some ATase C-terminal domain homologs are either single-domain proteins that lack an N-terminal domain, or have a tryptophan substituted in place of the acceptor cysteine (i.e. the motif PCHR is replaced by PWHR). ATase null mutant mice are viable, fertile, and have a normal lifespan.


Pssm-ID: 119438 [Multi-domain]  Cd Length: 79  Bit Score: 122.20  E-value: 2.17e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1550318548 209 FQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRAILGWE 286
Cdd:cd06445     1 FQRRVWEALRQIPYGEVTTYGQIAKLAGTPKAARAVGSALARNPIPILIPCHRVVRSDGGLGGYRGGLERKRELLELE 78
ogt TIGR00589
O-6-methylguanine DNA methyltransferase; All proteins in this family for which functions are ...
 207-286 2.83e-32

O-6-methylguanine DNA methyltransferase; All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. 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: 273157  Cd Length: 80  Bit Score: 114.33  E-value: 2.83e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 207 SDFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRAILGWE 286
Cdd:TIGR00589   1 TPFQQKVWKALRTIPYGETKSYGQLAKAIGNPKAARAVGGANGRNPLAILVPCHRVVGKNGTLTGYGGGLERKEFLLEHE 80
HTH_18 pfam12833
Helix-turn-helix domain;
41-120 3.12e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 82.64  E-value: 3.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  41 LARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQE-DMPLLETSIEVGLSGPSRLHDLFVTHEAMSPGEWKA 119
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 1550318548 120 R 120
Cdd:pfam12833  81 R 81
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
37-122 8.65e-18

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 80.98  E-value: 8.65e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  37 SLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLLETSIEVGLSGPSRLHDLFVTHEAMSPGE 116
Cdd:COG2207   170 TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                  ....*.
gi 1550318548 117 WKARGA 122
Cdd:COG2207   250 YRKRLR 255
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
35-118 8.46e-17

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 73.74  E-value: 8.46e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548   35 QPSLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLLETSIEVGLSGPSRLHDLFVTHEAMSP 114
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1550318548  115 GEWK 118
Cdd:smart00342  81 SEYR 84
PRK10371 PRK10371
transcriptional regulator MelR;
21-118 4.73e-07

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 50.20  E-value: 4.73e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  21 VRRVIAMLTEDYREQPSLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLLETSIEVGLSGPS 100
Cdd:PRK10371  193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSS 272

                          90
                  ....*....|....*...
gi 1550318548 101 RLHDLFVTHEAMSPGEWK 118
Cdd:PRK10371  273 RFYSTFGKYVGMSPQQYR 290
 
Name Accession Description Interval E-value
AdaB COG0350
DNA repair enzyme Ada (O6-methylguanine-DNA--protein-cysteine methyltransferase) [Replication, ...
 125-290 9.88e-62

DNA repair enzyme Ada (O6-methylguanine-DNA--protein-cysteine methyltransferase) [Replication, recombination and repair];


Pssm-ID: 440119 [Multi-domain]  Cd Length: 163  Bit Score: 192.78  E-value: 9.88e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 125 TIRYGFHPSPFGTALVMVTDRGLAGLAFADSGEERAsfedmAARWPNAtYVEDSAATARYAARI---FDPDRWCAEEPLR 201
Cdd:COG0350     1 TIRYAIFDTPLGPLLIAATDRGLCALSFGDDREEAL-----LARFPAA-LREDPPLLAEAARQLdayFAGERKDFDLPLD 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 202 ifLIGSDFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRA 281
Cdd:COG0350    75 --LRGTPFQRRVWEALRKIPYGETVTYGELARAIGRPKAARAVGSACGANPIPIIIPCHRVIGADGSLGGYAGGLERKRA 152


                  ....*....
gi 1550318548 282 ILGWEAGKA 290
Cdd:COG0350   153 LLELEGALA 161
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 19-290 7.22e-55

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];


Pssm-ID: 441772 [Multi-domain]  Cd Length: 358  Bit Score: 181.41  E-value: 7.22e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  19 DTVRRVIAMLTEDYREQPSLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQeDMPLLETSIEVGLSG 98
Cdd:COG2169    84 DLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQT-GLSVTDAAYAAGFGS 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  99 PSRLHDLFVTHEAMSPGEWKARGAGLTIRYGFHPSPFGTALVMVTDRGLAGLAFADSGEERasFEDMAARWPNATYVEDS 178
Cdd:COG2169   163 LSRFYEAFKKLLGMTPSAYRRGGAGAAIRFAPTPCSLGLLLVAASARGVCAILLGDDPEAL--LRDLQDRFPAAELIGGD 240

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 179 AATARYAARIFDPDRWCAEEP-LRIFLIGSDFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVV 257
Cdd:COG2169   241 AAFEQLVAEVVGFVEGPLLGLdLPLDLRGTAFQQRVWQALRAIPAGETASYAEIAARIGAPKAVRAVAAACAANQLAVAI 320

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1550318548 258 PCHRALGKTGDLTGYHWGLTRKRAILGWEAGKA 290
Cdd:COG2169   321 PCHRVVRADGALSGYRWGVERKRALLEREAAAA 353
DNA_binding_1 pfam01035
6-O-methylguanine DNA methyltransferase, DNA binding domain; This is the C-terminal ...
 208-287 4.77e-38

6-O-methylguanine DNA methyltransferase, DNA binding domain; This is the C-terminal DNA-binding domain of 6-O-methylguanine-DNA methyltransferases.


Pssm-ID: 460036  Cd Length: 81  Bit Score: 129.02  E-value: 4.77e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 208 DFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRAILGWEA 287
Cdd:pfam01035   1 PFQRRVWEALRQIPYGKTTTYGEIAKLLGRPKAARAVGNALGANPIPIIVPCHRVVGSDGSLGGYAGGLERKRALLELEG 80
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
8-287 1.38e-36

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 133.38  E-value: 1.38e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548   8 PTDITPEGTDYDTVRRVIAMLTEDyreQP-SLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVtldHAKRL---LRQe 83
Cdd:PRK15435   74 PDKANPQQHRLDKITHACRLLEQE---TPvTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAW---RARRLreaLAK- 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  84 DMPLLETSIEVGLSGPSRLHDLFVTHEAMSPGEWKARGAGLTIRYGFHPSPFGTALVMVTDRGLAGLAFADSgeERASFE 163
Cdd:PRK15435  147 GESVTTSILNAGFPDSSSYYRKADETLGMTAKQFRHGGENLAVRYALADCELGRCLVAESERGICAILLGDD--DAALIS 224

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 164 DMAARWPNAtyvEDSAATARYAARIFDPDRWC--AEEPLRIFL--IGSDFQIRVWQTLLQIPLGKATTYSRIAENLGQPT 239
Cdd:PRK15435  225 ELQQMFPAA---DNAPADLTFQQHVREVIASLnqRDTPLTLPLdiRGTAFQQQVWQALRTIPCGETVSYQQLANAIGKPK 301

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1550318548 240 ASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRAILGWEA 287
Cdd:PRK15435  302 AVRAVASACAANKLAIVIPCHRVVRGDGALSGYRWGVSRKAQLLRREA 349
ATase cd06445
The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT ...
 209-286 2.17e-35

The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of the C-terminal domain, suggesting an important structural role for the N-terminal domain in orienting the C-terminal domain for proper catalysis. Some ATase C-terminal domain homologs are either single-domain proteins that lack an N-terminal domain, or have a tryptophan substituted in place of the acceptor cysteine (i.e. the motif PCHR is replaced by PWHR). ATase null mutant mice are viable, fertile, and have a normal lifespan.


Pssm-ID: 119438 [Multi-domain]  Cd Length: 79  Bit Score: 122.20  E-value: 2.17e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1550318548 209 FQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRAILGWE 286
Cdd:cd06445     1 FQRRVWEALRQIPYGEVTTYGQIAKLAGTPKAARAVGSALARNPIPILIPCHRVVRSDGGLGGYRGGLERKRELLELE 78
ogt TIGR00589
O-6-methylguanine DNA methyltransferase; All proteins in this family for which functions are ...
 207-286 2.83e-32

O-6-methylguanine DNA methyltransferase; All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. 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: 273157  Cd Length: 80  Bit Score: 114.33  E-value: 2.83e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 207 SDFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRAILGWE 286
Cdd:TIGR00589   1 TPFQQKVWKALRTIPYGETKSYGQLAKAIGNPKAARAVGGANGRNPLAILVPCHRVVGKNGTLTGYGGGLERKEFLLEHE 80
PRK00901 PRK00901
methylated-DNA--protein-cysteine methyltransferase; Provisional
 206-286 1.74e-27

methylated-DNA--protein-cysteine methyltransferase; Provisional


Pssm-ID: 234860 [Multi-domain]  Cd Length: 155  Bit Score: 103.98  E-value: 1.74e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 206 GSDFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRAILGW 285
Cdd:PRK00901   71 GTEFQKKVWKALQEIPYGETRSYKEIAVNIGNPKACRAVGLANNKNPIPIFIPCHRVIGANGKLVGYAGGLDIKEKLLKL 150


                  .
gi 1550318548 286 E 286
Cdd:PRK00901  151 E 151
PRK10286 PRK10286
methylated-DNA--[protein]-cysteine S-methyltransferase;
206-286 3.23e-25

methylated-DNA--[protein]-cysteine S-methyltransferase;


Pssm-ID: 182355 [Multi-domain]  Cd Length: 171  Bit Score: 98.79  E-value: 3.23e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548 206 GSDFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLTGYHWGLTRKRAILGW 285
Cdd:PRK10286   86 GTPFQREVWQTLRTIPCGQVMHYGQLAEQLGRPGAARAVGAANGSNPISIVVPCHRVIGRNGTMTGYAGGVQRKEWLLRH 165


                  .
gi 1550318548 286 E 286
Cdd:PRK10286  166 E 166
HTH_18 pfam12833
Helix-turn-helix domain;
41-120 3.12e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 82.64  E-value: 3.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  41 LARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQE-DMPLLETSIEVGLSGPSRLHDLFVTHEAMSPGEWKA 119
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDtGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 1550318548 120 R 120
Cdd:pfam12833  81 R 81
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
37-122 8.65e-18

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 80.98  E-value: 8.65e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  37 SLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLLETSIEVGLSGPSRLHDLFVTHEAMSPGE 116
Cdd:COG2207   170 TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                  ....*.
gi 1550318548 117 WKARGA 122
Cdd:COG2207   250 YRKRLR 255
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
35-118 8.46e-17

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 73.74  E-value: 8.46e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548   35 QPSLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLLETSIEVGLSGPSRLHDLFVTHEAMSP 114
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1550318548  115 GEWK 118
Cdd:smart00342  81 SEYR 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 13-123 1.74e-16

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 77.89  E-value: 1.74e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  13 PEGTDYDTVRRVIAMLTEDYREQPSLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLLETSI 92
Cdd:COG4977   204 PLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAA 283

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1550318548  93 EVGLSGPSRLHDLFVTHEAMSPGEWKARGAG 123
Cdd:COG4977   284 ACGFGSASHFRRAFRRRFGVSPSAYRRRFRA 314
Atl1 COG3695
Alkylated DNA nucleotide flippase Atl1, participates in nucleotide excision repair, Ada-like ...
 208-283 5.28e-14

Alkylated DNA nucleotide flippase Atl1, participates in nucleotide excision repair, Ada-like DNA-binding domain [Transcription];


Pssm-ID: 442910  Cd Length: 104  Bit Score: 66.75  E-value: 5.28e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1550318548 208 DFQIRVWQTLLQIPLGKATTYSRIAENLGQPTASRAVGAAVGRNPISFVVPCHRALGKTGDLT-GYHWGLTRKRAIL 283
Cdd:COG3695     5 EFYERVYEVVAQIPPGRVATYGDIAALAGLPRGARQVGRALRALPEGSDLPWHRVVNADGRLSpGHAGGAEEQRELL 81
PRK03887 PRK03887
methylated-DNA--protein-cysteine methyltransferase; Provisional
 207-267 2.61e-10

methylated-DNA--protein-cysteine methyltransferase; Provisional


Pssm-ID: 167628 [Multi-domain]  Cd Length: 175  Bit Score: 58.21  E-value: 2.61e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1550318548 207 SDFQIRVWQTLLQ-IPLGKATTYSRIAENLGqpTASRAVGAAVGRNPISFVVPCHRALGKTG 267
Cdd:PRK03887   91 TPFERKVYEWLTKnVKRGEVITYGELAKALN--TSPRAVGGAMKRNPYPIIVPCHRVVGRKN 150
PRK10371 PRK10371
transcriptional regulator MelR;
21-118 4.73e-07

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 50.20  E-value: 4.73e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  21 VRRVIAMLTEDYREQPSLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLLETSIEVGLSGPS 100
Cdd:PRK10371  193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSS 272

                          90
                  ....*....|....*...
gi 1550318548 101 RLHDLFVTHEAMSPGEWK 118
Cdd:PRK10371  273 RFYSTFGKYVGMSPQQYR 290
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
16-132 3.87e-04

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 39.70  E-value: 3.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  16 TDYDTVRRVIAMLtEDYREQP-SLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLLETSIEV 94
Cdd:PRK11511    6 TDAITIHSILDWI-EDNLESPlSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERY 84

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1550318548  95 GLSGPSRLHDLFVTHEAMSPGEWKARGAGLTIRYgFHP 132
Cdd:PRK11511   85 GFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRF-LHP 121
ftrA PRK09393
transcriptional activator FtrA; Provisional
 23-120 4.06e-04

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 41.10  E-value: 4.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548  23 RVIAMLTEDYREQPSLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLLETSIEVGLSGPSRL 102
Cdd:PRK09393  222 PLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESL 301

                          90
                  ....*....|....*...
gi 1550318548 103 HDLFVTHEAMSPGEWKAR 120
Cdd:PRK09393  302 RHHFRRRAATSPAAYRKR 319
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
9-118 1.42e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 39.70  E-value: 1.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548   9 TDITPEGTDYDTVRRVIAMLTEDYREQPSLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLL 88
Cdd:PRK13500  196 SDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLIS 275

                          90       100       110
                  ....*....|....*....|....*....|
gi 1550318548  89 ETSIEVGLSGPSRLHDLFVTHEAMSPGEWK 118
Cdd:PRK13500  276 DISTECGFEDSNYFSVVFTRETGMTPSQWR 305
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
9-118 2.44e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 38.88  E-value: 2.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550318548   9 TDITPEGTDYDTVRRVIAMLTEDYREQPSLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQAVTLDHAKRLLRQEDMPLL 88
Cdd:PRK13502  166 TDDLPATSRETLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMIS 245

                          90       100       110
                  ....*....|....*....|....*....|
gi 1550318548  89 ETSIEVGLSGPSRLHDLFVTHEAMSPGEWK 118
Cdd:PRK13502  246 EISMQCGFEDSNYFSVVFTRETGMTPSQWR 275
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 37-69 2.92e-03

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 34.82  E-value: 2.92e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1550318548  37 SLESLARRLGQSPTQLQKVFTRWAGLSPKAFLQ 69
Cdd:pfam00165  10 TIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
 
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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