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Conserved domains on  [gi|239916007|ref|NP_033081|]
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MHC class II regulatory factor RFX1 [Mus musculus]

Protein Classification

RFX1_trans_act and RFX_DNA_binding domain-containing protein( domain architecture ID 12054117)

RFX1_trans_act and RFX_DNA_binding domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 214-357 7.04e-53

RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding proteins. RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region (pfam02257) in some mammalian RFX proteins, and is thought to activate transcription when associated with DNA. Deletion analysis has identified the region 233-351 in human RFX1 as being required for maximal activation.


:

Pssm-ID: 461362 [Multi-domain]  Cd Length: 163  Bit Score: 182.05  E-value: 7.04e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239916007  214 AGTPAATVQQLQVHSVQQSVPVTQERSVVQATPQ-TKAGPVQQLTVQGLQPVHVAQEVQQLPQVPVPHVYSSQVQYVEGG 292
Cdd:pfam04589   7 SAPPAAVLQQLAPTQVVQPVPASQQRSVVQATPSaPKGGHVQQLSVPRLQQVHVTQEVQQLQQVPVQHVYPNQVQYVEGG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 239916007  293 DASYTASAIRSSTYQYPETPIYTQTAGTSYYEASGTAAQVSTPATSQTV---ASSGSVPMYVSGSPIV 357
Cdd:pfam04589  87 DAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPATSLAVavsSSSVGIPMDVGGSQIV 154
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 421-498 1.79e-43

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


:

Pssm-ID: 460512  Cd Length: 79  Bit Score: 151.93  E-value: 1.79e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 239916007  421 PATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA 498
Cdd:pfam02257   2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
 
Name Accession Description Interval E-value
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 214-357 7.04e-53

RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding proteins. RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region (pfam02257) in some mammalian RFX proteins, and is thought to activate transcription when associated with DNA. Deletion analysis has identified the region 233-351 in human RFX1 as being required for maximal activation.


Pssm-ID: 461362 [Multi-domain]  Cd Length: 163  Bit Score: 182.05  E-value: 7.04e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239916007  214 AGTPAATVQQLQVHSVQQSVPVTQERSVVQATPQ-TKAGPVQQLTVQGLQPVHVAQEVQQLPQVPVPHVYSSQVQYVEGG 292
Cdd:pfam04589   7 SAPPAAVLQQLAPTQVVQPVPASQQRSVVQATPSaPKGGHVQQLSVPRLQQVHVTQEVQQLQQVPVQHVYPNQVQYVEGG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 239916007  293 DASYTASAIRSSTYQYPETPIYTQTAGTSYYEASGTAAQVSTPATSQTV---ASSGSVPMYVSGSPIV 357
Cdd:pfam04589  87 DAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPATSLAVavsSSSVGIPMDVGGSQIV 154
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 421-498 1.79e-43

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


Pssm-ID: 460512  Cd Length: 79  Bit Score: 151.93  E-value: 1.79e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 239916007  421 PATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA 498
Cdd:pfam02257   2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
425-500 8.55e-06

DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 49.17  E-value: 8.55e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 239916007 425 QWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRlgTRGNSKYHYYGLRIKASS 500
Cdd:COG3378  328 AFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--TNGGKRRGYRGIRLKDDS 401
rne PRK10811
ribonuclease E; Reviewed
 174-349 7.38e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 40.41  E-value: 7.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239916007  174 QSPAPGT--------KSGQV--SLTVHSAQQVHSAPERSPVQANNSTSKTAGTPAATVQQLQVHSVQQSVPVTQERSVVQ 243
Cdd:PRK10811  822 QSPMPLTvacaspemASGKVwiRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVV 901

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239916007  244 ATPQTKAGPVQ----------------QLTVQGLQPVHVAQEVQQLPQVPVPHVYSSQVQYVEGGDASYTASAIRSSTYQ 307
Cdd:PRK10811  902 AEPQPEEVVVVetthpeviaapvteqpQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAA 981

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 239916007  308 YPETPIYTQTAGTSYYEASGTAAQVSTPATSQTVASSgsvPM 349
Cdd:PRK10811  982 PVVAEVAAEVETVTAVEPEVAPAQVPEATVEHNHATA---PM 1020
 
Name Accession Description Interval E-value
RFX1_trans_act pfam04589
RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding ...
 214-357 7.04e-53

RFX1 transcription activation region; The RFX family is a family of winged-helix DNA binding proteins. RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region (pfam02257) in some mammalian RFX proteins, and is thought to activate transcription when associated with DNA. Deletion analysis has identified the region 233-351 in human RFX1 as being required for maximal activation.


Pssm-ID: 461362 [Multi-domain]  Cd Length: 163  Bit Score: 182.05  E-value: 7.04e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239916007  214 AGTPAATVQQLQVHSVQQSVPVTQERSVVQATPQ-TKAGPVQQLTVQGLQPVHVAQEVQQLPQVPVPHVYSSQVQYVEGG 292
Cdd:pfam04589   7 SAPPAAVLQQLAPTQVVQPVPASQQRSVVQATPSaPKGGHVQQLSVPRLQQVHVTQEVQQLQQVPVQHVYPNQVQYVEGG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 239916007  293 DASYTASAIRSSTYQYPETPIYTQTAGTSYYEASGTAAQVSTPATSQTV---ASSGSVPMYVSGSPIV 357
Cdd:pfam04589  87 DAVYTTSTIRSSAYPYTETPLYTQGSGASYYEAQGGGAQVSTPATSLAVavsSSSVGIPMDVGGSQIV 154
RFX_DNA_binding pfam02257
RFX DNA-binding domain; RFX is a regulatory factor which binds to the X box of MHC class II ...
 421-498 1.79e-43

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


Pssm-ID: 460512  Cd Length: 79  Bit Score: 151.93  E-value: 1.79e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 239916007  421 PATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA 498
Cdd:pfam02257   2 VFALQWLNANYEVAEGSSVPRSRVYAHYLSFCSKLGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKA 79
COG3378 COG3378
DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];
425-500 8.55e-06

DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons];


Pssm-ID: 442605 [Multi-domain]  Cd Length: 403  Bit Score: 49.17  E-value: 8.55e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 239916007 425 QWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRlgTRGNSKYHYYGLRIKASS 500
Cdd:COG3378  328 AFLEECCELDPGARVPKKDLYEAYREWCEDNGEKPLSKRTFGKELKKLGFEYEKRR--TNGGKRRGYRGIRLKDDS 401
rne PRK10811
ribonuclease E; Reviewed
 174-349 7.38e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 40.41  E-value: 7.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239916007  174 QSPAPGT--------KSGQV--SLTVHSAQQVHSAPERSPVQANNSTSKTAGTPAATVQQLQVHSVQQSVPVTQERSVVQ 243
Cdd:PRK10811  822 QSPMPLTvacaspemASGKVwiRYPVVRPQDVQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVV 901

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239916007  244 ATPQTKAGPVQ----------------QLTVQGLQPVHVAQEVQQLPQVPVPHVYSSQVQYVEGGDASYTASAIRSSTYQ 307
Cdd:PRK10811  902 AEPQPEEVVVVetthpeviaapvteqpQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAA 981

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 239916007  308 YPETPIYTQTAGTSYYEASGTAAQVSTPATSQTVASSgsvPM 349
Cdd:PRK10811  982 PVVAEVAAEVETVTAVEPEVAPAQVPEATVEHNHATA---PM 1020
 
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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