RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins; NF-X1, also known as nuclear transcription factor, X box-binding protein 1, is a novel cysteine-rich sequence-specific DNA-binding protein that interacts with the conserved X-box motif of the human major histocompatibility complex (MHC) class II genes via a repeated Cys-His domain. It functions as a cytokine-inducible transcriptional repressor that plays an important role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by interferon gamma (IFN- gamma). NFX1 contains an N-terminal PAM2 motif, a C4HC3-type RING-CH finger, a Cys-rich region that harbors several NFX1-type zinc fingers, and a C-terminal R3H domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 974005235  356 YECMVCCELVRVTAPVWSCQSCYHVFHLNCIKKWARSPASQA-DGQSGWRCPACQ 409
Cdd:cd16696     1 YECMVCCEVVRVMAPVWSCSSCYHVFHLNCIKKWARSPAAQAeDNSGGWRCPACQ 55

Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 974005235  496 CSNPCENILNCGQHQCAELCHGGQCQPCQIILNQVCYCGSTSRDVLCGT 544
Cdd:cd06008     1 CGEVCGKPLPCGNHKCEQLCHEGPCPPCPETVKKKCRCGKTTKEVPCGE 49

Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 974005235  557 CLKICGKDLKCGNHTCSQVCHPQPCQQCPRLPQlvRCCPCGQT 599
Cdd:cd06008     1 CGEVCGKPLPCGNHKCEQLCHEGPCPPCPETVK--KKCRCGKT 41

Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 974005235  823 CGLPCSATLPCGMHKCQRLCHKGECL-VDEPCKQPCTTPRADCGHPC 868
Cdd:cd06008     1 CGEVCGKPLPCGNHKCEQLCHEGPCPpCPETVKKKCRCGKTTKEVPC 47

RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins; NF-X1, also known as nuclear transcription factor, X box-binding protein 1, is a novel cysteine-rich sequence-specific DNA-binding protein that interacts with the conserved X-box motif of the human major histocompatibility complex (MHC) class II genes via a repeated Cys-His domain. It functions as a cytokine-inducible transcriptional repressor that plays an important role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by interferon gamma (IFN- gamma). NFX1 contains an N-terminal PAM2 motif, a C4HC3-type RING-CH finger, a Cys-rich region that harbors several NFX1-type zinc fingers, and a C-terminal R3H domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 974005235  356 YECMVCCELVRVTAPVWSCQSCYHVFHLNCIKKWARSPASQA-DGQSGWRCPACQ 409
Cdd:cd16696     1 YECMVCCEVVRVMAPVWSCSSCYHVFHLNCIKKWARSPAAQAeDNSGGWRCPACQ 55

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 974005235   996 KFVSDVEKEMETLVeavnkgKNSKKSHSFPPMNRDHRRIIHDLAQVYGLESVSYDSEPKRNVVVT 1060
Cdd:pfam01424    1 EFLEQLAEKLAEFV------KDTGKSLELPPMSSYERRIIHELAQKYGLESESEGEEPNRRVVVY 59

Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 974005235  496 CSNPCENILNCGQHQCAELCHGGQCQPCQIILNQVCYCGSTSRDVLCGT 544
Cdd:cd06008     1 CGEVCGKPLPCGNHKCEQLCHEGPCPPCPETVKKKCRCGKTTKEVPCGE 49

Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 974005235  712 CPLICGRKLRCGLHRCEEPCHRGNCQTCWQASfdELTCHCGASviYPPVPCGT 764
Cdd:cd06008     1 CGEVCGKPLPCGNHKCEQLCHEGPCPPCPETV--KKKCRCGKT--TKEVPCGE 49

Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 974005235  685 CDKRCNKKRLCGRHKCNEICCVDKEHKCPLICGRKLRCGLHRCEEPCHR 733
Cdd:cd06008     1 CGEVCGKPLPCGNHKCEQLCHEGPCPPCPETVKKKCRCGKTTKEVPCGE 49

RNA-binding cell elongation regulator Jag/EloR; Members of this family are nucleic acid-binding proteins (RNA or single-stranded DNA) with a KH domain at the N-terminus, an R3H domain at the C-terminus, and additional regions of homology. The founding member of this family was JAG (spoIIIJ Associated Gene) from Bacillus subtilis, but later work in other lineages, such as Streptococcus pneumoniae, as established a role in controlling cell elongation and the operation of the elongasome. The S. pneumoniae protein, a protein that undergoes regulatory phosphorylation and dephosphorylation, is also called RNA-binding cell elongation regulator EloR, and also KhpB.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 974005235  995 LKFVSDVE----KEMETLVE-----AvNKGKNSKKSHSFPPMNRDHRRIIHD-LAQVYGLESVSYDSEPKRNVVVT 1060
Cdd:NF041568  128 VRVILDAEnyreRREETLEQlaerlA-DKVKRTKKPVVLEPMPSYERKIIHTaLQNHPDVETYSEGEEPNRKVVIA 202

NF-X1 type zinc finger; This domain is presumed to be a zinc binding domain. The following pattern describes the zinc finger. C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C Where X can be any amino acid, and numbers in brackets indicate the number of residues. Two position can be either his or cys. This family includes Swiss:P40798, Swiss:Q12986 and Swiss:P53971. The zinc fingers in Swiss:Q12986 bind to DNA.

                           10
                   ....*....|....*....
gi 974005235   567 CGNHTCSQVCHPQPCQQCP 585
Cdd:pfam01422    1 CGNHTCEEVCHEGPCPPCP 19

RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins; NF-X1, also known as nuclear transcription factor, X box-binding protein 1, is a novel cysteine-rich sequence-specific DNA-binding protein that interacts with the conserved X-box motif of the human major histocompatibility complex (MHC) class II genes via a repeated Cys-His domain. It functions as a cytokine-inducible transcriptional repressor that plays an important role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by interferon gamma (IFN- gamma). NFX1 contains an N-terminal PAM2 motif, a C4HC3-type RING-CH finger, a Cys-rich region that harbors several NFX1-type zinc fingers, and a C-terminal R3H domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 974005235  356 YECMVCCELVRVTAPVWSCQSCYHVFHLNCIKKWARSPASQA-DGQSGWRCPACQ 409
Cdd:cd16696     1 YECMVCCEVVRVMAPVWSCSSCYHVFHLNCIKKWARSPAAQAeDNSGGWRCPACQ 55

RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1, NF-X1-type zinc finger protein NFXL1, and similar proteins; NF-X1, also known as nuclear transcription factor, X box-binding protein 1, is a novel cysteine-rich sequence-specific DNA-binding protein that interacts with the conserved X-box motif of the human major histocompatibility complex (MHC) class II genes via a repeated Cys-His domain. It functions as a cytokine-inducible transcriptional repressor that plays an important role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by interferon gamma (IFN- gamma). NFXL1, also known as NF-X1-type zinc finger protein NFXL1 or ovarian zinc finger protein (OZFP), is encoded by a novel human cytoplasm-distribution zinc finger protein (CDZFP) gene. This subfamily also includes NF-X1 homologs from insects, plants, and fungi. Drosophila melanogaster shuttle craft (STC) is a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system. It functions as a putative transcription factor and plays an essential role in the completion of embryonic development. In contrast to NF-X1, STC contains an RD domain. The Arabidopsis genome encodes two NF-X1 homologs, AtNFXL1 and AtNFXL2, both of which function as regulators of salt stress responses. The AtNFXL1 protein is a nuclear factor that positively affects adaptation to salt stress. It also functions as a negative regulator of the type A trichothecene phytotoxin-induced defense response. AtNFXL2 controls abscisic acid (ABA) levels and suppresses ABA responses. It may also prevent unnecessary and costly stress adaptation under favorable conditions. FKBP12-associated protein 1 (FAP1) is a dosage suppressor of rapamycin toxicity in budding yeast. It is localized in the cytoplasm, but upon rapamycin treatment translocates to the nucleus. FAP1 interacts with FKBP12 in a rapamycin-sensitive manner. It is a proline-rich protein containing a novel cysteine-rich DNA-binding motif. Unique structural features of the NFX1 and NFXL proteins are the Cys-rich region and a specific RING-CH finger motif with an unusual arrangement of zinc-coordinating residues. The Cys-rich region is required for binding to specific promoter elements. It frequently comprises more than 500 amino acids and harbors several NFX1-type zinc finger domains, characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The RING-CH finger, also known as vRING or RINGv, may have E3 ligase activity. It is characterized by a C4HC3-type Zn ligand signature and additional conserved amino acids, rather than the C3H2C3-type cysteines and histidines arrangement in canonical RING-H2 finger. In addition to the Cys-rich region and RING-CH finger, NFX1 contains a PAM2 motif in the N-terminus and a R3H domain in the C-terminus.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 974005235  356 YECMVCCELVRVTAPVWSCQSCYHVFHLNCIKKWARSPASQADGQ----SGWRCPACQ 409
Cdd:cd16492     1 YECMICTENVGRNQSIWSCSRCYRVFHLSCIKKWAKNSEEKAEQVknddDSWRCPGCQ 58

R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 974005235  998 VSDVEKEMETLVEavnkgKNSKKSHSFPPMNRDHRRIIHDLAQVYGLESVSYDSEPKRNVVVT 1060
Cdd:cd02325     1 REEREEELEAFAK-----DAAGKSLELPPMNSYERKLIHDLAEYYGLKSESEGEGPNRRVVIT 58

Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 974005235  622 CGKVCGKPLPCGsldfIHTCEKLCHEGDCGPCSRTSVISCRCSFRTKELPCTS 674
Cdd:cd06008     1 CGEVCGKPLPCG----NHKCEQLCHEGPCPPCPETVKKKCRCGKTTKEVPCGE 49

Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 974005235  496 CSNPCENILNCGQHQCAELCHGGQCQPCQIILNQVCYCGSTSRDVLCGT 544
Cdd:cd06008     1 CGEVCGKPLPCGNHKCEQLCHEGPCPPCPETVKKKCRCGKTTKEVPCGE 49

R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 974005235 1002 EKEMETLVE-AVNKGKNSKKSHSFPPMNRDHRRIIHD-LAQVYGLESVSYDSEPKRNVVVT 1060
Cdd:cd02644     5 EETLIRLAErAAEKVRRTGKPVKLEPMNAYERRIIHDaLANDEDVETESEGEGPYRRVVIS 65

Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 974005235  557 CLKICGKDLKCGNHTCSQVCHPQPCQQCPRLPQlvRCCPCGQT 599
Cdd:cd06008     1 CGEVCGKPLPCGNHKCEQLCHEGPCPPCPETVK--KKCRCGKT 41

Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 974005235  823 CGLPCSATLPCGMHKCQRLCHKGECL-VDEPCKQPCTTPRADCGHPC 868
Cdd:cd06008     1 CGEVCGKPLPCGNHKCEQLCHEGPCPpCPETVKKKCRCGKTTKEVPC 47

R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 974005235  994 DLKFVSDVEKEMETLVEavNKGKNSKKshsFPPMNRDHRRIIHDLAQVYGLESVSYDSEPKRnVVVT 1060
Cdd:cd02642     1 DRLFVLKLEKDLLAFIK--DSTRQSLE---LPPMNSYYRLLAHRVAQYYGLDHNVDNSGGKC-VIVN 61

RNA-binding cell elongation regulator Jag/EloR; Members of this family are nucleic acid-binding proteins (RNA or single-stranded DNA) with a KH domain at the N-terminus, an R3H domain at the C-terminus, and additional regions of homology. The founding member of this family was JAG (spoIIIJ Associated Gene) from Bacillus subtilis, but later work in other lineages, such as Streptococcus pneumoniae, as established a role in controlling cell elongation and the operation of the elongasome. The S. pneumoniae protein, a protein that undergoes regulatory phosphorylation and dephosphorylation, is also called RNA-binding cell elongation regulator EloR, and also KhpB.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 974005235  995 LKFVSDVE----KEMETLVE-----AvNKGKNSKKSHSFPPMNRDHRRIIHD-LAQVYGLESVSYDSEPKRNVVVT 1060
Cdd:NF041568  128 VRVILDAEnyreRREETLEQlaerlA-DKVKRTKKPVVLEPMPSYERKIIHTaLQNHPDVETYSEGEEPNRKVVIA 202

R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 974005235 1023 SFPP-MNRDHRRIIHDLAQVYGLESVSYDSEPKRNVVVT 1060
Cdd:cd02640    21 VFSPeFSKEERALIHQIAQKYGLKSRSYGSGNDRYLVIS 59

NF-X1 type zinc finger; This domain is presumed to be a zinc binding domain. The following pattern describes the zinc finger. C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C Where X can be any amino acid, and numbers in brackets indicate the number of residues. Two position can be either his or cys. This family includes Swiss:P40798, Swiss:Q12986 and Swiss:P53971. The zinc fingers in Swiss:Q12986 bind to DNA.

                           10
                   ....*....|....*....
gi 974005235   567 CGNHTCSQVCHPQPCQQCP 585
Cdd:pfam01422    1 CGNHTCEEVCHEGPCPPCP 19

NF-X1 type zinc finger; This domain is presumed to be a zinc binding domain. The following pattern describes the zinc finger. C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C Where X can be any amino acid, and numbers in brackets indicate the number of residues. Two position can be either his or cys. This family includes Swiss:P40798, Swiss:Q12986 and Swiss:P53971. The zinc fingers in Swiss:Q12986 bind to DNA.

                           10
                   ....*....|....*....
gi 974005235   722 CGLHRCEEPCHRGNCQTCW 740
Cdd:pfam01422    1 CGNHTCEEVCHEGPCPPCP 19