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Conserved domains on  [gi|1958716625|ref|XP_038951851|]
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regulator of nonsense transcripts 2 isoform X1 [Rattus norvegicus]

Protein Classification

regulator of nonsense transcripts 2( domain architecture ID 10650500)

regulator of nonsense transcripts 2 (UPF2) is involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC)

CATH:  1.25.40.180
Gene Ontology:  GO:0000184|GO:0042162|GO:0003723
PubMed:  18066079

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MIF4G pfam02854
MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). ...
 774-984 1.68e-44

MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.


:

Pssm-ID: 397130  Cd Length: 203  Bit Score: 160.22  E-value: 1.68e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  774 RKLLYKDLSKVT---TEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCVANLLAGLVLY-QEDVGIHVVDGVLE 849
Cdd:pfam02854    1 LKKVKGILNKLSpenFEKLIKELLKLIMSDPELLKYLIELIFEKAVEEPNFIPAYARLCSGLNLRnPTDFGIHLLNRLQE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  850 DI--RLGMEVNQPKFNQRRISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNPDgspssldPPEHLFRIRLVCTILDTC 927
Cdd:pfam02854   81 EFekRFELEENEQGNRRRRLGLVRFLGELYKFGLLTEKILFECLKELLSSLTKED-------LKRDLFNLECLLTLLTTI 153

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958716625  928 GQYFDRGSSKRKLDCFLVYFQRYVWWKkslevwtKDHPFPIDIDYMISDTLELLRPK 984
Cdd:pfam02854  154 GKLLENEKLPKLMDQFLDEIQKYVLSK-------DDPKLSSRLRFMLQDLIELRKNK 203
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 569-756 8.37e-39

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


:

Pssm-ID: 214713  Cd Length: 200  Bit Score: 143.66  E-value: 8.37e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   569 FLQQLPNCVNRDLIDKAAMDFCM-NMNTKANRKKLVRALFIVPRQRLDLLPFYARLVATLHPCMSDVAEDLCSMLRGDFR 647
Cdd:smart00543    3 KVKGLINKLSPSNFESIIKELLKlNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEFE 82

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   648 FHVRKKDQINIETKNKTVRFIGELTKFKMFTKNDTLHCLKMLLSDF-------SHHHIEMACTLLETCGRFLFRsPESHL 720
Cdd:smart00543   83 KGLESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLtkldpprSDFSVECLLSLLPTCGKDLER-EKSPK 161

                           170       180       190
                    ....*....|....*....|....*....|....*....
gi 1958716625   721 RTSVLLEQMMR---KKQAMHLDARYVTMVENAYYYCNPP 756
Cdd:smart00543  162 LLDEILERLQDyllKKDKTELSSRLRFMLELLIELRKNK 200
Upf2 pfam04050
Up-frameshift suppressor 2; Transcripts harbouring premature signals for translation ...
 1086-1215 5.71e-38

Up-frameshift suppressor 2; Transcripts harbouring premature signals for translation termination are recognized and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay.


:

Pssm-ID: 461146  Cd Length: 133  Bit Score: 138.64  E-value: 5.71e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625 1086 DEENAEVMIkggGLKHVPCVEDEDFIQALDKMMLENLQQRSGESVKVHQLDVAIPLHLKSQLRKGPPLGGG------EGE 1159
Cdd:pfam04050    1 EEEGEEVRR---GEEEVDPEEEAEFERELAKMMQESLESRKNERKTVPQLDVPLPMNVKAKKKSGSGDDGGaegdaeEPE 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958716625 1160 TESADTMPFVMLTRKGNKQQFKILNVPMSSQLAANHWNQQQAEQEERMRMKKLTLD 1215
Cdd:pfam04050   78 TNPSGKVAFTLLTKKGNKQQTKTLELPSDSSFAVNTREQEEAEKEEKQRIKRLVLN 133
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 167-362 3.25e-25

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


:

Pssm-ID: 214713  Cd Length: 200  Bit Score: 104.36  E-value: 3.25e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   167 LKKNTAFVKKL-KTITEQQRDSLSHDFNGL-NLSKYIAEAVASIVEAKLkiSDVNCAVHLCSLFHQRYADFAPSLLQVWK 244
Cdd:smart00543    1 EKKVKGLINKLsPSNFESIIKELLKLNNSDkNLRKYILELIFEKAVEEP--NFIPAYARLCALLNAKNPDFGSLLLERLQ 78

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   245 KHFEARKE-EKTPNITKLRTDLRFIAELTIVGIFTDKEGLSLIYEQLKSIINADR-ESHTHVSVVISFCRHCGDDIA-GL 321
Cdd:smart00543   79 EEFEKGLEsEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTKLDPpRSDFSVECLLSLLPTCGKDLErEK 158

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|.
gi 1958716625   322 VPRKVKSAAEKFNLNFPPSEIISPEKQQPFQNLLKEYFTSL 362
Cdd:smart00543  159 SPKLLDEILERLQDYLLKKDKTELSSRLRFMLELLIELRKN 199
DUF1451 super family cl19727
Zinc-ribbon containing domain; This family consists of several hypothetical bacterial proteins ...
 357-420 9.97e-03

Zinc-ribbon containing domain; This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein.


The actual alignment was detected with superfamily member PRK11032:

Pssm-ID: 450347  Cd Length: 160  Bit Score: 38.05  E-value: 9.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  357 EYFTSLTKHLKRDHRELQNTERQNRRILHSKGELSEDRHKQ--------YEEFAMSYQ------------KLLANS--QS 414
Cdd:PRK11032    10 ELVASLTERLRNGERDIDALVESARKRVDAAGELTRDEVDLitravrrdLEEFARSYEeskeefsdsvfmRVIKESlwQE 89


                   ....*.
gi 1958716625  415 LADLLD 420
Cdd:PRK11032    90 LADITD 95
 
Name Accession Description Interval E-value
MIF4G pfam02854
MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). ...
 774-984 1.68e-44

MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.


Pssm-ID: 397130  Cd Length: 203  Bit Score: 160.22  E-value: 1.68e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  774 RKLLYKDLSKVT---TEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCVANLLAGLVLY-QEDVGIHVVDGVLE 849
Cdd:pfam02854    1 LKKVKGILNKLSpenFEKLIKELLKLIMSDPELLKYLIELIFEKAVEEPNFIPAYARLCSGLNLRnPTDFGIHLLNRLQE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  850 DI--RLGMEVNQPKFNQRRISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNPDgspssldPPEHLFRIRLVCTILDTC 927
Cdd:pfam02854   81 EFekRFELEENEQGNRRRRLGLVRFLGELYKFGLLTEKILFECLKELLSSLTKED-------LKRDLFNLECLLTLLTTI 153

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958716625  928 GQYFDRGSSKRKLDCFLVYFQRYVWWKkslevwtKDHPFPIDIDYMISDTLELLRPK 984
Cdd:pfam02854  154 GKLLENEKLPKLMDQFLDEIQKYVLSK-------DDPKLSSRLRFMLQDLIELRKNK 203
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 771-984 4.10e-44

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


Pssm-ID: 214713  Cd Length: 200  Bit Score: 158.68  E-value: 4.10e-44
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   771 EYVRKLLYKDLSKVTTEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCVANLLAGLVLYQEDVGIHVVDGVLED 850
Cdd:smart00543    1 EKKVKGLINKLSPSNFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEE 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   851 IRLGMEVNQPKFNQRRISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNpdgspssLDPPEHLFRIRLVCTILDTCGQY 930
Cdd:smart00543   81 FEKGLESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTK-------LDPPRSDFSVECLLSLLPTCGKD 153

                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|....
gi 1958716625   931 FDRGSSKRKLDCFLVYFQRYVWWKKSLEVwtkdhpfPIDIDYMISDTLELLRPK 984
Cdd:smart00543  154 LEREKSPKLLDEILERLQDYLLKKDKTEL-------SSRLRFMLELLIELRKNK 200
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 569-756 8.37e-39

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


Pssm-ID: 214713  Cd Length: 200  Bit Score: 143.66  E-value: 8.37e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   569 FLQQLPNCVNRDLIDKAAMDFCM-NMNTKANRKKLVRALFIVPRQRLDLLPFYARLVATLHPCMSDVAEDLCSMLRGDFR 647
Cdd:smart00543    3 KVKGLINKLSPSNFESIIKELLKlNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEFE 82

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   648 FHVRKKDQINIETKNKTVRFIGELTKFKMFTKNDTLHCLKMLLSDF-------SHHHIEMACTLLETCGRFLFRsPESHL 720
Cdd:smart00543   83 KGLESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLtkldpprSDFSVECLLSLLPTCGKDLER-EKSPK 161

                           170       180       190
                    ....*....|....*....|....*....|....*....
gi 1958716625   721 RTSVLLEQMMR---KKQAMHLDARYVTMVENAYYYCNPP 756
Cdd:smart00543  162 LLDEILERLQDyllKKDKTELSSRLRFMLELLIELRKNK 200
Upf2 pfam04050
Up-frameshift suppressor 2; Transcripts harbouring premature signals for translation ...
 1086-1215 5.71e-38

Up-frameshift suppressor 2; Transcripts harbouring premature signals for translation termination are recognized and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay.


Pssm-ID: 461146  Cd Length: 133  Bit Score: 138.64  E-value: 5.71e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625 1086 DEENAEVMIkggGLKHVPCVEDEDFIQALDKMMLENLQQRSGESVKVHQLDVAIPLHLKSQLRKGPPLGGG------EGE 1159
Cdd:pfam04050    1 EEEGEEVRR---GEEEVDPEEEAEFERELAKMMQESLESRKNERKTVPQLDVPLPMNVKAKKKSGSGDDGGaegdaeEPE 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958716625 1160 TESADTMPFVMLTRKGNKQQFKILNVPMSSQLAANHWNQQQAEQEERMRMKKLTLD 1215
Cdd:pfam04050   78 TNPSGKVAFTLLTKKGNKQQTKTLELPSDSSFAVNTREQEEAEKEEKQRIKRLVLN 133
MIF4G pfam02854
MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). ...
 569-756 1.97e-25

MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.


Pssm-ID: 397130  Cd Length: 203  Bit Score: 105.14  E-value: 1.97e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  569 FLQQLPNCVNRDLIDKAAMDFC-MNMNTKANRKKLVRALFIVPRQRLDLLPFYARLVATLHPCM-SDVAEDLCSMLRGDF 646
Cdd:pfam02854    3 KVKGILNKLSPENFEKLIKELLkLIMSDPELLKYLIELIFEKAVEEPNFIPAYARLCSGLNLRNpTDFGIHLLNRLQEEF 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  647 --RFHVRKKDQINIETKNKTVRFIGELTKFKMFTKNDTLHCLKMLLSDF-------SHHHIEMACTLLETCGRFLFRsPE 717
Cdd:pfam02854   83 ekRFELEENEQGNRRRRLGLVRFLGELYKFGLLTEKILFECLKELLSSLtkedlkrDLFNLECLLTLLTTIGKLLEN-EK 161

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1958716625  718 SHLRTSVLLEQM---MRKKQAMHLDARYVTMVENAYYYCNPP 756
Cdd:pfam02854  162 LPKLMDQFLDEIqkyVLSKDDPKLSSRLRFMLQDLIELRKNK 203
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 167-362 3.25e-25

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


Pssm-ID: 214713  Cd Length: 200  Bit Score: 104.36  E-value: 3.25e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   167 LKKNTAFVKKL-KTITEQQRDSLSHDFNGL-NLSKYIAEAVASIVEAKLkiSDVNCAVHLCSLFHQRYADFAPSLLQVWK 244
Cdd:smart00543    1 EKKVKGLINKLsPSNFESIIKELLKLNNSDkNLRKYILELIFEKAVEEP--NFIPAYARLCALLNAKNPDFGSLLLERLQ 78

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   245 KHFEARKE-EKTPNITKLRTDLRFIAELTIVGIFTDKEGLSLIYEQLKSIINADR-ESHTHVSVVISFCRHCGDDIA-GL 321
Cdd:smart00543   79 EEFEKGLEsEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTKLDPpRSDFSVECLLSLLPTCGKDLErEK 158

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|.
gi 1958716625   322 VPRKVKSAAEKFNLNFPPSEIISPEKQQPFQNLLKEYFTSL 362
Cdd:smart00543  159 SPKLLDEILERLQDYLLKKDKTELSSRLRFMLELLIELRKN 199
MIF4G pfam02854
MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). ...
 167-315 1.35e-06

MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.


Pssm-ID: 397130  Cd Length: 203  Bit Score: 50.44  E-value: 1.35e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  167 LKKNTAFVKKLK-----TITEQQRDSLSHDfngLNLSKYIAEAVASIVEAKLkiSDVNCAVHLCS-LFHQRYADFAPSLL 240
Cdd:pfam02854    1 LKKVKGILNKLSpenfeKLIKELLKLIMSD---PELLKYLIELIFEKAVEEP--NFIPAYARLCSgLNLRNPTDFGIHLL 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958716625  241 QVWKKHFEARK---EEKTPNITKLRTDLRFIAELTIVGIFTDKEGLSLIYEQLKSIINAD-RESHTHVSVVISFCRHCG 315
Cdd:pfam02854   76 NRLQEEFEKRFeleENEQGNRRRRLGLVRFLGELYKFGLLTEKILFECLKELLSSLTKEDlKRDLFNLECLLTLLTTIG 154
PRK11032 PRK11032
zinc ribbon-containing protein;
357-420 9.97e-03

zinc ribbon-containing protein;


Pssm-ID: 182915  Cd Length: 160  Bit Score: 38.05  E-value: 9.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  357 EYFTSLTKHLKRDHRELQNTERQNRRILHSKGELSEDRHKQ--------YEEFAMSYQ------------KLLANS--QS 414
Cdd:PRK11032    10 ELVASLTERLRNGERDIDALVESARKRVDAAGELTRDEVDLitravrrdLEEFARSYEeskeefsdsvfmRVIKESlwQE 89


                   ....*.
gi 1958716625  415 LADLLD 420
Cdd:PRK11032    90 LADITD 95
 
Name Accession Description Interval E-value
MIF4G pfam02854
MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). ...
 774-984 1.68e-44

MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.


Pssm-ID: 397130  Cd Length: 203  Bit Score: 160.22  E-value: 1.68e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  774 RKLLYKDLSKVT---TEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCVANLLAGLVLY-QEDVGIHVVDGVLE 849
Cdd:pfam02854    1 LKKVKGILNKLSpenFEKLIKELLKLIMSDPELLKYLIELIFEKAVEEPNFIPAYARLCSGLNLRnPTDFGIHLLNRLQE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  850 DI--RLGMEVNQPKFNQRRISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNPDgspssldPPEHLFRIRLVCTILDTC 927
Cdd:pfam02854   81 EFekRFELEENEQGNRRRRLGLVRFLGELYKFGLLTEKILFECLKELLSSLTKED-------LKRDLFNLECLLTLLTTI 153

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958716625  928 GQYFDRGSSKRKLDCFLVYFQRYVWWKkslevwtKDHPFPIDIDYMISDTLELLRPK 984
Cdd:pfam02854  154 GKLLENEKLPKLMDQFLDEIQKYVLSK-------DDPKLSSRLRFMLQDLIELRKNK 203
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 771-984 4.10e-44

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


Pssm-ID: 214713  Cd Length: 200  Bit Score: 158.68  E-value: 4.10e-44
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   771 EYVRKLLYKDLSKVTTEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCVANLLAGLVLYQEDVGIHVVDGVLED 850
Cdd:smart00543    1 EKKVKGLINKLSPSNFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEE 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   851 IRLGMEVNQPKFNQRRISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNpdgspssLDPPEHLFRIRLVCTILDTCGQY 930
Cdd:smart00543   81 FEKGLESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTK-------LDPPRSDFSVECLLSLLPTCGKD 153

                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|....
gi 1958716625   931 FDRGSSKRKLDCFLVYFQRYVWWKKSLEVwtkdhpfPIDIDYMISDTLELLRPK 984
Cdd:smart00543  154 LEREKSPKLLDEILERLQDYLLKKDKTEL-------SSRLRFMLELLIELRKNK 200
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 569-756 8.37e-39

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


Pssm-ID: 214713  Cd Length: 200  Bit Score: 143.66  E-value: 8.37e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   569 FLQQLPNCVNRDLIDKAAMDFCM-NMNTKANRKKLVRALFIVPRQRLDLLPFYARLVATLHPCMSDVAEDLCSMLRGDFR 647
Cdd:smart00543    3 KVKGLINKLSPSNFESIIKELLKlNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEFE 82

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   648 FHVRKKDQINIETKNKTVRFIGELTKFKMFTKNDTLHCLKMLLSDF-------SHHHIEMACTLLETCGRFLFRsPESHL 720
Cdd:smart00543   83 KGLESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLtkldpprSDFSVECLLSLLPTCGKDLER-EKSPK 161

                           170       180       190
                    ....*....|....*....|....*....|....*....
gi 1958716625   721 RTSVLLEQMMR---KKQAMHLDARYVTMVENAYYYCNPP 756
Cdd:smart00543  162 LLDEILERLQDyllKKDKTELSSRLRFMLELLIELRKNK 200
Upf2 pfam04050
Up-frameshift suppressor 2; Transcripts harbouring premature signals for translation ...
 1086-1215 5.71e-38

Up-frameshift suppressor 2; Transcripts harbouring premature signals for translation termination are recognized and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay.


Pssm-ID: 461146  Cd Length: 133  Bit Score: 138.64  E-value: 5.71e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625 1086 DEENAEVMIkggGLKHVPCVEDEDFIQALDKMMLENLQQRSGESVKVHQLDVAIPLHLKSQLRKGPPLGGG------EGE 1159
Cdd:pfam04050    1 EEEGEEVRR---GEEEVDPEEEAEFERELAKMMQESLESRKNERKTVPQLDVPLPMNVKAKKKSGSGDDGGaegdaeEPE 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958716625 1160 TESADTMPFVMLTRKGNKQQFKILNVPMSSQLAANHWNQQQAEQEERMRMKKLTLD 1215
Cdd:pfam04050   78 TNPSGKVAFTLLTKKGNKQQTKTLELPSDSSFAVNTREQEEAEKEEKQRIKRLVLN 133
MIF4G pfam02854
MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). ...
 569-756 1.97e-25

MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.


Pssm-ID: 397130  Cd Length: 203  Bit Score: 105.14  E-value: 1.97e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  569 FLQQLPNCVNRDLIDKAAMDFC-MNMNTKANRKKLVRALFIVPRQRLDLLPFYARLVATLHPCM-SDVAEDLCSMLRGDF 646
Cdd:pfam02854    3 KVKGILNKLSPENFEKLIKELLkLIMSDPELLKYLIELIFEKAVEEPNFIPAYARLCSGLNLRNpTDFGIHLLNRLQEEF 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  647 --RFHVRKKDQINIETKNKTVRFIGELTKFKMFTKNDTLHCLKMLLSDF-------SHHHIEMACTLLETCGRFLFRsPE 717
Cdd:pfam02854   83 ekRFELEENEQGNRRRRLGLVRFLGELYKFGLLTEKILFECLKELLSSLtkedlkrDLFNLECLLTLLTTIGKLLEN-EK 161

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1958716625  718 SHLRTSVLLEQM---MRKKQAMHLDARYVTMVENAYYYCNPP 756
Cdd:pfam02854  162 LPKLMDQFLDEIqkyVLSKDDPKLSSRLRFMLQDLIELRKNK 203
MIF4G smart00543
Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The ...
 167-362 3.25e-25

Middle domain of eukaryotic initiation factor 4G (eIF4G); Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)


Pssm-ID: 214713  Cd Length: 200  Bit Score: 104.36  E-value: 3.25e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   167 LKKNTAFVKKL-KTITEQQRDSLSHDFNGL-NLSKYIAEAVASIVEAKLkiSDVNCAVHLCSLFHQRYADFAPSLLQVWK 244
Cdd:smart00543    1 EKKVKGLINKLsPSNFESIIKELLKLNNSDkNLRKYILELIFEKAVEEP--NFIPAYARLCALLNAKNPDFGSLLLERLQ 78

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625   245 KHFEARKE-EKTPNITKLRTDLRFIAELTIVGIFTDKEGLSLIYEQLKSIINADR-ESHTHVSVVISFCRHCGDDIA-GL 321
Cdd:smart00543   79 EEFEKGLEsEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTKLDPpRSDFSVECLLSLLPTCGKDLErEK 158

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|.
gi 1958716625   322 VPRKVKSAAEKFNLNFPPSEIISPEKQQPFQNLLKEYFTSL 362
Cdd:smart00543  159 SPKLLDEILERLQDYLLKKDKTELSSRLRFMLELLIELRKN 199
MIF4G pfam02854
MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). ...
 167-315 1.35e-06

MIF4G domain; MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.


Pssm-ID: 397130  Cd Length: 203  Bit Score: 50.44  E-value: 1.35e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  167 LKKNTAFVKKLK-----TITEQQRDSLSHDfngLNLSKYIAEAVASIVEAKLkiSDVNCAVHLCS-LFHQRYADFAPSLL 240
Cdd:pfam02854    1 LKKVKGILNKLSpenfeKLIKELLKLIMSD---PELLKYLIELIFEKAVEEP--NFIPAYARLCSgLNLRNPTDFGIHLL 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958716625  241 QVWKKHFEARK---EEKTPNITKLRTDLRFIAELTIVGIFTDKEGLSLIYEQLKSIINAD-RESHTHVSVVISFCRHCG 315
Cdd:pfam02854   76 NRLQEEFEKRFeleENEQGNRRRRLGLVRFLGELYKFGLLTEKILFECLKELLSSLTKEDlKRDLFNLECLLTLLTTIG 154
PRK11032 PRK11032
zinc ribbon-containing protein;
357-420 9.97e-03

zinc ribbon-containing protein;


Pssm-ID: 182915  Cd Length: 160  Bit Score: 38.05  E-value: 9.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958716625  357 EYFTSLTKHLKRDHRELQNTERQNRRILHSKGELSEDRHKQ--------YEEFAMSYQ------------KLLANS--QS 414
Cdd:PRK11032    10 ELVASLTERLRNGERDIDALVESARKRVDAAGELTRDEVDLitravrrdLEEFARSYEeskeefsdsvfmRVIKESlwQE 89


                   ....*.
gi 1958716625  415 LADLLD 420
Cdd:PRK11032    90 LADITD 95
 
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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