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Conserved domains on  [gi|1720372725|ref|XP_030102708|]
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ribosome quality control complex subunit NEMF isoform X2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RqcH_arch super family cl49222
ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) ...
 107-290 9.42e-62

ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) describes archaeal homologs of the RqcH (Ribosome-associated Quality Control H), involved in release of defective mRNAs that lack a stop codons and so are stuck on ribosomes. Conservation of a role in ribosome rescue for this archaeal family is supported by presence in a conserved gene neighborhood with homologs of Pelota/Dom34 and ABCE1/Rli1 homologs, proteins involved in splitting the ribosome into large and small subunits.


The actual alignment was detected with superfamily member NF041120:

Pssm-ID: 469043 [Multi-domain]  Cd Length: 642  Bit Score: 218.23  E-value: 9.42e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 107 VDVDLSLSAYANAKKYYDH-KRYAAKK--TQRTVEAAEKAFKSAEKKTKQTLKEVQTVtsiqkARKVYWFEKFLWFISSE 183
Cdd:NF041120  378 VELDIRKSVEENASRYYEKaKKLKRKIegALEAIEETKKELEKLEKKREEKKEEARRV-----RRKKEWYERFRWFITSD 452

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 184 NYLIIGGRDQQQNEIIVKRYLTPGDIYVHADLHGATSCVIKNpTGEPIPPRTLTEAGTMALCYSAAW-DARVITSAWWVY 262
Cdd:NF041120  453 GFLVIGGRDADQNEELVKKYLEDNDIFFHADIHGAPAVVIKT-GGESVPEEDLREAAQFAASYSKAWkAGLGSGDVYWVY 531

                         170       180
                  ....*....|....*....|....*...
gi 1720372725 263 HHQVSKTAPTGEYLTTGSFMIRGKKNFL 290
Cdd:NF041120  532 PDQVSKTPPSGEYLAKGSFMIRGKRNYI 559
NFACT-C pfam11923
NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, ...
 611-702 4.10e-39

NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins involved in the ribosomal quality control pathway. This context is conserved in archaea and eukaryotes, but NFACT proteins in bacteria lack the NFACT-C domain.


:

Pssm-ID: 432191  Cd Length: 104  Bit Score: 139.58  E-value: 4.10e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 611 NEENLFDSLTGQPHPEDVLMFAIPICAPYTIMTNYKYKVKLTPGVQKKGKAAKTALNSFMH---------SKEATAREKD 681
Cdd:pfam11923   3 NYLTLLDSLTGTPLPDDELLEAIPVCAPWAALQKYKYKVKLQPGTTKKGKAVKEILEYFLKrkvdessrdKERDWPREKE 82

                          90       100
                  ....*....|....*....|..
gi 1720372725 682 LFRSVKDTDLSRNIP-GKVKVS 702
Cdd:pfam11923  83 LIKALKDEELVNVIPvGKVKVS 104
 
Name Accession Description Interval E-value
RqcH_arch NF041120
ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) ...
 107-290 9.42e-62

ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) describes archaeal homologs of the RqcH (Ribosome-associated Quality Control H), involved in release of defective mRNAs that lack a stop codons and so are stuck on ribosomes. Conservation of a role in ribosome rescue for this archaeal family is supported by presence in a conserved gene neighborhood with homologs of Pelota/Dom34 and ABCE1/Rli1 homologs, proteins involved in splitting the ribosome into large and small subunits.


Pssm-ID: 469043 [Multi-domain]  Cd Length: 642  Bit Score: 218.23  E-value: 9.42e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 107 VDVDLSLSAYANAKKYYDH-KRYAAKK--TQRTVEAAEKAFKSAEKKTKQTLKEVQTVtsiqkARKVYWFEKFLWFISSE 183
Cdd:NF041120  378 VELDIRKSVEENASRYYEKaKKLKRKIegALEAIEETKKELEKLEKKREEKKEEARRV-----RRKKEWYERFRWFITSD 452

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 184 NYLIIGGRDQQQNEIIVKRYLTPGDIYVHADLHGATSCVIKNpTGEPIPPRTLTEAGTMALCYSAAW-DARVITSAWWVY 262
Cdd:NF041120  453 GFLVIGGRDADQNEELVKKYLEDNDIFFHADIHGAPAVVIKT-GGESVPEEDLREAAQFAASYSKAWkAGLGSGDVYWVY 531

                         170       180
                  ....*....|....*....|....*...
gi 1720372725 263 HHQVSKTAPTGEYLTTGSFMIRGKKNFL 290
Cdd:NF041120  532 PDQVSKTPPSGEYLAKGSFMIRGKRNYI 559
NFACT-R_1 pfam05670
NFACT protein RNA binding domain; This domain occurs in proteins that have been annotated as ...
 175-285 2.20e-51

NFACT protein RNA binding domain; This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from Swiss:O34693 where the N-terminal region is involved in this activity. It is an RNA binding domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. This NFACT-R family is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing and as a standalone domain. Additionally this domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.


Pssm-ID: 428576 [Multi-domain]  Cd Length: 111  Bit Score: 173.95  E-value: 2.20e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 175 KFLWFISSENYLIIGGRDQQQNEIIVKRYLTPGDIYVHADLHGATSCVIKNPTGEPIPPRTLTEAGTMALCYSAAWDARV 254
Cdd:pfam05670   1 KFYWFVSSEGYLVIGGRDKQENELLIKKYLEEGDLWFHADKHGSAHVYLKLPEGEDIPPETLEEAAQLAKANSIAWGNKQ 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1720372725 255 -ITSAWWVYHHQVSKTAPTGeYLTTGSFMIRG 285
Cdd:pfam05670  81 nNISVWYTPASQVSKTGPSG-YLDTGSFMFKG 111
NFACT-C pfam11923
NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, ...
 611-702 4.10e-39

NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins involved in the ribosomal quality control pathway. This context is conserved in archaea and eukaryotes, but NFACT proteins in bacteria lack the NFACT-C domain.


Pssm-ID: 432191  Cd Length: 104  Bit Score: 139.58  E-value: 4.10e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 611 NEENLFDSLTGQPHPEDVLMFAIPICAPYTIMTNYKYKVKLTPGVQKKGKAAKTALNSFMH---------SKEATAREKD 681
Cdd:pfam11923   3 NYLTLLDSLTGTPLPDDELLEAIPVCAPWAALQKYKYKVKLQPGTTKKGKAVKEILEYFLKrkvdessrdKERDWPREKE 82

                          90       100
                  ....*....|....*....|..
gi 1720372725 682 LFRSVKDTDLSRNIP-GKVKVS 702
Cdd:pfam11923  83 LIKALKDEELVNVIPvGKVKVS 104
RqcH COG1293
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) ...
 102-290 2.31e-36

Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) and RNA- (NFACT) binding domains [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440904 [Multi-domain]  Cd Length: 578  Bit Score: 144.60  E-value: 2.31e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 102 NKPLLVDVDLSLSAYANAKKYYdhKRYaaKKTQRTVEAAEKAFKSAEKK--------------TKQTLKEVQT------- 160
Cdd:COG1293   365 YEEVTIPLDPRLSPSENAQRYY--KKY--KKLKRKKEGAEEQLEETEEEleylesvlaqleqaEDEDLEEIREelieqgy 440

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 161 --VTSIQKARKVYWFEKFLWFISSENYLIIGGRDQQQNEIIVKRYLTPGDIYVHADLHGATSCVIKNpTGEPIPPRTLTE 238
Cdd:COG1293   441 lkKKKKKKKKKKKWYEKPRWFISSDGFLILVGRNNRQNDELTKKYARKNDIWFHAKDIPGSHVIIKT-EGKEPPEETLEE 519

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1720372725 239 AGTMALCYSAAWDARVITsAWWVYHHQVSKtaPTGEyltTGSFMIRGKKNFL 290
Cdd:COG1293   520 AAQLAAYYSKARKSGSVP-VDYTEPKQVSK--PKGA---KPGFVIYGNRKTL 565
 
Name Accession Description Interval E-value
RqcH_arch NF041120
ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) ...
 107-290 9.42e-62

ribosome rescue protein RqcH, archaeal type; This HMM (built with support from arCOG01695) describes archaeal homologs of the RqcH (Ribosome-associated Quality Control H), involved in release of defective mRNAs that lack a stop codons and so are stuck on ribosomes. Conservation of a role in ribosome rescue for this archaeal family is supported by presence in a conserved gene neighborhood with homologs of Pelota/Dom34 and ABCE1/Rli1 homologs, proteins involved in splitting the ribosome into large and small subunits.


Pssm-ID: 469043 [Multi-domain]  Cd Length: 642  Bit Score: 218.23  E-value: 9.42e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 107 VDVDLSLSAYANAKKYYDH-KRYAAKK--TQRTVEAAEKAFKSAEKKTKQTLKEVQTVtsiqkARKVYWFEKFLWFISSE 183
Cdd:NF041120  378 VELDIRKSVEENASRYYEKaKKLKRKIegALEAIEETKKELEKLEKKREEKKEEARRV-----RRKKEWYERFRWFITSD 452

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 184 NYLIIGGRDQQQNEIIVKRYLTPGDIYVHADLHGATSCVIKNpTGEPIPPRTLTEAGTMALCYSAAW-DARVITSAWWVY 262
Cdd:NF041120  453 GFLVIGGRDADQNEELVKKYLEDNDIFFHADIHGAPAVVIKT-GGESVPEEDLREAAQFAASYSKAWkAGLGSGDVYWVY 531

                         170       180
                  ....*....|....*....|....*...
gi 1720372725 263 HHQVSKTAPTGEYLTTGSFMIRGKKNFL 290
Cdd:NF041120  532 PDQVSKTPPSGEYLAKGSFMIRGKRNYI 559
NFACT-R_1 pfam05670
NFACT protein RNA binding domain; This domain occurs in proteins that have been annotated as ...
 175-285 2.20e-51

NFACT protein RNA binding domain; This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from Swiss:O34693 where the N-terminal region is involved in this activity. It is an RNA binding domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. This NFACT-R family is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing and as a standalone domain. Additionally this domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.


Pssm-ID: 428576 [Multi-domain]  Cd Length: 111  Bit Score: 173.95  E-value: 2.20e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 175 KFLWFISSENYLIIGGRDQQQNEIIVKRYLTPGDIYVHADLHGATSCVIKNPTGEPIPPRTLTEAGTMALCYSAAWDARV 254
Cdd:pfam05670   1 KFYWFVSSEGYLVIGGRDKQENELLIKKYLEEGDLWFHADKHGSAHVYLKLPEGEDIPPETLEEAAQLAKANSIAWGNKQ 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1720372725 255 -ITSAWWVYHHQVSKTAPTGeYLTTGSFMIRG 285
Cdd:pfam05670  81 nNISVWYTPASQVSKTGPSG-YLDTGSFMFKG 111
NFACT-C pfam11923
NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, ...
 611-702 4.10e-39

NFACT protein C-terminal domain; This is the C-terminal domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins involved in the ribosomal quality control pathway. This context is conserved in archaea and eukaryotes, but NFACT proteins in bacteria lack the NFACT-C domain.


Pssm-ID: 432191  Cd Length: 104  Bit Score: 139.58  E-value: 4.10e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 611 NEENLFDSLTGQPHPEDVLMFAIPICAPYTIMTNYKYKVKLTPGVQKKGKAAKTALNSFMH---------SKEATAREKD 681
Cdd:pfam11923   3 NYLTLLDSLTGTPLPDDELLEAIPVCAPWAALQKYKYKVKLQPGTTKKGKAVKEILEYFLKrkvdessrdKERDWPREKE 82

                          90       100
                  ....*....|....*....|..
gi 1720372725 682 LFRSVKDTDLSRNIP-GKVKVS 702
Cdd:pfam11923  83 LIKALKDEELVNVIPvGKVKVS 104
RqcH COG1293
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) ...
 102-290 2.31e-36

Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) and RNA- (NFACT) binding domains [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440904 [Multi-domain]  Cd Length: 578  Bit Score: 144.60  E-value: 2.31e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 102 NKPLLVDVDLSLSAYANAKKYYdhKRYaaKKTQRTVEAAEKAFKSAEKK--------------TKQTLKEVQT------- 160
Cdd:COG1293   365 YEEVTIPLDPRLSPSENAQRYY--KKY--KKLKRKKEGAEEQLEETEEEleylesvlaqleqaEDEDLEEIREelieqgy 440

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720372725 161 --VTSIQKARKVYWFEKFLWFISSENYLIIGGRDQQQNEIIVKRYLTPGDIYVHADLHGATSCVIKNpTGEPIPPRTLTE 238
Cdd:COG1293   441 lkKKKKKKKKKKKWYEKPRWFISSDGFLILVGRNNRQNDELTKKYARKNDIWFHAKDIPGSHVIIKT-EGKEPPEETLEE 519

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1720372725 239 AGTMALCYSAAWDARVITsAWWVYHHQVSKtaPTGEyltTGSFMIRGKKNFL 290
Cdd:COG1293   520 AAQLAAYYSKARKSGSVP-VDYTEPKQVSK--PKGA---KPGFVIYGNRKTL 565
 
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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