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Conserved domains on  [gi|392900915|ref|NP_502212|]
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Nucleolar protein 9 [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG5099 super family cl34901
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 371-591 1.51e-07

RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis];


The actual alignment was detected with superfamily member COG5099:

Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 54.75  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900915 371 GSRVWDKLMETCSEDARSLLwIEFCSKNVDELTDNRFSNFPLQKMINSSTSLEMVTEIIETMAPKCSSLLEHQNSGvfLS 450
Cdd:COG5099  488 GNYLIQKLFEYGSEIQKSIM-LSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGN--HV 564

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900915 451 VIRCAARYPSSektmlqqlrkyfraaseakKGQFLLNVLTLNGCDGSIfdtqkfTQKGTMLVSELVNFSKTKTLatgfEQ 530
Cdd:COG5099  565 IQKCIEKFNKE-------------------KNQFIFDSINENLYDLST------HRYGSRVVQRCLENCNSEDK----EN 615

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392900915 531 LSEQQIQEM---SCNKYTSRLIQAVLASKTMPEeiKEKIIGAFDKNSWETLITDTFGSRVFEKI 591
Cdd:COG5099  616 LVEEIISNSkylSQDQYGNYVVQHILDNGAEPN--KERIIIKLLSKRVVELSTHKFASNVVEKC 677
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 371-591 1.51e-07

RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis];


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 54.75  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900915 371 GSRVWDKLMETCSEDARSLLwIEFCSKNVDELTDNRFSNFPLQKMINSSTSLEMVTEIIETMAPKCSSLLEHQNSGvfLS 450
Cdd:COG5099  488 GNYLIQKLFEYGSEIQKSIM-LSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGN--HV 564

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900915 451 VIRCAARYPSSektmlqqlrkyfraaseakKGQFLLNVLTLNGCDGSIfdtqkfTQKGTMLVSELVNFSKTKTLatgfEQ 530
Cdd:COG5099  565 IQKCIEKFNKE-------------------KNQFIFDSINENLYDLST------HRYGSRVVQRCLENCNSEDK----EN 615

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392900915 531 LSEQQIQEM---SCNKYTSRLIQAVLASKTMPEeiKEKIIGAFDKNSWETLITDTFGSRVFEKI 591
Cdd:COG5099  616 LVEEIISNSkylSQDQYGNYVVQHILDNGAEPN--KERIIIKLLSKRVVELSTHKFASNVVEKC 677
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 352-439 4.72e-03

Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats.


Pssm-ID: 153420 [Multi-domain]  Cd Length: 322  Bit Score: 39.50  E-value: 4.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900915 352 KKLEKEDIEGISKA----WYS----SNGSRVWDKLMETCSEDARSLLwIEFCSKNVDELTDNRFSNFPLQKMINSSTSlE 423
Cdd:cd07920  138 EKFPPEDLQFIIDAfkgnCVAlsthPYGCRVIQRCLEHCSEEQREPL-LEEILEHALELVQDQFGNYVVQHVLELGDP-D 215

                         90
                 ....*....|....*.
gi 392900915 424 MVTEIIETMAPKCSSL 439
Cdd:cd07920  216 DTSRIIEKLLGNIVQL 231
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 371-591 1.51e-07

RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis];


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 54.75  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900915 371 GSRVWDKLMETCSEDARSLLwIEFCSKNVDELTDNRFSNFPLQKMINSSTSLEMVTEIIETMAPKCSSLLEHQNSGvfLS 450
Cdd:COG5099  488 GNYLIQKLFEYGSEIQKSIM-LSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGN--HV 564

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900915 451 VIRCAARYPSSektmlqqlrkyfraaseakKGQFLLNVLTLNGCDGSIfdtqkfTQKGTMLVSELVNFSKTKTLatgfEQ 530
Cdd:COG5099  565 IQKCIEKFNKE-------------------KNQFIFDSINENLYDLST------HRYGSRVVQRCLENCNSEDK----EN 615

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392900915 531 LSEQQIQEM---SCNKYTSRLIQAVLASKTMPEeiKEKIIGAFDKNSWETLITDTFGSRVFEKI 591
Cdd:COG5099  616 LVEEIISNSkylSQDQYGNYVVQHILDNGAEPN--KERIIIKLLSKRVVELSTHKFASNVVEKC 677
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 352-439 4.72e-03

Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats.


Pssm-ID: 153420 [Multi-domain]  Cd Length: 322  Bit Score: 39.50  E-value: 4.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900915 352 KKLEKEDIEGISKA----WYS----SNGSRVWDKLMETCSEDARSLLwIEFCSKNVDELTDNRFSNFPLQKMINSSTSlE 423
Cdd:cd07920  138 EKFPPEDLQFIIDAfkgnCVAlsthPYGCRVIQRCLEHCSEEQREPL-LEEILEHALELVQDQFGNYVVQHVLELGDP-D 215

                         90
                 ....*....|....*.
gi 392900915 424 MVTEIIETMAPKCSSL 439
Cdd:cd07920  216 DTSRIIEKLLGNIVQL 231
 
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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