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Conserved domains on  [gi|2024381351|ref|XP_040507623|]
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pumilio homolog 1 isoform X8 [Gallus gallus]

Protein Classification

Pumilio-family RNA binding repeat-containing protein( domain architecture ID 10167778)

Pumilio-family RNA binding repeat-containing protein harbors PUF repeats, which mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio; it may function as a translational repressor in early embryonic development by binding to sequences in the 3' UTR of target mRNAs

CATH:  1.25.10.10
Gene Ontology:  GO:0003723
PubMed:  14584586|29385744|17003467|9404893

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 842-1165 0e+00

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: 544.11  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  842 NLQLREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 920
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  921 RGHVLSLALQMYGCRVIQKALEFIPPDQqvINEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFA 1000
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQ--ISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351 1001 LSTHPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFAS 1080
Cdd:cd07920    159 LSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFAS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351 1081 NVVEKCVTHASRTERAMLIDEVCTmNDGPHSALYTMMKDQYANYVVQKMIDVAEPAQRKIVMHKIRPHIATLRKYTYGKH 1160
Cdd:cd07920    239 NVVEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKH 317


                   ....*
gi 2024381351 1161 ILAKL 1165
Cdd:cd07920    318 ILAKL 322
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 842-1165 0e+00

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: 544.11  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  842 NLQLREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 920
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  921 RGHVLSLALQMYGCRVIQKALEFIPPDQqvINEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFA 1000
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQ--ISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351 1001 LSTHPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFAS 1080
Cdd:cd07920    159 LSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFAS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351 1081 NVVEKCVTHASRTERAMLIDEVCTmNDGPHSALYTMMKDQYANYVVQKMIDVAEPAQRKIVMHKIRPHIATLRKYTYGKH 1160
Cdd:cd07920    239 NVVEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKH 317


                   ....*
gi 2024381351 1161 ILAKL 1165
Cdd:cd07920    318 ILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 682-1167 1.22e-101

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 339.80  E-value: 1.22e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  682 ATLGSALGGFGTAVANSNTgsgSRRDSLTGSSDLYKRTSSSLTPIGHSFYNGLGfSSSPGPVGMPLPSQGPGHSQtppps 761
Cdd:COG5099    271 VPSIRNLRGLNSALVSFLN---VSSSSLAFSALNGKEVSPTGSPSTRSFARVLP-KSSPNNLLTEILTTGVNPPQ----- 341

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  762 lsshgsssslNLGGLTNGSgrYISAAPGAEAKYRSASSASSLFSPSSTLFPSSRLRYGMSDVMPSG----RSRLLEDFRN 837
Cdd:COG5099    342 ----------SLPSLLNPV--FLSTSTGFSLTNLSGYLNPNKNLKKNTLSSLSNLGYSSNVPSPSSsestRNILGNISPN 409

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  838 N--RYPNLQLR----------------EIAGHIMEFSQ-DQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGN 898
Cdd:COG5099    410 FktSSNLTNLNsllkeklsnsssvsatDILGPSIIVSCkDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGN 489

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  899 YVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPPDQQvINEMVRELDGHVLKCVKDQNGNHVVQKC 978
Cdd:COG5099    490 YLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQ-ISLLVEELRPYCLQLIKDQNGNHVIQKC 568

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  979 IECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPED 1058
Cdd:COG5099    569 IEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPN 648

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351 1059 KSKIVAEIRGNVLV-LSQHKFASNVVEKCVTHASRTE-RAMLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPA 1136
Cdd:COG5099    649 KERIIIKLLSKRVVeLSTHKFASNVVEKCIKYASDSFkRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPEI 728

                          490       500       510
                   ....*....|....*....|....*....|.
gi 2024381351 1137 QRKIVMHKIRPHIATLRKYTYGKHILAKLEK 1167
Cdd:COG5099    729 QRSLLARAIKKVIPSLKKSMYGQHILALLEK 759
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 997-1031 1.85e-12

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. 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. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 62.32  E-value: 1.85e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2024381351  997 QVFALSTHPYGCRVIQRILEHCLPEQTLPILEELH 1031
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1029-1063 5.49e-08

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.74  E-value: 5.49e-08
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 2024381351  1029 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIV 1063
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 842-1165 0e+00

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: 544.11  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  842 NLQLREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 920
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  921 RGHVLSLALQMYGCRVIQKALEFIPPDQqvINEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFA 1000
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQ--ISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351 1001 LSTHPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFAS 1080
Cdd:cd07920    159 LSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFAS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351 1081 NVVEKCVTHASRTERAMLIDEVCTmNDGPHSALYTMMKDQYANYVVQKMIDVAEPAQRKIVMHKIRPHIATLRKYTYGKH 1160
Cdd:cd07920    239 NVVEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKH 317


                   ....*
gi 2024381351 1161 ILAKL 1165
Cdd:cd07920    318 ILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 682-1167 1.22e-101

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 339.80  E-value: 1.22e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  682 ATLGSALGGFGTAVANSNTgsgSRRDSLTGSSDLYKRTSSSLTPIGHSFYNGLGfSSSPGPVGMPLPSQGPGHSQtppps 761
Cdd:COG5099    271 VPSIRNLRGLNSALVSFLN---VSSSSLAFSALNGKEVSPTGSPSTRSFARVLP-KSSPNNLLTEILTTGVNPPQ----- 341

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  762 lsshgsssslNLGGLTNGSgrYISAAPGAEAKYRSASSASSLFSPSSTLFPSSRLRYGMSDVMPSG----RSRLLEDFRN 837
Cdd:COG5099    342 ----------SLPSLLNPV--FLSTSTGFSLTNLSGYLNPNKNLKKNTLSSLSNLGYSSNVPSPSSsestRNILGNISPN 409

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  838 N--RYPNLQLR----------------EIAGHIMEFSQ-DQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGN 898
Cdd:COG5099    410 FktSSNLTNLNsllkeklsnsssvsatDILGPSIIVSCkDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGN 489

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  899 YVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPPDQQvINEMVRELDGHVLKCVKDQNGNHVVQKC 978
Cdd:COG5099    490 YLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQ-ISLLVEELRPYCLQLIKDQNGNHVIQKC 568

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  979 IECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPED 1058
Cdd:COG5099    569 IEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPN 648

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351 1059 KSKIVAEIRGNVLV-LSQHKFASNVVEKCVTHASRTE-RAMLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPA 1136
Cdd:COG5099    649 KERIIIKLLSKRVVeLSTHKFASNVVEKCIKYASDSFkRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPEI 728

                          490       500       510
                   ....*....|....*....|....*....|.
gi 2024381351 1137 QRKIVMHKIRPHIATLRKYTYGKHILAKLEK 1167
Cdd:COG5099    729 QRSLLARAIKKVIPSLKKSMYGQHILALLEK 759
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 997-1031 1.85e-12

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. 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. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 62.32  E-value: 1.85e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2024381351  997 QVFALSTHPYGCRVIQRILEHCLPEQTLPILEELH 1031
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 851-885 1.34e-09

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. 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. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 54.23  E-value: 1.34e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2024381351  851 HIMEFSQDQHGSRFIQLKLERATPAERQLVFNEIL 885
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1033-1066 7.79e-09

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. 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. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 52.30  E-value: 7.79e-09
                           10        20        30
                   ....*....|....*....|....*....|....
gi 2024381351 1033 HTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEI 1066
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1029-1063 5.49e-08

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.74  E-value: 5.49e-08
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 2024381351  1029 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIV 1063
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 923-954 1.02e-07

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. 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. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 48.84  E-value: 1.02e-07
                           10        20        30
                   ....*....|....*....|....*....|....
gi 2024381351  923 HVLSLALQMYGCRVIQKALEFIPPDQ--QVINEM 954
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQreQILDEI 34
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1069-1103 1.48e-07

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. 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. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 48.45  E-value: 1.48e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2024381351 1069 NVLVLSQHKFASNVVEKCVTHASRTERAMLIDEVC 1103
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 957-992 3.30e-07

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 47.43  E-value: 3.30e-07
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 2024381351   957 ELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIID 992
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 993-1028 6.42e-07

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 46.66  E-value: 6.42e-07
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 2024381351   993 AFKGQVFALSTHPYGCRVIQRILEHCLPEQTLPILE 1028
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1110-1143 7.22e-07

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 46.66  E-value: 7.22e-07
                            10        20        30
                    ....*....|....*....|....*....|....
gi 2024381351  1110 HSALYTMMKDQYANYVVQKMIDVAEPAQRKIVMH 1143
Cdd:smart00025    3 KGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1114-1145 1.29e-06

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. 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. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 45.75  E-value: 1.29e-06
                           10        20        30
                   ....*....|....*....|....*....|..
gi 2024381351 1114 YTMMKDQYANYVVQKMIDVAEPAQRKIVMHKI 1145
Cdd:pfam00806    3 VELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1065-1100 2.74e-06

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.12  E-value: 2.74e-06
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 2024381351  1065 EIRGNVLVLSQHKFASNVVEKCVTHASRTERAMLID 1100
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 889-920 6.33e-06

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. 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. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 43.83  E-value: 6.33e-06
                           10        20        30
                   ....*....|....*....|....*....|..
gi 2024381351  889 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 920
Cdd:pfam00806    3 VELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 920-949 6.69e-06

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.96  E-value: 6.69e-06
                            10        20        30
                    ....*....|....*....|....*....|
gi 2024381351   920 IRGHVLSLALQMYGCRVIQKALEFIPPDQQ 949
Cdd:smart00025    2 IKGHLLELSKDQYGNRVVQKLLEHASESQR 31
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 883-913 1.10e-05

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.19  E-value: 1.10e-05
                            10        20        30
                    ....*....|....*....|....*....|.
gi 2024381351   883 EILQAAYQLMVDVFGNYVIQKFFEFGSLEQK 913
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQR 31
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 961-992 1.39e-05

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. 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. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 43.06  E-value: 1.39e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 2024381351  961 HVLKCVKDQNGNHVVQKCIECVQPQSLQFIID 992
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILD 32
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 847-882 1.48e-05

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 42.81  E-value: 1.48e-05
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 2024381351   847 EIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFN 882
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 848-954 5.66e-03

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 40.89  E-value: 5.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381351  848 IAGHIMEFSQDQHGSRFIQlKLERATPA--ERQLVFNEILQAA-------YQLMVDVFGNYVIQKFFEFGSLEQKLALAE 918
Cdd:COG5099    657 LSKRVVELSTHKFASNVVE-KCIKYASDsfKRSRILNELTNRGiekpgflMLILDDQYANYVIQYLLDVSPEIQRSLLAR 735

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 2024381351  919 RIRGHVLSLALQMYGCRVIQKALEFIPPDQQVINEM 954
Cdd:COG5099    736 AIKKVIPSLKKSMYGQHILALLEKVGSSSQSSISNK 771
 
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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