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Conserved domains on  [gi|2024381375|ref|XP_040507633|]
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pumilio homolog 1 isoform X24 [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 ...
 747-1068 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: 548.35  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  747 NLQLREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 825
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  826 RGHVLSLALQMYGCRVIQKALEFIPPDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALS 905
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  906 THPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 985
Cdd:cd07920    161 THPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  986 VEKCVTHASRTERAMLIDEVCTmNDGPHSALYTMMKDQYANYVVQKMIDVAEPAQRKIVMHKIRPHIATLRKYTYGKHIL 1065
Cdd:cd07920    241 VEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHIL 319


                   ...
gi 2024381375 1066 AKL 1068
Cdd:cd07920    320 AKL 322
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 747-1068 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: 548.35  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  747 NLQLREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 825
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  826 RGHVLSLALQMYGCRVIQKALEFIPPDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALS 905
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  906 THPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 985
Cdd:cd07920    161 THPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  986 VEKCVTHASRTERAMLIDEVCTmNDGPHSALYTMMKDQYANYVVQKMIDVAEPAQRKIVMHKIRPHIATLRKYTYGKHIL 1065
Cdd:cd07920    241 VEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHIL 319


                   ...
gi 2024381375 1066 AKL 1068
Cdd:cd07920    320 AKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 587-1070 1.04e-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: 338.26  E-value: 1.04e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  587 ATLGSALGGFGTAVANSNTgsgSRRDSLTGSSDLYKRTSSSLTPIGHSFYNGLGfSSSPGPVGMPLPSQGPGHSQtppps 666
Cdd:COG5099    271 VPSIRNLRGLNSALVSFLN---VSSSSLAFSALNGKEVSPTGSPSTRSFARVLP-KSSPNNLLTEILTTGVNPPQ----- 341

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  667 lsshgsssslNLGGLTNGSgrYISAAPGAEAKYRSASSASSLFSPSSTLFPSSRLRYGMSDVMPSG----RSRLLEDFRN 742
Cdd:COG5099    342 ----------SLPSLLNPV--FLSTSTGFSLTNLSGYLNPNKNLKKNTLSSLSNLGYSSNVPSPSSsestRNILGNISPN 409

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  743 N--RYPNLQLR----------------EIAGHIMEFSQ-DQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGN 803
Cdd:COG5099    410 FktSSNLTNLNsllkeklsnsssvsatDILGPSIIVSCkDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGN 489

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  804 YVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPPDQQ-NEMVRELDGHVLKCVKDQNGNHVVQKCI 882
Cdd:COG5099    490 YLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQiSLLVEELRPYCLQLIKDQNGNHVIQKCI 569

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  883 ECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDK 962
Cdd:COG5099    570 EKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNK 649

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  963 SKIVAEIRGNVLV-LSQHKFASNVVEKCVTHASRTE-RAMLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPAQ 1040
Cdd:COG5099    650 ERIIIKLLSKRVVeLSTHKFASNVVEKCIKYASDSFkRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPEIQ 729

                          490       500       510
                   ....*....|....*....|....*....|
gi 2024381375 1041 RKIVMHKIRPHIATLRKYTYGKHILAKLEK 1070
Cdd:COG5099    730 RSLLARAIKKVIPSLKKSMYGQHILALLEK 759
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 900-934 1.70e-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: 1.70e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2024381375  900 QVFALSTHPYGCRVIQRILEHCLPEQTLPILEELH 934
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 932-966 5.04e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.74  E-value: 5.04e-08
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 2024381375   932 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIV 966
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 ...
 747-1068 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: 548.35  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  747 NLQLREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 825
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  826 RGHVLSLALQMYGCRVIQKALEFIPPDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALS 905
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  906 THPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNV 985
Cdd:cd07920    161 THPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  986 VEKCVTHASRTERAMLIDEVCTmNDGPHSALYTMMKDQYANYVVQKMIDVAEPAQRKIVMHKIRPHIATLRKYTYGKHIL 1065
Cdd:cd07920    241 VEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHIL 319


                   ...
gi 2024381375 1066 AKL 1068
Cdd:cd07920    320 AKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 587-1070 1.04e-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: 338.26  E-value: 1.04e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  587 ATLGSALGGFGTAVANSNTgsgSRRDSLTGSSDLYKRTSSSLTPIGHSFYNGLGfSSSPGPVGMPLPSQGPGHSQtppps 666
Cdd:COG5099    271 VPSIRNLRGLNSALVSFLN---VSSSSLAFSALNGKEVSPTGSPSTRSFARVLP-KSSPNNLLTEILTTGVNPPQ----- 341

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  667 lsshgsssslNLGGLTNGSgrYISAAPGAEAKYRSASSASSLFSPSSTLFPSSRLRYGMSDVMPSG----RSRLLEDFRN 742
Cdd:COG5099    342 ----------SLPSLLNPV--FLSTSTGFSLTNLSGYLNPNKNLKKNTLSSLSNLGYSSNVPSPSSsestRNILGNISPN 409

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  743 N--RYPNLQLR----------------EIAGHIMEFSQ-DQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGN 803
Cdd:COG5099    410 FktSSNLTNLNsllkeklsnsssvsatDILGPSIIVSCkDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGN 489

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  804 YVIQKFFEFGSLEQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPPDQQ-NEMVRELDGHVLKCVKDQNGNHVVQKCI 882
Cdd:COG5099    490 YLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQiSLLVEELRPYCLQLIKDQNGNHVIQKCI 569

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  883 ECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDK 962
Cdd:COG5099    570 EKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNK 649

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024381375  963 SKIVAEIRGNVLV-LSQHKFASNVVEKCVTHASRTE-RAMLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPAQ 1040
Cdd:COG5099    650 ERIIIKLLSKRVVeLSTHKFASNVVEKCIKYASDSFkRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPEIQ 729

                          490       500       510
                   ....*....|....*....|....*....|
gi 2024381375 1041 RKIVMHKIRPHIATLRKYTYGKHILAKLEK 1070
Cdd:COG5099    730 RSLLARAIKKVIPSLKKSMYGQHILALLEK 759
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 900-934 1.70e-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: 1.70e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2024381375  900 QVFALSTHPYGCRVIQRILEHCLPEQTLPILEELH 934
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 756-790 1.23e-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: 1.23e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2024381375  756 HIMEFSQDQHGSRFIQLKLERATPAERQLVFNEIL 790
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 828-861 4.98e-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: 52.69  E-value: 4.98e-09
                           10        20        30
                   ....*....|....*....|....*....|....
gi 2024381375  828 HVLSLALQMYGCRVIQKALEFIPPDQQNEMVREL 861
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEI 34
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 936-969 7.16e-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: 7.16e-09
                           10        20        30
                   ....*....|....*....|....*....|....
gi 2024381375  936 HTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEI 969
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 932-966 5.04e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.74  E-value: 5.04e-08
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 2024381375   932 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIV 966
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 972-1006 1.36e-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: 1.36e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2024381375  972 NVLVLSQHKFASNVVEKCVTHASRTERAMLIDEVC 1006
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 825-859 2.39e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 47.81  E-value: 2.39e-07
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 2024381375   825 IRGHVLSLALQMYGCRVIQKALEFIPPDQQNEMVR 859
Cdd:smart00025    2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 860-895 3.03e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 47.43  E-value: 3.03e-07
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 2024381375   860 ELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIID 895
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 896-931 5.90e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 46.66  E-value: 5.90e-07
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 2024381375   896 AFKGQVFALSTHPYGCRVIQRILEHCLPEQTLPILE 931
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1013-1046 6.63e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 46.66  E-value: 6.63e-07
                            10        20        30
                    ....*....|....*....|....*....|....
gi 2024381375  1013 HSALYTMMKDQYANYVVQKMIDVAEPAQRKIVMH 1046
Cdd:smart00025    3 KGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1017-1048 1.19e-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: 1.19e-06
                           10        20        30
                   ....*....|....*....|....*....|..
gi 2024381375 1017 YTMMKDQYANYVVQKMIDVAEPAQRKIVMHKI 1048
Cdd:pfam00806    3 VELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 968-1003 2.52e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.12  E-value: 2.52e-06
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 2024381375   968 EIRGNVLVLSQHKFASNVVEKCVTHASRTERAMLID 1003
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 794-825 5.81e-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: 5.81e-06
                           10        20        30
                   ....*....|....*....|....*....|..
gi 2024381375  794 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 825
Cdd:pfam00806    3 VELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 788-818 1.01e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.19  E-value: 1.01e-05
                            10        20        30
                    ....*....|....*....|....*....|.
gi 2024381375   788 EILQAAYQLMVDVFGNYVIQKFFEFGSLEQK 818
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQR 31
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 864-895 1.27e-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: 1.27e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 2024381375  864 HVLKCVKDQNGNHVVQKCIECVQPQSLQFIID 895
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILD 32
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 752-787 1.36e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 42.81  E-value: 1.36e-05
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 2024381375   752 EIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFN 787
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
 
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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