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Conserved domains on  [gi|1250124233|ref|XP_022603449|]
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pumilio homolog 1 isoform X1 [Seriola dumerili]

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
SCOP:  4003086

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 ...
 818-1141 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: 532.17  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  818 NLQLRDIA-GHIMEFSQDQHGSRFIQLKLERASSAERQLVFSEILQAAYQLMVDVFGNYVIQKFFEFGSLDQKLALAERI 896
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  897 RGHVLSLALQMYGCRVIQKALEFIPSDQqvISEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPHALHFIIDAFKGQVFA 976
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQ--ISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  977 LSTHPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRAEDKSKIVAEIRGNVLGLSQHKFAS 1056
Cdd:cd07920    159 LSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFAS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233 1057 NVVEKCVTHASRAERAVLIDEVCSlTEGPHSALYTMMKDQYANYVVQKMIDVAEPTQRKIVMHKIRPHISTLRKYTYGKH 1136
Cdd:cd07920    239 NVVEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKH 317


                   ....*
gi 1250124233 1137 ILAKL 1141
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 ...
 818-1141 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: 532.17  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  818 NLQLRDIA-GHIMEFSQDQHGSRFIQLKLERASSAERQLVFSEILQAAYQLMVDVFGNYVIQKFFEFGSLDQKLALAERI 896
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  897 RGHVLSLALQMYGCRVIQKALEFIPSDQqvISEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPHALHFIIDAFKGQVFA 976
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQ--ISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  977 LSTHPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRAEDKSKIVAEIRGNVLGLSQHKFAS 1056
Cdd:cd07920    159 LSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFAS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233 1057 NVVEKCVTHASRAERAVLIDEVCSlTEGPHSALYTMMKDQYANYVVQKMIDVAEPTQRKIVMHKIRPHISTLRKYTYGKH 1136
Cdd:cd07920    239 NVVEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKH 317


                   ....*
gi 1250124233 1137 ILAKL 1141
Cdd:cd07920    318 ILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 823-1143 5.69e-103

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 343.27  E-value: 5.69e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  823 DIAGHIMEFSQ-DQHGSRFIQLKLERASSAERQLVFSEILQAAYQLMVDVFGNYVIQKFFEFGSLDQKLALAERIRGHVL 901
Cdd:COG5099    437 DILGPSIIVSCkDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLV 516

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  902 SLALQMYGCRVIQKALEFIPSDQQvISEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPHALHFIIDAFKGQVFALSTHP 981
Cdd:COG5099    517 SLSVHKYGTRVLQKAIDIVSTDIQ-ISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHR 595

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  982 YGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRAEDKSKIVAEIRG-NVLGLSQHKFASNVVE 1060
Cdd:COG5099    596 YGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSkRVVELSTHKFASNVVE 675

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233 1061 KCVTHASRAER-----AVLIDEVCSLTegphSALYTMMKDQYANYVVQKMIDVAEPTQRKIVMHKIRPHISTLRKYTYGK 1135
Cdd:COG5099    676 KCIKYASDSFKrsrilNELTNRGIEKP----GFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQ 751


                   ....*...
gi 1250124233 1136 HILAKLEK 1143
Cdd:COG5099    752 HILALLEK 759
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 973-1007 1.81e-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: 1.81e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1250124233  973 QVFALSTHPYGCRVIQRILEHCLPEQTLPILEELH 1007
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1005-1039 9.87e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 48.97  E-value: 9.87e-08
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 1250124233  1005 ELHQHTEQLVQDQYGNYVIQHVLEHGRAEDKSKIV 1039
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 ...
 818-1141 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: 532.17  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  818 NLQLRDIA-GHIMEFSQDQHGSRFIQLKLERASSAERQLVFSEILQAAYQLMVDVFGNYVIQKFFEFGSLDQKLALAERI 896
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  897 RGHVLSLALQMYGCRVIQKALEFIPSDQqvISEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPHALHFIIDAFKGQVFA 976
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQ--ISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  977 LSTHPYGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRAEDKSKIVAEIRGNVLGLSQHKFAS 1056
Cdd:cd07920    159 LSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFAS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233 1057 NVVEKCVTHASRAERAVLIDEVCSlTEGPHSALYTMMKDQYANYVVQKMIDVAEPTQRKIVMHKIRPHISTLRKYTYGKH 1136
Cdd:cd07920    239 NVVEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKH 317


                   ....*
gi 1250124233 1137 ILAKL 1141
Cdd:cd07920    318 ILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 823-1143 5.69e-103

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 343.27  E-value: 5.69e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  823 DIAGHIMEFSQ-DQHGSRFIQLKLERASSAERQLVFSEILQAAYQLMVDVFGNYVIQKFFEFGSLDQKLALAERIRGHVL 901
Cdd:COG5099    437 DILGPSIIVSCkDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLV 516

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  902 SLALQMYGCRVIQKALEFIPSDQQvISEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPHALHFIIDAFKGQVFALSTHP 981
Cdd:COG5099    517 SLSVHKYGTRVLQKAIDIVSTDIQ-ISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHR 595

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  982 YGCRVIQRILEHCLPEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRAEDKSKIVAEIRG-NVLGLSQHKFASNVVE 1060
Cdd:COG5099    596 YGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSkRVVELSTHKFASNVVE 675

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233 1061 KCVTHASRAER-----AVLIDEVCSLTegphSALYTMMKDQYANYVVQKMIDVAEPTQRKIVMHKIRPHISTLRKYTYGK 1135
Cdd:COG5099    676 KCIKYASDSFKrsrilNELTNRGIEKP----GFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQ 751


                   ....*...
gi 1250124233 1136 HILAKLEK 1143
Cdd:COG5099    752 HILALLEK 759
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 973-1007 1.81e-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: 1.81e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1250124233  973 QVFALSTHPYGCRVIQRILEHCLPEQTLPILEELH 1007
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 827-861 8.09e-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: 51.92  E-value: 8.09e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1250124233  827 HIMEFSQDQHGSRFIQLKLERASSAERQLVFSEIL 861
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1009-1042 2.64e-08

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: 50.76  E-value: 2.64e-08
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1250124233 1009 HTEQLVQDQYGNYVIQHVLEHGRAEDKSKIVAEI 1042
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1005-1039 9.87e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 48.97  E-value: 9.87e-08
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 1250124233  1005 ELHQHTEQLVQDQYGNYVIQHVLEHGRAEDKSKIV 1039
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1045-1079 2.59e-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: 47.68  E-value: 2.59e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1250124233 1045 NVLGLSQHKFASNVVEKCVTHASRAERAVLIDEVC 1079
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 899-930 5.35e-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: 46.91  E-value: 5.35e-07
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1250124233  899 HVLSLALQMYGCRVIQKALEFIPSDQ--QVISEM 930
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQreQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 969-1004 6.29e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 46.66  E-value: 6.29e-07
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1250124233   969 AFKGQVFALSTHPYGCRVIQRILEHCLPEQTLPILE 1004
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1086-1119 1.05e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 46.27  E-value: 1.05e-06
                            10        20        30
                    ....*....|....*....|....*....|....
gi 1250124233  1086 HSALYTMMKDQYANYVVQKMIDVAEPTQRKIVMH 1119
Cdd:smart00025    3 KGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 933-968 2.23e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.12  E-value: 2.23e-06
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1250124233   933 ELDGHVLKCVKDQNGNHVVQKCIECVQPHALHFIID 968
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1090-1121 2.30e-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: 44.98  E-value: 2.30e-06
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1250124233 1090 YTMMKDQYANYVVQKMIDVAEPTQRKIVMHKI 1121
Cdd:pfam00806    3 VELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1041-1076 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 1250124233  1041 EIRGNVLGLSQHKFASNVVEKCVTHASRAERAVLID 1076
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 859-889 1.57e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 42.81  E-value: 1.57e-05
                            10        20        30
                    ....*....|....*....|....*....|.
gi 1250124233   859 EILQAAYQLMVDVFGNYVIQKFFEFGSLDQK 889
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQR 31
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 865-896 1.82e-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: 42.67  E-value: 1.82e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1250124233  865 YQLMVDVFGNYVIQKFFEFGSLDQKLALAERI 896
Cdd:pfam00806    3 VELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 896-925 2.01e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 42.42  E-value: 2.01e-05
                            10        20        30
                    ....*....|....*....|....*....|
gi 1250124233   896 IRGHVLSLALQMYGCRVIQKALEFIPSDQQ 925
Cdd:smart00025    2 IKGHLLELSKDQYGNRVVQKLLEHASESQR 31
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 937-968 8.86e-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: 40.75  E-value: 8.86e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1250124233  937 HVLKCVKDQNGNHVVQKCIECVQPHALHFIID 968
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILD 32
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 812-930 1.37e-04

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 46.28  E-value: 1.37e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1250124233  812 RNNRYPNLQLRDIA---GHIMEFSQDQHGSRFIQlKLERASSA--ERQLVFSEILQAA-------YQLMVDVFGNYVIQK 879
Cdd:COG5099    642 DNGAEPNKERIIIKllsKRVVELSTHKFASNVVE-KCIKYASDsfKRSRILNELTNRGiekpgflMLILDDQYANYVIQY 720

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1250124233  880 FFEFGSLDQKLALAERIRGHVLSLALQMYGCRVIQKALEFIPSDQQVISEM 930
Cdd:COG5099    721 LLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALLEKVGSSSQSSISNK 771
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 824-857 3.17e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 38.95  E-value: 3.17e-04
                            10        20        30
                    ....*....|....*....|....*....|....
gi 1250124233   824 IAGHIMEFSQDQHGSRFIQLKLERASSAERQLVF 857
Cdd:smart00025    2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
 
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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