NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1622833718|ref|XP_028692684|]
View 

pumilio homolog 1 isoform X4 [Macaca mulatta]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 880-1203 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: 539.10  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  880 NLQLREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 958
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  959 RGHVLSLALQMYGCRVIQKALEFIPSDQqvINEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFA 1038
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQ--ISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718 1039 LSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFAS 1118
Cdd:cd07920    159 LSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFAS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718 1119 NVVEKCVTHASRTERAVLIDEVCTmNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKH 1198
Cdd:cd07920    239 NVVEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKH 317


                   ....*
gi 1622833718 1199 ILAKL 1203
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 ...
 880-1203 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: 539.10  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  880 NLQLREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 958
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  959 RGHVLSLALQMYGCRVIQKALEFIPSDQqvINEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFA 1038
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQ--ISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718 1039 LSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFAS 1118
Cdd:cd07920    159 LSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFAS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718 1119 NVVEKCVTHASRTERAVLIDEVCTmNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKH 1198
Cdd:cd07920    239 NVVEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKH 317


                   ....*
gi 1622833718 1199 ILAKL 1203
Cdd:cd07920    318 ILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 885-1205 1.24e-100

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 337.87  E-value: 1.24e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  885 EIAGHIMEFSQ-DQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVL 963
Cdd:COG5099    437 DILGPSIIVSCkDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLV 516

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  964 SLALQMYGCRVIQKALEFIPSDQQvINEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHP 1043
Cdd:COG5099    517 SLSVHKYGTRVLQKAIDIVSTDIQ-ISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHR 595

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718 1044 YGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLV-LSQHKFASNVVE 1122
Cdd:COG5099    596 YGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVeLSTHKFASNVVE 675

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718 1123 KCVTHASRTERAVLIDEVCTMNDGPH-SALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILA 1201
Cdd:COG5099    676 KCIKYASDSFKRSRILNELTNRGIEKpGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILA 755


                   ....
gi 1622833718 1202 KLEK 1205
Cdd:COG5099    756 LLEK 759
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1035-1069 5.58e-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: 61.16  E-value: 5.58e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1622833718 1035 QVFALSTHPYGCRVIQRILEHCLPDQTLPILEELH 1069
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1067-1101 5.67e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.74  E-value: 5.67e-08
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 1622833718  1067 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIV 1101
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 ...
 880-1203 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: 539.10  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  880 NLQLREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 958
Cdd:cd07920      1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  959 RGHVLSLALQMYGCRVIQKALEFIPSDQqvINEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFA 1038
Cdd:cd07920     81 LGHVVRLSLDMYGCRVIQKLLESISEEQ--ISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718 1039 LSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFAS 1118
Cdd:cd07920    159 LSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFAS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718 1119 NVVEKCVTHASRTERAVLIDEVCTmNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKH 1198
Cdd:cd07920    239 NVVEKCLKHASKEERELIIDEILA-SGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKH 317


                   ....*
gi 1622833718 1199 ILAKL 1203
Cdd:cd07920    318 ILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 885-1205 1.24e-100

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 337.87  E-value: 1.24e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  885 EIAGHIMEFSQ-DQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRGHVL 963
Cdd:COG5099    437 DILGPSIIVSCkDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLV 516

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  964 SLALQMYGCRVIQKALEFIPSDQQvINEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHP 1043
Cdd:COG5099    517 SLSVHKYGTRVLQKAIDIVSTDIQ-ISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHR 595

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718 1044 YGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLV-LSQHKFASNVVE 1122
Cdd:COG5099    596 YGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVeLSTHKFASNVVE 675

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718 1123 KCVTHASRTERAVLIDEVCTMNDGPH-SALYTMMKDQYANYVVQKMIDVAEPGQRKIVMHKIRPHIATLRKYTYGKHILA 1201
Cdd:COG5099    676 KCIKYASDSFKRSRILNELTNRGIEKpGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILA 755


                   ....
gi 1622833718 1202 KLEK 1205
Cdd:COG5099    756 LLEK 759
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1035-1069 5.58e-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: 61.16  E-value: 5.58e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1622833718 1035 QVFALSTHPYGCRVIQRILEHCLPDQTLPILEELH 1069
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 889-923 1.38e-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: 1.38e-09
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1622833718  889 HIMEFSQDQHGSRFIQLKLERATPAERQLVFNEIL 923
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1071-1104 8.04e-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: 8.04e-09
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1622833718 1071 HTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEI 1104
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1067-1101 5.67e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.74  E-value: 5.67e-08
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 1622833718  1067 ELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIV 1101
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 961-992 2.92e-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: 2.92e-07
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1622833718  961 HVLSLALQMYGCRVIQKALEFIPSDQ--QVINEM 992
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQreQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 995-1030 3.40e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 47.43  E-value: 3.40e-07
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1622833718   995 ELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIID 1030
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1107-1141 6.98e-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: 46.52  E-value: 6.98e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1622833718 1107 NVLVLSQHKFASNVVEKCVTHASRTERAVLIDEVC 1141
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1031-1066 9.61e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 46.27  E-value: 9.61e-07
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1622833718  1031 AFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILE 1066
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1152-1183 3.66e-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: 44.60  E-value: 3.66e-06
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1622833718 1152 YTMMKDQYANYVVQKMIDVAEPGQRKIVMHKI 1183
Cdd:pfam00806    3 VELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1148-1181 3.98e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 44.35  E-value: 3.98e-06
                            10        20        30
                    ....*....|....*....|....*....|....
gi 1622833718  1148 HSALYTMMKDQYANYVVQKMIDVAEPGQRKIVMH 1181
Cdd:smart00025    3 KGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 927-958 6.53e-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: 6.53e-06
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1622833718  927 YQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 958
Cdd:pfam00806    3 VELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1103-1138 7.84e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.58  E-value: 7.84e-06
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1622833718  1103 EIRGNVLVLSQHKFASNVVEKCVTHASRTERAVLID 1138
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 921-951 1.14e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.19  E-value: 1.14e-05
                            10        20        30
                    ....*....|....*....|....*....|.
gi 1622833718   921 EILQAAYQLMVDVFGNYVIQKFFEFGSLEQK 951
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQR 31
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 999-1030 1.43e-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: 1.43e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1622833718  999 HVLKCVKDQNGNHVVQKCIECVQPQSLQFIID 1030
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILD 32
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 885-920 1.53e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 42.81  E-value: 1.53e-05
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 1622833718   885 EIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFN 920
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 958-987 2.11e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 42.42  E-value: 2.11e-05
                            10        20        30
                    ....*....|....*....|....*....|
gi 1622833718   958 IRGHVLSLALQMYGCRVIQKALEFIPSDQQ 987
Cdd:smart00025    2 IKGHLLELSKDQYGNRVVQKLLEHASESQR 31
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 886-992 1.01e-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: 43.58  E-value: 1.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622833718  886 IAGHIMEFSQDQHGSRFIQlKLERATPA--ERQLVFNEILQAA-------YQLMVDVFGNYVIQKFFEFGSLEQKLALAE 956
Cdd:COG5099    657 LSKRVVELSTHKFASNVVE-KCIKYASDsfKRSRILNELTNRGiekpgflMLILDDQYANYVIQYLLDVSPEIQRSLLAR 735

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1622833718  957 RIRGHVLSLALQMYGCRVIQKALEFIPSDQQVINEM 992
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH