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Conserved domains on  [gi|28573153|ref|NP_788604|]
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pumilio, isoform E [Drosophila melanogaster]

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 ...
 508-826 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: 527.16  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 508 NLQLRDLA-NHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQV 586
Cdd:cd07920   1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 587 KGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLS 666
Cdd:cd07920  81 LGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALS 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 667 THPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNV 746
Cdd:cd07920 161 THPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 747 VEKCVTHATRGERTGLIDEVCTFNDN--ALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAALRKYTYGKHINA 824
Cdd:cd07920 241 VEKCLKHASKEERELIIDEILASGNEtsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILA 320


                ..
gi 28573153 825 KL 826
Cdd:cd07920 321 KL 322
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 508-826 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: 527.16  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 508 NLQLRDLA-NHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQV 586
Cdd:cd07920   1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 587 KGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLS 666
Cdd:cd07920  81 LGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALS 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 667 THPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNV 746
Cdd:cd07920 161 THPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 747 VEKCVTHATRGERTGLIDEVCTFNDN--ALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAALRKYTYGKHINA 824
Cdd:cd07920 241 VEKCLKHASKEERELIIDEILASGNEtsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILA 320


                ..
gi 28573153 825 KL 826
Cdd:cd07920 321 KL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 502-839 2.68e-99

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 328.63  E-value: 2.68e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 502 RNQRYPNLQLRDLANHIvefSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNT 581
Cdd:COG5099 430 SSSVSATDILGPSIIVS---CKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSI 506

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 582 LGMQVKGHVLQLALQMYGCRVIQKALESISPEQQ-QEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKG 660
Cdd:COG5099 507 MLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQiSLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINE 586

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 661 QVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLV-LSQ 739
Cdd:COG5099 587 NLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVeLST 666

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 740 HKFASNVVEKCV---THATRGERtgLIDEVCTFN---DNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAAL 813
Cdd:COG5099 667 HKFASNVVEKCIkyaSDSFKRSR--ILNELTNRGiekPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSL 744

                       330       340
                ....*....|....*....|....*.
gi 28573153 814 RKYTYGKHINAKLEKYYMKITNPITV 839
Cdd:COG5099 745 KKSMYGQHILALLEKVGSSSQSSISN 770
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 661-695 2.83e-14

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: 67.33  E-value: 2.83e-14
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 28573153   661 QVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELH 695
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 657-692 8.45e-09

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 51.67  E-value: 8.45e-09
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 28573153    657 AFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILD 692
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 508-826 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: 527.16  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 508 NLQLRDLA-NHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQV 586
Cdd:cd07920   1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 587 KGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLS 666
Cdd:cd07920  81 LGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALS 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 667 THPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNV 746
Cdd:cd07920 161 THPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 747 VEKCVTHATRGERTGLIDEVCTFNDN--ALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAALRKYTYGKHINA 824
Cdd:cd07920 241 VEKCLKHASKEERELIIDEILASGNEtsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILA 320


                ..
gi 28573153 825 KL 826
Cdd:cd07920 321 KL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 502-839 2.68e-99

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 328.63  E-value: 2.68e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 502 RNQRYPNLQLRDLANHIvefSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNT 581
Cdd:COG5099 430 SSSVSATDILGPSIIVS---CKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSI 506

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 582 LGMQVKGHVLQLALQMYGCRVIQKALESISPEQQ-QEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKG 660
Cdd:COG5099 507 MLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQiSLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINE 586

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 661 QVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLV-LSQ 739
Cdd:COG5099 587 NLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVeLST 666

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573153 740 HKFASNVVEKCV---THATRGERtgLIDEVCTFN---DNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAAL 813
Cdd:COG5099 667 HKFASNVVEKCIkyaSDSFKRSR--ILNELTNRGiekPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSL 744

                       330       340
                ....*....|....*....|....*.
gi 28573153 814 RKYTYGKHINAKLEKYYMKITNPITV 839
Cdd:COG5099 745 KKSMYGQHILALLEKVGSSSQSSISN 770
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 661-695 2.83e-14

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: 67.33  E-value: 2.83e-14
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 28573153   661 QVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELH 695
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 517-551 5.06e-11

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: 58.08  E-value: 5.06e-11
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 28573153   517 HIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEIL 551
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 589-622 6.85e-11

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: 57.70  E-value: 6.85e-11
                          10        20        30
                  ....*....|....*....|....*....|....
gi 28573153   589 HVLQLALQMYGCRVIQKALESISPEQQQEIVHEL 622
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 657-692 8.45e-09

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 51.67  E-value: 8.45e-09
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 28573153    657 AFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILD 692
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 586-620 2.82e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 50.13  E-value: 2.82e-08
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 28573153    586 VKGHVLQLALQMYGCRVIQKALESISPEQQQEIVH 620
Cdd:smart00025   2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 621-656 6.41e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.35  E-value: 6.41e-08
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 28573153    621 ELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIIN 656
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 693-728 9.39e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 48.97  E-value: 9.39e-08
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 28573153    693 ELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILIN 728
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 697-728 5.34e-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: 5.34e-07
                          10        20        30
                  ....*....|....*....|....*....|..
gi 28573153   697 HTEQLIQDQYGNYVIQHVLEHGKQEDKSILIN 728
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILD 32
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 549-582 8.77e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.89  E-value: 8.77e-07
                           10        20        30
                   ....*....|....*....|....*....|....
gi 28573153    549 EILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTL 582
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQI 34
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 555-582 9.16e-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: 46.14  E-value: 9.16e-07
                          10        20
                  ....*....|....*....|....*...
gi 28573153   555 YSLMTDVFGNYVIQKFFEFGTPEQKNTL 582
Cdd:pfam00806   3 VELATDQYGCRVIQKCLEHATEEQREQI 30
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 772-803 1.92e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.12  E-value: 1.92e-06
                           10        20        30
                   ....*....|....*....|....*....|..
gi 28573153    772 NALHVMMKDQYANYVVQKMIDVSEPTQLKKLM 803
Cdd:smart00025   4 GHLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 733-767 1.23e-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: 1.23e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 28573153   733 KVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVC 767
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 516-547 1.82e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 42.42  E-value: 1.82e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 28573153    516 NHIVEFSQDQHGSRFIQQKLERATAAEKQMVF 547
Cdd:smart00025   4 GHLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 625-656 2.62e-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: 41.90  E-value: 2.62e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 28573153   625 HVLKCVKDQNGNHVVQKCIECVDPVALQFIIN 656
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILD 32
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 777-806 1.08e-04

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: 39.98  E-value: 1.08e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 28573153   777 MMKDQYANYVVQKMIDVSEPTQLKKLMTKI 806
Cdd:pfam00806   5 LATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 729-764 1.84e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 39.34  E-value: 1.84e-04
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 28573153    729 SVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLID 764
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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