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Conserved domains on  [gi|22330712|ref|NP_177940|]
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pumilio 7 [Arabidopsis thaliana]

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 ...
 325-645 9.16e-142

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: 415.45  E-value: 9.16e-142
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 325 HPSLPNMCDiqGYVYLMAKDQHGCRFLQRIFDEGTSVDAMIIFNEVIAHVVELMMDPFGNYLMQKLLDVCTEEQRTQIVL 404
Cdd:cd07920   1 SLTLQDIKA--GHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLE 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 405 VATeepGQLIRISLNAYGTRVVQRLVETIRSgKQISLVKLALRPGFLDLIKDLNGNHVIQRCLQCLSTEDNKFIFDAATK 484
Cdd:cd07920  79 KIL---GHVVRLSLDMYGCRVIQKLLESISE-EQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKG 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 485 FCTEIATHRHGCCVLQKCIAYSMRQQREKLIAEISRNSLLLAQDPFGNYAVQFVIELRIPSAVAMMLAQLKGHYVQLSMQ 564
Cdd:cd07920 155 NCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCH 234

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 565 KFSSHMVERCLMHCP--ESRPQIVRELVSV---PHFDQLLQDPYANFVIQAALAATKGPLHASLVEVIRPHS-ILRNNPY 638
Cdd:cd07920 235 KFASNVVEKCLKHASkeERELIIDEILASGnetSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLpSLRKSPY 314


                ....*..
gi 22330712 639 CKRIFSR 645
Cdd:cd07920 315 GKHILAK 321
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 325-645 9.16e-142

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: 415.45  E-value: 9.16e-142
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 325 HPSLPNMCDiqGYVYLMAKDQHGCRFLQRIFDEGTSVDAMIIFNEVIAHVVELMMDPFGNYLMQKLLDVCTEEQRTQIVL 404
Cdd:cd07920   1 SLTLQDIKA--GHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLE 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 405 VATeepGQLIRISLNAYGTRVVQRLVETIRSgKQISLVKLALRPGFLDLIKDLNGNHVIQRCLQCLSTEDNKFIFDAATK 484
Cdd:cd07920  79 KIL---GHVVRLSLDMYGCRVIQKLLESISE-EQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKG 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 485 FCTEIATHRHGCCVLQKCIAYSMRQQREKLIAEISRNSLLLAQDPFGNYAVQFVIELRIPSAVAMMLAQLKGHYVQLSMQ 564
Cdd:cd07920 155 NCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCH 234

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 565 KFSSHMVERCLMHCP--ESRPQIVRELVSV---PHFDQLLQDPYANFVIQAALAATKGPLHASLVEVIRPHS-ILRNNPY 638
Cdd:cd07920 235 KFASNVVEKCLKHASkeERELIIDEILASGnetSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLpSLRKSPY 314


                ....*..
gi 22330712 639 CKRIFSR 645
Cdd:cd07920 315 GKHILAK 321
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 272-642 2.02e-67

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 235.03  E-value: 2.02e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 272 PLFCQRTQVPMVSKCSEPFSSDESFF---MNGKSIDHQRSNT----RALMSNNGNPTEIchpslpnmcdIQGYVYLMAKD 344
Cdd:COG5099 380 SLSNLGYSSNVPSPSSSESTRNILGNispNFKTSSNLTNLNSllkeKLSNSSSVSATDI----------LGPSIIVSCKD 449

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 345 QHGCRFLQRIFDEGTSVDAMIIFNEVIAHVVELMMDPFGNYLMQKLLDVCTEEQRTQIVLVATeepGQLIRISLNAYGTR 424
Cdd:COG5099 450 QHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSS---KHLVSLSVHKYGTR 526

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 425 VVQRLVETIRSGKQISLVKLALRPGFLDLIKDLNGNHVIQRCLQCLSTEDNKFIFDAATKFCTEIATHRHGCCVLQKCIA 504
Cdd:COG5099 527 VLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLE 606

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 505 YSMRQQREKLIAEISRNSLLLAQDPFGNYAVQFVIELRIPSAVAMML-AQLKGHYVQLSMQKFSSHMVERCLMHC--PES 581
Cdd:COG5099 607 NCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIiKLLSKRVVELSTHKFASNVVEKCIKYAsdSFK 686

                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 22330712 582 RPQIVRELVSVP-HFD----QLLQDPYANFVIQAALAATKGPLHASLVEVIRPH-SILRNNPYCKRI 642
Cdd:COG5099 687 RSRILNELTNRGiEKPgflmLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKViPSLKKSMYGQHI 753
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 486-519 6.07e-10

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: 54.61  E-value: 6.07e-10
                          10        20        30
                  ....*....|....*....|....*....|....
gi 22330712   486 CTEIATHRHGCCVLQKCIAYSMRQQREKLIAEIS 519
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 369-403 4.65e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.35  E-value: 4.65e-08
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 22330712    369 EVIAHVVELMMDPFGNYLMQKLLDVCTEEQRTQIV 403
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 ...
 325-645 9.16e-142

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: 415.45  E-value: 9.16e-142
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 325 HPSLPNMCDiqGYVYLMAKDQHGCRFLQRIFDEGTSVDAMIIFNEVIAHVVELMMDPFGNYLMQKLLDVCTEEQRTQIVL 404
Cdd:cd07920   1 SLTLQDIKA--GHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLE 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 405 VATeepGQLIRISLNAYGTRVVQRLVETIRSgKQISLVKLALRPGFLDLIKDLNGNHVIQRCLQCLSTEDNKFIFDAATK 484
Cdd:cd07920  79 KIL---GHVVRLSLDMYGCRVIQKLLESISE-EQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKG 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 485 FCTEIATHRHGCCVLQKCIAYSMRQQREKLIAEISRNSLLLAQDPFGNYAVQFVIELRIPSAVAMMLAQLKGHYVQLSMQ 564
Cdd:cd07920 155 NCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCH 234

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 565 KFSSHMVERCLMHCP--ESRPQIVRELVSV---PHFDQLLQDPYANFVIQAALAATKGPLHASLVEVIRPHS-ILRNNPY 638
Cdd:cd07920 235 KFASNVVEKCLKHASkeERELIIDEILASGnetSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLpSLRKSPY 314


                ....*..
gi 22330712 639 CKRIFSR 645
Cdd:cd07920 315 GKHILAK 321
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 272-642 2.02e-67

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 235.03  E-value: 2.02e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 272 PLFCQRTQVPMVSKCSEPFSSDESFF---MNGKSIDHQRSNT----RALMSNNGNPTEIchpslpnmcdIQGYVYLMAKD 344
Cdd:COG5099 380 SLSNLGYSSNVPSPSSSESTRNILGNispNFKTSSNLTNLNSllkeKLSNSSSVSATDI----------LGPSIIVSCKD 449

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 345 QHGCRFLQRIFDEGTSVDAMIIFNEVIAHVVELMMDPFGNYLMQKLLDVCTEEQRTQIVLVATeepGQLIRISLNAYGTR 424
Cdd:COG5099 450 QHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSS---KHLVSLSVHKYGTR 526

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 425 VVQRLVETIRSGKQISLVKLALRPGFLDLIKDLNGNHVIQRCLQCLSTEDNKFIFDAATKFCTEIATHRHGCCVLQKCIA 504
Cdd:COG5099 527 VLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLE 606

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22330712 505 YSMRQQREKLIAEISRNSLLLAQDPFGNYAVQFVIELRIPSAVAMML-AQLKGHYVQLSMQKFSSHMVERCLMHC--PES 581
Cdd:COG5099 607 NCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIiKLLSKRVVELSTHKFASNVVEKCIKYAsdSFK 686

                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 22330712 582 RPQIVRELVSVP-HFD----QLLQDPYANFVIQAALAATKGPLHASLVEVIRPH-SILRNNPYCKRI 642
Cdd:COG5099 687 RSRILNELTNRGiEKPgflmLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKViPSLKKSMYGQHI 753
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 486-519 6.07e-10

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: 54.61  E-value: 6.07e-10
                          10        20        30
                  ....*....|....*....|....*....|....
gi 22330712   486 CTEIATHRHGCCVLQKCIAYSMRQQREKLIAEIS 519
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 373-403 1.52e-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: 53.46  E-value: 1.52e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 22330712   373 HVVELMMDPFGNYLMQKLLDVCTEEQRTQIV 403
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQIL 31
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 337-371 2.20e-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: 49.99  E-value: 2.20e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 22330712   337 YVYLMAKDQHGCRFLQRIFDEGTSVDAMIIFNEVI 371
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 369-403 4.65e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.35  E-value: 4.65e-08
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 22330712    369 EVIAHVVELMMDPFGNYLMQKLLDVCTEEQRTQIV 403
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 445-480 5.08e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.58  E-value: 5.08e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 22330712    445 ALRPGFLDLIKDLNGNHVIQRCLQCLSTEDNKFIFD 480
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 450-480 3.00e-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: 38.44  E-value: 3.00e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 22330712   450 FLDLIKDLNGNHVIQRCLQCLSTEDNKFIFD 480
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQILD 32
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 557-589 3.22e-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: 38.44  E-value: 3.22e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 22330712   557 HYVQLSMQKFSSHMVERCLMHC-PESRPQIVREL 589
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHAtEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 334-368 7.04e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 37.41  E-value: 7.04e-04
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 22330712    334 IQGYVYLMAKDQHGCRFLQRIFDEGTSVDAMIIFN 368
Cdd:smart00025   2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 483-515 1.08e-03

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 37.03  E-value: 1.08e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 22330712    483 TKFCTEIATHRHGCCVLQKCIAYSMRQQREKLI 515
Cdd:smart00025   3 KGHLLELSKDQYGNRVVQKLLEHASESQREQII 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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