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Conserved domains on  [gi|2842704|sp|Q92359|]
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RecName: Full=Pumilio domain-containing protein C6G9.14

Protein Classification

COG5099 family protein( domain architecture ID 11473804)

COG5099 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 1-678 0e+00

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


:

Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 535.87  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704    1 MTEQSSKSHPSFMSTEYSLPVFSSQYSDIENKDVLKSNSWDPYAANAPIALSEIPSSSKSGKTNGSKAAVESGLASGAFG 80
Cdd:COG5099 100 MELPSSSFNPSTSSRNKSNSALSSTQQGNANSSVTLSSSTASSMFNSNKLPLPNPNHSNSATTNQSGSSFINTPASSSSQ 179

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704   81 NRTGNMNRNTSMSGYTFGSSNFVPYNLLSNTPSFTTSHSSSTTFVPPATMGGglNNLSSPSSSLYLPGSASYQRSNSKNS 160
Cdd:COG5099 180 PLTNLVVSSIKRFPYLTSLSPFFNYLIDPSSDSATASADTSPSFNPPPNLSP--NNLFSTSDLSPLPDTQSVENNIILNS 257

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  161 SASILQMNTTLDDIPILLRRPGLSSYTPGPSTSRRSISSSSNLGGNPGLIANNPSASKnFAFTSGSSSTNNSTTSSSSMA 240
Cdd:COG5099 258 SSSINELTSIYGSVPSIRNLRGLNSALVSFLNVSSSSLAFSALNGKEVSPTGSPSTRS-FARVLPKSSPNNLLTEILTTG 336

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  241 NGLQSISKHSAAFPLLSNATSFFGENLTPSLAASTASTGSTDSSGSNIANTLIAPTPTISPPSANTVGNPSPADTPGFNV 320
Cdd:COG5099 337 VNPPQSLPSLLNPVFLSTSTGFSLTNLSGYLNPNKNLKKNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPNFKTSSNL 416

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  321 PSLISDDPSVSSSLSSSVASLSLQNSNILSfCKDQHGCRYLQRLLEKKNQSHIDAVFAETHPYLAVLMVDAFGNYLCQKL 400
Cdd:COG5099 417 TNLNSLLKEKLSNSSSVSATDILGPSIIVS-CKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKL 495

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  401 FEHASEAQRSTFIQIIAPKLVPISFNMHGTRALQKIIDLVSSPDQISCIVNALRPNVVLLTKDLNGNHVIQKCLNKFSQE 480
Cdd:COG5099 496 FEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKE 575

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  481 DCQFIFDAICEDPLDVSTHRHGCCVVQRCFDHASPAQIEQLVEHIVPHALTLVQDAFGNYVLQYVLELNNPNHTEAIISY 560
Cdd:COG5099 576 KNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIK 655

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  561 FLYK-VRALSTQKFSSNVMEKCIFFAPAAIK-EKLISELMDEK-HLP----KLLRDSFANYVIQTALDNASVKQRAELVE 633
Cdd:COG5099 656 LLSKrVVELSTHKFASNVVEKCIKYASDSFKrSRILNELTNRGiEKPgflmLILDDQYANYVIQYLLDVSPEIQRSLLAR 735

                       650       660       670       680
                ....*....|....*....|....*....|....*....|....*
gi 2842704  634 RIKPLIPSIKNTPCGRRILSKLERRHPSSKEKpivYSNSERVNTS 678
Cdd:COG5099 736 AIKKVIPSLKKSMYGQHILALLEKVGSSSQSS---ISNKECMNTS 777
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 1-678 0e+00

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 535.87  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704    1 MTEQSSKSHPSFMSTEYSLPVFSSQYSDIENKDVLKSNSWDPYAANAPIALSEIPSSSKSGKTNGSKAAVESGLASGAFG 80
Cdd:COG5099 100 MELPSSSFNPSTSSRNKSNSALSSTQQGNANSSVTLSSSTASSMFNSNKLPLPNPNHSNSATTNQSGSSFINTPASSSSQ 179

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704   81 NRTGNMNRNTSMSGYTFGSSNFVPYNLLSNTPSFTTSHSSSTTFVPPATMGGglNNLSSPSSSLYLPGSASYQRSNSKNS 160
Cdd:COG5099 180 PLTNLVVSSIKRFPYLTSLSPFFNYLIDPSSDSATASADTSPSFNPPPNLSP--NNLFSTSDLSPLPDTQSVENNIILNS 257

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  161 SASILQMNTTLDDIPILLRRPGLSSYTPGPSTSRRSISSSSNLGGNPGLIANNPSASKnFAFTSGSSSTNNSTTSSSSMA 240
Cdd:COG5099 258 SSSINELTSIYGSVPSIRNLRGLNSALVSFLNVSSSSLAFSALNGKEVSPTGSPSTRS-FARVLPKSSPNNLLTEILTTG 336

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  241 NGLQSISKHSAAFPLLSNATSFFGENLTPSLAASTASTGSTDSSGSNIANTLIAPTPTISPPSANTVGNPSPADTPGFNV 320
Cdd:COG5099 337 VNPPQSLPSLLNPVFLSTSTGFSLTNLSGYLNPNKNLKKNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPNFKTSSNL 416

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  321 PSLISDDPSVSSSLSSSVASLSLQNSNILSfCKDQHGCRYLQRLLEKKNQSHIDAVFAETHPYLAVLMVDAFGNYLCQKL 400
Cdd:COG5099 417 TNLNSLLKEKLSNSSSVSATDILGPSIIVS-CKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKL 495

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  401 FEHASEAQRSTFIQIIAPKLVPISFNMHGTRALQKIIDLVSSPDQISCIVNALRPNVVLLTKDLNGNHVIQKCLNKFSQE 480
Cdd:COG5099 496 FEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKE 575

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  481 DCQFIFDAICEDPLDVSTHRHGCCVVQRCFDHASPAQIEQLVEHIVPHALTLVQDAFGNYVLQYVLELNNPNHTEAIISY 560
Cdd:COG5099 576 KNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIK 655

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  561 FLYK-VRALSTQKFSSNVMEKCIFFAPAAIK-EKLISELMDEK-HLP----KLLRDSFANYVIQTALDNASVKQRAELVE 633
Cdd:COG5099 656 LLSKrVVELSTHKFASNVVEKCIKYASDSFKrSRILNELTNRGiEKPgflmLILDDQYANYVIQYLLDVSPEIQRSLLAR 735

                       650       660       670       680
                ....*....|....*....|....*....|....*....|....*
gi 2842704  634 RIKPLIPSIKNTPCGRRILSKLERRHPSSKEKpivYSNSERVNTS 678
Cdd:COG5099 736 AIKKVIPSLKKSMYGQHILALLEKVGSSSQSS---ISNKECMNTS 777
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 344-655 4.17e-156

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: 453.20  E-value: 4.17e-156
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  344 QNSNILSFCKDQHGCRYLQRLLEKKNQSHIDAVFAETHPYLAVLMVDAFGNYLCQKLFEHASEAQRSTFIQIIAPKLVPI 423
Cdd:cd07920   8 KAGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVVRL 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  424 SFNMHGTRALQKIIDLVSsPDQISCIVNALRPNVVLLTKDLNGNHVIQKCLNKFSQEDCQFIFDAICEDPLDVSTHRHGC 503
Cdd:cd07920  88 SLDMYGCRVIQKLLESIS-EEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGC 166

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  504 CVVQRCFDHASPAQIEQLVEHIVPHALTLVQDAFGNYVLQYVLELNNPNHTEAIISYFLYKVRALSTQKFSSNVMEKCIF 583
Cdd:cd07920 167 RVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEKCLK 246

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2842704  584 FAPAAIKEKLISELMDEK----HLPKLLRDSFANYVIQTALDNASVKQRAELVERIKPLIPSIKNTPCGRRILSKL 655
Cdd:cd07920 247 HASKEERELIIDEILASGnetsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILAKL 322
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 494-525 1.58e-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: 59.24  E-value: 1.58e-11
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2842704    494 LDVSTHRHGCCVVQRCFDHASPAQIEQLVEHI 525
Cdd:pfam00806   3 VELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 379-414 1.72e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 44.73  E-value: 1.72e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 2842704     379 ETHPYLAVLMVDAFGNYLCQKLFEHASEAQRSTFIQ 414
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 1-678 0e+00

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 535.87  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704    1 MTEQSSKSHPSFMSTEYSLPVFSSQYSDIENKDVLKSNSWDPYAANAPIALSEIPSSSKSGKTNGSKAAVESGLASGAFG 80
Cdd:COG5099 100 MELPSSSFNPSTSSRNKSNSALSSTQQGNANSSVTLSSSTASSMFNSNKLPLPNPNHSNSATTNQSGSSFINTPASSSSQ 179

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704   81 NRTGNMNRNTSMSGYTFGSSNFVPYNLLSNTPSFTTSHSSSTTFVPPATMGGglNNLSSPSSSLYLPGSASYQRSNSKNS 160
Cdd:COG5099 180 PLTNLVVSSIKRFPYLTSLSPFFNYLIDPSSDSATASADTSPSFNPPPNLSP--NNLFSTSDLSPLPDTQSVENNIILNS 257

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  161 SASILQMNTTLDDIPILLRRPGLSSYTPGPSTSRRSISSSSNLGGNPGLIANNPSASKnFAFTSGSSSTNNSTTSSSSMA 240
Cdd:COG5099 258 SSSINELTSIYGSVPSIRNLRGLNSALVSFLNVSSSSLAFSALNGKEVSPTGSPSTRS-FARVLPKSSPNNLLTEILTTG 336

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  241 NGLQSISKHSAAFPLLSNATSFFGENLTPSLAASTASTGSTDSSGSNIANTLIAPTPTISPPSANTVGNPSPADTPGFNV 320
Cdd:COG5099 337 VNPPQSLPSLLNPVFLSTSTGFSLTNLSGYLNPNKNLKKNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPNFKTSSNL 416

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  321 PSLISDDPSVSSSLSSSVASLSLQNSNILSfCKDQHGCRYLQRLLEKKNQSHIDAVFAETHPYLAVLMVDAFGNYLCQKL 400
Cdd:COG5099 417 TNLNSLLKEKLSNSSSVSATDILGPSIIVS-CKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKL 495

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  401 FEHASEAQRSTFIQIIAPKLVPISFNMHGTRALQKIIDLVSSPDQISCIVNALRPNVVLLTKDLNGNHVIQKCLNKFSQE 480
Cdd:COG5099 496 FEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKE 575

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  481 DCQFIFDAICEDPLDVSTHRHGCCVVQRCFDHASPAQIEQLVEHIVPHALTLVQDAFGNYVLQYVLELNNPNHTEAIISY 560
Cdd:COG5099 576 KNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIK 655

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  561 FLYK-VRALSTQKFSSNVMEKCIFFAPAAIK-EKLISELMDEK-HLP----KLLRDSFANYVIQTALDNASVKQRAELVE 633
Cdd:COG5099 656 LLSKrVVELSTHKFASNVVEKCIKYASDSFKrSRILNELTNRGiEKPgflmLILDDQYANYVIQYLLDVSPEIQRSLLAR 735

                       650       660       670       680
                ....*....|....*....|....*....|....*....|....*
gi 2842704  634 RIKPLIPSIKNTPCGRRILSKLERRHPSSKEKpivYSNSERVNTS 678
Cdd:COG5099 736 AIKKVIPSLKKSMYGQHILALLEKVGSSSQSS---ISNKECMNTS 777
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 344-655 4.17e-156

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: 453.20  E-value: 4.17e-156
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  344 QNSNILSFCKDQHGCRYLQRLLEKKNQSHIDAVFAETHPYLAVLMVDAFGNYLCQKLFEHASEAQRSTFIQIIAPKLVPI 423
Cdd:cd07920   8 KAGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVVRL 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  424 SFNMHGTRALQKIIDLVSsPDQISCIVNALRPNVVLLTKDLNGNHVIQKCLNKFSQEDCQFIFDAICEDPLDVSTHRHGC 503
Cdd:cd07920  88 SLDMYGCRVIQKLLESIS-EEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGC 166

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2842704  504 CVVQRCFDHASPAQIEQLVEHIVPHALTLVQDAFGNYVLQYVLELNNPNHTEAIISYFLYKVRALSTQKFSSNVMEKCIF 583
Cdd:cd07920 167 RVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEKCLK 246

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2842704  584 FAPAAIKEKLISELMDEK----HLPKLLRDSFANYVIQTALDNASVKQRAELVERIKPLIPSIKNTPCGRRILSKL 655
Cdd:cd07920 247 HASKEERELIIDEILASGnetsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILAKL 322
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 494-525 1.58e-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: 59.24  E-value: 1.58e-11
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2842704    494 LDVSTHRHGCCVVQRCFDHASPAQIEQLVEHI 525
Cdd:pfam00806   3 VELATDQYGCRVIQKCLEHATEEQREQILDEI 34
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 456-490 1.60e-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: 1.60e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2842704    456 NVVLLTKDLNGNHVIQKCLNKFSQEDCQFIFDAIC 490
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 347-379 9.06e-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: 45.75  E-value: 9.06e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2842704    347 NILSFCKDQHGCRYLQRLLEKKNQSHIDAVFAE 379
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDE 33
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 379-414 1.72e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 44.73  E-value: 1.72e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 2842704     379 ETHPYLAVLMVDAFGNYLCQKLFEHASEAQRSTFIQ 414
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 452-487 4.00e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.96  E-value: 4.00e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 2842704     452 ALRPNVVLLTKDLNGNHVIQKCLNKFSQEDCQFIFD 487
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 494-523 5.81e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.19  E-value: 5.81e-06
                           10        20        30
                   ....*....|....*....|....*....|
gi 2842704     494 LDVSTHRHGCCVVQRCFDHASPAQIEQLVE 523
Cdd:smart00025   7 LELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 601-633 1.13e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 42.42  E-value: 1.13e-05
                           10        20        30
                   ....*....|....*....|....*....|...
gi 2842704     601 KHLPKLLRDSFANYVIQTALDNASVKQRAELVE 633
Cdd:smart00025   4 GHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 525-558 2.99e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 41.27  E-value: 2.99e-05
                           10        20        30
                   ....*....|....*....|....*....|....
gi 2842704     525 IVPHALTLVQDAFGNYVLQYVLELNNPNHTEAII 558
Cdd:smart00025   2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 387-417 1.25e-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: 39.59  E-value: 1.25e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2842704    387 LMVDAFGNYLCQKLFEHASEAQRSTFIQIIA 417
Cdd:pfam00806   5 LATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 347-377 4.17e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 38.18  E-value: 4.17e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 2842704     347 NILSFCKDQHGCRYLQRLLEKKNQSHIDAVF 377
Cdd:smart00025   5 HLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 564-598 1.21e-03

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: 36.89  E-value: 1.21e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2842704    564 KVRALSTQKFSSNVMEKCIFFAPAAIKEKLISELM 598
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 528-559 4.52e-03

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: 34.97  E-value: 4.52e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2842704    528 HALTLVQDAFGNYVLQYVLELNNPNHTEAIIS 559
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILD 32
 
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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