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Conserved domains on  [gi|1723801|sp|P25339|]
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RecName: Full=Pumilio homology domain family member 4

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 ...
65-888 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: 652.97  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801   65 PHPQMMGGMGFMPYSQMMQVPHnpcpffpppdfndpTAPLS--SSPLNAGGPPMlfkNDSLPFQMLSSGAAVATQggqnL 142
Cdd:COG5099   1 PNSDTMNNLLPSIKSQLHHSKK--------------SPPSSttSQELMNGNSTP---NSFSPIPSKASSSATFTL----N 59
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  143 NPLINDNSMKVLPIASADPLWthsnvPGSASVAIEETTATLQESLPSKGRESNNKASSFRRQTFHALSPTDLINAANNVT 222
Cdd:COG5099  60 LPINNSVNHKITSSSSSRRKP-----SGSWSVAISSSTSGSQSLLMELPSSSFNPSTSSRNKSNSALSSTQQGNANSSVT 134
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  223 LSKDFQSDMQNFSKAKKPSVGANNTAKTRTQSISFDNTPSSTSFIPPTNSVSEKLSDFKIETSKEDLINKTAPAKKESPT 302
Cdd:COG5099 135 LSSSTASSMFNSNKLPLPNPNHSNSATTNQSGSSFINTPASSSSQPLTNLVVSSIKRFPYLTSLSPFFNYLIDPSSDSAT 214
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  303 TYGAAYPYGGPLLQPNPimpghpHNISSPIYGIRSPFPNSYEMGAQFQPFSPILNPTSHSLNANSPIPLTQSPIHLAPVL 382
Cdd:COG5099 215 ASADTSPSFNPPPNLSP------NNLFSTSDLSPLPDTQSVENNIILNSSSSINELTSIYGSVPSIRNLRGLNSALVSFL 288
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  383 NPSSNSVAFSDMKNDGGKPTTDNDKAGPNVRMDLINPNLgpsmqpfhilppqqntppppwlYSTPPPFNAMVPPHLLAQN 462
Cdd:COG5099 289 NVSSSSLAFSALNGKEVSPTGSPSTRSFARVLPKSSPNN----------------------LLTEILTTGVNPPQSLPSL 346
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  463 HMPLMNSANNKHHGRNNNSmsshndNDNIGNSNYNNKDTGRSNVGKMKNMKNSYHGYYNNNNNNNNNNNNNNNSNATNSN 542
Cdd:COG5099 347 LNPVFLSTSTGFSLTNLSG------YLNPNKNLKKNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPNFKTSSNLTNLN 420
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  543 SAEKQRKIEESSRFADAVLDQYIGSihsLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 622
Cdd:COG5099 421 SLLKEKLSNSSSVSATDILGPSIIV---SCKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFE 497
                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  623 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENF 702
Cdd:COG5099 498 YGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKN 577
                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  703 QFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIV 782
Cdd:COG5099 578 QFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLL 657
                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  783 HLlkpRAIELSIHKFGSNVIEKILKTAIVSEP---MILEILNNGGE--TGIQSLLNDSYGNYVLQTALDISHKQNDYLYK 857
Cdd:COG5099 658 SK---RVVELSTHKFASNVVEKCIKYASDSFKrsrILNELTNRGIEkpGFLMLILDDQYANYVIQYLLDVSPEIQRSLLA 734
                       810       820       830
                ....*....|....*....|....*....|.
gi 1723801  858 RLSEIVAPLLVGPiRNTPHGKRIIGMLHLDS 888
Cdd:COG5099 735 RAIKKVIPSLKKS-MYGQHILALLEKVGSSS 764
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
65-888 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: 652.97  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801   65 PHPQMMGGMGFMPYSQMMQVPHnpcpffpppdfndpTAPLS--SSPLNAGGPPMlfkNDSLPFQMLSSGAAVATQggqnL 142
Cdd:COG5099   1 PNSDTMNNLLPSIKSQLHHSKK--------------SPPSSttSQELMNGNSTP---NSFSPIPSKASSSATFTL----N 59
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  143 NPLINDNSMKVLPIASADPLWthsnvPGSASVAIEETTATLQESLPSKGRESNNKASSFRRQTFHALSPTDLINAANNVT 222
Cdd:COG5099  60 LPINNSVNHKITSSSSSRRKP-----SGSWSVAISSSTSGSQSLLMELPSSSFNPSTSSRNKSNSALSSTQQGNANSSVT 134
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  223 LSKDFQSDMQNFSKAKKPSVGANNTAKTRTQSISFDNTPSSTSFIPPTNSVSEKLSDFKIETSKEDLINKTAPAKKESPT 302
Cdd:COG5099 135 LSSSTASSMFNSNKLPLPNPNHSNSATTNQSGSSFINTPASSSSQPLTNLVVSSIKRFPYLTSLSPFFNYLIDPSSDSAT 214
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  303 TYGAAYPYGGPLLQPNPimpghpHNISSPIYGIRSPFPNSYEMGAQFQPFSPILNPTSHSLNANSPIPLTQSPIHLAPVL 382
Cdd:COG5099 215 ASADTSPSFNPPPNLSP------NNLFSTSDLSPLPDTQSVENNIILNSSSSINELTSIYGSVPSIRNLRGLNSALVSFL 288
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  383 NPSSNSVAFSDMKNDGGKPTTDNDKAGPNVRMDLINPNLgpsmqpfhilppqqntppppwlYSTPPPFNAMVPPHLLAQN 462
Cdd:COG5099 289 NVSSSSLAFSALNGKEVSPTGSPSTRSFARVLPKSSPNN----------------------LLTEILTTGVNPPQSLPSL 346
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  463 HMPLMNSANNKHHGRNNNSmsshndNDNIGNSNYNNKDTGRSNVGKMKNMKNSYHGYYNNNNNNNNNNNNNNNSNATNSN 542
Cdd:COG5099 347 LNPVFLSTSTGFSLTNLSG------YLNPNKNLKKNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPNFKTSSNLTNLN 420
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  543 SAEKQRKIEESSRFADAVLDQYIGSihsLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 622
Cdd:COG5099 421 SLLKEKLSNSSSVSATDILGPSIIV---SCKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFE 497
                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  623 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENF 702
Cdd:COG5099 498 YGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKN 577
                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  703 QFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIV 782
Cdd:COG5099 578 QFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLL 657
                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  783 HLlkpRAIELSIHKFGSNVIEKILKTAIVSEP---MILEILNNGGE--TGIQSLLNDSYGNYVLQTALDISHKQNDYLYK 857
Cdd:COG5099 658 SK---RVVELSTHKFASNVVEKCIKYASDSFKrsrILNELTNRGIEkpGFLMLILDDQYANYVIQYLLDVSPEIQRSLLA 734
                       810       820       830
                ....*....|....*....|....*....|.
gi 1723801  858 RLSEIVAPLLVGPiRNTPHGKRIIGMLHLDS 888
Cdd:COG5099 735 RAIKKVIPSLKKS-MYGQHILALLEKVGSSS 764
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
562-884 2.43e-141

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: 422.00  E-value: 2.43e-141
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  562 DQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFV 641
Cdd:cd07920   6 DIKAGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVV 85
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  642 EISLNPHGTRALQKLIECIKtDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRH 721
Cdd:cd07920  86 RLSLDMYGCRVIQKLLESIS-EEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPY 164
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  722 GCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIItkeaEKNKYDYTHKIVHLLKPRAIELSIHKFGSNV 801
Cdd:cd07920 165 GCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVL----ELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  802 IEKILKTA--IVSEPMILEILNNGGET-GIQSLLNDSYGNYVLQTALDIShkqNDYLYKRLSEIVAPLLVGpIRNTPHGK 878
Cdd:cd07920 241 VEKCLKHAskEERELIIDEILASGNETsALDTLMKDQYGNYVIQTALDVA---KEEQRELLVEAIRPHLPS-LRKSPYGK 316

                ....*.
gi 1723801  879 RIIGML 884
Cdd:cd07920 317 HILAKL 322
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
713-746 5.50e-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: 60.78  E-value: 5.50e-12
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1723801    713 CIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLL 746
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
672-707 8.25e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.89  E-value: 8.25e-07
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1723801     672 SLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFD 707
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
65-888 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: 652.97  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801   65 PHPQMMGGMGFMPYSQMMQVPHnpcpffpppdfndpTAPLS--SSPLNAGGPPMlfkNDSLPFQMLSSGAAVATQggqnL 142
Cdd:COG5099   1 PNSDTMNNLLPSIKSQLHHSKK--------------SPPSSttSQELMNGNSTP---NSFSPIPSKASSSATFTL----N 59
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  143 NPLINDNSMKVLPIASADPLWthsnvPGSASVAIEETTATLQESLPSKGRESNNKASSFRRQTFHALSPTDLINAANNVT 222
Cdd:COG5099  60 LPINNSVNHKITSSSSSRRKP-----SGSWSVAISSSTSGSQSLLMELPSSSFNPSTSSRNKSNSALSSTQQGNANSSVT 134
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  223 LSKDFQSDMQNFSKAKKPSVGANNTAKTRTQSISFDNTPSSTSFIPPTNSVSEKLSDFKIETSKEDLINKTAPAKKESPT 302
Cdd:COG5099 135 LSSSTASSMFNSNKLPLPNPNHSNSATTNQSGSSFINTPASSSSQPLTNLVVSSIKRFPYLTSLSPFFNYLIDPSSDSAT 214
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  303 TYGAAYPYGGPLLQPNPimpghpHNISSPIYGIRSPFPNSYEMGAQFQPFSPILNPTSHSLNANSPIPLTQSPIHLAPVL 382
Cdd:COG5099 215 ASADTSPSFNPPPNLSP------NNLFSTSDLSPLPDTQSVENNIILNSSSSINELTSIYGSVPSIRNLRGLNSALVSFL 288
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  383 NPSSNSVAFSDMKNDGGKPTTDNDKAGPNVRMDLINPNLgpsmqpfhilppqqntppppwlYSTPPPFNAMVPPHLLAQN 462
Cdd:COG5099 289 NVSSSSLAFSALNGKEVSPTGSPSTRSFARVLPKSSPNN----------------------LLTEILTTGVNPPQSLPSL 346
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  463 HMPLMNSANNKHHGRNNNSmsshndNDNIGNSNYNNKDTGRSNVGKMKNMKNSYHGYYNNNNNNNNNNNNNNNSNATNSN 542
Cdd:COG5099 347 LNPVFLSTSTGFSLTNLSG------YLNPNKNLKKNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPNFKTSSNLTNLN 420
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  543 SAEKQRKIEESSRFADAVLDQYIGSihsLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLE 622
Cdd:COG5099 421 SLLKEKLSNSSSVSATDILGPSIIV---SCKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFE 497
                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  623 EVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENF 702
Cdd:COG5099 498 YGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKN 577
                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  703 QFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIV 782
Cdd:COG5099 578 QFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLL 657
                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  783 HLlkpRAIELSIHKFGSNVIEKILKTAIVSEP---MILEILNNGGE--TGIQSLLNDSYGNYVLQTALDISHKQNDYLYK 857
Cdd:COG5099 658 SK---RVVELSTHKFASNVVEKCIKYASDSFKrsrILNELTNRGIEkpGFLMLILDDQYANYVIQYLLDVSPEIQRSLLA 734
                       810       820       830
                ....*....|....*....|....*....|.
gi 1723801  858 RLSEIVAPLLVGPiRNTPHGKRIIGMLHLDS 888
Cdd:COG5099 735 RAIKKVIPSLKKS-MYGQHILALLEKVGSSS 764
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
562-884 2.43e-141

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: 422.00  E-value: 2.43e-141
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  562 DQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFV 641
Cdd:cd07920   6 DIKAGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVV 85
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  642 EISLNPHGTRALQKLIECIKtDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRH 721
Cdd:cd07920  86 RLSLDMYGCRVIQKLLESIS-EEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPY 164
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  722 GCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIItkeaEKNKYDYTHKIVHLLKPRAIELSIHKFGSNV 801
Cdd:cd07920 165 GCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVL----ELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1723801  802 IEKILKTA--IVSEPMILEILNNGGET-GIQSLLNDSYGNYVLQTALDIShkqNDYLYKRLSEIVAPLLVGpIRNTPHGK 878
Cdd:cd07920 241 VEKCLKHAskEERELIIDEILASGNETsALDTLMKDQYGNYVIQTALDVA---KEEQRELLVEAIRPHLPS-LRKSPYGK 316

                ....*.
gi 1723801  879 RIIGML 884
Cdd:cd07920 317 HILAKL 322
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
713-746 5.50e-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: 60.78  E-value: 5.50e-12
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1723801    713 CIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLL 746
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
672-707 8.25e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.89  E-value: 8.25e-07
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1723801     672 SLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFD 707
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
678-710 1.52e-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: 45.37  E-value: 1.52e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1723801    678 VQLSKDLNGNHVIQKCLQRLKPENFQFIFDAIS 710
Cdd:pfam00806   3 VELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
605-632 6.43e-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: 43.44  E-value: 6.43e-06
                          10        20
                  ....*....|....*....|....*...
gi 1723801    605 VELMTDSFGNYLIQKLLEEVTTEQRIVL 632
Cdd:pfam00806   3 VELATDQYGCRVIQKCLEHATEEQREQI 30
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
708-743 7.27e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 43.58  E-value: 7.27e-06
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1723801     708 AISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCD 743
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
599-634 1.24e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 42.81  E-value: 1.24e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1723801     599 ETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTK 634
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
568-599 5.15e-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: 41.13  E-value: 5.15e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1723801    568 IHSLCKDQHGCRFLQKQLDILGSKAADAIFEE 599
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQILDE 33
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
639-671 1.00e-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: 39.98  E-value: 1.00e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1723801    639 HFVEISLNPHGTRALQKLIECIkTDEEAQIVVD 671
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHA-TEEQREQILD 32
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
565-598 1.86e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 39.34  E-value: 1.86e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1723801     565 IGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFE 598
Cdd:smart00025   3 KGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
784-821 1.89e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 39.34  E-value: 1.89e-04
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1723801     784 LLKPRAIELSIHKFGSNVIEKILKTAivSEPMILEILN 821
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHA--SESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
790-820 7.99e-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: 7.99e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1723801    790 IELSIHKFGSNVIEKILK--TAIVSEPMILEIL 820
Cdd:pfam00806   3 VELATDQYGCRVIQKCLEhaTEEQREQILDEIL 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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