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Conserved domains on  [gi|74676554|sp|Q12221|]
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RecName: Full=mRNA-binding protein PUF2; AltName: Full=Pumilio homology domain family member 2

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 ...
 70-884 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: 658.36  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554   70 RFSDTLTNLLPSISAKLHHSKKStpvvvvPPTSSTPDSLNSTTYAPrvsSDSFTVATPLSLQSTTTRTRTRNNTVSSQIT 149
Cdd:COG5099    1 PNSDTMNNLLPSIKSQLHHSKKS------PPSSTTSQELMNGNSTP---NSFSPIPSKASSSATFTLNLPINNSVNHKIT 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  150 ASSSLTTDvgnatSANIWSANAESNTSSSPLFDYPLATSYFEPLTRFKSTDNYTLPQTAQLNSFLEKNGNPNIWSSAGNS 229
Cdd:COG5099   72 SSSSSRRK-----PSGSWSVAISSSTSGSQSLLMELPSSSFNPSTSSRNKSNSALSSTQQGNANSSVTLSSSTASSMFNS 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  230 NTDHLNTPIVNRQRSQSQSTTNRVYTDAPYYQQPAQNYQVQVPPRVPKSTSISPVILDDVDPASINWITANQKVPLVNQI 309
Cdd:COG5099  147 NKLPLPNPNHSNSATTNQSGSSFINTPASSSSQPLTNLVVSSIKRFPYLTSLSPFFNYLIDPSSDSATASADTSPSFNPP 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  310 SALLPTNTISISNVFPLQPTQQHQQNAVNLTSTSLATLCSQYGKVLSARTLRGLNMALVEFSTVESAICALEALQGKELS 389
Cdd:COG5099  227 PNLSPNNLFSTSDLSPLPDTQSVENNIILNSSSSINELTSIYGSVPSIRNLRGLNSALVSFLNVSSSSLAFSALNGKEVS 306

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  390 KVGAPSTVSFARVLPMYEQPlnvngfnntpkqPLLQEQLNHGVLNYQLQQSLQQPELQQQPTSFNQPNLT-YCNPTQNLS 468
Cdd:COG5099  307 PTGSPSTRSFARVLPKSSPN------------NLLTEILTTGVNPPQSLPSLLNPVFLSTSTGFSLTNLSgYLNPNKNLK 374

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  469 HLQLSSNENEPYPFPLPPPSLSDSKKDILHTISS-FKLEYDHLELNHLLQNALKNKG-VSDTNYFGPLPEHNSKvpkrkd 546
Cdd:COG5099  375 KNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPnFKTSSNLTNLNSLLKEKLSNSSsVSATDILGPSIIVSCK------ 448

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  547 tfDAPKLRELRKQFDSNslSTIEMEQLAIVMLDQLPELSSDYLGNTVIQKLFENSSNIIRDIMLRKCNKYLTSMGVHKNG 626
Cdd:COG5099  449 --DQHGSRFLQKLLDSN--SSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYG 524

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  627 TWVCQKIIKMANTPRQINLVTSGVSDYCTPLFNDQFGNYVIQ-GILKFGFPWNSFIFESVLSHFWTIVQNRYGSRAVRAC 705
Cdd:COG5099  525 TRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQkCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRC 604

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  706 LEADSIITQcqlLTITSLIIVLSPYLATDTNGTLLITWLLDTCTLPNKNLILCdKLVNKNLVKLCCHKLGSLTVLKILNL 785
Cdd:COG5099  605 LENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIII-KLLSKRVVELSTHKFASNVVEKCIKY 680

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  786 RGGEEealSKNKIIHAIFDGPISSDSILFQILDEGNYGPTFIYKVLTSRILDNSVRDEAITKIRQLILNSNINLQSRQLL 865
Cdd:COG5099  681 ASDSF---KRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALL 757

                        810       820
                 ....*....|....*....|
gi 74676554  866 EEVGLSSAG-ISPKQSSKNH 884
Cdd:COG5099  758 EKVGSSSQSsISNKECMNTS 777
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 70-884 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: 658.36  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554   70 RFSDTLTNLLPSISAKLHHSKKStpvvvvPPTSSTPDSLNSTTYAPrvsSDSFTVATPLSLQSTTTRTRTRNNTVSSQIT 149
Cdd:COG5099    1 PNSDTMNNLLPSIKSQLHHSKKS------PPSSTTSQELMNGNSTP---NSFSPIPSKASSSATFTLNLPINNSVNHKIT 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  150 ASSSLTTDvgnatSANIWSANAESNTSSSPLFDYPLATSYFEPLTRFKSTDNYTLPQTAQLNSFLEKNGNPNIWSSAGNS 229
Cdd:COG5099   72 SSSSSRRK-----PSGSWSVAISSSTSGSQSLLMELPSSSFNPSTSSRNKSNSALSSTQQGNANSSVTLSSSTASSMFNS 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  230 NTDHLNTPIVNRQRSQSQSTTNRVYTDAPYYQQPAQNYQVQVPPRVPKSTSISPVILDDVDPASINWITANQKVPLVNQI 309
Cdd:COG5099  147 NKLPLPNPNHSNSATTNQSGSSFINTPASSSSQPLTNLVVSSIKRFPYLTSLSPFFNYLIDPSSDSATASADTSPSFNPP 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  310 SALLPTNTISISNVFPLQPTQQHQQNAVNLTSTSLATLCSQYGKVLSARTLRGLNMALVEFSTVESAICALEALQGKELS 389
Cdd:COG5099  227 PNLSPNNLFSTSDLSPLPDTQSVENNIILNSSSSINELTSIYGSVPSIRNLRGLNSALVSFLNVSSSSLAFSALNGKEVS 306

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  390 KVGAPSTVSFARVLPMYEQPlnvngfnntpkqPLLQEQLNHGVLNYQLQQSLQQPELQQQPTSFNQPNLT-YCNPTQNLS 468
Cdd:COG5099  307 PTGSPSTRSFARVLPKSSPN------------NLLTEILTTGVNPPQSLPSLLNPVFLSTSTGFSLTNLSgYLNPNKNLK 374

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  469 HLQLSSNENEPYPFPLPPPSLSDSKKDILHTISS-FKLEYDHLELNHLLQNALKNKG-VSDTNYFGPLPEHNSKvpkrkd 546
Cdd:COG5099  375 KNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPnFKTSSNLTNLNSLLKEKLSNSSsVSATDILGPSIIVSCK------ 448

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  547 tfDAPKLRELRKQFDSNslSTIEMEQLAIVMLDQLPELSSDYLGNTVIQKLFENSSNIIRDIMLRKCNKYLTSMGVHKNG 626
Cdd:COG5099  449 --DQHGSRFLQKLLDSN--SSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYG 524

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  627 TWVCQKIIKMANTPRQINLVTSGVSDYCTPLFNDQFGNYVIQ-GILKFGFPWNSFIFESVLSHFWTIVQNRYGSRAVRAC 705
Cdd:COG5099  525 TRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQkCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRC 604

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  706 LEADSIITQcqlLTITSLIIVLSPYLATDTNGTLLITWLLDTCTLPNKNLILCdKLVNKNLVKLCCHKLGSLTVLKILNL 785
Cdd:COG5099  605 LENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIII-KLLSKRVVELSTHKFASNVVEKCIKY 680

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  786 RGGEEealSKNKIIHAIFDGPISSDSILFQILDEGNYGPTFIYKVLTSRILDNSVRDEAITKIRQLILNSNINLQSRQLL 865
Cdd:COG5099  681 ASDSF---KRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALL 757

                        810       820
                 ....*....|....*....|
gi 74676554  866 EEVGLSSAG-ISPKQSSKNH 884
Cdd:COG5099  758 EKVGSSSQSsISNKECMNTS 777
RRM_ScJSN1_like cd21616
RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar ...
 287-404 2.53e-53

RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar proteins; JSN1, also called Pumilio homology domain family member 1 (PUF1), is a member of the PUF family of proteins. It facilitates association of Arp2/3 complex to yeast mitochondria. It may play a role in mitosis, perhaps by affecting the stability of microtubules. Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410195 [Multi-domain]  Cd Length: 118  Bit Score: 181.88  E-value: 2.53e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  287 DDVDPASINWITANQKVPLVNQISALLPTNTISISNVFPLQPTQQHQQNAVNLTSTSLATLCSQYGKVLSARTLRGLNMA 366
Cdd:cd21616    1 DDVDPTSINWITTSPYVPPINQVNNLLPTNTILVSNIFPIQQTSPQPPNPINLTSTSLASLCSKFGDIISSRTLRGLNMA 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 74676554  367 LVEFSTVESAICALEALQGKELSKVGAPSTVSFARVLP 404
Cdd:cd21616   81 LIEFESVDSAILALESLQGKEISIIGVPSDITFAKILP 118
RRM smart00360
RNA recognition motif;
338-388 6.55e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 44.89  E-value: 6.55e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 74676554     338 NLTSTSLATLCSQYGKVLSAR------TLRGLNMALVEFSTVESAICALEALQGKEL 388
Cdd:smart00360   10 DTTEEELRELFSKFGKVESVRlvrdkeTGKSKGFAFVEFESEEDAEKALEALNGKEL 66
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 338-388 7.61e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 44.53  E-value: 7.61e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 74676554    338 NLTSTSLATLCSQYGKVLSAR-----TLRGLNMALVEFSTVESAICALEALQGKEL 388
Cdd:pfam00076    9 DTTEEDLKDLFSKFGPIKSIRlvrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKEL 64
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 70-884 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: 658.36  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554   70 RFSDTLTNLLPSISAKLHHSKKStpvvvvPPTSSTPDSLNSTTYAPrvsSDSFTVATPLSLQSTTTRTRTRNNTVSSQIT 149
Cdd:COG5099    1 PNSDTMNNLLPSIKSQLHHSKKS------PPSSTTSQELMNGNSTP---NSFSPIPSKASSSATFTLNLPINNSVNHKIT 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  150 ASSSLTTDvgnatSANIWSANAESNTSSSPLFDYPLATSYFEPLTRFKSTDNYTLPQTAQLNSFLEKNGNPNIWSSAGNS 229
Cdd:COG5099   72 SSSSSRRK-----PSGSWSVAISSSTSGSQSLLMELPSSSFNPSTSSRNKSNSALSSTQQGNANSSVTLSSSTASSMFNS 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  230 NTDHLNTPIVNRQRSQSQSTTNRVYTDAPYYQQPAQNYQVQVPPRVPKSTSISPVILDDVDPASINWITANQKVPLVNQI 309
Cdd:COG5099  147 NKLPLPNPNHSNSATTNQSGSSFINTPASSSSQPLTNLVVSSIKRFPYLTSLSPFFNYLIDPSSDSATASADTSPSFNPP 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  310 SALLPTNTISISNVFPLQPTQQHQQNAVNLTSTSLATLCSQYGKVLSARTLRGLNMALVEFSTVESAICALEALQGKELS 389
Cdd:COG5099  227 PNLSPNNLFSTSDLSPLPDTQSVENNIILNSSSSINELTSIYGSVPSIRNLRGLNSALVSFLNVSSSSLAFSALNGKEVS 306

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  390 KVGAPSTVSFARVLPMYEQPlnvngfnntpkqPLLQEQLNHGVLNYQLQQSLQQPELQQQPTSFNQPNLT-YCNPTQNLS 468
Cdd:COG5099  307 PTGSPSTRSFARVLPKSSPN------------NLLTEILTTGVNPPQSLPSLLNPVFLSTSTGFSLTNLSgYLNPNKNLK 374

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  469 HLQLSSNENEPYPFPLPPPSLSDSKKDILHTISS-FKLEYDHLELNHLLQNALKNKG-VSDTNYFGPLPEHNSKvpkrkd 546
Cdd:COG5099  375 KNTLSSLSNLGYSSNVPSPSSSESTRNILGNISPnFKTSSNLTNLNSLLKEKLSNSSsVSATDILGPSIIVSCK------ 448

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  547 tfDAPKLRELRKQFDSNslSTIEMEQLAIVMLDQLPELSSDYLGNTVIQKLFENSSNIIRDIMLRKCNKYLTSMGVHKNG 626
Cdd:COG5099  449 --DQHGSRFLQKLLDSN--SSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYG 524

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  627 TWVCQKIIKMANTPRQINLVTSGVSDYCTPLFNDQFGNYVIQ-GILKFGFPWNSFIFESVLSHFWTIVQNRYGSRAVRAC 705
Cdd:COG5099  525 TRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQkCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRC 604

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  706 LEADSIITQcqlLTITSLIIVLSPYLATDTNGTLLITWLLDTCTLPNKNLILCdKLVNKNLVKLCCHKLGSLTVLKILNL 785
Cdd:COG5099  605 LENCNSEDK---ENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIII-KLLSKRVVELSTHKFASNVVEKCIKY 680

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  786 RGGEEealSKNKIIHAIFDGPISSDSILFQILDEGNYGPTFIYKVLTSRILDNSVRDEAITKIRQLILNSNINLQSRQLL 865
Cdd:COG5099  681 ASDSF---KRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALL 757

                        810       820
                 ....*....|....*....|
gi 74676554  866 EEVGLSSAG-ISPKQSSKNH 884
Cdd:COG5099  758 EKVGSSSQSsISNKECMNTS 777
RRM_ScJSN1_like cd21616
RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar ...
 287-404 2.53e-53

RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar proteins; JSN1, also called Pumilio homology domain family member 1 (PUF1), is a member of the PUF family of proteins. It facilitates association of Arp2/3 complex to yeast mitochondria. It may play a role in mitosis, perhaps by affecting the stability of microtubules. Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410195 [Multi-domain]  Cd Length: 118  Bit Score: 181.88  E-value: 2.53e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  287 DDVDPASINWITANQKVPLVNQISALLPTNTISISNVFPLQPTQQHQQNAVNLTSTSLATLCSQYGKVLSARTLRGLNMA 366
Cdd:cd21616    1 DDVDPTSINWITTSPYVPPINQVNNLLPTNTILVSNIFPIQQTSPQPPNPINLTSTSLASLCSKFGDIISSRTLRGLNMA 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 74676554  367 LVEFSTVESAICALEALQGKELSKVGAPSTVSFARVLP 404
Cdd:cd21616   81 LIEFESVDSAILALESLQGKEISIIGVPSDITFAKILP 118
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 554-852 3.12e-27

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: 113.84  E-value: 3.12e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  554 RELRKQFDSNSLSTIEMEQLAIvmLDQLPELSSDYLGNTVIQKLFENSSNIIRDIMLRKCNKYLTSMGVHKNGTWVCQKI 633
Cdd:cd07920   23 RFLQQKLEEATPEEKELIFDEI--LPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVVRLSLDMYGCRVIQKL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  634 IKMANtPRQINLVTSGVSDYCTPLFNDQFGNYVIQGIL-KFGFPWNSFIFESVLSHFWTIVQNRYGSRAVRACLEadsii 712
Cdd:cd07920  101 LESIS-EEQISLLVKELRGHVVELVKDQNGNHVIQKCIeKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLE----- 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74676554  713 tQC---QLLTITSLIIVLSPYLATDTNGTLLITWLLDTCTLPNKNLILcdKLVNKNLVKLCCHKLGSLTVLKILNLRGGE 789
Cdd:cd07920  175 -HCseeQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRII--EKLLGNIVQLSCHKFASNVVEKCLKHASKE 251

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 74676554  790 EealsKNKIIHAIFDGPISSDSILFQILDE-GNYgptfiykVLtSRILDNS---VRDEAITKIRQLI 852
Cdd:cd07920  252 E----RELIIDEILASGNETSALDTLMKDQyGNY-------VI-QTALDVAkeeQRELLVEAIRPHL 306
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 338-388 2.30e-06

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 46.12  E-value: 2.30e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 74676554  338 NLTSTSLATLCSQYGKVLSARTLRGL-----NMALVEFSTVESAICALEALQGKEL 388
Cdd:cd00590    9 DTTEEDLRELFSKFGEVVSVRIVRDRdgkskGFAFVEFESPEDAEKALEALNGTEL 64
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
 343-401 5.00e-06

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 45.22  E-value: 5.00e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 74676554  343 SLATLCSQYGKVLSARTLRGLNM---ALVEFSTVESAICALEALQGKELskVGAPSTVSFAR 401
Cdd:cd12246   19 SLYALFSQFGPVLDIVASKSLKMrgqAFVVFKDVESATNALRALQGFPF--YGKPMRIQYAK 78
RRM smart00360
RNA recognition motif;
338-388 6.55e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 44.89  E-value: 6.55e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 74676554     338 NLTSTSLATLCSQYGKVLSAR------TLRGLNMALVEFSTVESAICALEALQGKEL 388
Cdd:smart00360   10 DTTEEELRELFSKFGKVESVRlvrdkeTGKSKGFAFVEFESEEDAEKALEALNGKEL 66
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 338-388 7.61e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 44.53  E-value: 7.61e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 74676554    338 NLTSTSLATLCSQYGKVLSAR-----TLRGLNMALVEFSTVESAICALEALQGKEL 388
Cdd:pfam00076    9 DTTEEDLKDLFSKFGPIKSIRlvrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKEL 64
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
 343-401 1.27e-04

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 41.28  E-value: 1.27e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 74676554  343 SLATLCSQYGKVLSARTLRglNMALVEFSTVESAICALEALQGKELSkvGAPSTVSFAR 401
Cdd:cd12233   16 DIEKLFEPFGPLVRCDIRK--TFAFVEFEDSEDATKALEALHGSRID--GSVLTVEFVK 70
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 338-388 9.99e-04

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 38.69  E-value: 9.99e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 74676554  338 NLTSTSLATLCSQYGKVLSAR------TLRGLNMALVEFSTVESAICALEALQGKEL 388
Cdd:cd21608   10 DTTEDDLRDLFSEFGEVESAKvitdreTGRSRGFGFVTFSTAEAAEAAIDALNGKEL 66
RRM2_U1A_like cd12247
RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily ...
 338-390 2.20e-03

RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding.


Pssm-ID: 409693 [Multi-domain]  Cd Length: 72  Bit Score: 37.93  E-value: 2.20e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 74676554  338 NLTSTSLATLCSQYGKVLSARTLRGLNMALVEFSTVESAICALEALQGKELSK 390
Cdd:cd12247   13 ETTKEMLEMLFNQFPGFKEVRLVPRRGIAFVEFETEEQATVALQALQGFKITP 65
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 339-388 2.81e-03

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 37.56  E-value: 2.81e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 74676554  339 LTSTSLATLCSQYGKVLSARTLRGLNMALVEFSTVESAICALEALQGKEL 388
Cdd:cd12431   15 VSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKEL 64
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
 340-389 7.70e-03

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 36.46  E-value: 7.70e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 74676554  340 TSTSLATLCSQYGKVLSA------RTLRGLNMALVEFSTVESAICALEALQGKELS 389
Cdd:cd12417   12 KAADLKKIFSKYGKVVSAkvvtsaRTPGSRCYGYVTMASVEEADLCIKSLNKTELH 67
RRM2_hnRNPL_like cd12694
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 344-388 9.00e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both nuclear and cytoplasmic roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410094 [Multi-domain]  Cd Length: 86  Bit Score: 36.48  E-value: 9.00e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 74676554  344 LATLCSQYGKVLSARTLR--GLNmALVEFSTVESAICALEALQGKEL 388
Cdd:cd12694   20 IHTICSPYGKVLRIVIFRknGVQ-AMVEFDSVESAQRAKAALNGADI 65
 
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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