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Conserved domains on  [gi|71983283|ref|NP_495523|]
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PUM-HD domain-containing protein [Caenorhabditis elegans]

Protein Classification

Pumilio-family RNA binding repeat-containing protein( domain architecture ID 10167778)

Pumilio-family RNA binding repeat-containing protein harbors PUF repeats, which mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio; it may function as a translational repressor in early embryonic development by binding to sequences in the 3' UTR of target mRNAs

CATH:  1.25.10.10
Gene Ontology:  GO:0003723
PubMed:  14584586|29385744|17003467|9404893
SCOP:  4003086

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 189-514 2.96e-124

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: 366.92  E-value: 2.96e-124
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 189 NLKLSDIR-GALLKFAKDQVGSRFIQQELASSKDRfEKDSIFDEVVSNADELVDDIFGNYVVQKFFEYGEERHWARLVDA 267
Cdd:cd07920   1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPE-EKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEK 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 268 IIDRVPEYAFQMYACRVLQKALEKINEPLQIKILSQIRHVIHRCMKDQNGNHVVQKAIEKVSPQYVQFIVDTLLESsntI 347
Cdd:cd07920  80 ILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGN---C 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 348 YEMSVDPYGCRVVQRCLEHCSPSQTKPVIGQIHKRFDEIANNQYGNYVVQHVIEHGSEEDRMVIVTRVSNNLFEFATHKY 427
Cdd:cd07920 157 VALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKF 236

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 428 SSNVIEKCLEQGAVYHKSMIVGAACHHQEGSVPIvVQMMKDQYANYVVQKMFDQVTSEQRRELILTVRPHIPVLRQFPHG 507
Cdd:cd07920 237 ASNVVEKCLKHASKEERELIIDEILASGNETSAL-DTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYG 315


                ....*..
gi 71983283 508 KHILAKL 514
Cdd:cd07920 316 KHILAKL 322
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 189-514 2.96e-124

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: 366.92  E-value: 2.96e-124
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 189 NLKLSDIR-GALLKFAKDQVGSRFIQQELASSKDRfEKDSIFDEVVSNADELVDDIFGNYVVQKFFEYGEERHWARLVDA 267
Cdd:cd07920   1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPE-EKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEK 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 268 IIDRVPEYAFQMYACRVLQKALEKINEPLQIKILSQIRHVIHRCMKDQNGNHVVQKAIEKVSPQYVQFIVDTLLESsntI 347
Cdd:cd07920  80 ILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGN---C 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 348 YEMSVDPYGCRVVQRCLEHCSPSQTKPVIGQIHKRFDEIANNQYGNYVVQHVIEHGSEEDRMVIVTRVSNNLFEFATHKY 427
Cdd:cd07920 157 VALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKF 236

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 428 SSNVIEKCLEQGAVYHKSMIVGAACHHQEGSVPIvVQMMKDQYANYVVQKMFDQVTSEQRRELILTVRPHIPVLRQFPHG 507
Cdd:cd07920 237 ASNVVEKCLKHASKEERELIIDEILASGNETSAL-DTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYG 315


                ....*..
gi 71983283 508 KHILAKL 514
Cdd:cd07920 316 KHILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 72-516 7.39e-82

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 270.85  E-value: 7.39e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283  72 GGKVIGQNTLHMFGTPPSCYCA----QENIPISSN----VGHVLSTINNNY--MNHQYNGS-NMFSNQMTQMLQAQAYND 140
Cdd:COG5099 304 EVSPTGSPSTRSFARVLPKSSPnnllTEILTTGVNppqsLPSLLNPVFLSTstGFSLTNLSgYLNPNKNLKKNTLSSLSN 383

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 141 LQ-MHQAHSQSIRVPVQPSATGIFSNPYREPTTTDDLLTRYRANpAMMKNLKLSDIRGALLKF-AKDQVGSRFIQQELAS 218
Cdd:COG5099 384 LGySSNVPSPSSSESTRNILGNISPNFKTSSNLTNLNSLLKEKL-SNSSSVSATDILGPSIIVsCKDQHGSRFLQKLLDS 462

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 219 SkDRFEKDSIFDEVVSNADELVDDIFGNYVVQKFFEYGEERHWARLVDAIIDRVPEYAFQMYACRVLQKALEKINEPLQI 298
Cdd:COG5099 463 N-SSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQI 541

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 299 K-ILSQIRHVIHRCMKDQNGNHVVQKAIEKVSPQYVQFIVDTLLESSNTIyemSVDPYGCRVVQRCLEHCSPSQTKPVIG 377
Cdd:COG5099 542 SlLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDL---STHRYGSRVVQRCLENCNSEDKENLVE 618

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 378 QIHKRFDEIANNQYGNYVVQHVIEHGSEEDR-MVIVTRVSNNLFEFATHKYSSNVIEKCLE-QGAVYHKSMIVGAACHHQ 455
Cdd:COG5099 619 EIISNSKYLSQDQYGNYVVQHILDNGAEPNKeRIIIKLLSKRVVELSTHKFASNVVEKCIKyASDSFKRSRILNELTNRG 698

                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 71983283 456 EGSVPIVVQMMKDQYANYVVQKMFDQVTSEQRRELILTVRPHIPVLRQFPHGKHILAKLEK 516
Cdd:COG5099 699 IEKPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALLEK 759
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 347-380 1.98e-10

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA). Other proteins that contain Puf domains are also plausible RNA binding proteins. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 55.77  E-value: 1.98e-10
                          10        20        30
                  ....*....|....*....|....*....|....
gi 71983283   347 IYEMSVDPYGCRVVQRCLEHCSPSQTKPVIGQIH 380
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 379-412 2.09e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 47.04  E-value: 2.09e-07
                           10        20        30
                   ....*....|....*....|....*....|....
gi 71983283    379 IHKRFDEIANNQYGNYVVQHVIEHGSEEDRMVIV 412
Cdd:smart00025   2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 189-514 2.96e-124

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: 366.92  E-value: 2.96e-124
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 189 NLKLSDIR-GALLKFAKDQVGSRFIQQELASSKDRfEKDSIFDEVVSNADELVDDIFGNYVVQKFFEYGEERHWARLVDA 267
Cdd:cd07920   1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPE-EKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEK 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 268 IIDRVPEYAFQMYACRVLQKALEKINEPLQIKILSQIRHVIHRCMKDQNGNHVVQKAIEKVSPQYVQFIVDTLLESsntI 347
Cdd:cd07920  80 ILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGN---C 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 348 YEMSVDPYGCRVVQRCLEHCSPSQTKPVIGQIHKRFDEIANNQYGNYVVQHVIEHGSEEDRMVIVTRVSNNLFEFATHKY 427
Cdd:cd07920 157 VALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKF 236

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 428 SSNVIEKCLEQGAVYHKSMIVGAACHHQEGSVPIvVQMMKDQYANYVVQKMFDQVTSEQRRELILTVRPHIPVLRQFPHG 507
Cdd:cd07920 237 ASNVVEKCLKHASKEERELIIDEILASGNETSAL-DTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYG 315


                ....*..
gi 71983283 508 KHILAKL 514
Cdd:cd07920 316 KHILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 72-516 7.39e-82

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 270.85  E-value: 7.39e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283  72 GGKVIGQNTLHMFGTPPSCYCA----QENIPISSN----VGHVLSTINNNY--MNHQYNGS-NMFSNQMTQMLQAQAYND 140
Cdd:COG5099 304 EVSPTGSPSTRSFARVLPKSSPnnllTEILTTGVNppqsLPSLLNPVFLSTstGFSLTNLSgYLNPNKNLKKNTLSSLSN 383

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 141 LQ-MHQAHSQSIRVPVQPSATGIFSNPYREPTTTDDLLTRYRANpAMMKNLKLSDIRGALLKF-AKDQVGSRFIQQELAS 218
Cdd:COG5099 384 LGySSNVPSPSSSESTRNILGNISPNFKTSSNLTNLNSLLKEKL-SNSSSVSATDILGPSIIVsCKDQHGSRFLQKLLDS 462

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 219 SkDRFEKDSIFDEVVSNADELVDDIFGNYVVQKFFEYGEERHWARLVDAIIDRVPEYAFQMYACRVLQKALEKINEPLQI 298
Cdd:COG5099 463 N-SSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQI 541

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 299 K-ILSQIRHVIHRCMKDQNGNHVVQKAIEKVSPQYVQFIVDTLLESSNTIyemSVDPYGCRVVQRCLEHCSPSQTKPVIG 377
Cdd:COG5099 542 SlLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDL---STHRYGSRVVQRCLENCNSEDKENLVE 618

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71983283 378 QIHKRFDEIANNQYGNYVVQHVIEHGSEEDR-MVIVTRVSNNLFEFATHKYSSNVIEKCLE-QGAVYHKSMIVGAACHHQ 455
Cdd:COG5099 619 EIISNSKYLSQDQYGNYVVQHILDNGAEPNKeRIIIKLLSKRVVELSTHKFASNVVEKCIKyASDSFKRSRILNELTNRG 698

                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 71983283 456 EGSVPIVVQMMKDQYANYVVQKMFDQVTSEQRRELILTVRPHIPVLRQFPHGKHILAKLEK 516
Cdd:COG5099 699 IEKPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALLEK 759
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 347-380 1.98e-10

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA). Other proteins that contain Puf domains are also plausible RNA binding proteins. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 55.77  E-value: 1.98e-10
                          10        20        30
                  ....*....|....*....|....*....|....
gi 71983283   347 IYEMSVDPYGCRVVQRCLEHCSPSQTKPVIGQIH 380
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 379-412 2.09e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 47.04  E-value: 2.09e-07
                           10        20        30
                   ....*....|....*....|....*....|....
gi 71983283    379 IHKRFDEIANNQYGNYVVQHVIEHGSEEDRMVIV 412
Cdd:smart00025   2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 342-376 4.99e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.89  E-value: 4.99e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 71983283    342 ESSNTIYEMSVDPYGCRVVQRCLEHCSPSQTKPVI 376
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 462-491 1.22e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.12  E-value: 1.22e-06
                           10        20        30
                   ....*....|....*....|....*....|
gi 71983283    462 VVQMMKDQYANYVVQKMFDQVTSEQRRELI 491
Cdd:smart00025   6 LLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 462-491 2.10e-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: 44.21  E-value: 2.10e-06
                          10        20        30
                  ....*....|....*....|....*....|
gi 71983283   462 VVQMMKDQYANYVVQKMFDQVTSEQRRELI 491
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQIL 31
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 385-412 3.82e-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: 3.82e-06
                          10        20
                  ....*....|....*....|....*...
gi 71983283   385 EIANNQYGNYVVQHVIEHGSEEDRMVIV 412
Cdd:pfam00806   4 ELATDQYGCRVIQKCLEHATEEQREQIL 31
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 304-338 2.47e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 41.27  E-value: 2.47e-05
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 71983283    304 IRHVIHRCMKDQNGNHVVQKAIEKVSPQYVQFIVD 338
Cdd:smart00025   2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 418-448 2.92e-04

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA). Other proteins that contain Puf domains are also plausible RNA binding proteins. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 38.05  E-value: 2.92e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 71983283   418 NLFEFATHKYSSNVIEKCLEQGAVYHKSMIV 448
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQIL 31
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 231-266 3.76e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 37.80  E-value: 3.76e-04
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 71983283    231 EVVSNADELVDDIFGNYVVQKFFEYGEERHWARLVD 266
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 308-341 3.89e-04

Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA). Other proteins that contain Puf domains are also plausible RNA binding proteins. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure.


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 38.05  E-value: 3.89e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 71983283   308 IHRCMKDQNGNHVVQKAIEKVSPQYVQFIVDTLL 341
Cdd:pfam00806   2 VVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 267-301 3.95e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 37.80  E-value: 3.95e-04
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 71983283    267 AIIDRVPEYAFQMYACRVLQKALEKINEPLQIKIL 301
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 415-448 4.45e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 37.80  E-value: 4.45e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 71983283    415 VSNNLFEFATHKYSSNVIEKCLEQGAVYHKSMIV 448
Cdd:smart00025   2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 462-517 2.41e-03

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 40.89  E-value: 2.41e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 71983283 462 VVQMMKDQYANYVVQKMFDQVTSEQRRELILTVRPHIPVLRQFPHGKHILAKLEKY 517
Cdd:COG5099 479 LVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDI 534
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 242-269 3.45e-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: 35.35  E-value: 3.45e-03
                          10        20
                  ....*....|....*....|....*...
gi 71983283   242 DIFGNYVVQKFFEYGEERHWARLVDAII 269
Cdd:pfam00806   8 DQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 271-304 4.00e-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: 4.00e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 71983283   271 RVPEYAFQMYACRVLQKALEKINEPLQIKILSQI 304
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEI 34
 
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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