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Conserved domains on  [gi|24645266|ref|NP_731315|]
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pumilio, isoform D [Drosophila melanogaster]

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 ...
 1106-1424 1.85e-177

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: 532.55  E-value: 1.85e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1106 NLQLRDLA-NHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQV 1184
Cdd:cd07920    1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1185 KGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLS 1264
Cdd:cd07920   81 LGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1265 THPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNV 1344
Cdd:cd07920  161 THPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1345 VEKCVTHATRGERTGLIDEVCTFNDN--ALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAALRKYTYGKHINA 1422
Cdd:cd07920  241 VEKCLKHASKEERELIIDEILASGNEtsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILA 320


                 ..
gi 24645266 1423 KL 1424
Cdd:cd07920  321 KL 322
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 1106-1424 1.85e-177

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: 532.55  E-value: 1.85e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1106 NLQLRDLA-NHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQV 1184
Cdd:cd07920    1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1185 KGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLS 1264
Cdd:cd07920   81 LGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1265 THPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNV 1344
Cdd:cd07920  161 THPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1345 VEKCVTHATRGERTGLIDEVCTFNDN--ALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAALRKYTYGKHINA 1422
Cdd:cd07920  241 VEKCLKHASKEERELIIDEILASGNEtsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILA 320


                 ..
gi 24645266 1423 KL 1424
Cdd:cd07920  321 KL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 1100-1437 3.66e-93

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 320.16  E-value: 3.66e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1100 RNQRYPNLQLRDLANHIvefSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNT 1179
Cdd:COG5099  430 SSSVSATDILGPSIIVS---CKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSI 506

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1180 LGMQVKGHVLQLALQMYGCRVIQKALESISPEQQ-QEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKG 1258
Cdd:COG5099  507 MLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQiSLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINE 586

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1259 QVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLV-LSQ 1337
Cdd:COG5099  587 NLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVeLST 666

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1338 HKFASNVVEKCV---THATRGERtgLIDEVCTFN---DNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAAL 1411
Cdd:COG5099  667 HKFASNVVEKCIkyaSDSFKRSR--ILNELTNRGiekPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSL 744

                        330       340
                 ....*....|....*....|....*.
gi 24645266 1412 RKYTYGKHINAKLEKYYMKITNPITV 1437
Cdd:COG5099  745 KKSMYGQHILALLEKVGSSSQSSISN 770
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1259-1293 3.38e-14

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: 67.71  E-value: 3.38e-14
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 24645266   1259 QVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELH 1293
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1255-1290 1.38e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 51.67  E-value: 1.38e-08
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 24645266    1255 AFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILD 1290
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 1106-1424 1.85e-177

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: 532.55  E-value: 1.85e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1106 NLQLRDLA-NHIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTLGMQV 1184
Cdd:cd07920    1 SLTLQDIKaGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1185 KGHVLQLALQMYGCRVIQKALESISPEQQQEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKGQVYSLS 1264
Cdd:cd07920   81 LGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1265 THPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLVLSQHKFASNV 1344
Cdd:cd07920  161 THPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1345 VEKCVTHATRGERTGLIDEVCTFNDN--ALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAALRKYTYGKHINA 1422
Cdd:cd07920  241 VEKCLKHASKEERELIIDEILASGNEtsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILA 320


                 ..
gi 24645266 1423 KL 1424
Cdd:cd07920  321 KL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 1100-1437 3.66e-93

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 320.16  E-value: 3.66e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1100 RNQRYPNLQLRDLANHIvefSQDQHGSRFIQQKLERATAAEKQMVFSEILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNT 1179
Cdd:COG5099  430 SSSVSATDILGPSIIVS---CKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSI 506

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1180 LGMQVKGHVLQLALQMYGCRVIQKALESISPEQQ-QEIVHELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIINAFKG 1258
Cdd:COG5099  507 MLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQiSLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINE 586

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1259 QVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILINSVRGKVLV-LSQ 1337
Cdd:COG5099  587 NLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVeLST 666

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24645266 1338 HKFASNVVEKCV---THATRGERtgLIDEVCTFN---DNALHVMMKDQYANYVVQKMIDVSEPTQLKKLMTKIRPHMAAL 1411
Cdd:COG5099  667 HKFASNVVEKCIkyaSDSFKRSR--ILNELTNRGiekPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSL 744

                        330       340
                 ....*....|....*....|....*.
gi 24645266 1412 RKYTYGKHINAKLEKYYMKITNPITV 1437
Cdd:COG5099  745 KKSMYGQHILALLEKVGSSSQSSISN 770
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1259-1293 3.38e-14

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: 67.71  E-value: 3.38e-14
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 24645266   1259 QVYSLSTHPYGCRVIQRILEHCTAEQTTPILDELH 1293
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1115-1149 6.41e-11

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


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 58.47  E-value: 6.41e-11
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 24645266   1115 HIVEFSQDQHGSRFIQQKLERATAAEKQMVFSEIL 1149
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1187-1220 8.26e-11

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


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 58.08  E-value: 8.26e-11
                           10        20        30
                   ....*....|....*....|....*....|....
gi 24645266   1187 HVLQLALQMYGCRVIQKALESISPEQQQEIVHEL 1220
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1255-1290 1.38e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 51.67  E-value: 1.38e-08
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 24645266    1255 AFKGQVYSLSTHPYGCRVIQRILEHCTAEQTTPILD 1290
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1184-1218 4.60e-08

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 50.13  E-value: 4.60e-08
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 24645266    1184 VKGHVLQLALQMYGCRVIQKALESISPEQQQEIVH 1218
Cdd:smart00025    2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1219-1254 1.05e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 49.35  E-value: 1.05e-07
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 24645266    1219 ELDGHVLKCVKDQNGNHVVQKCIECVDPVALQFIIN 1254
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1291-1326 1.54e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 48.97  E-value: 1.54e-07
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 24645266    1291 ELHEHTEQLIQDQYGNYVIQHVLEHGKQEDKSILIN 1326
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1295-1326 6.97e-07

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


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 46.91  E-value: 6.97e-07
                           10        20        30
                   ....*....|....*....|....*....|..
gi 24645266   1295 HTEQLIQDQYGNYVIQHVLEHGKQEDKSILIN 1326
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILD 32
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1153-1180 1.21e-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: 46.14  E-value: 1.21e-06
                           10        20
                   ....*....|....*....|....*...
gi 24645266   1153 YSLMTDVFGNYVIQKFFEFGTPEQKNTL 1180
Cdd:pfam00806    3 VELATDQYGCRVIQKCLEHATEEQREQI 30
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1147-1180 1.43e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.89  E-value: 1.43e-06
                            10        20        30
                    ....*....|....*....|....*....|....
gi 24645266    1147 EILAAAYSLMTDVFGNYVIQKFFEFGTPEQKNTL 1180
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1370-1401 3.14e-06

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 45.12  E-value: 3.14e-06
                            10        20        30
                    ....*....|....*....|....*....|..
gi 24645266    1370 NALHVMMKDQYANYVVQKMIDVSEPTQLKKLM 1401
Cdd:smart00025    4 GHLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1331-1365 1.67e-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: 43.06  E-value: 1.67e-05
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 24645266   1331 KVLVLSQHKFASNVVEKCVTHATRGERTGLIDEVC 1365
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1114-1145 2.97e-05

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 42.42  E-value: 2.97e-05
                            10        20        30
                    ....*....|....*....|....*....|..
gi 24645266    1114 NHIVEFSQDQHGSRFIQQKLERATAAEKQMVF 1145
Cdd:smart00025    4 GHLLELSKDQYGNRVVQKLLEHASESQREQII 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1223-1254 3.45e-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: 42.29  E-value: 3.45e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 24645266   1223 HVLKCVKDQNGNHVVQKCIECVDPVALQFIIN 1254
Cdd:pfam00806    1 HVVELATDQYGCRVIQKCLEHATEEQREQILD 32
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 1375-1404 1.42e-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: 40.36  E-value: 1.42e-04
                           10        20        30
                   ....*....|....*....|....*....|
gi 24645266   1375 MMKDQYANYVVQKMIDVSEPTQLKKLMTKI 1404
Cdd:pfam00806    5 LATDQYGCRVIQKCLEHATEEQREQILDEI 34
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 1327-1362 3.02e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 39.34  E-value: 3.02e-04
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 24645266    1327 SVRGKVLVLSQHKFASNVVEKCVTHATRGERTGLID 1362
Cdd:smart00025    1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
 
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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