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Conserved domains on  [gi|1063741624|ref|NP_001332599|]
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pumilio 12 [Arabidopsis thaliana]

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 ...
 264-592 4.00e-128

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: 378.86  E-value: 4.00e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 264 NLSLQPQKYNSIAEargkiyyLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQKLLEVCNEDQR 343
Cdd:cd07920     1 SLTLQDIKAGHIVE-------FAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 344 MQIVHSITrkpGLLIKISCDMHGTRAVQKIVETAkREEEISIIISALKHGIVHLIKNVNGNHVVQRCLQYLLPYCGKFLF 423
Cdd:cd07920    74 LQLLEKIL---GHVVRLSLDMYGCRVIQKLLESI-SEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFII 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 424 EAAITHCVELATDRHGCCVLQKCLGYSEGEQKQHLVSEIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYT 503
Cdd:cd07920   150 DAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIV 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 504 ELSMQKCSSNVVEKCLKLADDKHRARIIRELINYG----RLDQVMLDPYGNYVIQAALKQSKGNVHALLVDAIKLNISSL 579
Cdd:cd07920   230 QLSCHKFASNVVEKCLKHASKEERELIIDEILASGnetsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSL 309

                         330
                  ....*....|...
gi 1063741624 580 RTNPYGKKVLSAL 592
Cdd:cd07920   310 RKSPYGKHILAKL 322
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 264-592 4.00e-128

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: 378.86  E-value: 4.00e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 264 NLSLQPQKYNSIAEargkiyyLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQKLLEVCNEDQR 343
Cdd:cd07920     1 SLTLQDIKAGHIVE-------FAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 344 MQIVHSITrkpGLLIKISCDMHGTRAVQKIVETAkREEEISIIISALKHGIVHLIKNVNGNHVVQRCLQYLLPYCGKFLF 423
Cdd:cd07920    74 LQLLEKIL---GHVVRLSLDMYGCRVIQKLLESI-SEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFII 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 424 EAAITHCVELATDRHGCCVLQKCLGYSEGEQKQHLVSEIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYT 503
Cdd:cd07920   150 DAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIV 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 504 ELSMQKCSSNVVEKCLKLADDKHRARIIRELINYG----RLDQVMLDPYGNYVIQAALKQSKGNVHALLVDAIKLNISSL 579
Cdd:cd07920   230 QLSCHKFASNVVEKCLKHASKEERELIIDEILASGnetsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSL 309

                         330
                  ....*....|...
gi 1063741624 580 RTNPYGKKVLSAL 592
Cdd:cd07920   310 RKSPYGKHILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 253-592 4.09e-72

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 246.58  E-value: 4.09e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 253 QLNEDLTMSLNNLSlqpqKYNSIAEARGKIYYLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQ 332
Cdd:COG5099   418 NLNSLLKEKLSNSS----SVSATDILGPSIIVSCKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQ 493

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 333 KLLEVCNEDQRMQIVHSItrKPGLLiKISCDMHGTRAVQKIVETAKREEEISIIISALKHGIVHLIKNVNGNHVVQRCLQ 412
Cdd:COG5099   494 KLFEYGSEIQKSIMLSKS--SKHLV-SLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIE 570

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 413 YLLPYCGKFLFEAAITHCVELATDRHGCCVLQKCLGYSEGEQKQHLVSEIASNALLLSQDPFGNYVLQYVFELQLQWATF 492
Cdd:COG5099   571 KFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKE 650

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 493 EILE-QLEGNYTELSMQKCSSNVVEKCLKLA-DDKHRARIIRELINY-----GRLDQVMLDPYGNYVIQAALKQSKGNVH 565
Cdd:COG5099   651 RIIIkLLSKRVVELSTHKFASNVVEKCIKYAsDSFKRSRILNELTNRgiekpGFLMLILDDQYANYVIQYLLDVSPEIQR 730

                         330       340
                  ....*....|....*....|....*..
gi 1063741624 566 ALLVDAIKLNISSLRTNPYGKKVLSAL 592
Cdd:COG5099   731 SLLARAIKKVIPSLKKSMYGQHILALL 757
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 429-463 1.18e-12

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


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 61.93  E-value: 1.18e-12
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063741624 429 HCVELATDRHGCCVLQKCLGYSEGEQKQHLVSEIA 463
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 313-348 1.34e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 47.81  E-value: 1.34e-07
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1063741624  313 EIIDYISELMMDPFGNYLVQKLLEVCNEDQRMQIVH 348
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 ...
 264-592 4.00e-128

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: 378.86  E-value: 4.00e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 264 NLSLQPQKYNSIAEargkiyyLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQKLLEVCNEDQR 343
Cdd:cd07920     1 SLTLQDIKAGHIVE-------FAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 344 MQIVHSITrkpGLLIKISCDMHGTRAVQKIVETAkREEEISIIISALKHGIVHLIKNVNGNHVVQRCLQYLLPYCGKFLF 423
Cdd:cd07920    74 LQLLEKIL---GHVVRLSLDMYGCRVIQKLLESI-SEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFII 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 424 EAAITHCVELATDRHGCCVLQKCLGYSEGEQKQHLVSEIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYT 503
Cdd:cd07920   150 DAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIV 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 504 ELSMQKCSSNVVEKCLKLADDKHRARIIRELINYG----RLDQVMLDPYGNYVIQAALKQSKGNVHALLVDAIKLNISSL 579
Cdd:cd07920   230 QLSCHKFASNVVEKCLKHASKEERELIIDEILASGnetsALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSL 309

                         330
                  ....*....|...
gi 1063741624 580 RTNPYGKKVLSAL 592
Cdd:cd07920   310 RKSPYGKHILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 253-592 4.09e-72

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 246.58  E-value: 4.09e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 253 QLNEDLTMSLNNLSlqpqKYNSIAEARGKIYYLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQ 332
Cdd:COG5099   418 NLNSLLKEKLSNSS----SVSATDILGPSIIVSCKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQ 493

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 333 KLLEVCNEDQRMQIVHSItrKPGLLiKISCDMHGTRAVQKIVETAKREEEISIIISALKHGIVHLIKNVNGNHVVQRCLQ 412
Cdd:COG5099   494 KLFEYGSEIQKSIMLSKS--SKHLV-SLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIE 570

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 413 YLLPYCGKFLFEAAITHCVELATDRHGCCVLQKCLGYSEGEQKQHLVSEIASNALLLSQDPFGNYVLQYVFELQLQWATF 492
Cdd:COG5099   571 KFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKE 650

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063741624 493 EILE-QLEGNYTELSMQKCSSNVVEKCLKLA-DDKHRARIIRELINY-----GRLDQVMLDPYGNYVIQAALKQSKGNVH 565
Cdd:COG5099   651 RIIIkLLSKRVVELSTHKFASNVVEKCIKYAsDSFKRSRILNELTNRgiekpGFLMLILDDQYANYVIQYLLDVSPEIQR 730

                         330       340
                  ....*....|....*....|....*..
gi 1063741624 566 ALLVDAIKLNISSLRTNPYGKKVLSAL 592
Cdd:COG5099   731 SLLARAIKKVIPSLKKSMYGQHILALL 757
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 429-463 1.18e-12

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


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 61.93  E-value: 1.18e-12
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063741624 429 HCVELATDRHGCCVLQKCLGYSEGEQKQHLVSEIA 463
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 281-315 2.08e-08

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: 49.99  E-value: 2.08e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063741624 281 KIYYLAKDQHGCRFLQRIFSEKDGNDIEMIFNEII 315
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 317-351 3.14e-08

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: 49.61  E-value: 3.14e-08
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063741624 317 YISELMMDPFGNYLVQKLLEVCNEDQRMQIVHSIT 351
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 313-348 1.34e-07

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 47.81  E-value: 1.34e-07
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1063741624  313 EIIDYISELMMDPFGNYLVQKLLEVCNEDQRMQIVH 348
Cdd:smart00025   1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
PUF pfam00806
Pumilio-family RNA binding repeat; Puf repeats (aka PUM-HD, Pumilio homology domain) are ...
 501-535 3.20e-05

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


Pssm-ID: 459944 [Multi-domain]  Cd Length: 35  Bit Score: 41.13  E-value: 3.20e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063741624 501 NYTELSMQKCSSNVVEKCLKLADDKHRARIIRELI 535
Cdd:pfam00806   1 HVVELATDQYGCRVIQKCLEHATEEQREQILDEIL 35
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 427-456 3.18e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 38.18  E-value: 3.18e-04
                           10        20        30
                   ....*....|....*....|....*....|
gi 1063741624  427 ITHCVELATDRHGCCVLQKCLGYSEGEQKQ 456
Cdd:smart00025   3 KGHLLELSKDQYGNRVVQKLLEHASESQRE 32
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 279-312 6.27e-04

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 37.41  E-value: 6.27e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1063741624  279 RGKIYYLAKDQHGCRFLQRIFSEKDGNDIEMIFN 312
Cdd:smart00025   3 KGHLLELSKDQYGNRVVQKLLEHASESQREQIID 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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