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Conserved domains on  [gi|15219041|ref|NP_173581|]
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pumilio 20 [Arabidopsis thaliana]

Protein Classification

Pumilio-family RNA binding repeat-containing protein( domain architecture ID 1001700)

Pumilio-family RNA binding repeat-containing protein harbors PUF repeats, which mediate sequence specific RNA binding

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pumilio super family cl46378
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 92-304 4.81e-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.


The actual alignment was detected with superfamily member cd07920:

Pssm-ID: 480718 [Multi-domain]  Cd Length: 322  Bit Score: 107.68  E-value: 4.81e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041  92 DYFLMIARNMNGSKRIQKLLGKTDDVD-ALFAAAILRRFLHIITDKYASYVVRRGMTVFDKKKKK----AMYEHILHYAS 166
Cdd:cd07920  82 GHVVRLSLDMYGCRVIQKLLESISEEQiSLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQfiidAFKGNCVALST 161

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 167 H------IAR-----------------DKHALVLSNDAYGNFVIQRVLKLNDLRSKNNIVVSLRGHFVDLSFQKYGSYVV 223
Cdd:cd07920 162 HpygcrvIQRclehcseeqreplleeiLEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVV 241

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 224 DVLLE--TKESMVVVVEELMECEGDM--LMRLARNEYGNFLVCKALRVT---QKEMvrtdlfwgLVHKLKPFHNLLRWSR 296
Cdd:cd07920 242 EKCLKhaSKEERELIIDEILASGNETsaLDTLMKDQYGNYVIQTALDVAkeeQREL--------LVEAIRPHLPSLRKSP 313


                ....*....
gi 15219041 297 -GKNIASIL 304
Cdd:cd07920 314 yGKHILAKL 322
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 92-304 4.81e-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: 107.68  E-value: 4.81e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041  92 DYFLMIARNMNGSKRIQKLLGKTDDVD-ALFAAAILRRFLHIITDKYASYVVRRGMTVFDKKKKK----AMYEHILHYAS 166
Cdd:cd07920  82 GHVVRLSLDMYGCRVIQKLLESISEEQiSLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQfiidAFKGNCVALST 161

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 167 H------IAR-----------------DKHALVLSNDAYGNFVIQRVLKLNDLRSKNNIVVSLRGHFVDLSFQKYGSYVV 223
Cdd:cd07920 162 HpygcrvIQRclehcseeqreplleeiLEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVV 241

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 224 DVLLE--TKESMVVVVEELMECEGDM--LMRLARNEYGNFLVCKALRVT---QKEMvrtdlfwgLVHKLKPFHNLLRWSR 296
Cdd:cd07920 242 EKCLKhaSKEERELIIDEILASGNETsaLDTLMKDQYGNYVIQTALDVAkeeQREL--------LVEAIRPHLPSLRKSP 313


                ....*....
gi 15219041 297 -GKNIASIL 304
Cdd:cd07920 314 yGKHILAKL 322
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 92-306 2.33e-10

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 61.30  E-value: 2.33e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041  92 DYFLMIARNMNGSKRIQKLLGKTDDVDALFAA-AILRRFLHIITDKYASYVVRRGMTVFDKKKKKAMYEHILhyashiar 170
Cdd:COG5099 550 PYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFdSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEII-------- 621

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 171 dKHALVLSNDAYGNFVIQRVLKLNDLRSKNNIVVS-LRGHFVDLSFQKYGSYVVDVLLETK---ESMVVVVEELMECEGD 246
Cdd:COG5099 622 -SNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKlLSKRVVELSTHKFASNVVEKCIKYAsdsFKRSRILNELTNRGIE 700

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15219041 247 ---MLMRLARNEYGNFLVCKALRVTQKEmvrTDLFwgLVHKLKPFHNLLRWSR-GKNIASILNS 306
Cdd:COG5099 701 kpgFLMLILDDQYANYVIQYLLDVSPEI---QRSL--LARAIKKVIPSLKKSMyGQHILALLEK 759
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 172-203 1.06e-03

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 35.87  E-value: 1.06e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 15219041    172 KHALVLSNDAYGNFVIQRVLKLNDLRSKNNIV 203
Cdd:smart00025   4 GHLLELSKDQYGNRVVQKLLEHASESQREQII 35
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 92-304 4.81e-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: 107.68  E-value: 4.81e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041  92 DYFLMIARNMNGSKRIQKLLGKTDDVD-ALFAAAILRRFLHIITDKYASYVVRRGMTVFDKKKKK----AMYEHILHYAS 166
Cdd:cd07920  82 GHVVRLSLDMYGCRVIQKLLESISEEQiSLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQfiidAFKGNCVALST 161

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 167 H------IAR-----------------DKHALVLSNDAYGNFVIQRVLKLNDLRSKNNIVVSLRGHFVDLSFQKYGSYVV 223
Cdd:cd07920 162 HpygcrvIQRclehcseeqreplleeiLEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVV 241

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 224 DVLLE--TKESMVVVVEELMECEGDM--LMRLARNEYGNFLVCKALRVT---QKEMvrtdlfwgLVHKLKPFHNLLRWSR 296
Cdd:cd07920 242 EKCLKhaSKEERELIIDEILASGNETsaLDTLMKDQYGNYVIQTALDVAkeeQREL--------LVEAIRPHLPSLRKSP 313


                ....*....
gi 15219041 297 -GKNIASIL 304
Cdd:cd07920 314 yGKHILAKL 322
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 173-270 3.84e-12

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: 65.69  E-value: 3.84e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 173 HALVLSNDAYGNFVIQRVLKLNDLRSKNNIVVSLRGHFVDLSFQKYGSYVVDVLLET--KESMVVVVEELMECegdmLMR 250
Cdd:cd07920  47 HVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVVRLSLDMYGCRVIQKLLESisEEQISLLVKELRGH----VVE 122

                        90       100
                ....*....|....*....|
gi 15219041 251 LARNEYGNflvckalRVTQK 270
Cdd:cd07920 123 LVKDQNGN-------HVIQK 135
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 95-292 7.54e-12

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: 64.92  E-value: 7.54e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041  95 LMIARNMNGSKRIQKLL--GKTDDVDALFAAaILRRFLHIITDKYASYVVRRGMTVFDKKKKKAMYEHILhyashiardK 172
Cdd:cd07920  13 VEFAKDQHGSRFLQQKLeeATPEEKELIFDE-ILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKIL---------G 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 173 HALVLSNDAYGNFVIQRVLKLNDLRSKNNIVVSLRGHFVDLSFQKYGSYVVDVLLET--KESMVVVVEELMEcegdMLMR 250
Cdd:cd07920  83 HVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKfpPEDLQFIIDAFKG----NCVA 158

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 15219041 251 LARNEYGNFLVCKALRVTQKEMVRTdlfwgLVHKLKPFHNLL 292
Cdd:cd07920 159 LSTHPYGCRVIQRCLEHCSEEQREP-----LLEEILEHALEL 195
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 92-306 2.33e-10

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 61.30  E-value: 2.33e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041  92 DYFLMIARNMNGSKRIQKLLGKTDDVDALFAA-AILRRFLHIITDKYASYVVRRGMTVFDKKKKKAMYEHILhyashiar 170
Cdd:COG5099 550 PYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFdSINENLYDLSTHRYGSRVVQRCLENCNSEDKENLVEEII-------- 621

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 171 dKHALVLSNDAYGNFVIQRVLKLNDLRSKNNIVVS-LRGHFVDLSFQKYGSYVVDVLLETK---ESMVVVVEELMECEGD 246
Cdd:COG5099 622 -SNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKlLSKRVVELSTHKFASNVVEKCIKYAsdsFKRSRILNELTNRGIE 700

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15219041 247 ---MLMRLARNEYGNFLVCKALRVTQKEmvrTDLFwgLVHKLKPFHNLLRWSR-GKNIASILNS 306
Cdd:COG5099 701 kpgFLMLILDDQYANYVIQYLLDVSPEI---QRSL--LARAIKKVIPSLKKSMyGQHILALLEK 759
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 119-265 8.64e-09

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 56.68  E-value: 8.64e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 119 ALFAAAILRRFL-HIITDKYASYVVRRGMTVFDKKKKKAMYEHILHYAshiardkhaLVLSNDAYGNFVIQRVLKLNDLR 197
Cdd:COG5099 432 SVSATDILGPSIiVSCKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQL---------VELSSDYFGNYLIQKLFEYGSEI 502

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15219041 198 SKNNIVVSLRGHFVDLSFQKYGSYVVDVLLE---TKESMVVVVEELMECegdmLMRLARNEYGNFLVCKAL 265
Cdd:COG5099 503 QKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDivsTDIQISLLVEELRPY----CLQLIKDQNGNHVIQKCI 569
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 173-270 1.90e-06

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: 48.74  E-value: 1.90e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15219041 173 HALVLSNDAYGNFVIQRVLKLNDLRSKNNIVVSLRGHFVDLSFQKYGSYVVDVLLE--TKESMVVVVEELMeceGDMLmR 250
Cdd:cd07920  11 HIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEhgTEEQRLQLLEKIL---GHVV-R 86

                        90       100
                ....*....|....*....|
gi 15219041 251 LARNEYGNflvckalRVTQK 270
Cdd:cd07920  87 LSLDMYGC-------RVIQK 99
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 172-203 1.06e-03

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


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 35.87  E-value: 1.06e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 15219041    172 KHALVLSNDAYGNFVIQRVLKLNDLRSKNNIV 203
Cdd:smart00025   4 GHLLELSKDQYGNRVVQKLLEHASESQREQII 35
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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