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Conserved domains on  [gi|15230086|ref|NP_189070|]
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pumilio 25 [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 ...
 23-128 2.33e-08

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: 51.05  E-value: 2.33e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230086  23 EIGNKN--LLLLIHHAGSLL---LSMFGSFSnypVQKFLDMLDERCLTLIASEFDSYFENLVKDRVGNYVVQRLI----- 92
Cdd:cd07920  66 EHGTEEqrLQLLEKILGHVVrlsLDMYGCRV---IQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIekfpp 142

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 15230086  93 --WGFkrtgidlphsLTSVLVTRSIHLCKHRYGYQVIE 128
Cdd:cd07920 143 edLQF----------IIDAFKGNCVALSTHPYGCRVIQ 170
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 23-128 2.33e-08

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: 51.05  E-value: 2.33e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230086  23 EIGNKN--LLLLIHHAGSLL---LSMFGSFSnypVQKFLDMLDERCLTLIASEFDSYFENLVKDRVGNYVVQRLI----- 92
Cdd:cd07920  66 EHGTEEqrLQLLEKILGHVVrlsLDMYGCRV---IQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIekfpp 142

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 15230086  93 --WGFkrtgidlphsLTSVLVTRSIHLCKHRYGYQVIE 128
Cdd:cd07920 143 edLQF----------IIDAFKGNCVALSTHPYGCRVIQ 170
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 8-134 3.54e-05

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 42.04  E-value: 3.54e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230086   8 FLIQvgaTFVELSRNEIGNKNLLLLIHHAGSLLLSMFGSFSnypVQKFLDM-LDERCLTLIASEFDSYFENLVKDRVGNY 86
Cdd:COG5099 490 YLIQ---KLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRV---LQKAIDIvSTDIQISLLVEELRPYCLQLIKDQNGNH 563

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 15230086  87 VVQRLIWGFKrtgIDLPHSLTSVLVTRSIHLCKHRYGYQVIEA-FDRST 134
Cdd:COG5099 564 VIQKCIEKFN---KEKNQFIFDSINENLYDLSTHRYGSRVVQRcLENCN 609
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 23-128 2.33e-08

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: 51.05  E-value: 2.33e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230086  23 EIGNKN--LLLLIHHAGSLL---LSMFGSFSnypVQKFLDMLDERCLTLIASEFDSYFENLVKDRVGNYVVQRLI----- 92
Cdd:cd07920  66 EHGTEEqrLQLLEKILGHVVrlsLDMYGCRV---IQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIekfpp 142

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 15230086  93 --WGFkrtgidlphsLTSVLVTRSIHLCKHRYGYQVIE 128
Cdd:cd07920 143 edLQF----------IIDAFKGNCVALSTHPYGCRVIQ 170
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 8-134 3.54e-05

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


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 42.04  E-value: 3.54e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230086   8 FLIQvgaTFVELSRNEIGNKNLLLLIHHAGSLLLSMFGSFSnypVQKFLDM-LDERCLTLIASEFDSYFENLVKDRVGNY 86
Cdd:COG5099 490 YLIQ---KLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRV---LQKAIDIvSTDIQISLLVEELRPYCLQLIKDQNGNH 563

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 15230086  87 VVQRLIWGFKrtgIDLPHSLTSVLVTRSIHLCKHRYGYQVIEA-FDRST 134
Cdd:COG5099 564 VIQKCIEKFN---KEKNQFIFDSINENLYDLSTHRYGSRVVQRcLENCN 609
 
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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