NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|169646352|ref|NP_080679|]
View 

nucleolar protein 9 [Mus musculus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 512-600 5.62e-04

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: 42.58  E-value: 5.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169646352 512 PQLLTLAQSPAGSHVFDAILSSpsVTHKQRRRVLKTLKGQYVALACSRHGSRVLDAIWSGAALGARKEIAAELGEKNQEL 591
Cdd:cd07920  118 GHVVELVKDQNGNHVIQKCIEK--FPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALEL 195


                 ....*....
gi 169646352 592 IQDPFGHHV 600
Cdd:cd07920  196 VQDQFGNYV 204
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 512-600 5.62e-04

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: 42.58  E-value: 5.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169646352 512 PQLLTLAQSPAGSHVFDAILSSpsVTHKQRRRVLKTLKGQYVALACSRHGSRVLDAIWSGAALGARKEIAAELGEKNQEL 591
Cdd:cd07920  118 GHVVELVKDQNGNHVIQKCIEK--FPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALEL 195


                 ....*....
gi 169646352 592 IQDPFGHHV 600
Cdd:cd07920  196 VQDQFGNYV 204
 
Name Accession Description Interval E-value
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 512-600 5.62e-04

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: 42.58  E-value: 5.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169646352 512 PQLLTLAQSPAGSHVFDAILSSpsVTHKQRRRVLKTLKGQYVALACSRHGSRVLDAIWSGAALGARKEIAAELGEKNQEL 591
Cdd:cd07920  118 GHVVELVKDQNGNHVIQKCIEK--FPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHALEL 195


                 ....*....
gi 169646352 592 IQDPFGHHV 600
Cdd:cd07920  196 VQDQFGNYV 204
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 341-600 1.29e-03

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: 41.42  E-value: 1.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169646352 341 AERLQRLYKdHFQGQLCSLAEHPIANFPLQRLLDAItSPELLSLVFEELSPalemvlaqghpgVVVALVeaCRRVGTHqa 420
Cdd:cd07920   70 EEQRLQLLE-KILGHVVRLSLDMYGCRVIQKLLESI-SEEQISLLVKELRG------------HVVELV--KDQNGNH-- 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169646352 421 qVLQLLFEafhCAEPPSRQaacvPLFAALlayevyyelmeeegavpAEHQVEMAT--------ARALREVTvlgslllqh 492
Cdd:cd07920  132 -VIQKCIE---KFPPEDLQ----FIIDAF-----------------KGNCVALSThpygcrviQRCLEHCS--------- 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169646352 493 llyfsnPGLVLRSLSALTgPQLLTLAQSPAGSHVFDAILS--SPSVTHkqrrRVLKTLKGQYVALACSRHGSRVLD-AIW 569
Cdd:cd07920  178 ------EEQREPLLEEIL-EHALELVQDQFGNYVVQHVLElgDPDDTS----RIIEKLLGNIVQLSCHKFASNVVEkCLK 246

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 169646352 570 SGAALGARKEIAAELGEKNQE-----LIQDPFGHHV 600
Cdd:cd07920  247 HASKEERELIIDEILASGNETsaldtLMKDQYGNYV 282
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 512-600 9.70e-03

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: 38.73  E-value: 9.70e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169646352 512 PQLLTLAQSPAGSHVFDAILssPSVTHKQRRRVLKTLKGQYVALACSRHGSRVLDAIWSGAALGARKEIAAELGEKNQEL 591
Cdd:cd07920   46 PHVVELMVDPFGNYVIQKLF--EHGTEEQRLQLLEKILGHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVEL 123


                 ....*....
gi 169646352 592 IQDPFGHHV 600
Cdd:cd07920  124 VKDQNGNHV 132
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH