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Conserved domains on  [gi|398364467|ref|NP_011393|]
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mRNA-binding protein NAB2 [Saccharomyces cerevisiae S288C]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nab2 pfam11517
Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); Nab2 is a yeast heterogeneous nuclear ...
 1-101 1.58e-61

Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1.The N-terminal domain of Nab2 shows a structure of a helical fold. The N terminal domain of Nab2 is thought to mediate protein protein interactions that facilitate the nuclear export of mRNA. An essential hydrophobic Phe73 patch on the N terminal domain is thought to be a important component of the interface between Nab2 and Mlp1.


:

Pssm-ID: 402904  Cd Length: 101  Bit Score: 196.90  E-value: 1.58e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364467    1 MSQEQYTENLKVIVAEKLAGIPNFNEDIKYVAEYIVLLIVNGGTVESVVDELASLFDSVSRDTLANVVQTAFFALEALQQ 80
Cdd:pfam11517   1 MSQEQISENLKVIVAEKLKTLPNFNEDVNYVAEYIVLLMSNGGTVESVVQELSTLFDTVSTEALTDVVQTAFFALEALQQ 80

                          90       100
                  ....*....|....*....|.
gi 398364467   81 GESAENIVSKIRMMNAQSLGQ 101
Cdd:pfam11517  81 GETVETIVSKIRGMSAAPSQQ 101
Nab2p_Zf1 super family cl39611
Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1; This domain is found in ...
 252-278 3.64e-08

Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1; This domain is found in nuclear polyadenylated RNA-binding 2 protein (Nab2p) present in Saccharomyces cerevisiae. Nab2p is a major family of Poly A-binding proteins whose interactions are thought to be crucial for the control of poly(A) tail length. This domain is the first of seven CCCH zinc fingers which are responsible for polyadenosine RNA binding. When combined with the next three zinc fingers (Zf1-4), these four zinc fingers together may bind RNA in the 3' to 5' direction.


The actual alignment was detected with superfamily member pfam18260:

Pssm-ID: 436370  Cd Length: 26  Bit Score: 49.08  E-value: 3.64e-08
                          10        20
                  ....*....|....*....|....*..
gi 398364467  252 NFTPtKKEGRCRLFPHCPLGRSCPHAH 278
Cdd:pfam18260   1 NFVP-KKQGRCKLFPRCPLGKNCPHAH 26
 
Name Accession Description Interval E-value
Nab2 pfam11517
Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); Nab2 is a yeast heterogeneous nuclear ...
 1-101 1.58e-61

Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1.The N-terminal domain of Nab2 shows a structure of a helical fold. The N terminal domain of Nab2 is thought to mediate protein protein interactions that facilitate the nuclear export of mRNA. An essential hydrophobic Phe73 patch on the N terminal domain is thought to be a important component of the interface between Nab2 and Mlp1.


Pssm-ID: 402904  Cd Length: 101  Bit Score: 196.90  E-value: 1.58e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364467    1 MSQEQYTENLKVIVAEKLAGIPNFNEDIKYVAEYIVLLIVNGGTVESVVDELASLFDSVSRDTLANVVQTAFFALEALQQ 80
Cdd:pfam11517   1 MSQEQISENLKVIVAEKLKTLPNFNEDVNYVAEYIVLLMSNGGTVESVVQELSTLFDTVSTEALTDVVQTAFFALEALQQ 80

                          90       100
                  ....*....|....*....|.
gi 398364467   81 GESAENIVSKIRMMNAQSLGQ 101
Cdd:pfam11517  81 GETVETIVSKIRGMSAAPSQQ 101
Nab2p_Zf1 pfam18260
Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1; This domain is found in ...
 252-278 3.64e-08

Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1; This domain is found in nuclear polyadenylated RNA-binding 2 protein (Nab2p) present in Saccharomyces cerevisiae. Nab2p is a major family of Poly A-binding proteins whose interactions are thought to be crucial for the control of poly(A) tail length. This domain is the first of seven CCCH zinc fingers which are responsible for polyadenosine RNA binding. When combined with the next three zinc fingers (Zf1-4), these four zinc fingers together may bind RNA in the 3' to 5' direction.


Pssm-ID: 436370  Cd Length: 26  Bit Score: 49.08  E-value: 3.64e-08
                          10        20
                  ....*....|....*....|....*..
gi 398364467  252 NFTPtKKEGRCRLFPHCPLGRSCPHAH 278
Cdd:pfam18260   1 NFVP-KKQGRCKLFPRCPLGKNCPHAH 26
 
Name Accession Description Interval E-value
Nab2 pfam11517
Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); Nab2 is a yeast heterogeneous nuclear ...
 1-101 1.58e-61

Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1.The N-terminal domain of Nab2 shows a structure of a helical fold. The N terminal domain of Nab2 is thought to mediate protein protein interactions that facilitate the nuclear export of mRNA. An essential hydrophobic Phe73 patch on the N terminal domain is thought to be a important component of the interface between Nab2 and Mlp1.


Pssm-ID: 402904  Cd Length: 101  Bit Score: 196.90  E-value: 1.58e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364467    1 MSQEQYTENLKVIVAEKLAGIPNFNEDIKYVAEYIVLLIVNGGTVESVVDELASLFDSVSRDTLANVVQTAFFALEALQQ 80
Cdd:pfam11517   1 MSQEQISENLKVIVAEKLKTLPNFNEDVNYVAEYIVLLMSNGGTVESVVQELSTLFDTVSTEALTDVVQTAFFALEALQQ 80

                          90       100
                  ....*....|....*....|.
gi 398364467   81 GESAENIVSKIRMMNAQSLGQ 101
Cdd:pfam11517  81 GETVETIVSKIRGMSAAPSQQ 101
Nab2p_Zf1 pfam18260
Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1; This domain is found in ...
 252-278 3.64e-08

Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1; This domain is found in nuclear polyadenylated RNA-binding 2 protein (Nab2p) present in Saccharomyces cerevisiae. Nab2p is a major family of Poly A-binding proteins whose interactions are thought to be crucial for the control of poly(A) tail length. This domain is the first of seven CCCH zinc fingers which are responsible for polyadenosine RNA binding. When combined with the next three zinc fingers (Zf1-4), these four zinc fingers together may bind RNA in the 3' to 5' direction.


Pssm-ID: 436370  Cd Length: 26  Bit Score: 49.08  E-value: 3.64e-08
                          10        20
                  ....*....|....*....|....*..
gi 398364467  252 NFTPtKKEGRCRLFPHCPLGRSCPHAH 278
Cdd:pfam18260   1 NFVP-KKQGRCKLFPRCPLGKNCPHAH 26
 
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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