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Conserved domains on  [gi|1789593964|emb|CAA0264372|]
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unnamed protein product [Arabidopsis thaliana]

Protein Classification

pre-mRNA-splicing factor SPP2; KOW domain-containing RNA-binding protein( domain architecture ID 10576972)

pre-mRNA-splicing factor SPP2 is involved in pre-mRNA splicing; specifically in the final stages of spliceosome maturation| KOW domain-containing RNA-binding protein similar to the KOW motif in 60S ribosomal protein L27, which is a component of the large ribosomal subunit; the KOW domain is known as an RNA-binding motif that is shared among some families of ribosomal proteins

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
G-patch_2 pfam12656
G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ...
 143-202 7.89e-22

G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2.


:

Pssm-ID: 432700 [Multi-domain]  Cd Length: 61  Bit Score: 88.49  E-value: 7.89e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789593964 143 ADDPTLEDFESVPVDGFGAALMAGYGWKPGKGIGKNAKEDVEIKEYKKWTAKEGLGFDPD 202
Cdd:pfam12656   1 PDEASLEDYEKVPVEEFGAAMLRGMGWKPGQGIGKNKKGDVKPKEYKRRPGGLGLGAKPA 60
KOW_GPKOW_B cd13153
KOW motif of the "G-patch domain and KOW motifs-containing protein" (GPKOW) repeat B; GPKOW ...
 405-455 1.28e-14

KOW motif of the "G-patch domain and KOW motifs-containing protein" (GPKOW) repeat B; GPKOW contains one G-patch domain and two KOW motifs. GPKOW is a nuclear protein that regulated by catalytic (C) subunit of Protein Kinase A (PKA) and bind RNA in vivo. PKA may be involved in regulating multiple steps in post-transcriptional processing of pre-mRNAs. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. GPKOW is also known as the T54 protein or MOS2 homolog.


:

Pssm-ID: 240517  Cd Length: 51  Bit Score: 67.96  E-value: 1.28e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1789593964 405 GGPVLVLSGKHKGVYGNLVEKDLDKETGVVRDLDNHKMLDVRLDQVAEYMG 455
Cdd:cd13153     1 GAYVMVVRGKHRGQVGKLLERDKKKETAVVQLLDDFSVVTLSYDDICEYTG 51
 
Name Accession Description Interval E-value
G-patch_2 pfam12656
G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ...
 143-202 7.89e-22

G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2.


Pssm-ID: 432700 [Multi-domain]  Cd Length: 61  Bit Score: 88.49  E-value: 7.89e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789593964 143 ADDPTLEDFESVPVDGFGAALMAGYGWKPGKGIGKNAKEDVEIKEYKKWTAKEGLGFDPD 202
Cdd:pfam12656   1 PDEASLEDYEKVPVEEFGAAMLRGMGWKPGQGIGKNKKGDVKPKEYKRRPGGLGLGAKPA 60
KOW_GPKOW_B cd13153
KOW motif of the "G-patch domain and KOW motifs-containing protein" (GPKOW) repeat B; GPKOW ...
 405-455 1.28e-14

KOW motif of the "G-patch domain and KOW motifs-containing protein" (GPKOW) repeat B; GPKOW contains one G-patch domain and two KOW motifs. GPKOW is a nuclear protein that regulated by catalytic (C) subunit of Protein Kinase A (PKA) and bind RNA in vivo. PKA may be involved in regulating multiple steps in post-transcriptional processing of pre-mRNAs. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. GPKOW is also known as the T54 protein or MOS2 homolog.


Pssm-ID: 240517  Cd Length: 51  Bit Score: 67.96  E-value: 1.28e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1789593964 405 GGPVLVLSGKHKGVYGNLVEKDLDKETGVVRDLDNHKMLDVRLDQVAEYMG 455
Cdd:cd13153     1 GAYVMVVRGKHRGQVGKLLERDKKKETAVVQLLDDFSVVTLSYDDICEYTG 51
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 154-199 4.17e-06

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 43.69  E-value: 4.17e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1789593964  154 VPVDGFGAALMAGYGWKPGKGIGKNA---KEDVEIKEYKKwtaKEGLGF 199
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEqgiVEPISAEIKKD---RKGLGA 46
 
Name Accession Description Interval E-value
G-patch_2 pfam12656
G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ...
 143-202 7.89e-22

G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2.


Pssm-ID: 432700 [Multi-domain]  Cd Length: 61  Bit Score: 88.49  E-value: 7.89e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789593964 143 ADDPTLEDFESVPVDGFGAALMAGYGWKPGKGIGKNAKEDVEIKEYKKWTAKEGLGFDPD 202
Cdd:pfam12656   1 PDEASLEDYEKVPVEEFGAAMLRGMGWKPGQGIGKNKKGDVKPKEYKRRPGGLGLGAKPA 60
KOW_GPKOW_B cd13153
KOW motif of the "G-patch domain and KOW motifs-containing protein" (GPKOW) repeat B; GPKOW ...
 405-455 1.28e-14

KOW motif of the "G-patch domain and KOW motifs-containing protein" (GPKOW) repeat B; GPKOW contains one G-patch domain and two KOW motifs. GPKOW is a nuclear protein that regulated by catalytic (C) subunit of Protein Kinase A (PKA) and bind RNA in vivo. PKA may be involved in regulating multiple steps in post-transcriptional processing of pre-mRNAs. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. GPKOW is also known as the T54 protein or MOS2 homolog.


Pssm-ID: 240517  Cd Length: 51  Bit Score: 67.96  E-value: 1.28e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1789593964 405 GGPVLVLSGKHKGVYGNLVEKDLDKETGVVRDLDNHKMLDVRLDQVAEYMG 455
Cdd:cd13153     1 GAYVMVVRGKHRGQVGKLLERDKKKETAVVQLLDDFSVVTLSYDDICEYTG 51
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 154-199 4.17e-06

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 43.69  E-value: 4.17e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1789593964  154 VPVDGFGAALMAGYGWKPGKGIGKNA---KEDVEIKEYKKwtaKEGLGF 199
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEqgiVEPISAEIKKD---RKGLGA 46
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 157-198 8.84e-04

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 37.10  E-value: 8.84e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1789593964 157 DGFGAALMAGYGWKPGKGIGKNA---KEDVEIKEYKKwtaKEGLG 198
Cdd:pfam01585   2 SNIGFKLLQKMGWKEGQGLGKNEqgiAEPIEAKIKKD---RRGLG 43
 
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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