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Conserved domains on  [gi|47058996|ref|NP_997680|]
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NHP2-like protein 1 [Rattus norvegicus]

Protein Classification

SNU13 family protein( domain architecture ID 15340004)

SNU13 family protein similar to yeast Snu13p which is a bifunctional yeast protein involved in both messenger RNA splicing as well as ribosomal RNA maturation

Gene Ontology:  GO:0003723|GO:0030490

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SNU13 cd21104
U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, ...
 7-128 2.26e-90

U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, also known as NHP2-like protein 1 or U4/U6.U5 tri-snRNP 15.5 kDa protein, is a component of the spliceosome B complex, involved in pre-mRNA splicing. It binds to the 5'-stem-loop of U4 snRNA.


:

Pssm-ID: 411046  Cd Length: 122  Bit Score: 257.26  E-value: 2.26e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47058996   7 NPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSK 86
Cdd:cd21104   1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 47058996  87 QALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
Cdd:cd21104  81 QALGRACGVSRPVIACSVTTNEGSQLKSQIQSLKDAIEKLLI 122
 
Name Accession Description Interval E-value
SNU13 cd21104
U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, ...
 7-128 2.26e-90

U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, also known as NHP2-like protein 1 or U4/U6.U5 tri-snRNP 15.5 kDa protein, is a component of the spliceosome B complex, involved in pre-mRNA splicing. It binds to the 5'-stem-loop of U4 snRNA.


Pssm-ID: 411046  Cd Length: 122  Bit Score: 257.26  E-value: 2.26e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47058996   7 NPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSK 86
Cdd:cd21104   1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 47058996  87 QALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
Cdd:cd21104  81 QALGRACGVSRPVIACSVTTNEGSQLKSQIQSLKDAIEKLLI 122
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 18-110 3.45e-29

ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version of the large ribosomal complex protein eL8, previously designated L8 in yeast and L7Ae in the archaea. The family is a narrower version of the pfam01248 model which also recognizes the L30 protein.


Pssm-ID: 188367 [Multi-domain]  Cd Length: 117  Bit Score: 102.14  E-value: 3.45e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47058996    18 LTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSR 97
Cdd:TIGR03677  10 LADKALEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVKSKEDLGAAAGLEV 89

                          90
                  ....*....|...
gi 47058996    98 PVIACSVtIKEGS 110
Cdd:TIGR03677  90 GAASAAI-VDAGK 101
Ribosomal_L7Ae pfam01248
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from ...
 20-111 2.20e-27

Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118.


Pssm-ID: 426153 [Multi-domain]  Cd Length: 95  Bit Score: 96.90  E-value: 2.20e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47058996    20 KKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPV 99
Cdd:pfam01248   1 DAIYEVLKKALKTGKLVLGLKEVTKALERGEAKLVIIAEDCDPEEKVKLIPALCKEKNVPYVKVPSKKELGEACGKKRPV 80

                          90
                  ....*....|..
gi 47058996   100 IACSVTIKEGSQ 111
Cdd:pfam01248  81 SALAIKDEGDSK 92
Rpl7Ae COG1358
Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure ...
 20-101 2.58e-15

Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure and biogenesis]; Ribosomal protein L7Ae or related RNA K-turn-binding protein is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 440969 [Multi-domain]  Cd Length: 98  Bit Score: 65.95  E-value: 2.58e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47058996  20 KKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPlEIILHLPLLCEDKNVPYVFVRSKQALGRACG-VSRP 98
Cdd:COG1358   1 DKILNLLGLARRAGKLVSGEEQVLKAIRKGKAKLVIIAEDASE-NTKKKLLDLCEEYGVPVVEVGTKEELGKAIGkVGRA 79


                ...
gi 47058996  99 VIA 101
Cdd:COG1358  80 VVA 82
PTZ00222 PTZ00222
60S ribosomal protein L7a; Provisional
 38-94 1.20e-08

60S ribosomal protein L7a; Provisional


Pssm-ID: 140249  Cd Length: 263  Bit Score: 51.24  E-value: 1.20e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 47058996   38 GANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACG 94
Cdd:PTZ00222 136 GLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAIVKDMARLGDAIG 192
 
Name Accession Description Interval E-value
SNU13 cd21104
U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, ...
 7-128 2.26e-90

U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, also known as NHP2-like protein 1 or U4/U6.U5 tri-snRNP 15.5 kDa protein, is a component of the spliceosome B complex, involved in pre-mRNA splicing. It binds to the 5'-stem-loop of U4 snRNA.


Pssm-ID: 411046  Cd Length: 122  Bit Score: 257.26  E-value: 2.26e-90
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47058996   7 NPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSK 86
Cdd:cd21104   1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 47058996  87 QALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
Cdd:cd21104  81 QALGRACGVSRPVIACSVTTNEGSQLKSQIQSLKDAIEKLLI 122
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 18-110 3.45e-29

ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version of the large ribosomal complex protein eL8, previously designated L8 in yeast and L7Ae in the archaea. The family is a narrower version of the pfam01248 model which also recognizes the L30 protein.


Pssm-ID: 188367 [Multi-domain]  Cd Length: 117  Bit Score: 102.14  E-value: 3.45e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47058996    18 LTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSR 97
Cdd:TIGR03677  10 LADKALEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVKSKEDLGAAAGLEV 89

                          90
                  ....*....|...
gi 47058996    98 PVIACSVtIKEGS 110
Cdd:TIGR03677  90 GAASAAI-VDAGK 101
Ribosomal_L7Ae pfam01248
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from ...
 20-111 2.20e-27

Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118.


Pssm-ID: 426153 [Multi-domain]  Cd Length: 95  Bit Score: 96.90  E-value: 2.20e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47058996    20 KKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPV 99
Cdd:pfam01248   1 DAIYEVLKKALKTGKLVLGLKEVTKALERGEAKLVIIAEDCDPEEKVKLIPALCKEKNVPYVKVPSKKELGEACGKKRPV 80

                          90
                  ....*....|..
gi 47058996   100 IACSVTIKEGSQ 111
Cdd:pfam01248  81 SALAIKDEGDSK 92
Rpl7Ae COG1358
Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure ...
 20-101 2.58e-15

Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure and biogenesis]; Ribosomal protein L7Ae or related RNA K-turn-binding protein is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 440969 [Multi-domain]  Cd Length: 98  Bit Score: 65.95  E-value: 2.58e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47058996  20 KKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPlEIILHLPLLCEDKNVPYVFVRSKQALGRACG-VSRP 98
Cdd:COG1358   1 DKILNLLGLARRAGKLVSGEEQVLKAIRKGKAKLVIIAEDASE-NTKKKLLDLCEEYGVPVVEVGTKEELGKAIGkVGRA 79


                ...
gi 47058996  99 VIA 101
Cdd:COG1358  80 VVA 82
PTZ00222 PTZ00222
60S ribosomal protein L7a; Provisional
 38-94 1.20e-08

60S ribosomal protein L7a; Provisional


Pssm-ID: 140249  Cd Length: 263  Bit Score: 51.24  E-value: 1.20e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 47058996   38 GANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACG 94
Cdd:PTZ00222 136 GLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAIVKDMARLGDAIG 192
PTZ00365 PTZ00365
60S ribosomal protein L7Ae-like; Provisional
 35-108 4.93e-08

60S ribosomal protein L7Ae-like; Provisional


Pssm-ID: 240382  Cd Length: 266  Bit Score: 49.46  E-value: 4.93e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 47058996   35 LRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGV-SRPVIACSVTIKE 108
Cdd:PTZ00365 133 LKYGLNHVTDLVEYKKAKLVVIAHDVDPIELVCFLPALCRKKEVPYCIIKGKSRLGKLVHQkTAAVVAIDNVRKE 207
PRK13602 PRK13602
50S ribosomal protein L7ae-like protein;
33-107 7.79e-07

50S ribosomal protein L7ae-like protein;


Pssm-ID: 184174 [Multi-domain]  Cd Length: 82  Bit Score: 44.00  E-value: 7.79e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 47058996   33 KQLRKGANEATKTLNRGISEFIVMAADAEPlEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSrpVIACSVTIK 107
Cdd:PRK13602  10 KSIVIGTKQTVKALKRGSVKEVVVAEDADP-RLTEKVEALANEKGVPVSKVDSMKKLGKACGIE--VGAAAVAII 81
 
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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