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Conserved domains on  [gi|297799776|ref|XP_002867772|]
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NHP2-like protein 1 homolog [Arabidopsis lyrata subsp. lyrata]

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 2.35e-84

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: 241.85  E-value: 2.35e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297799776   7 NPKAYPLADSQLSITILDLVQQATNYKQLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLLAEDKNVPYVFVPSK 86
Cdd:cd21104    1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 297799776  87 QALGRACGVTRSVIACSVTSNEASQLKSQIQHLKDAIEKLLI 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 2.35e-84

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: 241.85  E-value: 2.35e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297799776   7 NPKAYPLADSQLSITILDLVQQATNYKQLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLLAEDKNVPYVFVPSK 86
Cdd:cd21104    1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 297799776  87 QALGRACGVTRSVIACSVTSNEASQLKSQIQHLKDAIEKLLI 128
Cdd:cd21104   81 QALGRACGVSRPVIACSVTTNEGSQLKSQIQSLKDAIEKLLI 122
Ribosomal_L7Ae pfam01248
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from ...
 22-111 2.31e-23

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: 86.49  E-value: 2.31e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297799776   22 ILDLVQQATNYKQLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRSVIA 101
Cdd:pfam01248   3 IYEVLKKALKTGKLVLGLKEVTKALERGEAKLVIIAEDCDPEEKVKLIPALCKEKNVPYVKVPSKKELGEACGKKRPVSA 82

                          90
                  ....*....|
gi 297799776  102 CSVTSNEASQ 111
Cdd:pfam01248  83 LAIKDEGDSK 92
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 23-126 2.06e-20

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: 79.80  E-value: 2.06e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297799776   23 LDLVQQATNYKQLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRSVIAC 102
Cdd:TIGR03677  15 LEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVKSKEDLGAAAGLEVGAASA 94

                          90       100
                  ....*....|....*....|....*
gi 297799776  103 SVT-SNEASQLksqiqhLKDAIEKL 126
Cdd:TIGR03677  95 AIVdAGKAEEL------LKEIIEKV 113
Rpl7Ae COG1358
Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure ...
 22-101 1.20e-13

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: 61.71  E-value: 1.20e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297799776  22 ILDLVQQATNYKQLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLlAEDKNVPYVFVPSKQALGRACG-VTRSVI 100
Cdd:COG1358    3 ILNLLGLARRAGKLVSGEEQVLKAIRKGKAKLVIIAEDASENTKKKLLDL-CEEYGVPVVEVGTKEELGKAIGkVGRAVV 81


                 .
gi 297799776 101 A 101
Cdd:COG1358   82 A 82
PRK13602 PRK13602
50S ribosomal protein L7ae-like protein;
24-95 4.03e-05

50S ribosomal protein L7ae-like protein;


Pssm-ID: 184174 [Multi-domain]  Cd Length: 82  Bit Score: 39.38  E-value: 4.03e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 297799776  24 DLVQQATNykqLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLlAEDKNVPYVFVPSKQALGRACGV 95
Cdd:PRK13602   4 EKVSQAKS---IVIGTKQTVKALKRGSVKEVVVAEDADPRLTEKVEAL-ANEKGVPVSKVDSMKKLGKACGI 71
 
Name Accession Description Interval E-value
SNU13 cd21104
U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, ...
 7-128 2.35e-84

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: 241.85  E-value: 2.35e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297799776   7 NPKAYPLADSQLSITILDLVQQATNYKQLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLLAEDKNVPYVFVPSK 86
Cdd:cd21104    1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 297799776  87 QALGRACGVTRSVIACSVTSNEASQLKSQIQHLKDAIEKLLI 128
Cdd:cd21104   81 QALGRACGVSRPVIACSVTTNEGSQLKSQIQSLKDAIEKLLI 122
Ribosomal_L7Ae pfam01248
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from ...
 22-111 2.31e-23

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: 86.49  E-value: 2.31e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297799776   22 ILDLVQQATNYKQLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRSVIA 101
Cdd:pfam01248   3 IYEVLKKALKTGKLVLGLKEVTKALERGEAKLVIIAEDCDPEEKVKLIPALCKEKNVPYVKVPSKKELGEACGKKRPVSA 82

                          90
                  ....*....|
gi 297799776  102 CSVTSNEASQ 111
Cdd:pfam01248  83 LAIKDEGDSK 92
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 23-126 2.06e-20

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: 79.80  E-value: 2.06e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297799776   23 LDLVQQATNYKQLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRSVIAC 102
Cdd:TIGR03677  15 LEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVKSKEDLGAAAGLEVGAASA 94

                          90       100
                  ....*....|....*....|....*
gi 297799776  103 SVT-SNEASQLksqiqhLKDAIEKL 126
Cdd:TIGR03677  95 AIVdAGKAEEL------LKEIIEKV 113
Rpl7Ae COG1358
Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure ...
 22-101 1.20e-13

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: 61.71  E-value: 1.20e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297799776  22 ILDLVQQATNYKQLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLlAEDKNVPYVFVPSKQALGRACG-VTRSVI 100
Cdd:COG1358    3 ILNLLGLARRAGKLVSGEEQVLKAIRKGKAKLVIIAEDASENTKKKLLDL-CEEYGVPVVEVGTKEELGKAIGkVGRAVV 81


                 .
gi 297799776 101 A 101
Cdd:COG1358   82 A 82
PRK13602 PRK13602
50S ribosomal protein L7ae-like protein;
24-95 4.03e-05

50S ribosomal protein L7ae-like protein;


Pssm-ID: 184174 [Multi-domain]  Cd Length: 82  Bit Score: 39.38  E-value: 4.03e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 297799776  24 DLVQQATNykqLKKGANEATKTLNRGISEFVVMAADAEPLEILLHLPLlAEDKNVPYVFVPSKQALGRACGV 95
Cdd:PRK13602   4 EKVSQAKS---IVIGTKQTVKALKRGSVKEVVVAEDADPRLTEKVEAL-ANEKGVPVSKVDSMKKLGKACGI 71
 
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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