NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1972254412|ref|NP_001379076|]
View 

Small nuclear ribonucleoprotein associated homolog 13 [Caenorhabditis elegans]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 3.75e-81

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: 233.76  E-value: 3.75e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972254412   7 NPKAFPLADTNLSQKLMDLVQQAMNYKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLLCEDKNVPYVFVRSK 86
Cdd:cd21104     1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1972254412  87 AALGRACGVTRPVIAASITQNEGSQLKSQIQKIKEDVEKLLI 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 3.75e-81

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: 233.76  E-value: 3.75e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972254412   7 NPKAFPLADTNLSQKLMDLVQQAMNYKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLLCEDKNVPYVFVRSK 86
Cdd:cd21104     1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1972254412  87 AALGRACGVTRPVIAASITQNEGSQLKSQIQKIKEDVEKLLI 128
Cdd:cd21104    81 QALGRACGVSRPVIACSVTTNEGSQLKSQIQSLKDAIEKLLI 122
Ribosomal_L7Ae pfam01248
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from ...
 20-111 5.09e-25

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: 90.73  E-value: 5.09e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972254412  20 QKLMDLVQQAMNYKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLLCEDKNVPYVFVRSKAALGRACGVTRPV 99
Cdd:pfam01248   1 DAIYEVLKKALKTGKLVLGLKEVTKALERGEAKLVIIAEDCDPEEKVKLIPALCKEKNVPYVKVPSKKELGEACGKKRPV 80

                          90
                  ....*....|..
gi 1972254412 100 IAASITQNEGSQ 111
Cdd:pfam01248  81 SALAIKDEGDSK 92
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 18-121 4.76e-24

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: 89.05  E-value: 4.76e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972254412  18 LSQKLMDLVQQAMNYKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLLCEDKNVPYVFVRSKAALGRACGVTR 97
Cdd:TIGR03677  10 LADKALEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVKSKEDLGAAAGLEV 89

                          90       100
                  ....*....|....*....|....*..
gi 1972254412  98 PVIAASITqNEGS---QLKSQIQKIKE 121
Cdd:TIGR03677  90 GAASAAIV-DAGKaeeLLKEIIEKVEA 115
Rpl7Ae COG1358
Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure ...
 20-118 3.57e-12

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: 57.86  E-value: 3.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972254412  20 QKLMDLVQQAMNYKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLlCEDKNVPYVFVRSKAALGRACGVTRPV 99
Cdd:COG1358     1 DKILNLLGLARRAGKLVSGEEQVLKAIRKGKAKLVIIAEDASENTKKKLLDL-CEEYGVPVVEVGTKEELGKAIGKVGRA 79

                          90
                  ....*....|....*....
gi 1972254412 100 IAASITQNEGSQLKSQIQK 118
Cdd:COG1358    80 VVAITDEGFAKKLLELLEE 98
PRK13602 PRK13602
50S ribosomal protein L7ae-like protein;
24-95 2.92e-04

50S ribosomal protein L7ae-like protein;


Pssm-ID: 184174 [Multi-domain]  Cd Length: 82  Bit Score: 37.07  E-value: 2.92e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1972254412  24 DLVQQAmnyKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLlCEDKNVPYVFVRSKAALGRACGV 95
Cdd:PRK13602    4 EKVSQA---KSIVIGTKQTVKALKRGSVKEVVVAEDADPRLTEKVEAL-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 3.75e-81

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: 233.76  E-value: 3.75e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972254412   7 NPKAFPLADTNLSQKLMDLVQQAMNYKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLLCEDKNVPYVFVRSK 86
Cdd:cd21104     1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1972254412  87 AALGRACGVTRPVIAASITQNEGSQLKSQIQKIKEDVEKLLI 128
Cdd:cd21104    81 QALGRACGVSRPVIACSVTTNEGSQLKSQIQSLKDAIEKLLI 122
Ribosomal_L7Ae pfam01248
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from ...
 20-111 5.09e-25

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: 90.73  E-value: 5.09e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972254412  20 QKLMDLVQQAMNYKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLLCEDKNVPYVFVRSKAALGRACGVTRPV 99
Cdd:pfam01248   1 DAIYEVLKKALKTGKLVLGLKEVTKALERGEAKLVIIAEDCDPEEKVKLIPALCKEKNVPYVKVPSKKELGEACGKKRPV 80

                          90
                  ....*....|..
gi 1972254412 100 IAASITQNEGSQ 111
Cdd:pfam01248  81 SALAIKDEGDSK 92
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 18-121 4.76e-24

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: 89.05  E-value: 4.76e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972254412  18 LSQKLMDLVQQAMNYKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLLCEDKNVPYVFVRSKAALGRACGVTR 97
Cdd:TIGR03677  10 LADKALEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVKSKEDLGAAAGLEV 89

                          90       100
                  ....*....|....*....|....*..
gi 1972254412  98 PVIAASITqNEGS---QLKSQIQKIKE 121
Cdd:TIGR03677  90 GAASAAIV-DAGKaeeLLKEIIEKVEA 115
Rpl7Ae COG1358
Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure ...
 20-118 3.57e-12

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: 57.86  E-value: 3.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972254412  20 QKLMDLVQQAMNYKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLlCEDKNVPYVFVRSKAALGRACGVTRPV 99
Cdd:COG1358     1 DKILNLLGLARRAGKLVSGEEQVLKAIRKGKAKLVIIAEDASENTKKKLLDL-CEEYGVPVVEVGTKEELGKAIGKVGRA 79

                          90
                  ....*....|....*....
gi 1972254412 100 IAASITQNEGSQLKSQIQK 118
Cdd:COG1358    80 VVAITDEGFAKKLLELLEE 98
PRK13602 PRK13602
50S ribosomal protein L7ae-like protein;
24-95 2.92e-04

50S ribosomal protein L7ae-like protein;


Pssm-ID: 184174 [Multi-domain]  Cd Length: 82  Bit Score: 37.07  E-value: 2.92e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1972254412  24 DLVQQAmnyKQLKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLlCEDKNVPYVFVRSKAALGRACGV 95
Cdd:PRK13602    4 EKVSQA---KSIVIGTKQTVKALKRGSVKEVVVAEDADPRLTEKVEAL-ANEKGVPVSKVDSMKKLGKACGI 71
PTZ00222 PTZ00222
60S ribosomal protein L7a; Provisional
 38-94 5.14e-04

60S ribosomal protein L7a; Provisional


Pssm-ID: 140249  Cd Length: 263  Bit Score: 38.14  E-value: 5.14e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1972254412  38 GANEATKTLNRGISEIIVMAADAEPLEILLHLPLLCEDKNVPYVFVRSKAALGRACG 94
Cdd:PTZ00222  136 GLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAIVKDMARLGDAIG 192
PTZ00365 PTZ00365
60S ribosomal protein L7Ae-like; Provisional
 35-101 1.79e-03

60S ribosomal protein L7Ae-like; Provisional


Pssm-ID: 240382  Cd Length: 266  Bit Score: 36.75  E-value: 1.79e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1972254412  35 LKKGANEATKTLNRGISEIIVMAADAEPLEILLHLPLLCEDKNVPYVFVRSKAALGRACGV-TRPVIA 101
Cdd:PTZ00365  133 LKYGLNHVTDLVEYKKAKLVVIAHDVDPIELVCFLPALCRKKEVPYCIIKGKSRLGKLVHQkTAAVVA 200
 
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