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Conserved domains on  [gi|13386120|ref|NP_080907|]
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H/ACA ribonucleoprotein complex subunit 2 isoform 1 [Mus musculus]

Protein Classification

ribosomal eL8 family protein( domain architecture ID 1903236)

ribosomal eL8 family protein such as large ribosomal subunit protein eL8 and H/ACA ribonucleoprotein complex subunit 2

Gene Ontology:  GO:0003723
SCOP:  4001513

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SNU13 super family cl42391
U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, ...
 32-130 3.25e-30

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.


The actual alignment was detected with superfamily member cd21104:

Pssm-ID: 455736  Cd Length: 122  Bit Score: 105.87  E-value: 3.25e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120  32 NPIAQPLASRRLTRKLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVLCEDQNLPYVYIPSK 111
Cdd:cd21104   1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                        90       100
                ....*....|....*....|.
gi 13386120 112 TDLGAATGSKRP--TCVIMVK 130
Cdd:cd21104  81 QALGRACGVSRPviACSVTTN 101
 
Name Accession Description Interval E-value
SNU13 cd21104
U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, ...
 32-130 3.25e-30

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: 105.87  E-value: 3.25e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120  32 NPIAQPLASRRLTRKLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVLCEDQNLPYVYIPSK 111
Cdd:cd21104   1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                        90       100
                ....*....|....*....|.
gi 13386120 112 TDLGAATGSKRP--TCVIMVK 130
Cdd:cd21104  81 QALGRACGVSRPviACSVTTN 101
Ribosomal_L7Ae pfam01248
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from ...
 46-137 9.25e-24

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: 88.42  E-value: 9.25e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120    46 KLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVLCEDQNLPYVYIPSKTDLGAATGSKRPTC 125
Cdd:pfam01248   2 AIYEVLKKALKTGKLVLGLKEVTKALERGEAKLVIIAEDCDPEEKVKLIPALCKEKNVPYVKVPSKKELGEACGKKRPVS 81

                          90
                  ....*....|..
gi 13386120   126 VIMVKPHEEYQE 137
Cdd:pfam01248  82 ALAIKDEGDSKI 93
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 43-149 8.79e-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: 79.03  E-value: 8.79e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120    43 LTRKLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVLCEDQNLPYVYIPSKTDLGAATGSKR 122
Cdd:TIGR03677  10 LADKALEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVKSKEDLGAAAGLEV 89

                          90       100
                  ....*....|....*....|....*..
gi 13386120   123 PTCVIMVKPHEEYQETYDKCLEEVQAL 149
Cdd:TIGR03677  90 GAASAAIVDAGKAEELLKEIIEKVEAL 116
PTZ00222 PTZ00222
60S ribosomal protein L7a; Provisional
 52-148 3.05e-09

60S ribosomal protein L7a; Provisional


Pssm-ID: 140249  Cd Length: 263  Bit Score: 53.93  E-value: 3.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120   52 KKAVKQKQ---IRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVLCEDQNLPYVYIPSKTDLGAATGSKRPTCVIM 128
Cdd:PTZ00222 122 KKTVSTKAplaVVTGLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAIVKDMARLGDAIGRKTATCVAI 201

                         90       100
                 ....*....|....*....|
gi 13386120  129 VKPHEEYQETYDKCLEEVQA 148
Cdd:PTZ00222 202 TDVNAEDEAALKNLIRSVNA 221
Rpl7Ae COG1358
Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure ...
 45-130 1.40e-08

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: 49.39  E-value: 1.40e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120  45 RKLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPiEVYCHLPVLCEDQNLPYVYIPSKTDLGAATGsKRPT 124
Cdd:COG1358   1 DKILNLLGLARRAGKLVSGEEQVLKAIRKGKAKLVIIAEDASE-NTKKKLLDLCEEYGVPVVEVGTKEELGKAIG-KVGR 78


                ....*.
gi 13386120 125 CVIMVK 130
Cdd:COG1358  79 AVVAIT 84
 
Name Accession Description Interval E-value
SNU13 cd21104
U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, ...
 32-130 3.25e-30

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: 105.87  E-value: 3.25e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120  32 NPIAQPLASRRLTRKLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVLCEDQNLPYVYIPSK 111
Cdd:cd21104   1 NPKAYPLADAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVPSK 80

                        90       100
                ....*....|....*....|.
gi 13386120 112 TDLGAATGSKRP--TCVIMVK 130
Cdd:cd21104  81 QALGRACGVSRPviACSVTTN 101
Ribosomal_L7Ae pfam01248
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from ...
 46-137 9.25e-24

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: 88.42  E-value: 9.25e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120    46 KLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVLCEDQNLPYVYIPSKTDLGAATGSKRPTC 125
Cdd:pfam01248   2 AIYEVLKKALKTGKLVLGLKEVTKALERGEAKLVIIAEDCDPEEKVKLIPALCKEKNVPYVKVPSKKELGEACGKKRPVS 81

                          90
                  ....*....|..
gi 13386120   126 VIMVKPHEEYQE 137
Cdd:pfam01248  82 ALAIKDEGDSKI 93
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 43-149 8.79e-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: 79.03  E-value: 8.79e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120    43 LTRKLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVLCEDQNLPYVYIPSKTDLGAATGSKR 122
Cdd:TIGR03677  10 LADKALEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVKSKEDLGAAAGLEV 89

                          90       100
                  ....*....|....*....|....*..
gi 13386120   123 PTCVIMVKPHEEYQETYDKCLEEVQAL 149
Cdd:TIGR03677  90 GAASAAIVDAGKAEELLKEIIEKVEAL 116
PTZ00222 PTZ00222
60S ribosomal protein L7a; Provisional
 52-148 3.05e-09

60S ribosomal protein L7a; Provisional


Pssm-ID: 140249  Cd Length: 263  Bit Score: 53.93  E-value: 3.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120   52 KKAVKQKQ---IRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVLCEDQNLPYVYIPSKTDLGAATGSKRPTCVIM 128
Cdd:PTZ00222 122 KKTVSTKAplaVVTGLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAIVKDMARLGDAIGRKTATCVAI 201

                         90       100
                 ....*....|....*....|
gi 13386120  129 VKPHEEYQETYDKCLEEVQA 148
Cdd:PTZ00222 202 TDVNAEDEAALKNLIRSVNA 221
Rpl7Ae COG1358
Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure ...
 45-130 1.40e-08

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: 49.39  E-value: 1.40e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120  45 RKLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPiEVYCHLPVLCEDQNLPYVYIPSKTDLGAATGsKRPT 124
Cdd:COG1358   1 DKILNLLGLARRAGKLVSGEEQVLKAIRKGKAKLVIIAEDASE-NTKKKLLDLCEEYGVPVVEVGTKEELGKAIG-KVGR 78


                ....*.
gi 13386120 125 CVIMVK 130
Cdd:COG1358  79 AVVAIT 84
PTZ00365 PTZ00365
60S ribosomal protein L7Ae-like; Provisional
 60-140 2.41e-06

60S ribosomal protein L7Ae-like; Provisional


Pssm-ID: 240382  Cd Length: 266  Bit Score: 45.61  E-value: 2.41e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13386120   60 IRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVLCEDQNLPYVYIPSKTDLGAATGSKRPTCVIMVKPHEEYQETY 139
Cdd:PTZ00365 133 LKYGLNHVTDLVEYKKAKLVVIAHDVDPIELVCFLPALCRKKEVPYCIIKGKSRLGKLVHQKTAAVVAIDNVRKEDQAEF 212


                 .
gi 13386120  140 D 140
Cdd:PTZ00365 213 D 213
 
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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