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Conserved domains on  [gi|564397845|ref|XP_006256472|]
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activating signal cointegrator 1 complex subunit 1 isoform X3 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AKAP7_NLS pfam10469
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ...
 132-355 4.39e-77

AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes. AKAP7_NLS carries the nuclear localization signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein. Binding to the regulatory subunits RI and RII of PKA is mediated via the family AKAP7_RIRII_bdg. at the C-terminus. This family represents a region that contains two 2'5' RNA ligase like domains pfam02834. Presumably this domain carried out some as yet unknown enzymatic function.


:

Pssm-ID: 402204 [Multi-domain]  Cd Length: 207  Bit Score: 235.63  E-value: 4.39e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845  132 FTHFLSFFLNEVEVQERFLEFQAEVLKKcskDRGVDSTIFQNPKKLHLTIGMLVLLSEQEIQQTCEILQRCKEEFINDIS 211
Cdd:pfam10469   1 PTHFLSIPLNSPELRKRLEEFQESVLKQ---LPGLDESLFIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIKDILN 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845  212 GgKPLEVEMAGIEYMNDDPAMVDVLYAKVHMKDGSNRLQELVDRVLERFQSMGLVMKEW-TSVKLHATVMNTLLRKDPNa 290
Cdd:pfam10469  78 G-NPLSLRFKGLETFNDDPSAVRVLYAKVEEDDHSPKLQELADRIIRRFQEAGLLVKENnSRVKLHMTLMNTRYRKKKY- 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564397845  291 egrynlytadgkyiFKERESFDGRNILKTFENFYFGSLKLNSIHISQRFTVD-SFGNYASCGHVDF 355
Cdd:pfam10469 156 --------------AKSKESFDAREILDEFKDFDFGTQKVSELHLCSMGSSDeSDGFYHVEASVKL 207
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 58-123 1.06e-28

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.


:

Pssm-ID: 411847 [Multi-domain]  Cd Length: 66  Bit Score: 105.74  E-value: 1.06e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564397845  58 FRATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLGHEGEIVITGHHRNGVVSARTRIDVLL 123
Cdd:cd22419    1 FRLSLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
 
Name Accession Description Interval E-value
AKAP7_NLS pfam10469
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ...
 132-355 4.39e-77

AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes. AKAP7_NLS carries the nuclear localization signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein. Binding to the regulatory subunits RI and RII of PKA is mediated via the family AKAP7_RIRII_bdg. at the C-terminus. This family represents a region that contains two 2'5' RNA ligase like domains pfam02834. Presumably this domain carried out some as yet unknown enzymatic function.


Pssm-ID: 402204 [Multi-domain]  Cd Length: 207  Bit Score: 235.63  E-value: 4.39e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845  132 FTHFLSFFLNEVEVQERFLEFQAEVLKKcskDRGVDSTIFQNPKKLHLTIGMLVLLSEQEIQQTCEILQRCKEEFINDIS 211
Cdd:pfam10469   1 PTHFLSIPLNSPELRKRLEEFQESVLKQ---LPGLDESLFIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIKDILN 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845  212 GgKPLEVEMAGIEYMNDDPAMVDVLYAKVHMKDGSNRLQELVDRVLERFQSMGLVMKEW-TSVKLHATVMNTLLRKDPNa 290
Cdd:pfam10469  78 G-NPLSLRFKGLETFNDDPSAVRVLYAKVEEDDHSPKLQELADRIIRRFQEAGLLVKENnSRVKLHMTLMNTRYRKKKY- 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564397845  291 egrynlytadgkyiFKERESFDGRNILKTFENFYFGSLKLNSIHISQRFTVD-SFGNYASCGHVDF 355
Cdd:pfam10469 156 --------------AKSKESFDAREILDEFKDFDFGTQKVSELHLCSMGSSDeSDGFYHVEASVKL 207
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 58-123 1.06e-28

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.


Pssm-ID: 411847 [Multi-domain]  Cd Length: 66  Bit Score: 105.74  E-value: 1.06e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564397845  58 FRATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLGHEGEIVITGHHRNGVVSARTRIDVLL 123
Cdd:cd22419    1 FRLSLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
PLN00108 PLN00108
unknown protein; Provisional
 128-355 1.85e-21

unknown protein; Provisional


Pssm-ID: 177724  Cd Length: 257  Bit Score: 92.05  E-value: 1.85e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845 128 RRQPFTHFLSFFLN-EVEVQERFLEFQAEVLKKCSKD----------RGVDSTIFQNPKKLHLTIGMLVLLSEQEIQQTC 196
Cdd:PLN00108  32 HREVFTHFVSLPLAiYPDLKKNIEAFQNSVLGNNDKDplkfqstlaeMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQ 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845 197 EILQRCKEEfINDISGGKPLEVEMAGIEYMNDDPAMVDVLYAKVHMKDGSNRLQELVDRVLERFQSMGLVMKEWTS-VKL 275
Cdd:PLN00108 112 NILKSICSN-VRQALKDRPVFIRLRGLDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKDAKSrLKL 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845 276 HATVMNTLLRKDPNaegrynlytadgkyifKERESFDGRNILKTFENFYFGSLKLNSIHISQRFTVDSFGNYASCGHVDF 355
Cdd:PLN00108 191 HATLMNASYRKDKS----------------KKMDTFDAREIHKEFENKDWGTYLIREAHISQRYKYDPNGYFHCCASLPF 254
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 61-119 5.78e-06

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 43.42  E-value: 5.78e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564397845   61 TVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPK---LGHEGEIVITGhHRNGVVSARTRI 119
Cdd:pfam00013   3 EILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPsesEGNERIVTITG-TPEAVEAAKALI 63
KH smart00322
K homology RNA-binding domain;
59-119 2.29e-05

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 41.90  E-value: 2.29e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564397845    59 RATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLG-HEGEIVITGhHRNGVVSARTRI 119
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGsEERVVEITG-PPENVEKAAELI 64
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 135-259 8.09e-05

RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 42.71  E-value: 8.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845 135 FLSFFLNEvEVQERFLEFQAEvLKKCSKDRGVDstifqnPKKLHLTIGMLVLLSEQEIQQTCEILQRCKEEFindisggK 214
Cdd:COG1514    4 FIALPPPE-ELREALAALRAR-LKAAPGGRWVR------PENLHLTLAFLGEVDEERLEALAEALARAAAGA-------P 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 564397845 215 PLEVEMAGIEYMNDDPAmvDVLYAKVHMKDGSNRLQELVDRVLER 259
Cdd:COG1514   69 PFELRLDGLGAFPRPRP--RVLWLGVEPSPELLALHRRLRAALAR 111
 
Name Accession Description Interval E-value
AKAP7_NLS pfam10469
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ...
 132-355 4.39e-77

AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes. AKAP7_NLS carries the nuclear localization signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein. Binding to the regulatory subunits RI and RII of PKA is mediated via the family AKAP7_RIRII_bdg. at the C-terminus. This family represents a region that contains two 2'5' RNA ligase like domains pfam02834. Presumably this domain carried out some as yet unknown enzymatic function.


Pssm-ID: 402204 [Multi-domain]  Cd Length: 207  Bit Score: 235.63  E-value: 4.39e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845  132 FTHFLSFFLNEVEVQERFLEFQAEVLKKcskDRGVDSTIFQNPKKLHLTIGMLVLLSEQEIQQTCEILQRCKEEFINDIS 211
Cdd:pfam10469   1 PTHFLSIPLNSPELRKRLEEFQESVLKQ---LPGLDESLFIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIKDILN 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845  212 GgKPLEVEMAGIEYMNDDPAMVDVLYAKVHMKDGSNRLQELVDRVLERFQSMGLVMKEW-TSVKLHATVMNTLLRKDPNa 290
Cdd:pfam10469  78 G-NPLSLRFKGLETFNDDPSAVRVLYAKVEEDDHSPKLQELADRIIRRFQEAGLLVKENnSRVKLHMTLMNTRYRKKKY- 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564397845  291 egrynlytadgkyiFKERESFDGRNILKTFENFYFGSLKLNSIHISQRFTVD-SFGNYASCGHVDF 355
Cdd:pfam10469 156 --------------AKSKESFDAREILDEFKDFDFGTQKVSELHLCSMGSSDeSDGFYHVEASVKL 207
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 58-123 1.06e-28

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.


Pssm-ID: 411847 [Multi-domain]  Cd Length: 66  Bit Score: 105.74  E-value: 1.06e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564397845  58 FRATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLGHEGEIVITGHHRNGVVSARTRIDVLL 123
Cdd:cd22419    1 FRLSLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
PLN00108 PLN00108
unknown protein; Provisional
 128-355 1.85e-21

unknown protein; Provisional


Pssm-ID: 177724  Cd Length: 257  Bit Score: 92.05  E-value: 1.85e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845 128 RRQPFTHFLSFFLN-EVEVQERFLEFQAEVLKKCSKD----------RGVDSTIFQNPKKLHLTIGMLVLLSEQEIQQTC 196
Cdd:PLN00108  32 HREVFTHFVSLPLAiYPDLKKNIEAFQNSVLGNNDKDplkfqstlaeMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQ 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845 197 EILQRCKEEfINDISGGKPLEVEMAGIEYMNDDPAMVDVLYAKVHMKDGSNRLQELVDRVLERFQSMGLVMKEWTS-VKL 275
Cdd:PLN00108 112 NILKSICSN-VRQALKDRPVFIRLRGLDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKDAKSrLKL 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845 276 HATVMNTLLRKDPNaegrynlytadgkyifKERESFDGRNILKTFENFYFGSLKLNSIHISQRFTVDSFGNYASCGHVDF 355
Cdd:PLN00108 191 HATLMNASYRKDKS----------------KKMDTFDAREIHKEFENKDWGTYLIREAHISQRYKYDPNGYFHCCASLPF 254
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 59-119 5.98e-08

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.


Pssm-ID: 411839 [Multi-domain]  Cd Length: 62  Bit Score: 48.74  E-value: 5.98e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564397845  59 RATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLGHEGE-IVITGHHRNgVVSARTRI 119
Cdd:cd22411    1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDSDvITITGKKED-VEKARERI 61
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 65-120 5.11e-07

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 46.52  E-value: 5.11e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564397845  65 PSLLYKHIVGKRGDTKKKIEVETKTSINIPKLGH---EGEIVITGhHRNGVVSARTRID 120
Cdd:cd00105    6 PSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEgsgERVVTITG-TPEAVEKAKELIE 63
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 61-119 5.78e-06

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 43.42  E-value: 5.78e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564397845   61 TVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPK---LGHEGEIVITGhHRNGVVSARTRI 119
Cdd:pfam00013   3 EILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPsesEGNERIVTITG-TPEAVEAAKALI 63
KH smart00322
K homology RNA-binding domain;
59-119 2.29e-05

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 41.90  E-value: 2.29e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564397845    59 RATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLG-HEGEIVITGhHRNGVVSARTRI 119
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGsEERVVEITG-PPENVEKAAELI 64
KH-I_Vigilin_rpt2 cd22406
second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 59-119 2.79e-05

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.


Pssm-ID: 411834 [Multi-domain]  Cd Length: 75  Bit Score: 41.91  E-value: 2.79e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564397845  59 RATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLGHE-GEIVITGhHRNGVVSARTRI 119
Cdd:cd22406    6 SVTVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQEDNsDEIKITG-TKEGIEKARHEI 66
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 68-119 2.84e-05

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.


Pssm-ID: 411804 [Multi-domain]  Cd Length: 68  Bit Score: 41.40  E-value: 2.84e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564397845  68 LYKHIVGKRGDTKKKIEVETKTSINIPKLGHE-GEIVITGHHrNGVVSARTRI 119
Cdd:cd02394   12 FHGHIIGKGGANIKRIREESGVSIRIPDDEANsDEIRIEGSP-EGVKKAKAEI 63
KH-I_ScSCP160_rpt1 cd22446
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 60-122 4.81e-05

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411874 [Multi-domain]  Cd Length: 86  Bit Score: 41.62  E-value: 4.81e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564397845  60 ATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLGHEG-----------EIVITGHHrNGVVSARTRIDVL 122
Cdd:cd22446    9 ITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKRNEEGnydeddddetvEISIEGDA-EGVELAKKEIEAI 81
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 135-259 8.09e-05

RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 42.71  E-value: 8.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845 135 FLSFFLNEvEVQERFLEFQAEvLKKCSKDRGVDstifqnPKKLHLTIGMLVLLSEQEIQQTCEILQRCKEEFindisggK 214
Cdd:COG1514    4 FIALPPPE-ELREALAALRAR-LKAAPGGRWVR------PENLHLTLAFLGEVDEERLEALAEALARAAAGA-------P 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 564397845 215 PLEVEMAGIEYMNDDPAmvDVLYAKVHMKDGSNRLQELVDRVLER 259
Cdd:COG1514   69 PFELRLDGLGAFPRPRP--RVLWLGVEPSPELLALHRRLRAALAR 111
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 61-120 1.62e-04

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411875 [Multi-domain]  Cd Length: 80  Bit Score: 39.71  E-value: 1.62e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564397845  61 TVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPK------LGHEG-----EIVITGHHRNgVVSARTRID 120
Cdd:cd22447    7 TVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPrdadaaPADEDddtmvEVTITGDEFN-VQHAKQRIE 76
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 61-119 2.01e-04

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.


Pssm-ID: 411879 [Multi-domain]  Cd Length: 69  Bit Score: 39.36  E-value: 2.01e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564397845  61 TVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKL-GHEGEIVITGhHRNGVVSARTRI 119
Cdd:cd22451    4 DIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKdDPSGKIRITG-ARDGVEAATAKI 62
KH-I_ScSCP160_rpt4 cd22449
fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 56-124 3.00e-04

fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.


Pssm-ID: 411877 [Multi-domain]  Cd Length: 70  Bit Score: 38.79  E-value: 3.00e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564397845  56 HGFRATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLGHEGEIVITGhHRNGVVSARTRIDVLLD 124
Cdd:cd22449    2 NGYTVKFDVPAKYVPHIIGKKGANINKLREEYGVKIDFEDKTGEGNVEIKG-SKKNVEEAKKRILSQID 69
KH-I_ScSCP160_rpt7 cd22452
seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 57-119 8.19e-04

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.


Pssm-ID: 411880 [Multi-domain]  Cd Length: 65  Bit Score: 37.30  E-value: 8.19e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564397845  57 GFRATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLGHEGEIVITGHHRNGVVSARTRI 119
Cdd:cd22452    1 DFRGWIKVSPRYFGRIIGPGGSNINQIREKSGCFINVPKKNKESDVITLRGTKEGVEKAEEMI 63
KH-I_Vigilin_rpt5 cd22409
fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 60-106 2.69e-03

fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifth one.


Pssm-ID: 411837 [Multi-domain]  Cd Length: 70  Bit Score: 36.02  E-value: 2.69e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 564397845  60 ATVSAPSLLYKHIVGKRGDTKKKIEVET-KTSINIPKlgHEGEIVITG 106
Cdd:cd22409    4 AEVSAPSWLHRFIIGKKGANIKKITQDLpKVHIEFTE--GEDKIELEG 49
KH-I_Vigilin_rpt14 cd22417
fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 58-119 3.50e-03

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.


Pssm-ID: 411845 [Multi-domain]  Cd Length: 72  Bit Score: 35.65  E-value: 3.50e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564397845  58 FRATVSAPSLLYKHIVGKRGDTKKKIEVETKTSINIPKLGHEG--EIVITGhHRNGVVSARTRI 119
Cdd:cd22417    1 FTLTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDENddEITITG-YEKNAEAAKDAI 63
KH-I_Dim2p_like_rpt1 cd22389
first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ...
 72-105 5.95e-03

first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins; The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411817 [Multi-domain]  Cd Length: 70  Bit Score: 34.87  E-value: 5.95e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 564397845  72 IVGKRGDTKKKIEVETKTSINIpkLGHEGEIVIT 105
Cdd:cd22389   13 LIGKKGETKREIEERTGVKITV--DSETGEVIIE 44
KH-I_Vigilin_rpt3 cd22407
third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 65-119 8.34e-03

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.


Pssm-ID: 411835 [Multi-domain]  Cd Length: 62  Bit Score: 34.49  E-value: 8.34e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564397845  65 PSLLYKHIVGKRGDTKKKIEVETKTSINIPKLG-HEGEIVITGhHRNGVVSARTRI 119
Cdd:cd22407    7 PKVYHPFIAGPNNENVKELQEETGVRINIPPPSvNKDEIVVSG-EKEGVAQAVAKI 61
 
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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