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Conserved domains on  [gi|311771710|ref|NP_001185728|]
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activating signal cointegrator 1 complex subunit 1 isoform a [Homo sapiens]

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 ...
 161-349 1.48e-64

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: 205.20  E-value: 1.48e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710  161 FTHFLAFFLNEVEVQEGFLRFQEEVLAKCSmdhGVDSSIFQNPKKLHLTIGMLVLLSEEEIQQTCEMLQQCKEEFINDIS 240
Cdd:pfam10469   1 PTHFLSIPLNSPELRKRLEEFQESVLKQLP---GLDESLFIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIKDILN 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710  241 GgKPLEVEMAGIEYMNDDPGMVDVLYAKVHMKDGSNRLQELVDRVLERFQASGLIVKEWNS-VKLHATVMNTLFRKDPNa 319
Cdd:pfam10469  78 G-NPLSLRFKGLETFNDDPSAVRVLYAKVEEDDHSPKLQELADRIIRRFQEAGLLVKENNSrVKLHMTLMNTRYRKKKY- 155

                         170       180       190
                  ....*....|....*....|....*....|
gi 311771710  320 egrynlytaegkyiFKERESFDGRNILKSF 349
Cdd:pfam10469 156 --------------AKSKESFDAREILDEF 171
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 87-152 2.45e-29

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: 108.43  E-value: 2.45e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311771710  87 TLDCQNIYTWKSRHIVGKRGDTRKKIEMETKTSISIPKPGQDGEIVITGQHRNGVISARTRIDVLL 152
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 ...
 161-349 1.48e-64

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: 205.20  E-value: 1.48e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710  161 FTHFLAFFLNEVEVQEGFLRFQEEVLAKCSmdhGVDSSIFQNPKKLHLTIGMLVLLSEEEIQQTCEMLQQCKEEFINDIS 240
Cdd:pfam10469   1 PTHFLSIPLNSPELRKRLEEFQESVLKQLP---GLDESLFIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIKDILN 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710  241 GgKPLEVEMAGIEYMNDDPGMVDVLYAKVHMKDGSNRLQELVDRVLERFQASGLIVKEWNS-VKLHATVMNTLFRKDPNa 319
Cdd:pfam10469  78 G-NPLSLRFKGLETFNDDPSAVRVLYAKVEEDDHSPKLQELADRIIRRFQEAGLLVKENNSrVKLHMTLMNTRYRKKKY- 155

                         170       180       190
                  ....*....|....*....|....*....|
gi 311771710  320 egrynlytaegkyiFKERESFDGRNILKSF 349
Cdd:pfam10469 156 --------------AKSKESFDAREILDEF 171
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 87-152 2.45e-29

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: 108.43  E-value: 2.45e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311771710  87 TLDCQNIYTWKSRHIVGKRGDTRKKIEMETKTSISIPKPGQDGEIVITGQHRNGVISARTRIDVLL 152
Cdd:cd22419    1 FRLSLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
PLN00108 PLN00108
unknown protein; Provisional
 157-370 8.86e-15

unknown protein; Provisional


Pssm-ID: 177724  Cd Length: 257  Bit Score: 73.56  E-value: 8.86e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710 157 RKQPFTHFLAFFLN-EVEVQEGFLRFQEEVLAKCSMD----------HGVDSSIFQNPKKLHLTIGMLVLLSEEEIQQTC 225
Cdd:PLN00108  32 HREVFTHFVSLPLAiYPDLKKNIEAFQNSVLGNNDKDplkfqstlaeMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQ 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710 226 EMLQQCKEEfINDISGGKPLEVEMAGIEYMNDDPGMVDVLYAKVHMKDGSNRLQELVDRVLERFQASGLIVKEWNS-VKL 304
Cdd:PLN00108 112 NILKSICSN-VRQALKDRPVFIRLRGLDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKDAKSrLKL 190

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 311771710 305 HATVMNTLFRKDPNAEgrynLYTAEGKYIFKERESFD-GRNILKSFALLPRLEYNDAISAHCNLCLP 370
Cdd:PLN00108 191 HATLMNASYRKDKSKK----MDTFDAREIHKEFENKDwGTYLIREAHISQRYKYDPNGYFHCCASLP 253
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 99-148 5.27e-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: 43.81  E-value: 5.27e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 311771710   99 RHIVGKRGDTRKKIEMETKTSISIPKP---GQDGEIVITGQhRNGVISARTRI 148
Cdd:pfam00013  12 GLIIGKGGSNIKEIREETGAKIQIPPSeseGNERIVTITGT-PEAVEAAKALI 63
KH smart00322
K homology RNA-binding domain;
93-148 1.56e-05

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 42.28  E-value: 1.56e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 311771710    93 IYTWKSRHIVGKRGDTRKKIEMETKTSISIPKPG-QDGEIVITGqHRNGVISARTRI 148
Cdd:smart00322   9 IPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGsEERVVEITG-PPENVEKAAELI 64
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 164-288 9.65e-04

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


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 40.01  E-value: 9.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710 164 FLAFFLNEvEVQEGFLRFQEEVLAKCSMDhgvdssiFQNPKKLHLTIGMLVLLSEEEIQQTCEMLQQCKEEFindisggK 243
Cdd:COG1514    4 FIALPPPE-ELREALAALRARLKAAPGGR-------WVRPENLHLTLAFLGEVDEERLEALAEALARAAAGA-------P 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 311771710 244 PLEVEMAGIEYM-NDDPGmvdVLYAKVHMKDGSNRLQELVDRVLER 288
Cdd:COG1514   69 PFELRLDGLGAFpRPRPR---VLWLGVEPSPELLALHRRLRAALAR 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 ...
 161-349 1.48e-64

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: 205.20  E-value: 1.48e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710  161 FTHFLAFFLNEVEVQEGFLRFQEEVLAKCSmdhGVDSSIFQNPKKLHLTIGMLVLLSEEEIQQTCEMLQQCKEEFINDIS 240
Cdd:pfam10469   1 PTHFLSIPLNSPELRKRLEEFQESVLKQLP---GLDESLFIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIKDILN 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710  241 GgKPLEVEMAGIEYMNDDPGMVDVLYAKVHMKDGSNRLQELVDRVLERFQASGLIVKEWNS-VKLHATVMNTLFRKDPNa 319
Cdd:pfam10469  78 G-NPLSLRFKGLETFNDDPSAVRVLYAKVEEDDHSPKLQELADRIIRRFQEAGLLVKENNSrVKLHMTLMNTRYRKKKY- 155

                         170       180       190
                  ....*....|....*....|....*....|
gi 311771710  320 egrynlytaegkyiFKERESFDGRNILKSF 349
Cdd:pfam10469 156 --------------AKSKESFDAREILDEF 171
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 87-152 2.45e-29

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: 108.43  E-value: 2.45e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311771710  87 TLDCQNIYTWKSRHIVGKRGDTRKKIEMETKTSISIPKPGQDGEIVITGQHRNGVISARTRIDVLL 152
Cdd:cd22419    1 FRLSLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
PLN00108 PLN00108
unknown protein; Provisional
 157-370 8.86e-15

unknown protein; Provisional


Pssm-ID: 177724  Cd Length: 257  Bit Score: 73.56  E-value: 8.86e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710 157 RKQPFTHFLAFFLN-EVEVQEGFLRFQEEVLAKCSMD----------HGVDSSIFQNPKKLHLTIGMLVLLSEEEIQQTC 225
Cdd:PLN00108  32 HREVFTHFVSLPLAiYPDLKKNIEAFQNSVLGNNDKDplkfqstlaeMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQ 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710 226 EMLQQCKEEfINDISGGKPLEVEMAGIEYMNDDPGMVDVLYAKVHMKDGSNRLQELVDRVLERFQASGLIVKEWNS-VKL 304
Cdd:PLN00108 112 NILKSICSN-VRQALKDRPVFIRLRGLDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKDAKSrLKL 190

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 311771710 305 HATVMNTLFRKDPNAEgrynLYTAEGKYIFKERESFD-GRNILKSFALLPRLEYNDAISAHCNLCLP 370
Cdd:PLN00108 191 HATLMNASYRKDKSKK----MDTFDAREIHKEFENKDwGTYLIREAHISQRYKYDPNGYFHCCASLP 253
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 99-148 6.06e-08

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: 49.11  E-value: 6.06e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 311771710  99 RHIVGKRGDTRKKIEMETKTSISIPKPG-QDGEIVITGQHrNGVISARTRI 148
Cdd:cd02394   14 GHIIGKGGANIKRIREESGVSIRIPDDEaNSDEIRIEGSP-EGVKKAKAEI 63
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 99-149 2.74e-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: 47.29  E-value: 2.74e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 311771710  99 RHIVGKRGDTRKKIEMETKTSISIPKPG---QDGEIVITGqHRNGVISARTRID 149
Cdd:cd00105   11 GLIIGKGGSTIKEIEEETGARIQIPKEGegsGERVVTITG-TPEAVEKAKELIE 63
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 99-148 9.55e-07

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: 45.66  E-value: 9.55e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 311771710  99 RHIVGKRGDTRKKIEMETKTSISIPKPG-QDGEIVITGQHRNgVISARTRI 148
Cdd:cd22411   12 KNIIGKGGATIKKIREETNTRIDLPEENsDSDVITITGKKED-VEKARERI 61
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 99-148 5.27e-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: 43.81  E-value: 5.27e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 311771710   99 RHIVGKRGDTRKKIEMETKTSISIPKP---GQDGEIVITGQhRNGVISARTRI 148
Cdd:pfam00013  12 GLIIGKGGSNIKEIREETGAKIQIPPSeseGNERIVTITGT-PEAVEAAKALI 63
KH smart00322
K homology RNA-binding domain;
93-148 1.56e-05

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 42.28  E-value: 1.56e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 311771710    93 IYTWKSRHIVGKRGDTRKKIEMETKTSISIPKPG-QDGEIVITGqHRNGVISARTRI 148
Cdd:smart00322   9 IPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGsEERVVEITG-PPENVEKAAELI 64
KH-I_Vigilin_rpt2 cd22406
second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 99-148 1.90e-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: 42.30  E-value: 1.90e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 311771710  99 RHIVGKRGDTRKKIEMETKTSISIPKPGQD-GEIVITGQhRNGVISARTRI 148
Cdd:cd22406   17 RFILGKKGKKLQELELKTATKIVIPRQEDNsDEIKITGT-KEGIEKARHEI 66
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 99-148 3.46e-05

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: 41.67  E-value: 3.46e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 311771710  99 RHIVGKRGDTRKKIEMETKTSISIP-KPGQDGEIVITGQhRNGVISARTRI 148
Cdd:cd22451   13 RAIIGKGGAVLRELEAETGCRIQVPkKDDPSGKIRITGA-RDGVEAATAKI 62
KH-I_Vigilin_rpt4 cd22408
fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 97-148 2.88e-04

fourth 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 fourth one.


Pssm-ID: 411836 [Multi-domain]  Cd Length: 62  Bit Score: 38.69  E-value: 2.88e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 311771710  97 KSRH--IVGKRGDTRKKIEMETKTSISIPKPGQDGE-IVITGQHRNgVISARTRI 148
Cdd:cd22408    8 KSQHrfVIGPRGSTIQEILEETGCSVEVPPNDSDSEtITLRGPADK-LGAALTLV 61
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 164-288 9.65e-04

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


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 40.01  E-value: 9.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311771710 164 FLAFFLNEvEVQEGFLRFQEEVLAKCSMDhgvdssiFQNPKKLHLTIGMLVLLSEEEIQQTCEMLQQCKEEFindisggK 243
Cdd:COG1514    4 FIALPPPE-ELREALAALRARLKAAPGGR-------WVRPENLHLTLAFLGEVDEERLEALAEALARAAAGA-------P 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 311771710 244 PLEVEMAGIEYM-NDDPGmvdVLYAKVHMKDGSNRLQELVDRVLER 288
Cdd:COG1514   69 PFELRLDGLGAFpRPRPR---VLWLGVEPSPELLALHRRLRAALAR 111
KH-I_Vigilin_rpt3 cd22407
third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 101-148 2.01e-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: 36.42  E-value: 2.01e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 311771710 101 IVGKRGDTRKKIEMETKTSISIPKPG-QDGEIVITGQhRNGVISARTRI 148
Cdd:cd22407   14 IAGPNNENVKELQEETGVRINIPPPSvNKDEIVVSGE-KEGVAQAVAKI 61
KH-I_Dim2p_like_rpt2 cd22390
second type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ...
 97-153 2.46e-03

second 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 second one.


Pssm-ID: 411818  Cd Length: 96  Bit Score: 36.82  E-value: 2.46e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 311771710  97 KSRhIVGKRGDTRKKIEMETKTSISIpkpgQDGEIVITGQHRNGVIsARTRIDVLLD 153
Cdd:cd22390   30 KGR-VIGSGGKTRRLIEELTGCYISV----YGKTVSIIGDFENLQI-AKEAIEMLLN 80
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 97-149 4.27e-03

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.


Pssm-ID: 411803 [Multi-domain]  Cd Length: 70  Bit Score: 35.53  E-value: 4.27e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 311771710  97 KSRHIVGKRGDTRKKIEMETKTSISIpkpGQDGEIVITGQHRNGVISARTRID 149
Cdd:cd02393   14 KIGDVIGPGGKTIRAIIEETGAKIDI---EDDGTVTIFATDKESAEAAKAMIE 63
KH-I_Dim2p_like_rpt1 cd22389
first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ...
 101-151 4.28e-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: 35.64  E-value: 4.28e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 311771710 101 IVGKRGDTRKKIEMETKTSISIpkPGQDGEIVITGQHRNGVISARTRIDVL 151
Cdd:cd22389   13 LIGKKGETKREIEERTGVKITV--DSETGEVIIEPEDEEDPLNVMKAREVV 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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