NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|334185393|ref|NP_001189910|]
View 

Putative eukaryotic LigT [Arabidopsis thaliana]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PLN00108 super family cl42901
unknown protein; Provisional
 138-404 2.04e-86

unknown protein; Provisional


The actual alignment was detected with superfamily member PLN00108:

Pssm-ID: 177724  Cd Length: 257  Bit Score: 263.47  E-value: 2.04e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 138 YSHFVSLPLAIHPELVDKLVNFQNSILGihsiasdkqddqanrattsvavdlkaNSETNQVNVgiksipivsyppkaksk 217
Cdd:PLN00108  36 FTHFVSLPLAIYPDLKKNIEAFQNSVLG--------------------------NNDKDPLKF----------------- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 218 SSTLLDLGIEKSIFIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIFPSVMDALDNKPVFIRLKGLDCMRGPLDKTRVLYA 297
Cdd:PLN00108  73 QSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 298 PVEEIGDEGRLLRACQVITDAFVKAGLVlEKDAKQSLKLHVTVMNARHrkrRKNNKKKMETFDAREIHKQFGNEDWGEYL 377
Cdd:PLN00108 153 PVEEVGHEGRLLNACHVIIDAFENAGFA-GKDAKSRLKLHATLMNASY---RKDKSKKMDTFDAREIHKEFENKDWGTYL 228

                        250       260
                 ....*....|....*....|....*..
gi 334185393 378 IQEAHLSQRFVFDQNGYYRCCGSIPFP 404
Cdd:PLN00108 229 IREAHISQRYKYDPNGYFHCCASLPFP 255
KH-I super family cl00098
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 65-127 4.09e-08

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.


The actual alignment was detected with superfamily member cd22419:

Pssm-ID: 469614 [Multi-domain]  Cd Length: 66  Bit Score: 49.88  E-value: 4.09e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334185393  65 SLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSRNKDHISIEGGSVDCVTKASKRIATII 127
Cdd:cd22419    4 SLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
 
Name Accession Description Interval E-value
PLN00108 PLN00108
unknown protein; Provisional
 138-404 2.04e-86

unknown protein; Provisional


Pssm-ID: 177724  Cd Length: 257  Bit Score: 263.47  E-value: 2.04e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 138 YSHFVSLPLAIHPELVDKLVNFQNSILGihsiasdkqddqanrattsvavdlkaNSETNQVNVgiksipivsyppkaksk 217
Cdd:PLN00108  36 FTHFVSLPLAIYPDLKKNIEAFQNSVLG--------------------------NNDKDPLKF----------------- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 218 SSTLLDLGIEKSIFIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIFPSVMDALDNKPVFIRLKGLDCMRGPLDKTRVLYA 297
Cdd:PLN00108  73 QSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 298 PVEEIGDEGRLLRACQVITDAFVKAGLVlEKDAKQSLKLHVTVMNARHrkrRKNNKKKMETFDAREIHKQFGNEDWGEYL 377
Cdd:PLN00108 153 PVEEVGHEGRLLNACHVIIDAFENAGFA-GKDAKSRLKLHATLMNASY---RKDKSKKMDTFDAREIHKEFENKDWGTYL 228

                        250       260
                 ....*....|....*....|....*..
gi 334185393 378 IQEAHLSQRFVFDQNGYYRCCGSIPFP 404
Cdd:PLN00108 229 IREAHISQRYKYDPNGYFHCCASLPFP 255
AKAP7_NLS pfam10469
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ...
 138-403 3.58e-59

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: 191.72  E-value: 3.58e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393  138 YSHFVSLPLAIHpELVDKLVNFQNSILgihsiasdKQDDqanrattsvavdlkansetnqvnvgiksipivsyppkaksk 217
Cdd:pfam10469   1 PTHFLSIPLNSP-ELRKRLEEFQESVL--------KQLP----------------------------------------- 30

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393  218 sstlldlGIEKSIFIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIFPSVMDALDNKPVFIRLKGLDCMRGPLDKTRVLYA 297
Cdd:pfam10469  31 -------GLDESLFIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIKDILNGNPLSLRFKGLETFNDDPSAVRVLYA 103

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393  298 PVEEIGDEGRLLRACQVITDAFVKAGLVLEKDAKQsLKLHVTVMNARHRKRRKNNKKkmETFDAREIHKQFGNEDWGEYL 377
Cdd:pfam10469 104 KVEEDDHSPKLQELADRIIRRFQEAGLLVKENNSR-VKLHMTLMNTRYRKKKYAKSK--ESFDAREILDEFKDFDFGTQK 180

                         250       260
                  ....*....|....*....|....*..
gi 334185393  378 IQEAHLSQRFVFDQ-NGYYRCCGSIPF 403
Cdd:pfam10469 181 VSELHLCSMGSSDEsDGFYHVEASVKL 207
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 65-127 4.09e-08

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: 49.88  E-value: 4.09e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334185393  65 SLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSRNKDHISIEGGSVDCVTKASKRIATII 127
Cdd:cd22419    4 SLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 231-365 6.96e-06

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


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 46.18  E-value: 6.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 231 FIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIfpsvmdALDNKPVFIRLKGLDCMRGPldKTRVLYAPVEEigdEGRLLR 310
Cdd:COG1514   32 WVRPENLHLTLAFLGEVDEERLEALAEALARA------AAGAPPFELRLDGLGAFPRP--RPRVLWLGVEP---SPELLA 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334185393 311 ACQVITDAFVKAGLVLEkdaKQSLKLHVTVmnARHRKRRKNNKKKME--------TFDAREIH 365
Cdd:COG1514  101 LHRRLRAALARAGLPPE---RRPFVPHVTL--ARGKRPAPPLAPALAelrdfefpEFTVDEFV 158
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 63-123 8.76e-05

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: 40.34  E-value: 8.76e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334185393   63 SVSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSR---NKDHISIEgGSVDCVTKASKRI 123
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSEsegNERIVTIT-GTPEAVEAAKALI 63
 
Name Accession Description Interval E-value
PLN00108 PLN00108
unknown protein; Provisional
 138-404 2.04e-86

unknown protein; Provisional


Pssm-ID: 177724  Cd Length: 257  Bit Score: 263.47  E-value: 2.04e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 138 YSHFVSLPLAIHPELVDKLVNFQNSILGihsiasdkqddqanrattsvavdlkaNSETNQVNVgiksipivsyppkaksk 217
Cdd:PLN00108  36 FTHFVSLPLAIYPDLKKNIEAFQNSVLG--------------------------NNDKDPLKF----------------- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 218 SSTLLDLGIEKSIFIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIFPSVMDALDNKPVFIRLKGLDCMRGPLDKTRVLYA 297
Cdd:PLN00108  73 QSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 298 PVEEIGDEGRLLRACQVITDAFVKAGLVlEKDAKQSLKLHVTVMNARHrkrRKNNKKKMETFDAREIHKQFGNEDWGEYL 377
Cdd:PLN00108 153 PVEEVGHEGRLLNACHVIIDAFENAGFA-GKDAKSRLKLHATLMNASY---RKDKSKKMDTFDAREIHKEFENKDWGTYL 228

                        250       260
                 ....*....|....*....|....*..
gi 334185393 378 IQEAHLSQRFVFDQNGYYRCCGSIPFP 404
Cdd:PLN00108 229 IREAHISQRYKYDPNGYFHCCASLPFP 255
AKAP7_NLS pfam10469
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ...
 138-403 3.58e-59

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: 191.72  E-value: 3.58e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393  138 YSHFVSLPLAIHpELVDKLVNFQNSILgihsiasdKQDDqanrattsvavdlkansetnqvnvgiksipivsyppkaksk 217
Cdd:pfam10469   1 PTHFLSIPLNSP-ELRKRLEEFQESVL--------KQLP----------------------------------------- 30

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393  218 sstlldlGIEKSIFIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIFPSVMDALDNKPVFIRLKGLDCMRGPLDKTRVLYA 297
Cdd:pfam10469  31 -------GLDESLFIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIKDILNGNPLSLRFKGLETFNDDPSAVRVLYA 103

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393  298 PVEEIGDEGRLLRACQVITDAFVKAGLVLEKDAKQsLKLHVTVMNARHRKRRKNNKKkmETFDAREIHKQFGNEDWGEYL 377
Cdd:pfam10469 104 KVEEDDHSPKLQELADRIIRRFQEAGLLVKENNSR-VKLHMTLMNTRYRKKKYAKSK--ESFDAREILDEFKDFDFGTQK 180

                         250       260
                  ....*....|....*....|....*..
gi 334185393  378 IQEAHLSQRFVFDQ-NGYYRCCGSIPF 403
Cdd:pfam10469 181 VSELHLCSMGSSDEsDGFYHVEASVKL 207
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 65-127 4.09e-08

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: 49.88  E-value: 4.09e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334185393  65 SLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSRNKDHISIEGGSVDCVTKASKRIATII 127
Cdd:cd22419    4 SLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 231-365 6.96e-06

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


Pssm-ID: 441123 [Multi-domain]  Cd Length: 181  Bit Score: 46.18  E-value: 6.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393 231 FIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIfpsvmdALDNKPVFIRLKGLDCMRGPldKTRVLYAPVEEigdEGRLLR 310
Cdd:COG1514   32 WVRPENLHLTLAFLGEVDEERLEALAEALARA------AAGAPPFELRLDGLGAFPRP--RPRVLWLGVEP---SPELLA 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334185393 311 ACQVITDAFVKAGLVLEkdaKQSLKLHVTVmnARHRKRRKNNKKKME--------TFDAREIH 365
Cdd:COG1514  101 LHRRLRAALARAGLPPE---RRPFVPHVTL--ARGKRPAPPLAPALAelrdfefpEFTVDEFV 158
KH-I_Vigilin_rpt3 cd22407
third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 65-123 1.21e-05

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: 42.58  E-value: 1.21e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185393  65 SLEVGASLIKFIRGKEGTTQMKLEEEMGVKI-ILPSSRNKDHISIEGGSvDCVTKASKRI 123
Cdd:cd22407    3 RLDIPKVYHPFIAGPNNENVKELQEETGVRInIPPPSVNKDEIVVSGEK-EGVAQAVAKI 61
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 63-123 8.76e-05

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: 40.34  E-value: 8.76e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334185393   63 SVSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSR---NKDHISIEgGSVDCVTKASKRI 123
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSEsegNERIVTIT-GTPEAVEAAKALI 63
KH-I_Vigilin_rpt10 cd22413
tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 62-124 6.90e-04

tenth 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 tenth one.


Pssm-ID: 411841 [Multi-domain]  Cd Length: 66  Bit Score: 37.62  E-value: 6.90e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 334185393  62 HSVSLEVGAS--LIKFIRGKEGTTQMKLEEEMGVKIILPSSRNKDH--ISIEgGSVDCVTKASKRIA 124
Cdd:cd22413    1 NSFTVEIRAKpeYHRFLIGRGGANIRKIRDNTGARIIFPTARDEDQelITII-GTKEAVEKAKEELE 66
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 62-129 1.10e-03

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: 37.43  E-value: 1.10e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334185393  62 HSVSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPssrNKD----HISIEGGSvDCVTKASKRIATIIDE 129
Cdd:cd22451    1 ASIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVP---KKDdpsgKIRITGAR-DGVEAATAKILNISDE 68
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 64-123 3.20e-03

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: 35.74  E-value: 3.20e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334185393  64 VSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILP---SSRNKDHISIEgGSVDCVTKASKRI 123
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPkegEGSGERVVTIT-GTPEAVEKAKELI 62
KH-I_Vigilin_rpt2 cd22406
second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 63-129 4.94e-03

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: 35.75  E-value: 4.94e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 334185393  63 SVSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPS-SRNKDHISIEGGSvDCVTKASKRIATIIDE 129
Cdd:cd22406    6 SVTVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRqEDNSDEIKITGTK-EGIEKARHEIQLISDE 72
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 64-128 5.24e-03

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: 35.24  E-value: 5.24e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 334185393  64 VSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILP-SSRNKDHISIEgGSVDCVTKASKRIATIID 128
Cdd:cd02394    4 TTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPdDEANSDEIRIE-GSPEGVKKAKAEILELVD 68
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 63-123 8.27e-03

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: 34.49  E-value: 8.27e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334185393  63 SVSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSRNK-DHISIEGGSVDCvTKASKRI 123
Cdd:cd22411    1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDsDVITITGKKEDV-EKARERI 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH