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Conserved domains on  [gi|1063711867|ref|NP_001326073|]
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Putative eukaryotic LigT [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN00108 super family cl42901
unknown protein; Provisional
 178-378 8.63e-52

unknown protein; Provisional


The actual alignment was detected with superfamily member PLN00108:

Pssm-ID: 177724  Cd Length: 257  Bit Score: 173.33  E-value: 8.63e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 178 YSHFVSLPLAIHPELVDKLVNFQNSILGihsiasdkqddqanrattsvavdlkaNSETNQVNVgiksipivsyppkaksk 257
Cdd:PLN00108   36 FTHFVSLPLAIYPDLKKNIEAFQNSVLG--------------------------NNDKDPLKF----------------- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 258 SSTLLDLGIEKSIFIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIFPSVMDALDNKPVFIRLKGLDCMRGPLDKTRVLYA 337
Cdd:PLN00108   73 QSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYA 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1063711867 338 PVEEIGDEGRLLRACQVITDAFVKAGLVlEKDAKQSLKVKA 378
Cdd:PLN00108  153 PVEEVGHEGRLLNACHVIIDAFENAGFA-GKDAKSRLKLHA 192
KH-I super family cl00098
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 105-167 6.99e-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: 49.11  E-value: 6.99e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063711867 105 SLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSRNKDHISIEGGSVDCVTKASKRIATII 167
Cdd:cd22419     4 SLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
 
Name Accession Description Interval E-value
PLN00108 PLN00108
unknown protein; Provisional
 178-378 8.63e-52

unknown protein; Provisional


Pssm-ID: 177724  Cd Length: 257  Bit Score: 173.33  E-value: 8.63e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 178 YSHFVSLPLAIHPELVDKLVNFQNSILGihsiasdkqddqanrattsvavdlkaNSETNQVNVgiksipivsyppkaksk 257
Cdd:PLN00108   36 FTHFVSLPLAIYPDLKKNIEAFQNSVLG--------------------------NNDKDPLKF----------------- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 258 SSTLLDLGIEKSIFIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIFPSVMDALDNKPVFIRLKGLDCMRGPLDKTRVLYA 337
Cdd:PLN00108   73 QSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYA 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1063711867 338 PVEEIGDEGRLLRACQVITDAFVKAGLVlEKDAKQSLKVKA 378
Cdd:PLN00108  153 PVEEVGHEGRLLNACHVIIDAFENAGFA-GKDAKSRLKLHA 192
AKAP7_NLS pfam10469
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ...
 178-372 2.45e-32

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: 120.45  E-value: 2.45e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 178 YSHFVSLPLAIHpELVDKLVNFQNSILgihsiasdKQDDqanrattsvavdlkansetnqvnvgiksipivsyppkaksk 257
Cdd:pfam10469   1 PTHFLSIPLNSP-ELRKRLEEFQESVL--------KQLP----------------------------------------- 30

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 258 sstlldlGIEKSIFIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIFPSVMDALDNKPVFIRLKGLDCMRGPLDKTRVLYA 337
Cdd:pfam10469  31 -------GLDESLFIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIKDILNGNPLSLRFKGLETFNDDPSAVRVLYA 103

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1063711867 338 PVEEIGDEGRLLRACQVITDAFVKAGLVLEKDAKQ 372
Cdd:pfam10469 104 KVEEDDHSPKLQELADRIIRRFQEAGLLVKENNSR 138
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 105-167 6.99e-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: 49.11  E-value: 6.99e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063711867 105 SLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSRNKDHISIEGGSVDCVTKASKRIATII 167
Cdd:cd22419     4 SLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 271-368 4.36e-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: 43.86  E-value: 4.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 271 FIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIfpsvmdALDNKPVFIRLKGLDCMRGPldKTRVLYAPVEEigdEGRLLR 350
Cdd:COG1514    32 WVRPENLHLTLAFLGEVDEERLEALAEALARA------AAGAPPFELRLDGLGAFPRP--RPRVLWLGVEP---SPELLA 100

                          90
                  ....*....|....*...
gi 1063711867 351 ACQVITDAFVKAGLVLEK 368
Cdd:COG1514   101 LHRRLRAALARAGLPPER 118
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 103-163 8.83e-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: 8.83e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063711867 103 SVSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSR---NKDHISIEgGSVDCVTKASKRI 163
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSEsegNERIVTIT-GTPEAVEAAKALI 63
 
Name Accession Description Interval E-value
PLN00108 PLN00108
unknown protein; Provisional
 178-378 8.63e-52

unknown protein; Provisional


Pssm-ID: 177724  Cd Length: 257  Bit Score: 173.33  E-value: 8.63e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 178 YSHFVSLPLAIHPELVDKLVNFQNSILGihsiasdkqddqanrattsvavdlkaNSETNQVNVgiksipivsyppkaksk 257
Cdd:PLN00108   36 FTHFVSLPLAIYPDLKKNIEAFQNSVLG--------------------------NNDKDPLKF----------------- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 258 SSTLLDLGIEKSIFIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIFPSVMDALDNKPVFIRLKGLDCMRGPLDKTRVLYA 337
Cdd:PLN00108   73 QSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRGLDCMNGSLDKTRVLYA 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1063711867 338 PVEEIGDEGRLLRACQVITDAFVKAGLVlEKDAKQSLKVKA 378
Cdd:PLN00108  153 PVEEVGHEGRLLNACHVIIDAFENAGFA-GKDAKSRLKLHA 192
AKAP7_NLS pfam10469
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ...
 178-372 2.45e-32

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: 120.45  E-value: 2.45e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 178 YSHFVSLPLAIHpELVDKLVNFQNSILgihsiasdKQDDqanrattsvavdlkansetnqvnvgiksipivsyppkaksk 257
Cdd:pfam10469   1 PTHFLSIPLNSP-ELRKRLEEFQESVL--------KQLP----------------------------------------- 30

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 258 sstlldlGIEKSIFIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIFPSVMDALDNKPVFIRLKGLDCMRGPLDKTRVLYA 337
Cdd:pfam10469  31 -------GLDESLFIPPEKLHITLLVLVLLDDEEVARAKEALRECREEIKDILNGNPLSLRFKGLETFNDDPSAVRVLYA 103

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1063711867 338 PVEEIGDEGRLLRACQVITDAFVKAGLVLEKDAKQ 372
Cdd:pfam10469 104 KVEEDDHSPKLQELADRIIRRFQEAGLLVKENNSR 138
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 105-167 6.99e-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: 49.11  E-value: 6.99e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063711867 105 SLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSRNKDHISIEGGSVDCVTKASKRIATII 167
Cdd:cd22419     4 SLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKDRSGVDSARTRIEVLV 66
KH-I_Vigilin_rpt3 cd22407
third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 105-163 1.19e-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: 1.19e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 105 SLEVGASLIKFIRGKEGTTQMKLEEEMGVKI-ILPSSRNKDHISIEGGSvDCVTKASKRI 163
Cdd:cd22407     3 RLDIPKVYHPFIAGPNNENVKELQEETGVRInIPPPSVNKDEIVVSGEK-EGVAQAVAKI 61
ThpR COG1514
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ...
 271-368 4.36e-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: 43.86  E-value: 4.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063711867 271 FIKPSTFHLTVVMLKLWNKDRVNAACDVLKSIfpsvmdALDNKPVFIRLKGLDCMRGPldKTRVLYAPVEEigdEGRLLR 350
Cdd:COG1514    32 WVRPENLHLTLAFLGEVDEERLEALAEALARA------AAGAPPFELRLDGLGAFPRP--RPRVLWLGVEP---SPELLA 100

                          90
                  ....*....|....*...
gi 1063711867 351 ACQVITDAFVKAGLVLEK 368
Cdd:COG1514   101 LHRRLRAALARAGLPPER 118
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 103-163 8.83e-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: 8.83e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063711867 103 SVSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSR---NKDHISIEgGSVDCVTKASKRI 163
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, ...
 102-164 8.14e-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: 8.14e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063711867 102 HSVSLEVGAS--LIKFIRGKEGTTQMKLEEEMGVKIILPSSRNKDH--ISIEgGSVDCVTKASKRIA 164
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 ...
 102-169 1.13e-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: 37.05  E-value: 1.13e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063711867 102 HSVSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPssrNKD----HISIEGGSvDCVTKASKRIATIIDE 169
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 ...
 104-163 3.50e-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: 3.50e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063711867 104 VSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILP---SSRNKDHISIEgGSVDCVTKASKRI 163
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; ...
 103-169 4.55e-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: 4.55e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063711867 103 SVSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPS-SRNKDHISIEGGSvDCVTKASKRIATIIDE 169
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, ...
 104-168 5.66e-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: 5.66e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063711867 104 VSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILP-SSRNKDHISIEgGSVDCVTKASKRIATIID 168
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; ...
 103-163 9.30e-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: 9.30e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063711867 103 SVSLEVGASLIKFIRGKEGTTQMKLEEEMGVKIILPSSRNK-DHISIEGGSVDCvTKASKRI 163
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.
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