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Conserved domains on  [gi|2048774953|ref|NP_001382063|]
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LIX1-like protein [Rattus norvegicus]

Protein Classification

DSRM_SF domain-containing protein( domain architecture ID 10633134)

DSRM_SF domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LIX1 pfam14954
Limb expression 1; This entry represents the limb expression 1 (LIX1) family.
 87-328 1.78e-178

Limb expression 1; This entry represents the limb expression 1 (LIX1) family.


:

Pssm-ID: 464400  Cd Length: 242  Bit Score: 493.52  E-value: 1.78e-178
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953  87 SFAKHTQGYGRVNVVEALQEFWQMKQSRGADLKNGALVVYEMVPSNSPPYVCYVTLPGGSCFGSFQFCPTKAEARRSAAK 166
Cdd:pfam14954   1 SFAKHSQGYKDVNVVEALQEFWQMKQTRGAGFSSEALVVYESVPSPGPPYVCYVTLPGGSCFGNFQNCPTKAEARRSAAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953 167 IALMNSVFNEHPSRRITDEFIEKSVSEALASFNGNREEADNPNTGIGAFRFMLESNKGKSMLEFQELMTVFQLLHWNGSL 246
Cdd:pfam14954  81 IALMNSVFNEHPSRRITDEFIEKAVQEARASFSGSLGDAHDPNTGIGAFRFMLESNKGRTMLEFQELMTVFQLLHWNGSL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953 247 KAMRERQCSRQEVLAHYSHRALDDDIRHQMALDWVSREQSVPGALSRELASTERELDEARLAGKELRFHKEKKDILMLAA 326
Cdd:pfam14954 161 KAMRERQCSRQEVIAHYSQRALDDDMRSQMALDWIAREQESPGLISQELALAEKELEAARLAGRELRFYKEKKDILSLAL 240


                  ..
gi 2048774953 327 GQ 328
Cdd:pfam14954 241 SQ 242
 
Name Accession Description Interval E-value
LIX1 pfam14954
Limb expression 1; This entry represents the limb expression 1 (LIX1) family.
 87-328 1.78e-178

Limb expression 1; This entry represents the limb expression 1 (LIX1) family.


Pssm-ID: 464400  Cd Length: 242  Bit Score: 493.52  E-value: 1.78e-178
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953  87 SFAKHTQGYGRVNVVEALQEFWQMKQSRGADLKNGALVVYEMVPSNSPPYVCYVTLPGGSCFGSFQFCPTKAEARRSAAK 166
Cdd:pfam14954   1 SFAKHSQGYKDVNVVEALQEFWQMKQTRGAGFSSEALVVYESVPSPGPPYVCYVTLPGGSCFGNFQNCPTKAEARRSAAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953 167 IALMNSVFNEHPSRRITDEFIEKSVSEALASFNGNREEADNPNTGIGAFRFMLESNKGKSMLEFQELMTVFQLLHWNGSL 246
Cdd:pfam14954  81 IALMNSVFNEHPSRRITDEFIEKAVQEARASFSGSLGDAHDPNTGIGAFRFMLESNKGRTMLEFQELMTVFQLLHWNGSL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953 247 KAMRERQCSRQEVLAHYSHRALDDDIRHQMALDWVSREQSVPGALSRELASTERELDEARLAGKELRFHKEKKDILMLAA 326
Cdd:pfam14954 161 KAMRERQCSRQEVIAHYSQRALDDDMRSQMALDWIAREQESPGLISQELALAEKELEAARLAGRELRFYKEKKDILSLAL 240


                  ..
gi 2048774953 327 GQ 328
Cdd:pfam14954 241 SQ 242
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 119-169 4.01e-04

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 38.03  E-value: 4.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2048774953 119 KNGALVVYEMV---PSNSPPYVCYVTLPGGSCFGSfqfCPTKAEARRSAAKIAL 169
Cdd:cd00048     7 NKWPPPEYETVeegGPHNPRFTCTVTVNGQTFEGE---GKSKKEAKQAAAEKAL 57
DSRM smart00358
Double-stranded RNA binding motif;
101-169 2.46e-03

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 36.09  E-value: 2.46e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2048774953  101 VEALQEFWQmkqsrgadlKNGALVVYEMV----PSNSPPYVCYVTLpGGSCFGSFQfCPTKAEARRSAAKIAL 169
Cdd:smart00358   2 KSLLQELAQ---------KRKLPPEYELVkeegPDHAPRFTVTVKV-GGKRTGEGE-GSSKKEAKQRAAEAAL 63
 
Name Accession Description Interval E-value
LIX1 pfam14954
Limb expression 1; This entry represents the limb expression 1 (LIX1) family.
 87-328 1.78e-178

Limb expression 1; This entry represents the limb expression 1 (LIX1) family.


Pssm-ID: 464400  Cd Length: 242  Bit Score: 493.52  E-value: 1.78e-178
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953  87 SFAKHTQGYGRVNVVEALQEFWQMKQSRGADLKNGALVVYEMVPSNSPPYVCYVTLPGGSCFGSFQFCPTKAEARRSAAK 166
Cdd:pfam14954   1 SFAKHSQGYKDVNVVEALQEFWQMKQTRGAGFSSEALVVYESVPSPGPPYVCYVTLPGGSCFGNFQNCPTKAEARRSAAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953 167 IALMNSVFNEHPSRRITDEFIEKSVSEALASFNGNREEADNPNTGIGAFRFMLESNKGKSMLEFQELMTVFQLLHWNGSL 246
Cdd:pfam14954  81 IALMNSVFNEHPSRRITDEFIEKAVQEARASFSGSLGDAHDPNTGIGAFRFMLESNKGRTMLEFQELMTVFQLLHWNGSL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953 247 KAMRERQCSRQEVLAHYSHRALDDDIRHQMALDWVSREQSVPGALSRELASTERELDEARLAGKELRFHKEKKDILMLAA 326
Cdd:pfam14954 161 KAMRERQCSRQEVIAHYSQRALDDDMRSQMALDWIAREQESPGLISQELALAEKELEAARLAGRELRFYKEKKDILSLAL 240


                  ..
gi 2048774953 327 GQ 328
Cdd:pfam14954 241 SQ 242
CCDC158 pfam15921
Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. ...
 169-320 3.27e-05

Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. The function is not known.


Pssm-ID: 464943 [Multi-domain]  Cd Length: 1112  Bit Score: 45.88  E-value: 3.27e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953  169 LMNSVFNEHPSRRITDEFIEKSVSEALASFNGNREEADNPNTGIGAFRFMLEsnkgksmLEFQELMTVF----QLLHWNG 244
Cdd:pfam15921  476 MLRKVVEELTAKKMTLESSERTVSDLTASLQEKERAIEATNAEITKLRSRVD-------LKLQELQHLKnegdHLRNVQT 548

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2048774953  245 SLKAMRERQCSRQEVLahyshRALDDDIRHQMALdwVSREQSVPGALSRELASTERELDEARLAGKELRFHKEKKD 320
Cdd:pfam15921  549 ECEALKLQMAEKDKVI-----EILRQQIENMTQL--VGQHGRTAGAMQVEKAQLEKEINDRRLELQEFKILKDKKD 617
Dicer_dimer pfam03368
Dicer dimerization domain; This domain is found in members of the Dicer protein family which ...
 125-165 6.82e-05

Dicer dimerization domain; This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners.


Pssm-ID: 460900  Cd Length: 89  Bit Score: 40.94  E-value: 6.82e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2048774953 125 VYEMVPSNSPPYVCYVTLPGGSCFGSFQ--FCPTKAEARRSAA 165
Cdd:pfam03368  23 EYEVTEVEGGKFVCTVTLPINSPLRSIEgpPWRSKKLAKRSAA 65
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 119-169 4.01e-04

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 38.03  E-value: 4.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2048774953 119 KNGALVVYEMV---PSNSPPYVCYVTLPGGSCFGSfqfCPTKAEARRSAAKIAL 169
Cdd:cd00048     7 NKWPPPEYETVeegGPHNPRFTCTVTVNGQTFEGE---GKSKKEAKQAAAEKAL 57
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 104-170 5.30e-04

first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380736 [Multi-domain]  Cd Length: 69  Bit Score: 37.84  E-value: 5.30e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774953 104 LQEFwqmKQSRGADLKngalvVYEMV---PSNSPPYVCYVTLpGGSCFGSFQFCPTKAEARRSAAKIALM 170
Cdd:cd19907     6 LQEY---AQKSCLNLP-----VYACIregPDHAPRFRATVTF-NGVIFESPPGFPTLKAAEHSAAEVALN 66
DSRM smart00358
Double-stranded RNA binding motif;
101-169 2.46e-03

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 36.09  E-value: 2.46e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2048774953  101 VEALQEFWQmkqsrgadlKNGALVVYEMV----PSNSPPYVCYVTLpGGSCFGSFQfCPTKAEARRSAAKIAL 169
Cdd:smart00358   2 KSLLQELAQ---------KRKLPPEYELVkeegPDHAPRFTVTVKV-GGKRTGEGE-GSSKKEAKQRAAEAAL 63
DSRM_A1CF-like cd19872
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ...
 125-169 5.62e-03

double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding protein 46 (RBM46) and similar proteins; The family includes two dsRNA-binding motif-containing proteins, A1CF and RBM46. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. RBM46 (also called cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. Members of this family contain three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380701  Cd Length: 75  Bit Score: 35.34  E-value: 5.62e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2048774953 125 VYEMVPSNSPP----YVCYVTLPGGSC----FGSFQFCPTKAEARRSAAKIAL 169
Cdd:cd19872    19 VYQLLSTSSNNevqlFIYKVTIPNLPNgrltFQPDKLCRTPEEAKVLAAEFVL 71
 
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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