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Conserved domains on  [gi|1769767938|dbj|GES66653|]
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hypothetical protein ATETN484_0016020000 [Aspergillus terreus]

Protein Classification

RNA-binding protein( domain architecture ID 10350618)

RNA-binding protein containing an RNA recognition motif (RRM)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA12 pfam10443
RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM ...
 362-780 0e+00

RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM domain. This region is C-terminal to that and includes a P-loop motif suggesting this region binds to NTP. The RNA12 proteins is involved in pre-rRNA maturation.


:

Pssm-ID: 371055  Cd Length: 429  Bit Score: 727.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 362 RQGDISQLQSWLTENAETFIVIQGPRGSGKRELVMNQALAPYKYKVVIDCKQIQDARGDTAKIARAASQVGYRPVFSWMN 441
Cdd:pfam10443   1 RKEKIEQLQEWLLENVNTFIVVQGPRGSGKRELVMDRVLKDRKNVLVIDCDQLQKARGDAGFISTAASQVGYFPVFSWMN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 442 SISSFVDLAAQGMIGTKAGFSETLDAQLSNIWQNTATALKQITLENRRKSDKDASLTDEEYLEAHPEQRPVVIIDNFLHN 521
Cdd:pfam10443  81 SISSLIDLAAQGLTGQKAGFSETKEAQLRNILQTTATALKDIALEEYKKEDKDANLKEEDYLEAHPEAKPVVVIDNFLHK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 522 ASEDNVVYEKITEWAAGLTTGNIAHVIFLTTDVSFAKPLSKALPNAVFRTISLGDCSLDVARRFVLSHLA------GESK 595
Cdd:pfam10443 161 AEENGFVYKKLAEWAASLVQNNIAHVIFLTEDVSYSKPLSKALPNQVFKTISLGDASPDVARKYVLSQLDedtrkeENSS 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 596 GEDKQAEKR-----GDLAGLDSCIEILGGRVTDLEFMAHRIEAGETPEAAVNRIIEQSASEILKMFILD-GGASSTAWTH 669
Cdd:pfam10443 241 DEQNTDDKAataneKDLKELDSCIEPLGGRMTDLQAFARRIKSGESPSEAVNDIIEQSASEILKMFLLDsGDASDLPWTP 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 670 EQAWHLIKTLakAKHGSIPYNQVLLSDLFKENGEATLRALEQAELISIVSANGCPEAVKPGKPVYRTVFKRLTENKTLSS 749
Cdd:pfam10443 321 EQAWYLIKLL--SKNGSIPYNELLLSPLFKGSGETALRALEQAELISVTRDNGRPSTIRPGKPVYRAAFKRLLNDKVLSS 398

                         410       420       430
                  ....*....|....*....|....*....|.
gi 1769767938 750 RLDLEILSQLIAKENKSIGKHEEELRLLGGL 780
Cdd:pfam10443 399 RLDLEYLTALIAKENKKIKKYEEELRLLGKL 429
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 177-275 1.88e-28

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


The actual alignment was detected with superfamily member cd12433:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 86  Bit Score: 109.28  E-value: 1.88e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 177 RIPSQRLKVEFHPASadgaadiLTTETLYSLFRSYGKLRDIEKQPADSkvSPHYAYVEFTRPRYAVMAKNCMHGFTCSEs 256
Cdd:cd12433     1 RYPSRTIRVEFEGPE-------LSQEELYSLFRPYGRINDITPPPPDS--LPRYATVTFRRIRGAIAAKNCLHGYVVNE- 70

                          90
                  ....*....|....*....
gi 1769767938 257 qgggkFGTRVKIKYERKIK 275
Cdd:cd12433    71 -----GGTRLRIQYEPKLR 84
 
Name Accession Description Interval E-value
RNA12 pfam10443
RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM ...
 362-780 0e+00

RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM domain. This region is C-terminal to that and includes a P-loop motif suggesting this region binds to NTP. The RNA12 proteins is involved in pre-rRNA maturation.


Pssm-ID: 371055  Cd Length: 429  Bit Score: 727.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 362 RQGDISQLQSWLTENAETFIVIQGPRGSGKRELVMNQALAPYKYKVVIDCKQIQDARGDTAKIARAASQVGYRPVFSWMN 441
Cdd:pfam10443   1 RKEKIEQLQEWLLENVNTFIVVQGPRGSGKRELVMDRVLKDRKNVLVIDCDQLQKARGDAGFISTAASQVGYFPVFSWMN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 442 SISSFVDLAAQGMIGTKAGFSETLDAQLSNIWQNTATALKQITLENRRKSDKDASLTDEEYLEAHPEQRPVVIIDNFLHN 521
Cdd:pfam10443  81 SISSLIDLAAQGLTGQKAGFSETKEAQLRNILQTTATALKDIALEEYKKEDKDANLKEEDYLEAHPEAKPVVVIDNFLHK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 522 ASEDNVVYEKITEWAAGLTTGNIAHVIFLTTDVSFAKPLSKALPNAVFRTISLGDCSLDVARRFVLSHLA------GESK 595
Cdd:pfam10443 161 AEENGFVYKKLAEWAASLVQNNIAHVIFLTEDVSYSKPLSKALPNQVFKTISLGDASPDVARKYVLSQLDedtrkeENSS 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 596 GEDKQAEKR-----GDLAGLDSCIEILGGRVTDLEFMAHRIEAGETPEAAVNRIIEQSASEILKMFILD-GGASSTAWTH 669
Cdd:pfam10443 241 DEQNTDDKAataneKDLKELDSCIEPLGGRMTDLQAFARRIKSGESPSEAVNDIIEQSASEILKMFLLDsGDASDLPWTP 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 670 EQAWHLIKTLakAKHGSIPYNQVLLSDLFKENGEATLRALEQAELISIVSANGCPEAVKPGKPVYRTVFKRLTENKTLSS 749
Cdd:pfam10443 321 EQAWYLIKLL--SKNGSIPYNELLLSPLFKGSGETALRALEQAELISVTRDNGRPSTIRPGKPVYRAAFKRLLNDKVLSS 398

                         410       420       430
                  ....*....|....*....|....*....|.
gi 1769767938 750 RLDLEILSQLIAKENKSIGKHEEELRLLGGL 780
Cdd:pfam10443 399 RLDLEYLTALIAKENKKIKKYEEELRLLGKL 429
RRM_Yme2p_like cd12433
RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar ...
 177-275 1.88e-28

RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar proteins; This subfamily corresponds to the RRM of Yme2p, also termed protein RNA12, an inner mitochondrial membrane protein that plays a critical role in mitochondrial DNA transactions. It may serve as a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae. Yme2p contains an exonuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal domain.


Pssm-ID: 409867 [Multi-domain]  Cd Length: 86  Bit Score: 109.28  E-value: 1.88e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 177 RIPSQRLKVEFHPASadgaadiLTTETLYSLFRSYGKLRDIEKQPADSkvSPHYAYVEFTRPRYAVMAKNCMHGFTCSEs 256
Cdd:cd12433     1 RYPSRTIRVEFEGPE-------LSQEELYSLFRPYGRINDITPPPPDS--LPRYATVTFRRIRGAIAAKNCLHGYVVNE- 70

                          90
                  ....*....|....*....
gi 1769767938 257 qgggkFGTRVKIKYERKIK 275
Cdd:cd12433    71 -----GGTRLRIQYEPKLR 84
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 199-252 2.46e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 45.69  E-value: 2.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1769767938 199 LTTETLYSLFRSYGKLRDIEKQPADSKVSPHYAYVEFTRPRYAVMAKNCMHGFT 252
Cdd:pfam00076  10 TTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKE 63
RRM smart00360
RNA recognition motif;
200-251 8.46e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 41.43  E-value: 8.46e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1769767938  200 TTETLYSLFRSYGKLRDIE-KQPADSKVSPHYAYVEFTRPRYAVMAKNCMHGF 251
Cdd:smart00360  12 TEEELRELFSKFGKVESVRlVRDKETGKSKGFAFVEFESEEDAEKALEALNGK 64
 
Name Accession Description Interval E-value
RNA12 pfam10443
RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM ...
 362-780 0e+00

RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM domain. This region is C-terminal to that and includes a P-loop motif suggesting this region binds to NTP. The RNA12 proteins is involved in pre-rRNA maturation.


Pssm-ID: 371055  Cd Length: 429  Bit Score: 727.95  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 362 RQGDISQLQSWLTENAETFIVIQGPRGSGKRELVMNQALAPYKYKVVIDCKQIQDARGDTAKIARAASQVGYRPVFSWMN 441
Cdd:pfam10443   1 RKEKIEQLQEWLLENVNTFIVVQGPRGSGKRELVMDRVLKDRKNVLVIDCDQLQKARGDAGFISTAASQVGYFPVFSWMN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 442 SISSFVDLAAQGMIGTKAGFSETLDAQLSNIWQNTATALKQITLENRRKSDKDASLTDEEYLEAHPEQRPVVIIDNFLHN 521
Cdd:pfam10443  81 SISSLIDLAAQGLTGQKAGFSETKEAQLRNILQTTATALKDIALEEYKKEDKDANLKEEDYLEAHPEAKPVVVIDNFLHK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 522 ASEDNVVYEKITEWAAGLTTGNIAHVIFLTTDVSFAKPLSKALPNAVFRTISLGDCSLDVARRFVLSHLA------GESK 595
Cdd:pfam10443 161 AEENGFVYKKLAEWAASLVQNNIAHVIFLTEDVSYSKPLSKALPNQVFKTISLGDASPDVARKYVLSQLDedtrkeENSS 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 596 GEDKQAEKR-----GDLAGLDSCIEILGGRVTDLEFMAHRIEAGETPEAAVNRIIEQSASEILKMFILD-GGASSTAWTH 669
Cdd:pfam10443 241 DEQNTDDKAataneKDLKELDSCIEPLGGRMTDLQAFARRIKSGESPSEAVNDIIEQSASEILKMFLLDsGDASDLPWTP 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 670 EQAWHLIKTLakAKHGSIPYNQVLLSDLFKENGEATLRALEQAELISIVSANGCPEAVKPGKPVYRTVFKRLTENKTLSS 749
Cdd:pfam10443 321 EQAWYLIKLL--SKNGSIPYNELLLSPLFKGSGETALRALEQAELISVTRDNGRPSTIRPGKPVYRAAFKRLLNDKVLSS 398

                         410       420       430
                  ....*....|....*....|....*....|.
gi 1769767938 750 RLDLEILSQLIAKENKSIGKHEEELRLLGGL 780
Cdd:pfam10443 399 RLDLEYLTALIAKENKKIKKYEEELRLLGKL 429
RRM_Yme2p_like cd12433
RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar ...
 177-275 1.88e-28

RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar proteins; This subfamily corresponds to the RRM of Yme2p, also termed protein RNA12, an inner mitochondrial membrane protein that plays a critical role in mitochondrial DNA transactions. It may serve as a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae. Yme2p contains an exonuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal domain.


Pssm-ID: 409867 [Multi-domain]  Cd Length: 86  Bit Score: 109.28  E-value: 1.88e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1769767938 177 RIPSQRLKVEFHPASadgaadiLTTETLYSLFRSYGKLRDIEKQPADSkvSPHYAYVEFTRPRYAVMAKNCMHGFTCSEs 256
Cdd:cd12433     1 RYPSRTIRVEFEGPE-------LSQEELYSLFRPYGRINDITPPPPDS--LPRYATVTFRRIRGAIAAKNCLHGYVVNE- 70

                          90
                  ....*....|....*....
gi 1769767938 257 qgggkFGTRVKIKYERKIK 275
Cdd:cd12433    71 -----GGTRLRIQYEPKLR 84
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 199-252 1.31e-06

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 46.51  E-value: 1.31e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1769767938 199 LTTETLYSLFRSYGKLRDIEKQPADSKVSPHYAYVEFTRPRYAVMAKNCMHGFT 252
Cdd:cd00590    10 TTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTE 63
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 199-252 2.46e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 45.69  E-value: 2.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1769767938 199 LTTETLYSLFRSYGKLRDIEKQPADSKVSPHYAYVEFTRPRYAVMAKNCMHGFT 252
Cdd:pfam00076  10 TTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKE 63
RRM smart00360
RNA recognition motif;
200-251 8.46e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 41.43  E-value: 8.46e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1769767938  200 TTETLYSLFRSYGKLRDIE-KQPADSKVSPHYAYVEFTRPRYAVMAKNCMHGF 251
Cdd:smart00360  12 TEEELRELFSKFGKVESVRlVRDKETGKSKGFAFVEFESEEDAEKALEALNGK 64
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
 194-249 4.05e-03

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 36.82  E-value: 4.05e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1769767938 194 GAADILTTETLYSLFRSYGKLRDIEkQPADSKVSPH--YAYVEFTRPRYAVMAKNCMH 249
Cdd:cd12347     5 GLAEEVDEKVLHAAFIPFGDIVDIQ-IPLDYETEKHrgFAFVEFEEAEDAAAAIDNMN 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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