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Conserved domains on  [gi|367016243|ref|XP_003682620|]
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hypothetical protein TDEL_0G00420 [Torulaspora delbrueckii]

Protein Classification

RRM_Yme2p_like and RNA12 domain-containing protein( domain architecture ID 10189498)

RRM_Yme2p_like and RNA12 domain-containing protein

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 ...
 349-778 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: 668.63  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  349 RIEKVNDLKMWLEENNNTFVVIRGPRGSGKHELVMQHTLQNRDNVLYLDCDKFIKSRTDAKFLRNAANQLGYFPIFPWFN 428
Cdd:pfam10443   1 RKEKIEQLQEWLLENVNTFIVVQGPRGSGKRELVMDRVLKDRKNVLVIDCDQLQKARGDAGFISTAASQVGYFPVFSWMN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  429 SVTNVIDLMVQGLTGQKSGLSETKEAQFRNMLTTGLMSIRHIALKGYrttiKNGDESINIKEEDYLQQHPEEKPVIVIDR 508
Cdd:pfam10443  81 SISSLIDLAAQGLTGQKAGFSETKEAQLRNILQTTATALKDIALEEY----KKEDKDANLKEEDYLEAHPEAKPVVVIDN 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  509 FTGKSEINGFIYKELSDWAAMLVQMNIAHVIFLTETVAPNQILSESLPTQVFKTLILSDASKENSKKYVLAQLiDQNMQT 588
Cdd:pfam10443 157 FLHKAEENGFVYKKLAEWAASLVQNNIAHVIFLTEDVSYSKPLSKALPNQVFKTISLGDASPDVARKYVLSQL-DEDTRK 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  589 AKLVADGENTDvEKKVDIDEKIIKEIDEVLEPLGGRMLDLQAFVRRVKSGEEPKEALDKMVEQSSEQITQIFLSDKVD-- 666
Cdd:pfam10443 236 EENSSDEQNTD-DKAATANEKDLKELDSCIEPLGGRMTDLQAFARRIKSGESPSEAVNDIIEQSASEILKMFLLDSGDas 314

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  667 --PIKSAQAWELIELLTEHPKVTFEDIVFRPLFKAAPELGITELENNGLVSVSRERGVLKEIFPAKPLYRAAFQYLVNDP 744
Cdd:pfam10443 315 dlPWTPEQAWYLIKLLSKNGSIPYNELLLSPLFKGSGETALRALEQAELISVTRDNGRPSTIRPGKPVYRAAFKRLLNDK 394

                         410       420       430
                  ....*....|....*....|....*....|....
gi 367016243  745 DLSTILKTRYLLKVVGFEAGRIKKWEEELRPLGK 778
Cdd:pfam10443 395 VLSSRLDLEYLTALIAKENKKIKKYEEELRLLGK 428
RRM_Yme2p_like cd12433
RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar ...
 180-261 7.31e-33

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: 121.60  E-value: 7.31e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243 180 RLPNKTIVVKFQGPALTEEEIYSLFRRYGTISDIF--PVTGSDNTARVKYRSFRGAICAKNCVSGIEIH--NTVLHIQYE 255
Cdd:cd12433    1 RYPSRTIRVEFEGPELSQEELYSLFRPYGRINDITppPPDSLPRYATVTFRRIRGAIAAKNCLHGYVVNegGTRLRIQYE 80


                 ....*.
gi 367016243 256 KIEQGH 261
Cdd:cd12433   81 PKLRAH 86
 
Name Accession Description Interval E-value
RNA12 pfam10443
RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM ...
 349-778 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: 668.63  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  349 RIEKVNDLKMWLEENNNTFVVIRGPRGSGKHELVMQHTLQNRDNVLYLDCDKFIKSRTDAKFLRNAANQLGYFPIFPWFN 428
Cdd:pfam10443   1 RKEKIEQLQEWLLENVNTFIVVQGPRGSGKRELVMDRVLKDRKNVLVIDCDQLQKARGDAGFISTAASQVGYFPVFSWMN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  429 SVTNVIDLMVQGLTGQKSGLSETKEAQFRNMLTTGLMSIRHIALKGYrttiKNGDESINIKEEDYLQQHPEEKPVIVIDR 508
Cdd:pfam10443  81 SISSLIDLAAQGLTGQKAGFSETKEAQLRNILQTTATALKDIALEEY----KKEDKDANLKEEDYLEAHPEAKPVVVIDN 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  509 FTGKSEINGFIYKELSDWAAMLVQMNIAHVIFLTETVAPNQILSESLPTQVFKTLILSDASKENSKKYVLAQLiDQNMQT 588
Cdd:pfam10443 157 FLHKAEENGFVYKKLAEWAASLVQNNIAHVIFLTEDVSYSKPLSKALPNQVFKTISLGDASPDVARKYVLSQL-DEDTRK 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  589 AKLVADGENTDvEKKVDIDEKIIKEIDEVLEPLGGRMLDLQAFVRRVKSGEEPKEALDKMVEQSSEQITQIFLSDKVD-- 666
Cdd:pfam10443 236 EENSSDEQNTD-DKAATANEKDLKELDSCIEPLGGRMTDLQAFARRIKSGESPSEAVNDIIEQSASEILKMFLLDSGDas 314

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  667 --PIKSAQAWELIELLTEHPKVTFEDIVFRPLFKAAPELGITELENNGLVSVSRERGVLKEIFPAKPLYRAAFQYLVNDP 744
Cdd:pfam10443 315 dlPWTPEQAWYLIKLLSKNGSIPYNELLLSPLFKGSGETALRALEQAELISVTRDNGRPSTIRPGKPVYRAAFKRLLNDK 394

                         410       420       430
                  ....*....|....*....|....*....|....
gi 367016243  745 DLSTILKTRYLLKVVGFEAGRIKKWEEELRPLGK 778
Cdd:pfam10443 395 VLSSRLDLEYLTALIAKENKKIKKYEEELRLLGK 428
RRM_Yme2p_like cd12433
RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar ...
 180-261 7.31e-33

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: 121.60  E-value: 7.31e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243 180 RLPNKTIVVKFQGPALTEEEIYSLFRRYGTISDIF--PVTGSDNTARVKYRSFRGAICAKNCVSGIEIH--NTVLHIQYE 255
Cdd:cd12433    1 RYPSRTIRVEFEGPELSQEELYSLFRPYGRINDITppPPDSLPRYATVTFRRIRGAIAAKNCLHGYVVNegGTRLRIQYE 80


                 ....*.
gi 367016243 256 KIEQGH 261
Cdd:cd12433   81 PKLRAH 86
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 186-251 3.60e-08

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: 50.69  E-value: 3.60e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  186 IVVKFQGPALTEEEIYSLFRRYGTISDIFPVTG----SDNTARVKYRSFRGAICAKNCVSGIEIHNTVLH 251
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDetgrSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
COG1672 COG1672
Predicted ATPase, archaeal AAA+ ATPase superfamily [General function prediction only];
349-445 1.14e-05

Predicted ATPase, archaeal AAA+ ATPase superfamily [General function prediction only];


Pssm-ID: 441278 [Multi-domain]  Cd Length: 324  Bit Score: 48.37  E-value: 1.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243 349 RIEKVNDLKMWLEENNNTFVVIRGPRGSGKHELVmQHTLQNRDnVLYLDCDKFIKSRTDAKFLRNAANQLGYFPIFPWFN 428
Cdd:COG1672    5 REEELEELEKLYESDGGELVVVYGRRRVGKTSLI-KEFLKEKP-AIYFDAREESERESLRDFSEALAEALGDPLSKKEFE 82

                         90
                 ....*....|....*..
gi 367016243 429 SVTNVIDLMVQGLTGQK 445
Cdd:COG1672   83 SWEEAFEYLAELAEGKR 99
RRM smart00360
RNA recognition motif;
185-252 3.28e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.58  E-value: 3.28e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 367016243   185 TIVVKFQGPALTEEEIYSLFRRYGTISDIF----PVTG-SDNTARVKYRSFRGAICAKNCVSGIEIHNTVLHI 252
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRlvrdKETGkSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
 
Name Accession Description Interval E-value
RNA12 pfam10443
RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM ...
 349-778 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: 668.63  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  349 RIEKVNDLKMWLEENNNTFVVIRGPRGSGKHELVMQHTLQNRDNVLYLDCDKFIKSRTDAKFLRNAANQLGYFPIFPWFN 428
Cdd:pfam10443   1 RKEKIEQLQEWLLENVNTFIVVQGPRGSGKRELVMDRVLKDRKNVLVIDCDQLQKARGDAGFISTAASQVGYFPVFSWMN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  429 SVTNVIDLMVQGLTGQKSGLSETKEAQFRNMLTTGLMSIRHIALKGYrttiKNGDESINIKEEDYLQQHPEEKPVIVIDR 508
Cdd:pfam10443  81 SISSLIDLAAQGLTGQKAGFSETKEAQLRNILQTTATALKDIALEEY----KKEDKDANLKEEDYLEAHPEAKPVVVIDN 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  509 FTGKSEINGFIYKELSDWAAMLVQMNIAHVIFLTETVAPNQILSESLPTQVFKTLILSDASKENSKKYVLAQLiDQNMQT 588
Cdd:pfam10443 157 FLHKAEENGFVYKKLAEWAASLVQNNIAHVIFLTEDVSYSKPLSKALPNQVFKTISLGDASPDVARKYVLSQL-DEDTRK 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  589 AKLVADGENTDvEKKVDIDEKIIKEIDEVLEPLGGRMLDLQAFVRRVKSGEEPKEALDKMVEQSSEQITQIFLSDKVD-- 666
Cdd:pfam10443 236 EENSSDEQNTD-DKAATANEKDLKELDSCIEPLGGRMTDLQAFARRIKSGESPSEAVNDIIEQSASEILKMFLLDSGDas 314

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  667 --PIKSAQAWELIELLTEHPKVTFEDIVFRPLFKAAPELGITELENNGLVSVSRERGVLKEIFPAKPLYRAAFQYLVNDP 744
Cdd:pfam10443 315 dlPWTPEQAWYLIKLLSKNGSIPYNELLLSPLFKGSGETALRALEQAELISVTRDNGRPSTIRPGKPVYRAAFKRLLNDK 394

                         410       420       430
                  ....*....|....*....|....*....|....
gi 367016243  745 DLSTILKTRYLLKVVGFEAGRIKKWEEELRPLGK 778
Cdd:pfam10443 395 VLSSRLDLEYLTALIAKENKKIKKYEEELRLLGK 428
RRM_Yme2p_like cd12433
RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar ...
 180-261 7.31e-33

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: 121.60  E-value: 7.31e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243 180 RLPNKTIVVKFQGPALTEEEIYSLFRRYGTISDIF--PVTGSDNTARVKYRSFRGAICAKNCVSGIEIH--NTVLHIQYE 255
Cdd:cd12433    1 RYPSRTIRVEFEGPELSQEELYSLFRPYGRINDITppPPDSLPRYATVTFRRIRGAIAAKNCLHGYVVNegGTRLRIQYE 80


                 ....*.
gi 367016243 256 KIEQGH 261
Cdd:cd12433   81 PKLRAH 86
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 186-251 3.60e-08

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: 50.69  E-value: 3.60e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243  186 IVVKFQGPALTEEEIYSLFRRYGTISDIFPVTG----SDNTARVKYRSFRGAICAKNCVSGIEIHNTVLH 251
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDetgrSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
COG1672 COG1672
Predicted ATPase, archaeal AAA+ ATPase superfamily [General function prediction only];
349-445 1.14e-05

Predicted ATPase, archaeal AAA+ ATPase superfamily [General function prediction only];


Pssm-ID: 441278 [Multi-domain]  Cd Length: 324  Bit Score: 48.37  E-value: 1.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243 349 RIEKVNDLKMWLEENNNTFVVIRGPRGSGKHELVmQHTLQNRDnVLYLDCDKFIKSRTDAKFLRNAANQLGYFPIFPWFN 428
Cdd:COG1672    5 REEELEELEKLYESDGGELVVVYGRRRVGKTSLI-KEFLKEKP-AIYFDAREESERESLRDFSEALAEALGDPLSKKEFE 82

                         90
                 ....*....|....*..
gi 367016243 429 SVTNVIDLMVQGLTGQK 445
Cdd:COG1672   83 SWEEAFEYLAELAEGKR 99
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 186-253 1.25e-05

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: 43.81  E-value: 1.25e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 367016243 186 IVVKFQGPALTEEEIYSLFRRYGTISDIFPVTGSD----NTARVKYRSFRGAICAKNCVSGIEIHNTVLHIQ 253
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDgkskGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM smart00360
RNA recognition motif;
185-252 3.28e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.58  E-value: 3.28e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 367016243   185 TIVVKFQGPALTEEEIYSLFRRYGTISDIF----PVTG-SDNTARVKYRSFRGAICAKNCVSGIEIHNTVLHI 252
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRlvrdKETGkSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
 185-253 1.03e-03

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 38.39  E-value: 1.03e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 367016243 185 TIVVKFQGPALTEEEIYSLFRRYGTISDIFPvTGSDNTAR-VKYRSFRGAICAKNCVSGIEIHNTVLHIQ 253
Cdd:cd12276    3 TLLVFNLDAPVSNDELKSLFSKFGEIKEIRP-TPDKPSQKfVEFYDVRDAEAALDGLNGRELLGGKLKVA 71
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
 192-254 1.08e-03

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 38.15  E-value: 1.08e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 367016243 192 GPALTEEEIYSLFRRYGTISDIfPVTGSDNTARVKYRSFRGAICAKNCVSGIEIHNTVLHIQY 254
Cdd:cd12340    8 PPDTSESAIREIFSPYGPVKEV-KMLSDSNFAFVEFEELEDAIRAKDSVHGRVLNNEPLYVTY 69
AAA_14 pfam13173
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 364-399 1.38e-03

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 463799 [Multi-domain]  Cd Length: 128  Bit Score: 39.49  E-value: 1.38e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 367016243  364 NNTFVVIRGPRGSGKHELVMQ--HTLQNRDNVLYLDCD 399
Cdd:pfam13173   1 SRKILVITGPRQVGKTTLLLQliKELLPPENILYINLD 38
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
 197-254 1.91e-03

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 37.64  E-value: 1.91e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 367016243 197 EEEIYSLFRRYGTISDIFPVTGSDNTARVKYRSFRGAICAKNCVSGIEIHNTVLHIQY 254
Cdd:cd12524   15 DEELRALFEQFGEIRTLYTACKHRGFIMVSYYDIRAAQSAKRALQGTELGGRKLDIHF 72
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
 193-256 4.41e-03

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 36.61  E-value: 4.41e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 367016243 193 PALTEEEIYSLFRRYGTISDI---FPVTGSDNT-ARVKYRSFRGAICAKNCVSGIEIHNTVLHIQYEK 256
Cdd:cd12309   12 ITITEEELRRAFERYGVVEDVdikRPPRGQGNAyAFVKFLNLDMAHRAKVAMSGQYIGRNQIKIGYGK 79
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 349-384 9.49e-03

ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is involved in binding ATP. There are eukaryote members as well as archaeal members in this family.


Pssm-ID: 376582 [Multi-domain]  Cd Length: 222  Bit Score: 38.46  E-value: 9.49e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 367016243  349 RIEKVNDLKMWLEENNNTFVVIRGPRGSGKHELVMQ 384
Cdd:pfam01637   4 REKELKELEEWAERGPNLIYVIYGPEGCGKTALLRE 39
 
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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