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Conserved domains on  [gi|530409209|ref|XP_005255661|]
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RNA exonuclease 5 isoform X1 [Homo sapiens]

Protein Classification

REX1_like and RRM_SF domain-containing protein( domain architecture ID 10150244)

protein containing domains REX1_like, and RRM_SF

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 229-377 2.93e-80

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


:

Pssm-ID: 99848  Cd Length: 150  Bit Score: 253.56  E-value: 2.93e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 229 FGLDCEMCLTSKGRELTRISLVAEGGCCVMDELVKPENKILDYLTSFSGITKKILNPVTTKLKDVQRQLKALLPPDAVLV 308
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530409209 309 GHSLDLDLRALKMIHPYVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQCpDRLGHDATEDARTILELAR 377
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 506-576 1.69e-39

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 cd12273:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 71  Bit Score: 139.98  E-value: 1.69e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530409209 506 TVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQPHLCIQYEVLEAAQLAIESLDGILVDGICIKVQR 576
Cdd:cd12273    1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQPYVCVQYEVLEAAQLAVETLDGALVDGHCIKVQR 71
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 602-672 6.15e-31

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 cd12274:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 71  Bit Score: 115.73  E-value: 6.15e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530409209 602 IYLSGVSETFKEQLLQEPRLFL-GLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGkDWKLKGRHA 672
Cdd:cd12274    1 IYVSGFKKSLTEEDLQERFSQLsDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 229-377 2.93e-80

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 253.56  E-value: 2.93e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 229 FGLDCEMCLTSKGRELTRISLVAEGGCCVMDELVKPENKILDYLTSFSGITKKILNPVTTKLKDVQRQLKALLPPDAVLV 308
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530409209 309 GHSLDLDLRALKMIHPYVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQCpDRLGHDATEDARTILELAR 377
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150
RRM1_NEFsp cd12273
RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 506-576 1.69e-39

RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.


Pssm-ID: 409716 [Multi-domain]  Cd Length: 71  Bit Score: 139.98  E-value: 1.69e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530409209 506 TVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQPHLCIQYEVLEAAQLAIESLDGILVDGICIKVQR 576
Cdd:cd12273    1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQPYVCVQYEVLEAAQLAVETLDGALVDGHCIKVQR 71
RRM2_NEFsp cd12274
RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 602-672 6.15e-31

RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.


Pssm-ID: 409717 [Multi-domain]  Cd Length: 71  Bit Score: 115.73  E-value: 6.15e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530409209 602 IYLSGVSETFKEQLLQEPRLFL-GLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGkDWKLKGRHA 672
Cdd:cd12274    1 IYVSGFKKSLTEEDLQERFSQLsDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 228-384 1.86e-29

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 115.09  E-value: 1.86e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209   228 LFGLDCEM-CLTSKGRELTRISLV-AEGGC--CVMDELVKPENKILDYLTSFSGITKKILNPvTTKLKDVQRQLKALLPP 303
Cdd:smart00479   2 LVVIDCETtGLDPGKDEIIEIAAVdVDGGEiiEVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209   304 DAVLVGHSLDLDLRALKMIHP----------YVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQCpdrlGHDATEDART 371
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGLPKysLKKLAKRLLLEVIQR----AHRALDDARA 156

                          170
                   ....*....|...
gi 530409209   372 ILELARYFLKHGP 384
Cdd:smart00479 157 TAKLFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 231-375 5.96e-10

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 58.52  E-value: 5.96e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  231 LDCEM-CLTSKG---RELTRISLVAEGGC--CVMDELVKPE--NKILDYLTSFSGITKKILnPVTTKLKDVQRQLKALLP 302
Cdd:pfam00929   3 IDLETtGLDPEKdeiIEIAAVVIDGGENEigETFHTYVKPTrlPKLTDECTKFTGITQAML-DNKPSFEEVLEEFLEFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  303 PDAVLVGHS-------LDLDLRALKMIH----PYVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQcpdrLGHDATEDA 369
Cdd:pfam00929  82 KGNLLVAHNasfdvgfLRYDDKRFLKKPmpklNPVIDTLILDKATYKELPGrsLDALAEKLGLEHIG----RAHRALDDA 157


                  ....*.
gi 530409209  370 RTILEL 375
Cdd:pfam00929 158 RATAKL 163
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 494-657 9.74e-10

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 62.01  E-value: 9.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  494 NKRMRIKWTE----ISTVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQPH----LCIQYEVLEAAQLAIESLDGI 565
Cdd:TIGR01645  93 NQQRQQQRQQalaiMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKhkgfAFVEYEVPEAAQLALEQMNGQ 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  566 LVDGICIKVQRPVTelTLDCDTLVNELEGDSENQGSIYLSGVSETFKEQLLQEP-RLFLGLEAVILPKDLKSGKQKKYCF 644
Cdd:TIGR01645 173 MLGGRNIKVGRPSN--MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVfEAFGEIVKCQLARAPTGRGHKGYGF 250

                         170
                  ....*....|...
gi 530409209  645 LKFKSFGSAQQAL 657
Cdd:TIGR01645 251 IEYNNLQSQSEAI 263
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 259-390 1.51e-07

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 52.07  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 259 DELVKPENKILDYLTSFSGITKKILN--PvttKLKDVQRQLKALLPpDAVLVGHSLDLDLRALKM--------IHPYVID 328
Cdd:COG2176   45 STLVNPGRPIPPFITELTGITDEMVAdaP---PFEEVLPEFLEFLG-DAVLVAHNASFDLGFLNAalkrlglpFDNPVLD 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530409209 329 TSLLYVR--EQGRRFKLKFLAKVIlgkDIQCPDRlgHDATEDARTILELARYFLKH-GPKKIAEL 390
Cdd:COG2176  121 TLELARRllPELKSYKLDTLAERL---GIPLEDR--HRALGDAEATAELFLKLLEKlEEKGITTL 180
RRM smart00360
RNA recognition motif;
601-671 2.36e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 48.74  E-value: 2.36e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 530409209   601 SIYLSGVSETFKEQLLQEprLFL---GLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGKdwKLKGRH 671
Cdd:smart00360   1 TLFVGNLPPDTTEEELRE--LFSkfgKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK--ELDGRP 70
RRM smart00360
RNA recognition motif;
506-574 7.63e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 47.20  E-value: 7.63e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530409209   506 TVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVL--ETRQPHLC--IQYEVLEAAQLAIESLDGILVDGICIKV 574
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRdkETGKSKGFafVEFESEEDAEKALEALNGKELDGRPLKV 73
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 562-664 1.21e-06

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 51.82  E-value: 1.21e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  562 LDGILVDGICIKVQRPV----------------TELTLDCDTLVNELEGDSENQGSIYLSGVSETFKE-QLLQEPRLFLG 624
Cdd:TIGR01642 242 LDSIIYSNVFLKIRRPHdyipvpqitpevsqknPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEdQIKELLESFGD 321

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 530409209  625 LEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGKD 664
Cdd:TIGR01642 322 LKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKD 361
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 507-573 3.08e-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: 45.30  E-value: 3.08e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  507 VYAGPFSKNCNLRALKRLFKSFGPVQSMTFV-LETRQPHLC--IQYEVLEAAQLAIESLDGILVDGICIK 573
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVrDETGRSKGFafVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
521-574 1.82e-03

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 37.77  E-value: 1.82e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 530409209 521 LKRLFKSFGPVQSMTFVL--ETRQP--HLCIQYEVLEAAQLAIESLDGILVDGICIKV 574
Cdd:COG0724   18 LRELFSEYGEVTSVKLITdrETGRSrgFGFVEMPDDEEAQAAIEALNGAELMGRTLKV 75
PRK05755 PRK05755
DNA polymerase I; Provisional
 285-396 6.89e-03

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 40.08  E-value: 6.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 285 PVTTKLKDVQRQLKALLPPDAVL-VGHSLDLDLRALK----MIHPYVIDTSLL-YVREQGRRFKLKFLAKV--------- 349
Cdd:PRK05755 350 PLDQLDREVLAALKPLLEDPAIKkVGQNLKYDLHVLArygiELRGIAFDTMLAsYLLDPGRRHGLDSLAERylghktisf 429

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 530409209 350 --ILGKDIQC----PDRLGHDATEDARTILELARYFLkhgPKKIAELNLEALA 396
Cdd:PRK05755 430 eeVAGKQLTFaqvdLEEAAEYAAEDADVTLRLHEVLK---PKLLEEPGLLELY 479
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 229-377 2.93e-80

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 253.56  E-value: 2.93e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 229 FGLDCEMCLTSKGRELTRISLVAEGGCCVMDELVKPENKILDYLTSFSGITKKILNPVTTKLKDVQRQLKALLPPDAVLV 308
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530409209 309 GHSLDLDLRALKMIHPYVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQCpDRLGHDATEDARTILELAR 377
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150
RRM1_NEFsp cd12273
RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 506-576 1.69e-39

RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.


Pssm-ID: 409716 [Multi-domain]  Cd Length: 71  Bit Score: 139.98  E-value: 1.69e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530409209 506 TVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQPHLCIQYEVLEAAQLAIESLDGILVDGICIKVQR 576
Cdd:cd12273    1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQPYVCVQYEVLEAAQLAVETLDGALVDGHCIKVQR 71
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 230-377 6.14e-33

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.


Pssm-ID: 99840  Cd Length: 161  Bit Score: 124.70  E-value: 6.14e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 230 GLDCEMCLTSKGR-ELTRISLV-AEGGCCVMDELVKPENKILDYLTSFSGITKKIL---NPVTTKL--KDVQRQLK-ALL 301
Cdd:cd06137    2 ALDCEMVGLADGDsEVVRISAVdVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLeeaAKAGKTIfgWEAARAALwKFI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 302 PPDAVLVGHSLDLDLRALKMIHPYVIDTSLL---YV--REQGRRFKLKFLAKVILGKDIQcPDRLGHDATEDARTILELA 376
Cdd:cd06137   82 DPDTILVGHSLQNDLDALRMIHTRVVDTAILtreAVkgPLAKRQWSLRTLCRDFLGLKIQ-GGGEGHDSLEDALAAREVV 160


                 .
gi 530409209 377 R 377
Cdd:cd06137  161 L 161
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 231-377 2.33e-32

DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.


Pssm-ID: 99847  Cd Length: 152  Bit Score: 122.62  E-value: 2.33e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 231 LDCEMC-LTSKGRE--LTRISLVAEGGCCVMDELVKPENKILDYLTSFSGITKKILNPVTTkLKDVQRQLKALLpPDAVL 307
Cdd:cd06144    3 LDCEMVgVGPDGSEsaLARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPD-FEEVQKKVAELL-KGRIL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530409209 308 VGHSLDLDLRALKMIHPYVI--DTS--LLYVRE-QGRRFKLKFLAKVILGKDIQCpdrLGHDATEDARTILELAR 377
Cdd:cd06144   81 VGHALKNDLKVLKLDHPKKLirDTSkyKPLRKTaKGKSPSLKKLAKQLLGLDIQE---GEHSSVEDARAAMRLYR 152
RRM2_NEFsp cd12274
RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 602-672 6.15e-31

RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.


Pssm-ID: 409717 [Multi-domain]  Cd Length: 71  Bit Score: 115.73  E-value: 6.15e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530409209 602 IYLSGVSETFKEQLLQEPRLFL-GLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGkDWKLKGRHA 672
Cdd:cd12274    1 IYVSGFKKSLTEEDLQERFSQLsDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 228-384 1.86e-29

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 115.09  E-value: 1.86e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209   228 LFGLDCEM-CLTSKGRELTRISLV-AEGGC--CVMDELVKPENKILDYLTSFSGITKKILNPvTTKLKDVQRQLKALLPP 303
Cdd:smart00479   2 LVVIDCETtGLDPGKDEIIEIAAVdVDGGEiiEVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209   304 DAVLVGHSLDLDLRALKMIHP----------YVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQCpdrlGHDATEDART 371
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGLPKysLKKLAKRLLLEVIQR----AHRALDDARA 156

                          170
                   ....*....|...
gi 530409209   372 ILELARYFLKHGP 384
Cdd:smart00479 157 TAKLFKKLLERLE 169
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 244-377 1.25e-24

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.


Pssm-ID: 99846  Cd Length: 174  Bit Score: 101.15  E-value: 1.25e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 244 LTRISLV-AEG---GCCVMDELVKPENKILDYLTSFSGITKKILNPVT-----TKLKDVQRQLKALLPPDAVLVGHSLDL 314
Cdd:cd06143   33 LARVSVVrGEGeleGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKTssknlTTLKSAYLKLRLLVDLGCIFVGHGLAK 112

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530409209 315 DLRALKMIHP--YVIDTSLLYVREQGRRFKLKFLAKVILGKDIQCPdrlGHDATEDARTILELAR 377
Cdd:cd06143  113 DFRVINIQVPkeQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSE---THDSIEDARTALKLYR 174
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 231-377 8.84e-23

DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins; Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response.


Pssm-ID: 99852  Cd Length: 157  Bit Score: 95.58  E-value: 8.84e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 231 LDCEMCLTS-KGR--ELTRISLVAEGGCCVMDELVKPENKILDYLTSFSGITKK-ILNpvTTKLKDVQRQLKALLpPDAV 306
Cdd:cd06149    3 IDCEMVGTGpGGResELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQhLVN--ATPFAVAQKEILKIL-KGKV 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 530409209 307 LVGHSLDLDLRALKMIHP--YVIDTS---LLYVR---EQGRRFKLKFLAKVILGKDIQCpDRLGHDATEDARTILELAR 377
Cdd:cd06149   80 VVGHAIHNDFKALKYFHPkhMTRDTStipLLNRKagfPENCRVSLKVLAKRLLHRDIQV-GRQGHSSVEDARATMELYK 157
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 231-375 5.96e-10

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 58.52  E-value: 5.96e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  231 LDCEM-CLTSKG---RELTRISLVAEGGC--CVMDELVKPE--NKILDYLTSFSGITKKILnPVTTKLKDVQRQLKALLP 302
Cdd:pfam00929   3 IDLETtGLDPEKdeiIEIAAVVIDGGENEigETFHTYVKPTrlPKLTDECTKFTGITQAML-DNKPSFEEVLEEFLEFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  303 PDAVLVGHS-------LDLDLRALKMIH----PYVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQcpdrLGHDATEDA 369
Cdd:pfam00929  82 KGNLLVAHNasfdvgfLRYDDKRFLKKPmpklNPVIDTLILDKATYKELPGrsLDALAEKLGLEHIG----RAHRALDDA 157


                  ....*.
gi 530409209  370 RTILEL 375
Cdd:pfam00929 158 RATAKL 163
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 494-657 9.74e-10

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 62.01  E-value: 9.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  494 NKRMRIKWTE----ISTVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQPH----LCIQYEVLEAAQLAIESLDGI 565
Cdd:TIGR01645  93 NQQRQQQRQQalaiMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKhkgfAFVEYEVPEAAQLALEQMNGQ 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  566 LVDGICIKVQRPVTelTLDCDTLVNELEGDSENQGSIYLSGVSETFKEQLLQEP-RLFLGLEAVILPKDLKSGKQKKYCF 644
Cdd:TIGR01645 173 MLGGRNIKVGRPSN--MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVfEAFGEIVKCQLARAPTGRGHKGYGF 250

                         170
                  ....*....|...
gi 530409209  645 LKFKSFGSAQQAL 657
Cdd:TIGR01645 251 IEYNNLQSQSEAI 263
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
 505-576 1.72e-08

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 52.03  E-value: 1.72e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 530409209 505 STVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLET---RQPHLC-IQYEVLEAAQLAIESLDGILVDGICIKVQR 576
Cdd:cd12370    1 CRVYVGSIYFELGEDTIRQAFAPFGPIKSIDMSWDPvtmKHKGFAfVEYEVPEAAQLALEQMNGVMLGGRNIKVGR 76
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 231-377 2.83e-08

DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 53.84  E-value: 2.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 231 LDCEM-CLTSKGRELTRISLVA-EGGCCVMDE---LVKPENKILDYLTSFSGITKKILNPVTTkLKDVQRQLKALLPpDA 305
Cdd:cd06127    3 FDTETtGLDPKKDRIIEIGAVKvDGGIEIVERfetLVNPGRPIPPEATAIHGITDEMLADAPP-FEEVLPEFLEFLG-GR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 306 VLVGHSLDLDLRALK---------MIHPYVIDTSLLY--VREQGRRFKLKFLAKVILGkdiqCPDRLGHDATEDARTILE 374
Cdd:cd06127   81 VLVAHNASFDLRFLNrelrrlggpPLPNPWIDTLRLArrLLPGLRSHRLGLLLAERYG----IPLEGAHRALADALATAE 156


                 ...
gi 530409209 375 LAR 377
Cdd:cd06127  157 LLL 159
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 507-575 3.26e-08

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: 51.13  E-value: 3.26e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530409209 507 VYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQPHLC---IQYEVLEAAQLAIESLDGILVDGICIKVQ 575
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGfafVEFESPEDAEKALEALNGTELGGRPLKVS 72
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 259-390 1.51e-07

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 52.07  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 259 DELVKPENKILDYLTSFSGITKKILN--PvttKLKDVQRQLKALLPpDAVLVGHSLDLDLRALKM--------IHPYVID 328
Cdd:COG2176   45 STLVNPGRPIPPFITELTGITDEMVAdaP---PFEEVLPEFLEFLG-DAVLVAHNASFDLGFLNAalkrlglpFDNPVLD 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530409209 329 TSLLYVR--EQGRRFKLKFLAKVIlgkDIQCPDRlgHDATEDARTILELARYFLKH-GPKKIAEL 390
Cdd:COG2176  121 TLELARRllPELKSYKLDTLAERL---GIPLEDR--HRALGDAEATAELFLKLLEKlEEKGITTL 180
RRM smart00360
RNA recognition motif;
601-671 2.36e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 48.74  E-value: 2.36e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 530409209   601 SIYLSGVSETFKEQLLQEprLFL---GLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGKdwKLKGRH 671
Cdd:smart00360   1 TLFVGNLPPDTTEEELRE--LFSkfgKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK--ELDGRP 70
RRM smart00360
RNA recognition motif;
506-574 7.63e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 47.20  E-value: 7.63e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530409209   506 TVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVL--ETRQPHLC--IQYEVLEAAQLAIESLDGILVDGICIKV 574
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRdkETGKSKGFafVEFESEEDAEKALEALNGKELDGRPLKV 73
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 562-664 1.21e-06

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 51.82  E-value: 1.21e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  562 LDGILVDGICIKVQRPV----------------TELTLDCDTLVNELEGDSENQGSIYLSGVSETFKE-QLLQEPRLFLG 624
Cdd:TIGR01642 242 LDSIIYSNVFLKIRRPHdyipvpqitpevsqknPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEdQIKELLESFGD 321

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 530409209  625 LEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGKD 664
Cdd:TIGR01642 322 LKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKD 361
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 507-573 3.08e-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: 45.30  E-value: 3.08e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  507 VYAGPFSKNCNLRALKRLFKSFGPVQSMTFV-LETRQPHLC--IQYEVLEAAQLAIESLDGILVDGICIK 573
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVrDETGRSKGFafVEFEDEEDAEKAIEALNGKELGGRELK 70
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 506-670 5.12e-06

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 49.92  E-value: 5.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  506 TVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQPH----LCIQYEVLEAAQLAIeSLDGILVDGICIKVQRPVTEL 581
Cdd:TIGR01622 116 TVFVQQLAARARERDLYEFFSKVGKVRDVQIIKDRNSRRskgvGYVEFYDVDSVQAAL-ALTGQKLLGIPVIVQLSEAEK 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209  582 TLDCdTLVNELEGDSENQGS---IYLSGVSETFKEQLLQ---EPrlFLGLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQ 655
Cdd:TIGR01622 195 NRAA-RAATETSGHHPNSIPfhrLYVGNLHFNITEQDLRqifEP--FGEIEFVQLQKDPETGRSKGYGFIQFRDAEQAKE 271

                         170
                  ....*....|....*
gi 530409209  656 ALNILTGKDwkLKGR 670
Cdd:TIGR01622 272 ALEKMNGFE--LAGR 284
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 602-670 1.08e-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: 1.08e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 602 IYLSGVS-ETFKEQLLQEPRLFLGLEAVILPKDlKSGKQKKYCFLKFKSFGSAQQALNILTGKdwKLKGR 670
Cdd:cd00590    1 LFVGNLPpDTTEEDLRELFSKFGEVVSVRIVRD-RDGKSKGFAFVEFESPEDAEKALEALNGT--ELGGR 67
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 261-381 1.56e-04

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 42.86  E-value: 1.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 261 LVKPENKILDYLTSFSGITKKILN--PvttKLKDVQRQLKALLPpDAVLVGHSLDLDLRAL---------KMIHPYVIDT 329
Cdd:COG0847   39 LVNPERPIPPEATAIHGITDEDVAdaP---PFAEVLPELLEFLG-GAVLVAHNAAFDLGFLnaelrraglPLPPFPVLDT 114

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 530409209 330 SLLY--VREQGRRFKLKFLAKViLGKDIqcPDRlgHDATEDARTILELARYFLK 381
Cdd:COG0847  115 LRLArrLLPGLPSYSLDALCER-LGIPF--DER--HRALADAEATAELFLALLR 163
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
521-574 1.82e-03

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 37.77  E-value: 1.82e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 530409209 521 LKRLFKSFGPVQSMTFVL--ETRQP--HLCIQYEVLEAAQLAIESLDGILVDGICIKV 574
Cdd:COG0724   18 LRELFSEYGEVTSVKLITdrETGRSrgFGFVEMPDDEEAQAAIEALNGAELMGRTLKV 75
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
 613-670 1.99e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 37.61  E-value: 1.99e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530409209 613 EQLLQ---EPrlFLGLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGKDwkLKGR 670
Cdd:cd12284   12 EDMLRgifEP--FGKIEFVQLQKDPETGRSKGYGFIQFRDAEDAKKALEQLNGFE--LAGR 68
RRM1_SF3B4 cd12334
RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
 602-670 2.97e-03

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409771 [Multi-domain]  Cd Length: 74  Bit Score: 37.20  E-value: 2.97e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530409209 602 IYLSGVSETFKEQLLQEprLFLGLEAVI---LPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGKdwKLKGR 670
Cdd:cd12334    1 VYVGNLDEKVTEELLWE--LFIQAGPVVnvhMPKDRVTQQHQGYGFVEFLSEEDADYAIKIMNMI--KLYGK 68
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
 506-576 3.42e-03

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.


Pssm-ID: 410011 [Multi-domain]  Cd Length: 72  Bit Score: 36.65  E-value: 3.42e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530409209 506 TVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQPHLC-IQYEVLEAAQLAIESLDGILVDGICIKVQR 576
Cdd:cd12599    1 RVYVGNLPMDIREREVEDLFSKYGPVVSIDLKIPPRPPAYAfVEFEDARDAEDAIRGRDGYDFDGHRLRVEL 72
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 606-663 4.42e-03

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 36.79  E-value: 4.42e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 530409209 606 GVSEtfkEQLLQEPRLFLGLEAVILPKDlksgkqKKYCFLKFKSFGSAQQALNILTGK 663
Cdd:cd12431   14 GVSR---EQLLEVFEKYGTVEDIVMLPG------KPYSFVSFKSVEEAAKAYNALNGK 62
RRM_NELFE cd12305
RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This ...
 521-575 4.45e-03

RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif.


Pssm-ID: 409746 [Multi-domain]  Cd Length: 75  Bit Score: 36.53  E-value: 4.45e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 530409209 521 LKRLFKSFGPVQSMTFvletRQPHLC--IQYEVLEAAQLAIESLDGILVDGICIKVQ 575
Cdd:cd12305   19 LKKAFSPFGNIINISM----EIEKNCafVTFEKMESADQAIAELNGTTVEGVQLKVS 71
PRK05755 PRK05755
DNA polymerase I; Provisional
 285-396 6.89e-03

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 40.08  E-value: 6.89e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530409209 285 PVTTKLKDVQRQLKALLPPDAVL-VGHSLDLDLRALK----MIHPYVIDTSLL-YVREQGRRFKLKFLAKV--------- 349
Cdd:PRK05755 350 PLDQLDREVLAALKPLLEDPAIKkVGQNLKYDLHVLArygiELRGIAFDTMLAsYLLDPGRRHGLDSLAERylghktisf 429

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 530409209 350 --ILGKDIQC----PDRLGHDATEDARTILELARYFLkhgPKKIAELNLEALA 396
Cdd:PRK05755 430 eeVAGKQLTFaqvdLEEAAEYAAEDADVTLRLHEVLK---PKLLEEPGLLELY 479
 
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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