NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|767988839|ref|XP_011544267|]
View 

RNA exonuclease 5 isoform X4 [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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 6.87e-81

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: 6.87e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 229 FGLDCEMCLTSKGRELTRISLVAEGGCCVMDELVKPENKILDYLTSFSGITKKILNPVTTKLKDVQRQLKALLPPDAVLV 308
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767988839 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 ...
 536-606 5.65e-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: 5.65e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767988839 536 IYLSGVSETFKEQLLQEPRLFL-GLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGkDWKLKGRHA 606
Cdd:cd12274    1 IYVSGFKKSLTEEDLQERFSQLsDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 471-507 3.47e-15

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: 70.64  E-value: 3.47e-15
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 767988839 471 TVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQ 507
Cdd:cd12273    1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQ 37
 
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 6.87e-81

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: 6.87e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 229 FGLDCEMCLTSKGRELTRISLVAEGGCCVMDELVKPENKILDYLTSFSGITKKILNPVTTKLKDVQRQLKALLPPDAVLV 308
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767988839 309 GHSLDLDLRALKMIHPYVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQCpDRLGHDATEDARTILELAR 377
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150
RRM2_NEFsp cd12274
RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 536-606 5.65e-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: 5.65e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767988839 536 IYLSGVSETFKEQLLQEPRLFL-GLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGkDWKLKGRHA 606
Cdd:cd12274    1 IYVSGFKKSLTEEDLQERFSQLsDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 228-384 9.20e-30

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 115.48  E-value: 9.20e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839   228 LFGLDCEM-CLTSKGRELTRISLV-AEGGC--CVMDELVKPENKILDYLTSFSGITKKILNPvTTKLKDVQRQLKALLPP 303
Cdd:smart00479   2 LVVIDCETtGLDPGKDEIIEIAAVdVDGGEiiEVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839   304 DAVLVGHSLDLDLRALKMIHP----------YVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQCpdrlGHDATEDART 371
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGLPKysLKKLAKRLLLEVIQR----AHRALDDARA 156

                          170
                   ....*....|...
gi 767988839   372 ILELARYFLKHGP 384
Cdd:smart00479 157 TAKLFKKLLERLE 169
RRM1_NEFsp cd12273
RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 471-507 3.47e-15

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: 70.64  E-value: 3.47e-15
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 767988839 471 TVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQ 507
Cdd:cd12273    1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQ 37
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 231-375 5.38e-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: 5.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839  231 LDCEM-CLTSKG---RELTRISLVAEGGC--CVMDELVKPE--NKILDYLTSFSGITKKILnPVTTKLKDVQRQLKALLP 302
Cdd:pfam00929   3 IDLETtGLDPEKdeiIEIAAVVIDGGENEigETFHTYVKPTrlPKLTDECTKFTGITQAML-DNKPSFEEVLEEFLEFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839  303 PDAVLVGHS-------LDLDLRALKMIH----PYVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQcpdrLGHDATEDA 369
Cdd:pfam00929  82 KGNLLVAHNasfdvgfLRYDDKRFLKKPmpklNPVIDTLILDKATYKELPGrsLDALAEKLGLEHIG----RAHRALDDA 157


                  ....*.
gi 767988839  370 RTILEL 375
Cdd:pfam00929 158 RATAKL 163
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 259-395 1.25e-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: 1.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 259 DELVKPENKILDYLTSFSGITKKILN--PvttKLKDVQRQLKALLPpDAVLVGHSLDLDLRALKM--------IHPYVID 328
Cdd:COG2176   45 STLVNPGRPIPPFITELTGITDEMVAdaP---PFEEVLPEFLEFLG-DAVLVAHNASFDLGFLNAalkrlglpFDNPVLD 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767988839 329 TSLLYVR--EQGRRFKLKFLAKVIlgkDIQCPDRlgHDATEDARTILELARYFLkhgpKKIAELNLEAL 395
Cdd:COG2176  121 TLELARRllPELKSYKLDTLAERL---GIPLEDR--HRALGDAEATAELFLKLL----EKLEEKGITTL 180
RRM smart00360
RNA recognition motif;
535-605 2.15e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 48.74  E-value: 2.15e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767988839   535 SIYLSGVSETFKEQLLQEprLFL---GLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGKdwKLKGRH 605
Cdd:smart00360   1 TLFVGNLPPDTTEEELRE--LFSkfgKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK--ELDGRP 70
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 418-598 6.54e-04

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: 42.96  E-value: 6.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839  418 PNTSVLECLDSVGQKLLFLTRETDAGELPSSRNCQTikclsNKEMRIKWTEISTVYAGPFSKNCNLRALKRLFKSFGPVQ 497
Cdd:TIGR01642 184 PPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-----NKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPH 258

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839  498 SMTFVLE-TRQVQRPVTELTLDCDTLVNELEGDSENQGSIYLSGVSETFKE-QLLQEPRLFLGLEAVILPKDLKSGKQKK 575
Cdd:TIGR01642 259 DYIPVPQiTPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEdQIKELLESFGDLKAFNLIKDIATGLSKG 338

                         170       180
                  ....*....|....*....|...
gi 767988839  576 YCFLKFKSFGSAQQALNILTGKD 598
Cdd:TIGR01642 339 YAFCEYKDPSVTDVAIAALNGKD 361
PRK05755 PRK05755
DNA polymerase I; Provisional
 285-396 5.42e-03

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 40.08  E-value: 5.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 285 PVTTKLKDVQRQLKALLPPDAVL-VGHSLDLDLRALK----MIHPYVIDTSLL-YVREQGRRFKLKFLAKV--------- 349
Cdd:PRK05755 350 PLDQLDREVLAALKPLLEDPAIKkVGQNLKYDLHVLArygiELRGIAFDTMLAsYLLDPGRRHGLDSLAERylghktisf 429

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 767988839 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 6.87e-81

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: 6.87e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 229 FGLDCEMCLTSKGRELTRISLVAEGGCCVMDELVKPENKILDYLTSFSGITKKILNPVTTKLKDVQRQLKALLPPDAVLV 308
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767988839 309 GHSLDLDLRALKMIHPYVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQCpDRLGHDATEDARTILELAR 377
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKpsLKNLAKKYLGRDIQQ-GEGGHDSVEDARAALELVK 150
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 230-377 5.24e-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: 5.24e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 230 GLDCEMCLTSKGR-ELTRISLV-AEGGCCVMDELVKPENKILDYLTSFSGITKKIL---NPVTTKL--KDVQRQLK-ALL 301
Cdd:cd06137    2 ALDCEMVGLADGDsEVVRISAVdVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLeeaAKAGKTIfgWEAARAALwKFI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 302 PPDAVLVGHSLDLDLRALKMIHPYVIDTSLL---YV--REQGRRFKLKFLAKVILGKDIQcPDRLGHDATEDARTILELA 376
Cdd:cd06137   82 DPDTILVGHSLQNDLDALRMIHTRVVDTAILtreAVkgPLAKRQWSLRTLCRDFLGLKIQ-GGGEGHDSLEDALAAREVV 160


                 .
gi 767988839 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 2.01e-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: 2.01e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 231 LDCEMC-LTSKGRE--LTRISLVAEGGCCVMDELVKPENKILDYLTSFSGITKKILNPVTTkLKDVQRQLKALLpPDAVL 307
Cdd:cd06144    3 LDCEMVgVGPDGSEsaLARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPD-FEEVQKKVAELL-KGRIL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767988839 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 ...
 536-606 5.65e-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: 5.65e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767988839 536 IYLSGVSETFKEQLLQEPRLFL-GLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGkDWKLKGRHA 606
Cdd:cd12274    1 IYVSGFKKSLTEEDLQERFSQLsDLEAVFLPKDLQSGKHKKYCFLKFRSSQSAQAALDIITG-EWKLKGRRA 71
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 228-384 9.20e-30

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 115.48  E-value: 9.20e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839   228 LFGLDCEM-CLTSKGRELTRISLV-AEGGC--CVMDELVKPENKILDYLTSFSGITKKILNPvTTKLKDVQRQLKALLPP 303
Cdd:smart00479   2 LVVIDCETtGLDPGKDEIIEIAAVdVDGGEiiEVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839   304 DAVLVGHSLDLDLRALKMIHP----------YVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQCpdrlGHDATEDART 371
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLEHPrlgikqppklPVIDTLKLARATNPGLPKysLKKLAKRLLLEVIQR----AHRALDDARA 156

                          170
                   ....*....|...
gi 767988839   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 9.64e-25

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: 101.54  E-value: 9.64e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 244 LTRISLV-AEG---GCCVMDELVKPENKILDYLTSFSGITKKILNPVT-----TKLKDVQRQLKALLPPDAVLVGHSLDL 314
Cdd:cd06143   33 LARVSVVrGEGeleGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKTssknlTTLKSAYLKLRLLVDLGCIFVGHGLAK 112

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767988839 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 1.10e-22

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: 95.20  E-value: 1.10e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 231 LDCEMCLTS-KGR--ELTRISLVAEGGCCVMDELVKPENKILDYLTSFSGITKK-ILNpvTTKLKDVQRQLKALLpPDAV 306
Cdd:cd06149    3 IDCEMVGTGpGGResELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQhLVN--ATPFAVAQKEILKIL-KGKV 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767988839 307 LVGHSLDLDLRALKMIHP--YVIDTS---LLYVR---EQGRRFKLKFLAKVILGKDIQCpDRLGHDATEDARTILELAR 377
Cdd:cd06149   80 VVGHAIHNDFKALKYFHPkhMTRDTStipLLNRKagfPENCRVSLKVLAKRLLHRDIQV-GRQGHSSVEDARATMELYK 157
RRM1_NEFsp cd12273
RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp; This ...
 471-507 3.47e-15

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: 70.64  E-value: 3.47e-15
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 767988839 471 TVYAGPFSKNCNLRALKRLFKSFGPVQSMTFVLETRQ 507
Cdd:cd12273    1 TVYAGPFEKSFCLKSVKRLFRSCGPVQSLTVVTETYQ 37
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 231-375 5.38e-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: 5.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839  231 LDCEM-CLTSKG---RELTRISLVAEGGC--CVMDELVKPE--NKILDYLTSFSGITKKILnPVTTKLKDVQRQLKALLP 302
Cdd:pfam00929   3 IDLETtGLDPEKdeiIEIAAVVIDGGENEigETFHTYVKPTrlPKLTDECTKFTGITQAML-DNKPSFEEVLEEFLEFLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839  303 PDAVLVGHS-------LDLDLRALKMIH----PYVIDTSLLYVREQGRRFK--LKFLAKVILGKDIQcpdrLGHDATEDA 369
Cdd:pfam00929  82 KGNLLVAHNasfdvgfLRYDDKRFLKKPmpklNPVIDTLILDKATYKELPGrsLDALAEKLGLEHIG----RAHRALDDA 157


                  ....*.
gi 767988839  370 RTILEL 375
Cdd:pfam00929 158 RATAKL 163
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 231-377 2.56e-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: 2.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 231 LDCEM-CLTSKGRELTRISLVA-EGGCCVMDE---LVKPENKILDYLTSFSGITKKILNPVTTkLKDVQRQLKALLPpDA 305
Cdd:cd06127    3 FDTETtGLDPKKDRIIEIGAVKvDGGIEIVERfetLVNPGRPIPPEATAIHGITDEMLADAPP-FEEVLPEFLEFLG-GR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 306 VLVGHSLDLDLRALK---------MIHPYVIDTSLLY--VREQGRRFKLKFLAKVILGkdiqCPDRLGHDATEDARTILE 374
Cdd:cd06127   81 VLVAHNASFDLRFLNrelrrlggpPLPNPWIDTLRLArrLLPGLRSHRLGLLLAERYG----IPLEGAHRALADALATAE 156


                 ...
gi 767988839 375 LAR 377
Cdd:cd06127  157 LLL 159
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 259-395 1.25e-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: 1.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 259 DELVKPENKILDYLTSFSGITKKILN--PvttKLKDVQRQLKALLPpDAVLVGHSLDLDLRALKM--------IHPYVID 328
Cdd:COG2176   45 STLVNPGRPIPPFITELTGITDEMVAdaP---PFEEVLPEFLEFLG-DAVLVAHNASFDLGFLNAalkrlglpFDNPVLD 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767988839 329 TSLLYVR--EQGRRFKLKFLAKVIlgkDIQCPDRlgHDATEDARTILELARYFLkhgpKKIAELNLEAL 395
Cdd:COG2176  121 TLELARRllPELKSYKLDTLAERL---GIPLEDR--HRALGDAEATAELFLKLL----EKLEEKGITTL 180
RRM smart00360
RNA recognition motif;
535-605 2.15e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 48.74  E-value: 2.15e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767988839   535 SIYLSGVSETFKEQLLQEprLFL---GLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGKdwKLKGRH 605
Cdd:smart00360   1 TLFVGNLPPDTTEEELRE--LFSkfgKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK--ELDGRP 70
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 536-604 9.82e-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: 43.81  E-value: 9.82e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 536 IYLSGVS-ETFKEQLLQEPRLFLGLEAVILPKDlKSGKQKKYCFLKFKSFGSAQQALNILTGKdwKLKGR 604
Cdd:cd00590    1 LFVGNLPpDTTEEDLRELFSKFGEVVSVRIVRD-RDGKSKGFAFVEFESPEDAEKALEALNGT--ELGGR 67
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 261-381 1.22e-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: 43.24  E-value: 1.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 261 LVKPENKILDYLTSFSGITKKILN--PvttKLKDVQRQLKALLPpDAVLVGHSLDLDLRAL---------KMIHPYVIDT 329
Cdd:COG0847   39 LVNPERPIPPEATAIHGITDEDVAdaP---PFAEVLPELLEFLG-GAVLVAHNAAFDLGFLnaelrraglPLPPFPVLDT 114

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 767988839 330 SLLY--VREQGRRFKLKFLAKViLGKDIqcPDRlgHDATEDARTILELARYFLK 381
Cdd:COG0847  115 LRLArrLLPGLPSYSLDALCER-LGIPF--DER--HRALADAEATAELFLALLR 163
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 418-598 6.54e-04

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: 42.96  E-value: 6.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839  418 PNTSVLECLDSVGQKLLFLTRETDAGELPSSRNCQTikclsNKEMRIKWTEISTVYAGPFSKNCNLRALKRLFKSFGPVQ 497
Cdd:TIGR01642 184 PPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-----NKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPH 258

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839  498 SMTFVLE-TRQVQRPVTELTLDCDTLVNELEGDSENQGSIYLSGVSETFKE-QLLQEPRLFLGLEAVILPKDLKSGKQKK 575
Cdd:TIGR01642 259 DYIPVPQiTPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEdQIKELLESFGDLKAFNLIKDIATGLSKG 338

                         170       180
                  ....*....|....*....|...
gi 767988839  576 YCFLKFKSFGSAQQALNILTGKD 598
Cdd:TIGR01642 339 YAFCEYKDPSVTDVAIAALNGKD 361
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
 547-604 1.82e-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: 1.82e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767988839 547 EQLLQ---EPrlFLGLEAVILPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGKDwkLKGR 604
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 ...
 536-604 2.71e-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: 2.71e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767988839 536 IYLSGVSETFKEQLLQEprLFLGLEAVI---LPKDLKSGKQKKYCFLKFKSFGSAQQALNILTGKdwKLKGR 604
Cdd:cd12334    1 VYVGNLDEKVTEELLWE--LFIQAGPVVnvhMPKDRVTQQHQGYGFVEFLSEEDADYAIKIMNMI--KLYGK 68
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 540-597 4.03e-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: 4.03e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 767988839 540 GVSEtfkEQLLQEPRLFLGLEAVILPKDlksgkqKKYCFLKFKSFGSAQQALNILTGK 597
Cdd:cd12431   14 GVSR---EQLLEVFEKYGTVEDIVMLPG------KPYSFVSFKSVEEAAKAYNALNGK 62
PRK05755 PRK05755
DNA polymerase I; Provisional
 285-396 5.42e-03

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 40.08  E-value: 5.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988839 285 PVTTKLKDVQRQLKALLPPDAVL-VGHSLDLDLRALK----MIHPYVIDTSLL-YVREQGRRFKLKFLAKV--------- 349
Cdd:PRK05755 350 PLDQLDREVLAALKPLLEDPAIKkVGQNLKYDLHVLArygiELRGIAFDTMLAsYLLDPGRRHGLDSLAERylghktisf 429

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 767988839 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH