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Conserved domains on  [gi|1059842875|ref|NP_001317449|]
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trinucleotide repeat-containing gene 6A protein isoform 2 [Homo sapiens]

Protein Classification

RNA-binding protein; RNA-binding protein 43( domain architecture ID 11186870)

RNA-binding protein containing an RNA recognition motif (RRM)| RNA-binding protein 43 (RBM43) is an RNA-binding protein containing an RNA recognition motif (RRM)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TNRC6-PABC_bdg pfam16608
TNRC6-PABC binding domain; TNRC6-PABC_bdg is a natively unstructured region on the higher ...
 1457-1718 1.60e-102

TNRC6-PABC binding domain; TNRC6-PABC_bdg is a natively unstructured region on the higher eukaryote TNRC6 subset of GW182 proteins that carries the binding motif for the interaction with Polyadenylate-binding protein 1, PABC. TNRC6 are trinucleotide repeat-containing gene 6 proteins required for miRNA-mediated gene silencing that are localized to the P bodies (processing bodies). P bodies are cytoplasmic mRNP aggregates that are involved in general mRNA translation repression and decay, including nonsense-mediated decay. Thus GW182 proteins are essential for microRNA-mediated translational repression and deadenylation in animal cells being a major component of miRISCs. The interaction motif that binds to PABC is ShNWPPEFHPGVPWKGLQ. This region lies between a Q-rich region and the RRM, or RNA-recognition motif, pfam13893.


:

Pssm-ID: 465195  Cd Length: 290  Bit Score: 330.80  E-value: 1.60e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1457 NAFSNFPI-GLNSNLNV-NMDMN---SIKEP--QSRLRKWT-TVDSISVNTS-LDQNSSKHGAISSGFRLEESPFVPYDF 1527
Cdd:pfam16608    3 NTFSPYPLaGLNPNMNVsNMDITgglGGKEPqsQSRLKQWTnSMDNLSSAASpLDQNSSKHGAISAGLRLEDSSFGPYDL 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1528 MNSSTSPASPPGSIGDGWPRAKSPN----GSSSVNWPPEFRPGEPWKGYPNIDPETDPYVTPGSVINNLSINTVREVDH- 1602
Cdd:pfam16608   83 IPGSESPASPPGPVGDSWPRAKSPPdkisNSSNVNWPPEFRPGVPWKGLQNIDPETDPYVTPGSVINGLSINTIRDTDHq 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1603 -LRDRNSGSSSSLNTTLPSTSAWsSIRASNYNVPLSSTAQSTSARNSDSKLTWSPG--SVTNTSLAHELWKVPLPPKNIT 1679
Cdd:pfam16608  163 lLRDRNNGPSSSLNTTLPSNSAW-PISASNHSSSLSSTASSTSAKLSDSKSTWSPGpiSHTQASLSHELWKVPLPPRNTT 241

                          250       260       270
                   ....*....|....*....|....*....|....*....
gi 1059842875 1680 APSRPPPGLTGQKPPlSTWDNSPLRIgGGWGNSDARYTP 1718
Cdd:pfam16608  242 APTRPPPGLTNQKPS-STWGASALRL-GGWGSSESRYSS 278
RRM_TNRC6A cd12711
RNA recognition motif (RRM) found in vertebrate GW182 autoantigen; This subgroup corresponds ...
 1726-1817 5.72e-55

RNA recognition motif (RRM) found in vertebrate GW182 autoantigen; This subgroup corresponds to the RRM of the GW182 autoantigen, also termed trinucleotide repeat-containing gene 6A protein (TNRC6A), or CAG repeat protein 26, or EMSY interactor protein, or protein GW1, or glycine-tryptophan protein of 182 kDa, a phosphorylated cytoplasmic autoantigen involved in stabilizing and/or regulating translation and/or storing several different mRNAs. GW182 is characterized by multiple glycine/tryptophan (G/W) repeats and is a critical component of GW bodies (GWBs, also called mammalian processing bodies, or P bodies). The mRNAs associated with GW182 are presumed to reside within GWBs. GW182 has been shown to bind multiple Ago-miRNA complexes, and thus plays a key role in miRNA-mediated translational repression and mRNA degradation. In the absence of Ago2, GW182 may induce translational silencing effect. GW182 is composed of an N-terminal G/W-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred to as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation.


:

Pssm-ID: 410110  Cd Length: 92  Bit Score: 186.05  E-value: 5.72e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1726 SSGRITNWLVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPHGNALVRYSSKEEVVKAQKSLHMCVLGNTTILAEFASEE 1805
Cdd:cd12711      1 SSGRITNWLVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPHGNALVRYSSKEEAVKAQKSLHMCVLGNTTILAEFASEE 80

                           90
                   ....*....|..
gi 1059842875 1806 EISRFFAQSQSL 1817
Cdd:cd12711     81 EISRFFAQGQSL 92
Ago_hook super family cl44598
Argonaute hook; This region has been called the argonaute hook. It has been shown to bind to ...
 1075-1202 1.42e-07

Argonaute hook; This region has been called the argonaute hook. It has been shown to bind to the Piwi domain pfam02171 of Argnonaute proteins.


The actual alignment was detected with superfamily member pfam10427:

Pssm-ID: 463088 [Multi-domain]  Cd Length: 148  Bit Score: 52.74  E-value: 1.42e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1075 DNGTSAWGKPIDSGPSWGEPIAAASSTSTWGSSSVGPQALSKSGPKSMQDGWcGDDMPLPGNRPTGWEEEEDVEIGMWNS 1154
Cdd:pfam10427   28 DNGTAAWGHPNNSGPGWGGGRNEPSVVTGWGDDSHGAPNLSKPGSKSSQSNW-GDDKDEGSLGQNSWSDEDSYGGGWGNK 106

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1155 NS--SQELNSSLNWppytkkmSSKGLSGKKrrrergmMKGGNKQEEAWIN 1202
Cdd:pfam10427  107 QSqlSTSSGNSSGW-------GNASKKGMQ-------MVDGGDLGSEWKH 142
ser_rich_anae_1 super family cl41472
serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 ...
 405-693 1.24e-06

serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 amino acids), which a highly serine-rich central region that averages over 300 aa in length. Species encoding members of this family of proteins tend to be anaerobic bacteria, including Gram-positive bacteria of the human gut microbiome and Chloroflexi from marine sediments.


The actual alignment was detected with superfamily member NF033849:

Pssm-ID: 468206 [Multi-domain]  Cd Length: 1122  Bit Score: 53.86  E-value: 1.24e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  405 QSINSKVSGGSTHGTWGSLQETCESEVSGTQKVSFSGQPQNITTEMTGPNNTTNFMTSSlpnSGSVQNNELPSSNTGAWR 484
Cdd:NF033849   245 ESVGHSTSQGQSHSVGTSESHSVGTSQSQSHTTGHGSTRGWSHTQSTSESESTGQSSSV---GTSESQSHGTTEGTSTTD 321

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  485 VSTMNHPQMQAPSGMNGTSLSHLSNGESKSGGSYGTTWGAYGSNYSGDKCSGPNGQANGDTVNATlmqPGVNGPMGtnfq 564
Cdd:NF033849   322 SSSHSQSSSYNVSSGTGVSSSHSDGTSQSTSISHSESSSESTGTSVGHSTSSSVSSSESSSRSSS---SGVSGGFS---- 394

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  565 vNTNKGGGVWESGAANSQSTSWgsgngansggsrrGWGTpaqNTGTNLPSVEWNKLPSNQHSNDSANGNGKTFTNGWKST 644
Cdd:NF033849   395 -GGIAGGGVTSEGLGASQGGSE-------------GWGS---GDSVQSVSQSYGSSSSTGTSSGHSDSSSHSTSSGQADS 457

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1059842875  645 E------EEDQGSATSQTNEQSSVWAKTGGTVESDGSTESTGRLEEKGTGESQSR 693
Cdd:NF033849   458 VsqgtswSEGTGTSQGQSVGTSESWSTSQSETDSVGDSTGTSESVSQGDGRSTGR 512
M_domain super family cl15179
M domain of GW182;
1280-1432 3.68e-06

M domain of GW182;


The actual alignment was detected with superfamily member pfam12938:

Pssm-ID: 432890 [Multi-domain]  Cd Length: 243  Bit Score: 50.31  E-value: 3.68e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1280 NGNPSMFGVGNTAAQPRGMQQPP---AQPLSSSQPNLRAQVPPpLLSPQVPVSLLKYAPNNGGLNPL-----FGPQQVAM 1351
Cdd:pfam12938   65 QGGPQGVGGSSGAAVARGQQQPNppsVQPLNSSQASLRAQQPS-GQQLRMLVQQIQLAVQNGFLNHQiltqpLAPQTLNL 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1352 LNQLSQLNQLSQISQLQRLLAQQqraqsqrsvpSGNRPQQDQQGRPLSVQQQMMQQSRQLDPN--LLVKQQTPPSQQQPL 1429
Cdd:pfam12938  144 LNQLLNAIKQLQAAQQSLARRGV----------GGNANQMQQNVAINKYKQQIQQLQNQIAAQqaIYVKQQQQQQNSQQQ 213


                   ...
gi 1059842875 1430 HQP 1432
Cdd:pfam12938  214 QQP 216
ser_rich_anae_1 super family cl41472
serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 ...
 622-860 1.19e-04

serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 amino acids), which a highly serine-rich central region that averages over 300 aa in length. Species encoding members of this family of proteins tend to be anaerobic bacteria, including Gram-positive bacteria of the human gut microbiome and Chloroflexi from marine sediments.


The actual alignment was detected with superfamily member NF033849:

Pssm-ID: 468206 [Multi-domain]  Cd Length: 1122  Bit Score: 47.31  E-value: 1.19e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  622 SNQHSNDSANGNGKTFTNGWKSTEEEDQGSATSQTNEQSSV----WAKTGGTVESDGS--TESTGRLEEKGTGESQSrdr 695
Cdd:NF033849   266 SVGTSQSQSHTTGHGSTRGWSHTQSTSESESTGQSSSVGTSesqsHGTTEGTSTTDSSshSQSSSYNVSSGTGVSSS--- 342

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  696 rkidqhtllqsivnrtdldprvLSNSGWGQTPIKQNTAWdTETSPRGERKTDNGTEAWGSSATQTFNSGacidktspngn 775
Cdd:NF033849   343 ----------------------HSDGTSQSTSISHSESS-SESTGTSVGHSTSSSVSSSESSSRSSSSG----------- 388

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  776 dtSSVSGWGDPKPALRWGDSKGSNcQGGWEDDSAATGMVKSNQ-WGNCKEEKAAW--------------NDSQKNKQGWG 840
Cdd:NF033849   389 --VSGGFSGGIAGGGVTSEGLGAS-QGGSEGWGSGDSVQSVSQsYGSSSSTGTSSghsdssshstssgqADSVSQGTSWS 465

                          250       260
                   ....*....|....*....|
gi 1059842875  841 DGQKSSQGWSVSASDNWGET 860
Cdd:NF033849   466 EGTGTSQGQSVGTSESWSTS 485
 
Name Accession Description Interval E-value
TNRC6-PABC_bdg pfam16608
TNRC6-PABC binding domain; TNRC6-PABC_bdg is a natively unstructured region on the higher ...
 1457-1718 1.60e-102

TNRC6-PABC binding domain; TNRC6-PABC_bdg is a natively unstructured region on the higher eukaryote TNRC6 subset of GW182 proteins that carries the binding motif for the interaction with Polyadenylate-binding protein 1, PABC. TNRC6 are trinucleotide repeat-containing gene 6 proteins required for miRNA-mediated gene silencing that are localized to the P bodies (processing bodies). P bodies are cytoplasmic mRNP aggregates that are involved in general mRNA translation repression and decay, including nonsense-mediated decay. Thus GW182 proteins are essential for microRNA-mediated translational repression and deadenylation in animal cells being a major component of miRISCs. The interaction motif that binds to PABC is ShNWPPEFHPGVPWKGLQ. This region lies between a Q-rich region and the RRM, or RNA-recognition motif, pfam13893.


Pssm-ID: 465195  Cd Length: 290  Bit Score: 330.80  E-value: 1.60e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1457 NAFSNFPI-GLNSNLNV-NMDMN---SIKEP--QSRLRKWT-TVDSISVNTS-LDQNSSKHGAISSGFRLEESPFVPYDF 1527
Cdd:pfam16608    3 NTFSPYPLaGLNPNMNVsNMDITgglGGKEPqsQSRLKQWTnSMDNLSSAASpLDQNSSKHGAISAGLRLEDSSFGPYDL 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1528 MNSSTSPASPPGSIGDGWPRAKSPN----GSSSVNWPPEFRPGEPWKGYPNIDPETDPYVTPGSVINNLSINTVREVDH- 1602
Cdd:pfam16608   83 IPGSESPASPPGPVGDSWPRAKSPPdkisNSSNVNWPPEFRPGVPWKGLQNIDPETDPYVTPGSVINGLSINTIRDTDHq 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1603 -LRDRNSGSSSSLNTTLPSTSAWsSIRASNYNVPLSSTAQSTSARNSDSKLTWSPG--SVTNTSLAHELWKVPLPPKNIT 1679
Cdd:pfam16608  163 lLRDRNNGPSSSLNTTLPSNSAW-PISASNHSSSLSSTASSTSAKLSDSKSTWSPGpiSHTQASLSHELWKVPLPPRNTT 241

                          250       260       270
                   ....*....|....*....|....*....|....*....
gi 1059842875 1680 APSRPPPGLTGQKPPlSTWDNSPLRIgGGWGNSDARYTP 1718
Cdd:pfam16608  242 APTRPPPGLTNQKPS-STWGASALRL-GGWGSSESRYSS 278
RRM_TNRC6A cd12711
RNA recognition motif (RRM) found in vertebrate GW182 autoantigen; This subgroup corresponds ...
 1726-1817 5.72e-55

RNA recognition motif (RRM) found in vertebrate GW182 autoantigen; This subgroup corresponds to the RRM of the GW182 autoantigen, also termed trinucleotide repeat-containing gene 6A protein (TNRC6A), or CAG repeat protein 26, or EMSY interactor protein, or protein GW1, or glycine-tryptophan protein of 182 kDa, a phosphorylated cytoplasmic autoantigen involved in stabilizing and/or regulating translation and/or storing several different mRNAs. GW182 is characterized by multiple glycine/tryptophan (G/W) repeats and is a critical component of GW bodies (GWBs, also called mammalian processing bodies, or P bodies). The mRNAs associated with GW182 are presumed to reside within GWBs. GW182 has been shown to bind multiple Ago-miRNA complexes, and thus plays a key role in miRNA-mediated translational repression and mRNA degradation. In the absence of Ago2, GW182 may induce translational silencing effect. GW182 is composed of an N-terminal G/W-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred to as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation.


Pssm-ID: 410110  Cd Length: 92  Bit Score: 186.05  E-value: 5.72e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1726 SSGRITNWLVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPHGNALVRYSSKEEVVKAQKSLHMCVLGNTTILAEFASEE 1805
Cdd:cd12711      1 SSGRITNWLVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPHGNALVRYSSKEEAVKAQKSLHMCVLGNTTILAEFASEE 80

                           90
                   ....*....|..
gi 1059842875 1806 EISRFFAQSQSL 1817
Cdd:cd12711     81 EISRFFAQGQSL 92
Ago_hook pfam10427
Argonaute hook; This region has been called the argonaute hook. It has been shown to bind to ...
 1075-1202 1.42e-07

Argonaute hook; This region has been called the argonaute hook. It has been shown to bind to the Piwi domain pfam02171 of Argnonaute proteins.


Pssm-ID: 463088 [Multi-domain]  Cd Length: 148  Bit Score: 52.74  E-value: 1.42e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1075 DNGTSAWGKPIDSGPSWGEPIAAASSTSTWGSSSVGPQALSKSGPKSMQDGWcGDDMPLPGNRPTGWEEEEDVEIGMWNS 1154
Cdd:pfam10427   28 DNGTAAWGHPNNSGPGWGGGRNEPSVVTGWGDDSHGAPNLSKPGSKSSQSNW-GDDKDEGSLGQNSWSDEDSYGGGWGNK 106

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1155 NS--SQELNSSLNWppytkkmSSKGLSGKKrrrergmMKGGNKQEEAWIN 1202
Cdd:pfam10427  107 QSqlSTSSGNSSGW-------GNASKKGMQ-------MVDGGDLGSEWKH 142
ser_rich_anae_1 NF033849
serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 ...
 405-693 1.24e-06

serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 amino acids), which a highly serine-rich central region that averages over 300 aa in length. Species encoding members of this family of proteins tend to be anaerobic bacteria, including Gram-positive bacteria of the human gut microbiome and Chloroflexi from marine sediments.


Pssm-ID: 468206 [Multi-domain]  Cd Length: 1122  Bit Score: 53.86  E-value: 1.24e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  405 QSINSKVSGGSTHGTWGSLQETCESEVSGTQKVSFSGQPQNITTEMTGPNNTTNFMTSSlpnSGSVQNNELPSSNTGAWR 484
Cdd:NF033849   245 ESVGHSTSQGQSHSVGTSESHSVGTSQSQSHTTGHGSTRGWSHTQSTSESESTGQSSSV---GTSESQSHGTTEGTSTTD 321

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  485 VSTMNHPQMQAPSGMNGTSLSHLSNGESKSGGSYGTTWGAYGSNYSGDKCSGPNGQANGDTVNATlmqPGVNGPMGtnfq 564
Cdd:NF033849   322 SSSHSQSSSYNVSSGTGVSSSHSDGTSQSTSISHSESSSESTGTSVGHSTSSSVSSSESSSRSSS---SGVSGGFS---- 394

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  565 vNTNKGGGVWESGAANSQSTSWgsgngansggsrrGWGTpaqNTGTNLPSVEWNKLPSNQHSNDSANGNGKTFTNGWKST 644
Cdd:NF033849   395 -GGIAGGGVTSEGLGASQGGSE-------------GWGS---GDSVQSVSQSYGSSSSTGTSSGHSDSSSHSTSSGQADS 457

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1059842875  645 E------EEDQGSATSQTNEQSSVWAKTGGTVESDGSTESTGRLEEKGTGESQSR 693
Cdd:NF033849   458 VsqgtswSEGTGTSQGQSVGTSESWSTSQSETDSVGDSTGTSESVSQGDGRSTGR 512
M_domain pfam12938
M domain of GW182;
1280-1432 3.68e-06

M domain of GW182;


Pssm-ID: 432890 [Multi-domain]  Cd Length: 243  Bit Score: 50.31  E-value: 3.68e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1280 NGNPSMFGVGNTAAQPRGMQQPP---AQPLSSSQPNLRAQVPPpLLSPQVPVSLLKYAPNNGGLNPL-----FGPQQVAM 1351
Cdd:pfam12938   65 QGGPQGVGGSSGAAVARGQQQPNppsVQPLNSSQASLRAQQPS-GQQLRMLVQQIQLAVQNGFLNHQiltqpLAPQTLNL 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1352 LNQLSQLNQLSQISQLQRLLAQQqraqsqrsvpSGNRPQQDQQGRPLSVQQQMMQQSRQLDPN--LLVKQQTPPSQQQPL 1429
Cdd:pfam12938  144 LNQLLNAIKQLQAAQQSLARRGV----------GGNANQMQQNVAINKYKQQIQQLQNQIAAQqaIYVKQQQQQQNSQQQ 213


                   ...
gi 1059842875 1430 HQP 1432
Cdd:pfam12938  214 QQP 216
ser_rich_anae_1 NF033849
serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 ...
 622-860 1.19e-04

serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 amino acids), which a highly serine-rich central region that averages over 300 aa in length. Species encoding members of this family of proteins tend to be anaerobic bacteria, including Gram-positive bacteria of the human gut microbiome and Chloroflexi from marine sediments.


Pssm-ID: 468206 [Multi-domain]  Cd Length: 1122  Bit Score: 47.31  E-value: 1.19e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  622 SNQHSNDSANGNGKTFTNGWKSTEEEDQGSATSQTNEQSSV----WAKTGGTVESDGS--TESTGRLEEKGTGESQSrdr 695
Cdd:NF033849   266 SVGTSQSQSHTTGHGSTRGWSHTQSTSESESTGQSSSVGTSesqsHGTTEGTSTTDSSshSQSSSYNVSSGTGVSSS--- 342

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  696 rkidqhtllqsivnrtdldprvLSNSGWGQTPIKQNTAWdTETSPRGERKTDNGTEAWGSSATQTFNSGacidktspngn 775
Cdd:NF033849   343 ----------------------HSDGTSQSTSISHSESS-SESTGTSVGHSTSSSVSSSESSSRSSSSG----------- 388

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  776 dtSSVSGWGDPKPALRWGDSKGSNcQGGWEDDSAATGMVKSNQ-WGNCKEEKAAW--------------NDSQKNKQGWG 840
Cdd:NF033849   389 --VSGGFSGGIAGGGVTSEGLGAS-QGGSEGWGSGDSVQSVSQsYGSSSSTGTSSghsdssshstssgqADSVSQGTSWS 465

                          250       260
                   ....*....|....*....|
gi 1059842875  841 DGQKSSQGWSVSASDNWGET 860
Cdd:NF033849   466 EGTGTSQGQSVGTSESWSTS 485
COG4625 COG4625
Uncharacterized conserved protein, contains a C-terminal beta-barrel porin domain [Function ...
 267-687 6.67e-03

Uncharacterized conserved protein, contains a C-terminal beta-barrel porin domain [Function unknown];


Pssm-ID: 443664 [Multi-domain]  Cd Length: 900  Bit Score: 41.30  E-value: 6.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  267 NITIMASGNTGGEKDGLRNSTGLGSQNKFVVGSSSNNVGHGSSTGPWGFSHGAIISTCQVSVDAPESKSESSNNRMNAWG 346
Cdd:COG4625     91 GGVGGGGGGGGGGGGGGGGGGGGGGGGSAGGGGGGAGGAGGGGGGGAGGGGGGGGGGGAGGGGGGGAGGAGGGGGGGGGG 170

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  347 TVSSSSNGGLNPSTLNSASNHGAWPVLENNGLALKGPVGSGSSGINIQCSTIGQMPNNQSINSKVSGGSTHGTWGSLQET 426
Cdd:COG4625    171 GGGGGGGGGGGGGGGGGGGGGGNGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGG 250

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  427 CESEVSGTQKVSFSGQPQNITTEMTGPNNTTNFMTSSLPNSGSVQNNELPSSNTGAWRVSTMNHPQMQAPSGMNGTSLSH 506
Cdd:COG4625    251 GGGGGGGNGGGGGAGGGGGGGGGGSGGGGGGGGGGGSGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 330

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  507 LSNGESKS-------GGSYGTTWGAYGSNYSGDKCSGPNGQANGDTVNATLMQPGVNGPMGTNFQVNTNKGGGVWESGAA 579
Cdd:COG4625    331 GGGAGGGGgsggagaGGGGAGGGGAGGGGGGGTGGGGGGGGGGGGGSGGGGAGGGGGSGGGGGGGAGGGGGGGGAGGTGG 410

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  580 NSQS-TSWGSGNGANSGGSRRGWGTPAQNTGTNLPSVEWNKLPSNQHSNDSANGNGKTFTNGWKSTEEEDQGSATSQTNE 658
Cdd:COG4625    411 GGAGgGGGAAGGGGGGTGAGGGGGGGGTGAGGGGATGGGGGGGGGAGGSGGGAGAGGGSGSGAGTLTLTGNNTYTGTTTV 490

                          410       420       430
                   ....*....|....*....|....*....|.
gi 1059842875  659 QS--SVWAKTGGTVESDGSTESTGRLEEKGT 687
Cdd:COG4625    491 NGggNYTQSAGSTLAVEVDAANSDRLVVTGT 521
 
Name Accession Description Interval E-value
TNRC6-PABC_bdg pfam16608
TNRC6-PABC binding domain; TNRC6-PABC_bdg is a natively unstructured region on the higher ...
 1457-1718 1.60e-102

TNRC6-PABC binding domain; TNRC6-PABC_bdg is a natively unstructured region on the higher eukaryote TNRC6 subset of GW182 proteins that carries the binding motif for the interaction with Polyadenylate-binding protein 1, PABC. TNRC6 are trinucleotide repeat-containing gene 6 proteins required for miRNA-mediated gene silencing that are localized to the P bodies (processing bodies). P bodies are cytoplasmic mRNP aggregates that are involved in general mRNA translation repression and decay, including nonsense-mediated decay. Thus GW182 proteins are essential for microRNA-mediated translational repression and deadenylation in animal cells being a major component of miRISCs. The interaction motif that binds to PABC is ShNWPPEFHPGVPWKGLQ. This region lies between a Q-rich region and the RRM, or RNA-recognition motif, pfam13893.


Pssm-ID: 465195  Cd Length: 290  Bit Score: 330.80  E-value: 1.60e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1457 NAFSNFPI-GLNSNLNV-NMDMN---SIKEP--QSRLRKWT-TVDSISVNTS-LDQNSSKHGAISSGFRLEESPFVPYDF 1527
Cdd:pfam16608    3 NTFSPYPLaGLNPNMNVsNMDITgglGGKEPqsQSRLKQWTnSMDNLSSAASpLDQNSSKHGAISAGLRLEDSSFGPYDL 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1528 MNSSTSPASPPGSIGDGWPRAKSPN----GSSSVNWPPEFRPGEPWKGYPNIDPETDPYVTPGSVINNLSINTVREVDH- 1602
Cdd:pfam16608   83 IPGSESPASPPGPVGDSWPRAKSPPdkisNSSNVNWPPEFRPGVPWKGLQNIDPETDPYVTPGSVINGLSINTIRDTDHq 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1603 -LRDRNSGSSSSLNTTLPSTSAWsSIRASNYNVPLSSTAQSTSARNSDSKLTWSPG--SVTNTSLAHELWKVPLPPKNIT 1679
Cdd:pfam16608  163 lLRDRNNGPSSSLNTTLPSNSAW-PISASNHSSSLSSTASSTSAKLSDSKSTWSPGpiSHTQASLSHELWKVPLPPRNTT 241

                          250       260       270
                   ....*....|....*....|....*....|....*....
gi 1059842875 1680 APSRPPPGLTGQKPPlSTWDNSPLRIgGGWGNSDARYTP 1718
Cdd:pfam16608  242 APTRPPPGLTNQKPS-STWGASALRL-GGWGSSESRYSS 278
RRM_TNRC6A cd12711
RNA recognition motif (RRM) found in vertebrate GW182 autoantigen; This subgroup corresponds ...
 1726-1817 5.72e-55

RNA recognition motif (RRM) found in vertebrate GW182 autoantigen; This subgroup corresponds to the RRM of the GW182 autoantigen, also termed trinucleotide repeat-containing gene 6A protein (TNRC6A), or CAG repeat protein 26, or EMSY interactor protein, or protein GW1, or glycine-tryptophan protein of 182 kDa, a phosphorylated cytoplasmic autoantigen involved in stabilizing and/or regulating translation and/or storing several different mRNAs. GW182 is characterized by multiple glycine/tryptophan (G/W) repeats and is a critical component of GW bodies (GWBs, also called mammalian processing bodies, or P bodies). The mRNAs associated with GW182 are presumed to reside within GWBs. GW182 has been shown to bind multiple Ago-miRNA complexes, and thus plays a key role in miRNA-mediated translational repression and mRNA degradation. In the absence of Ago2, GW182 may induce translational silencing effect. GW182 is composed of an N-terminal G/W-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred to as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation.


Pssm-ID: 410110  Cd Length: 92  Bit Score: 186.05  E-value: 5.72e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1726 SSGRITNWLVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPHGNALVRYSSKEEVVKAQKSLHMCVLGNTTILAEFASEE 1805
Cdd:cd12711      1 SSGRITNWLVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPHGNALVRYSSKEEAVKAQKSLHMCVLGNTTILAEFASEE 80

                           90
                   ....*....|..
gi 1059842875 1806 EISRFFAQSQSL 1817
Cdd:cd12711     81 EISRFFAQGQSL 92
RRM_TNRC6C cd12713
RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6C ...
 1729-1813 1.37e-48

RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6C protein (TNRC6C); This subgroup corresponds to the RRM of TNRC6C, one of three GW182 paralogs in mammalian genomes. It is enriched in P-bodies and important for efficient miRNA-mediated repression. TNRC6C is composed of an N-terminal glycine/tryptophan (G/W)-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half containing the RRM domain functions as a key effector domain mediating protein synthesis repression by TNRC6C.


Pssm-ID: 410112 [Multi-domain]  Cd Length: 88  Bit Score: 167.96  E-value: 1.37e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1729 RITNWLVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPHGNALVRYSSKEEVVKAQKSLHMCVLGNTTILAEFASEEEIS 1808
Cdd:cd12713      4 RTSSWLVLRNLTPQIDGSTLRTLCLQHGPLITFHLNLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTILAEFASEEEVN 83


                   ....*
gi 1059842875 1809 RFFAQ 1813
Cdd:cd12713     84 RFLAQ 88
RRM_TNRC6B cd12712
RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6B ...
 1733-1813 2.31e-47

RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6B protein (TNRC6B); This subgroup corresponds to the RRM of TNRC6B, one of three GW182 paralogs in mammalian genomes. It is involved in miRNA-mediated mRNA degradation. TNRC6B is composed of an N-terminal glycine/tryptophan (G/W)-rich region; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. TNRC6B directly interacts with Argonaute (Ago) proteins through its N-terminal glycine/tryptophan (G/W)-rich region that is called Ago protein-binding domain. TNRC6B is enriched in P-bodies and its Q-rich domain is responsible for P-body localization. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half of TNRC6B comprising an RRM domain exerts a strong translation inhibition potential, which does not require either association with Agos or localization to P-bodies.


Pssm-ID: 410111  Cd Length: 83  Bit Score: 164.08  E-value: 2.31e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1733 WLVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPHGNALVRYSSKEEVVKAQKSLHMCVLGNTTILAEFASEEEISRFFA 1812
Cdd:cd12712      3 WLVLHNLTPQIDGSTLRTICMQHGPLLTFHLNLTQGTALIRYSTKQEAAKAQTALHMCVLGNTTILAEFATEEEVSRYFA 82


                   .
gi 1059842875 1813 Q 1813
Cdd:cd12712     83 Q 83
RRM_GW182_like cd12435
RNA recognition motif (RRM) found in the GW182 family proteins; This subfamily corresponds to ...
 1731-1801 3.43e-47

RNA recognition motif (RRM) found in the GW182 family proteins; This subfamily corresponds to the RRM of the GW182 family which includes three paralogs of TNRC6 (GW182-related) proteins comprising GW182/TNGW1, TNRC6B (containing three isoforms) and TNRC6C in mammal, a single Drosophila ortholog (dGW182, also called Gawky) and two Caenorhabditis elegans orthologs AIN-1 and AIN-2, which contain multiple miRNA-binding sites and have important functions in miRNA-mediated translational repression, as well as mRNA degradation in Metazoa. The GW182 family proteins directly interact with Argonaute (Ago) proteins, and thus function as downstream effectors in the miRNA pathway, responsible for inhibition of translation and acceleration of mRNA decay. Members in this family are characterized by an abnormally high content of glycine/tryptophan (G/W) repeats, one or more glutamine (Q)-rich motifs, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The only exception is the worm protein that does not contain a recognizable RRM domain. The GW182 family proteins are recruited to miRNA targets through an interaction between their N-terminal domain and an Argonaute protein. Then they promote translational repression and/or degradation of miRNA targets through their C-terminal silencing domain.


Pssm-ID: 409869 [Multi-domain]  Cd Length: 71  Bit Score: 162.99  E-value: 3.43e-47
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1059842875 1731 TNWLVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPHGNALVRYSSKEEVVKAQKSLHMCVLGNTTILAEF 1801
Cdd:cd12435      1 SNWLVLRNLTPQIDGSTLRTLCMQHGPLLTFHLNLNHGNALIRYSSREEAAKAQKALNMCVLGNTTILADF 71
Ago_hook pfam10427
Argonaute hook; This region has been called the argonaute hook. It has been shown to bind to ...
 1075-1202 1.42e-07

Argonaute hook; This region has been called the argonaute hook. It has been shown to bind to the Piwi domain pfam02171 of Argnonaute proteins.


Pssm-ID: 463088 [Multi-domain]  Cd Length: 148  Bit Score: 52.74  E-value: 1.42e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1075 DNGTSAWGKPIDSGPSWGEPIAAASSTSTWGSSSVGPQALSKSGPKSMQDGWcGDDMPLPGNRPTGWEEEEDVEIGMWNS 1154
Cdd:pfam10427   28 DNGTAAWGHPNNSGPGWGGGRNEPSVVTGWGDDSHGAPNLSKPGSKSSQSNW-GDDKDEGSLGQNSWSDEDSYGGGWGNK 106

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1155 NS--SQELNSSLNWppytkkmSSKGLSGKKrrrergmMKGGNKQEEAWIN 1202
Cdd:pfam10427  107 QSqlSTSSGNSSGW-------GNASKKGMQ-------MVDGGDLGSEWKH 142
ser_rich_anae_1 NF033849
serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 ...
 405-693 1.24e-06

serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 amino acids), which a highly serine-rich central region that averages over 300 aa in length. Species encoding members of this family of proteins tend to be anaerobic bacteria, including Gram-positive bacteria of the human gut microbiome and Chloroflexi from marine sediments.


Pssm-ID: 468206 [Multi-domain]  Cd Length: 1122  Bit Score: 53.86  E-value: 1.24e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  405 QSINSKVSGGSTHGTWGSLQETCESEVSGTQKVSFSGQPQNITTEMTGPNNTTNFMTSSlpnSGSVQNNELPSSNTGAWR 484
Cdd:NF033849   245 ESVGHSTSQGQSHSVGTSESHSVGTSQSQSHTTGHGSTRGWSHTQSTSESESTGQSSSV---GTSESQSHGTTEGTSTTD 321

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  485 VSTMNHPQMQAPSGMNGTSLSHLSNGESKSGGSYGTTWGAYGSNYSGDKCSGPNGQANGDTVNATlmqPGVNGPMGtnfq 564
Cdd:NF033849   322 SSSHSQSSSYNVSSGTGVSSSHSDGTSQSTSISHSESSSESTGTSVGHSTSSSVSSSESSSRSSS---SGVSGGFS---- 394

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  565 vNTNKGGGVWESGAANSQSTSWgsgngansggsrrGWGTpaqNTGTNLPSVEWNKLPSNQHSNDSANGNGKTFTNGWKST 644
Cdd:NF033849   395 -GGIAGGGVTSEGLGASQGGSE-------------GWGS---GDSVQSVSQSYGSSSSTGTSSGHSDSSSHSTSSGQADS 457

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1059842875  645 E------EEDQGSATSQTNEQSSVWAKTGGTVESDGSTESTGRLEEKGTGESQSR 693
Cdd:NF033849   458 VsqgtswSEGTGTSQGQSVGTSESWSTSQSETDSVGDSTGTSESVSQGDGRSTGR 512
M_domain pfam12938
M domain of GW182;
1280-1432 3.68e-06

M domain of GW182;


Pssm-ID: 432890 [Multi-domain]  Cd Length: 243  Bit Score: 50.31  E-value: 3.68e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1280 NGNPSMFGVGNTAAQPRGMQQPP---AQPLSSSQPNLRAQVPPpLLSPQVPVSLLKYAPNNGGLNPL-----FGPQQVAM 1351
Cdd:pfam12938   65 QGGPQGVGGSSGAAVARGQQQPNppsVQPLNSSQASLRAQQPS-GQQLRMLVQQIQLAVQNGFLNHQiltqpLAPQTLNL 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875 1352 LNQLSQLNQLSQISQLQRLLAQQqraqsqrsvpSGNRPQQDQQGRPLSVQQQMMQQSRQLDPN--LLVKQQTPPSQQQPL 1429
Cdd:pfam12938  144 LNQLLNAIKQLQAAQQSLARRGV----------GGNANQMQQNVAINKYKQQIQQLQNQIAAQqaIYVKQQQQQQNSQQQ 213


                   ...
gi 1059842875 1430 HQP 1432
Cdd:pfam12938  214 QQP 216
ser_rich_anae_1 NF033849
serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 ...
 622-860 1.19e-04

serine-rich protein; This serine-rich protein belongs to a family with large size (over 1000 amino acids), which a highly serine-rich central region that averages over 300 aa in length. Species encoding members of this family of proteins tend to be anaerobic bacteria, including Gram-positive bacteria of the human gut microbiome and Chloroflexi from marine sediments.


Pssm-ID: 468206 [Multi-domain]  Cd Length: 1122  Bit Score: 47.31  E-value: 1.19e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  622 SNQHSNDSANGNGKTFTNGWKSTEEEDQGSATSQTNEQSSV----WAKTGGTVESDGS--TESTGRLEEKGTGESQSrdr 695
Cdd:NF033849   266 SVGTSQSQSHTTGHGSTRGWSHTQSTSESESTGQSSSVGTSesqsHGTTEGTSTTDSSshSQSSSYNVSSGTGVSSS--- 342

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  696 rkidqhtllqsivnrtdldprvLSNSGWGQTPIKQNTAWdTETSPRGERKTDNGTEAWGSSATQTFNSGacidktspngn 775
Cdd:NF033849   343 ----------------------HSDGTSQSTSISHSESS-SESTGTSVGHSTSSSVSSSESSSRSSSSG----------- 388

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  776 dtSSVSGWGDPKPALRWGDSKGSNcQGGWEDDSAATGMVKSNQ-WGNCKEEKAAW--------------NDSQKNKQGWG 840
Cdd:NF033849   389 --VSGGFSGGIAGGGVTSEGLGAS-QGGSEGWGSGDSVQSVSQsYGSSSSTGTSSghsdssshstssgqADSVSQGTSWS 465

                          250       260
                   ....*....|....*....|
gi 1059842875  841 DGQKSSQGWSVSASDNWGET 860
Cdd:NF033849   466 EGTGTSQGQSVGTSESWSTS 485
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 1734-1797 2.75e-04

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: 41.11  E-value: 2.75e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1059842875 1734 LVLKNLTPQIDGSTLRTLCMQHGPLITFHLNLPH-----GNALVRYSSKEEVVKAQKSLHMCVLGNTTI 1797
Cdd:cd00590      1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRdgkskGFAFVEFESPEDAEKALEALNGTELGGRPL 69
COG4625 COG4625
Uncharacterized conserved protein, contains a C-terminal beta-barrel porin domain [Function ...
 267-687 6.67e-03

Uncharacterized conserved protein, contains a C-terminal beta-barrel porin domain [Function unknown];


Pssm-ID: 443664 [Multi-domain]  Cd Length: 900  Bit Score: 41.30  E-value: 6.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  267 NITIMASGNTGGEKDGLRNSTGLGSQNKFVVGSSSNNVGHGSSTGPWGFSHGAIISTCQVSVDAPESKSESSNNRMNAWG 346
Cdd:COG4625     91 GGVGGGGGGGGGGGGGGGGGGGGGGGGSAGGGGGGAGGAGGGGGGGAGGGGGGGGGGGAGGGGGGGAGGAGGGGGGGGGG 170

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  347 TVSSSSNGGLNPSTLNSASNHGAWPVLENNGLALKGPVGSGSSGINIQCSTIGQMPNNQSINSKVSGGSTHGTWGSLQET 426
Cdd:COG4625    171 GGGGGGGGGGGGGGGGGGGGGGNGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGG 250

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  427 CESEVSGTQKVSFSGQPQNITTEMTGPNNTTNFMTSSLPNSGSVQNNELPSSNTGAWRVSTMNHPQMQAPSGMNGTSLSH 506
Cdd:COG4625    251 GGGGGGGNGGGGGAGGGGGGGGGGSGGGGGGGGGGGSGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 330

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  507 LSNGESKS-------GGSYGTTWGAYGSNYSGDKCSGPNGQANGDTVNATLMQPGVNGPMGTNFQVNTNKGGGVWESGAA 579
Cdd:COG4625    331 GGGAGGGGgsggagaGGGGAGGGGAGGGGGGGTGGGGGGGGGGGGGSGGGGAGGGGGSGGGGGGGAGGGGGGGGAGGTGG 410

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1059842875  580 NSQS-TSWGSGNGANSGGSRRGWGTPAQNTGTNLPSVEWNKLPSNQHSNDSANGNGKTFTNGWKSTEEEDQGSATSQTNE 658
Cdd:COG4625    411 GGAGgGGGAAGGGGGGTGAGGGGGGGGTGAGGGGATGGGGGGGGGAGGSGGGAGAGGGSGSGAGTLTLTGNNTYTGTTTV 490

                          410       420       430
                   ....*....|....*....|....*....|.
gi 1059842875  659 QS--SVWAKTGGTVESDGSTESTGRLEEKGT 687
Cdd:COG4625    491 NGggNYTQSAGSTLAVEVDAANSDRLVVTGT 521
 
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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