Psyllid ID: psy3994

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280--
Protein Sequence
MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFDEDTVPLWLK
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEHHHccccccccccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEHHHHHHHHHccccccccHHHHHHHHHHHHHHHHcccHHcHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccccccccccccccccEEEEEccccccccHHHHHHHHHHcccEEEEEcccccccEEEEEccHHHHHHHHHHHccccccccEEEEEEcccccccHHHHHccccHcccEEEEcHHccccHHHHHEEccccEccHHHHcHHcc
Coil and Loop (DISEMBL)
MDVIKTFNQElsslydtkppiskaKITAITRSAIRAIKFYKHVVQSVEKFIIkckpeykvpaLYVIDSLVrqsrhqfqdkdvfgprfaRNLKATFQhlyqcppedksKIIRVLNLwqknevftpdiihplfdmadpnhpiHRELAEIQARNGVENMCSTTLWIGHLSKLVqeeelsdtfgeygdvvsinlipprgcaFVCMNRRQDAAKALYKLKNTKLQGKTItlawapgkgmkdkdwkdfwevqdgvsyipydrlskeidydyledggvfdedtvplwlk
Flexible Loop (DISEMBL)
MDVIKTFNQelsslydtkppiskaKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYklkntklqgktitlawapgkgmkdkdwKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFDEDTVPLWLK
Low Complexity Region (SEG)
MDVIKTFNQELSSLYDTKPPISkakitaitrsairaikFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFDEDTVPLWLK
Disordered region (IsUnstruct)
********************ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFDEDTVPLW**
Disordered Region (DISOPRED)
**VIKTFNQELSSLY************AITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVR*************PRFARNLKATFQHLYQCPPE*************************LFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL********************DGVSYIPYDRLSKEIDYDYLEDGGVFDE***P****
Disordered Region (DISEMBL)
MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFDEDTVPLWLK
Disordered Region (DISPRO)
MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFDEDTVPLWLK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFDEDTVPLWLK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	282	2.2.26 [Sep-21-2011]
Q9UPN6	1271	Protein SCAF8 OS=Homo sap	yes	N/A	0.475	0.105	0.748	2e-54
Q6DID3	1268	Protein SCAF8 OS=Mus musc	yes	N/A	0.475	0.105	0.748	2e-54
O95104	1147	Splicing factor, arginine	no	N/A	0.475	0.116	0.740	3e-53
Q63623	1268	Protein SCAF8 OS=Rattus n	no	N/A	0.475	0.105	0.733	2e-52
Q63627	1048	Splicing factor, arginine	no	N/A	0.464	0.125	0.433	7e-26
Q9LEB4	409	Polyadenylate-binding pro	N/A	N/A	0.468	0.322	0.291	2e-09
Q9SX79	432	Polyadenylate-binding pro	yes	N/A	0.319	0.208	0.326	2e-08
O60176	473	Uncharacterized RNA-bindi	yes	N/A	0.226	0.135	0.369	4e-08
Q9SX80	434	Polyadenylate-binding pro	no	N/A	0.255	0.165	0.361	4e-08
Q93W34	415	Polyadenylate-binding pro	no	N/A	0.294	0.2	0.313	1e-07

>sp|Q9UPN6|SCAF8_HUMAN Protein SCAF8 OS=Homo sapiens GN=SCAF8 PE=1 SV=1

 Score =  212 bits (540), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 101/135 (74%), Positives = 117/135 (86%), Gaps = 1/135 (0%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           M+ +KTFN EL SL D KPPISKAK+T IT++AI+AIKFYKHVVQSVEKFI KCKPEYKV
Sbjct: 1   MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 120

Query: 120 EVFTPDIIHPLFDMA 134
            VF  +II PL DMA
Sbjct: 121 NVFKSEIIQPLLDMA 135

May play a role in mRNA processing.
Homo sapiens (taxid: 9606)

>sp|Q6DID3|SCAF8_MOUSE Protein SCAF8 OS=Mus musculus GN=Scaf8 PE=1 SV=1

 Score =  212 bits (539), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 101/135 (74%), Positives = 117/135 (86%), Gaps = 1/135 (0%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           M+ +KTFN EL SL D KPPISKAK+T IT++AI+AIKFYKHVVQSVEKFI KCKPEYKV
Sbjct: 1   MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 120

Query: 120 EVFTPDIIHPLFDMA 134
            VF  +II PL DMA
Sbjct: 121 NVFKSEIIQPLLDMA 135

May play a role in mRNA processing.

Mus musculus (taxid: 10090)

>sp|O95104|SFR15_HUMAN Splicing factor, arginine/serine-rich 15 OS=Homo sapiens GN=SCAF4 PE=1 SV=3

 Score =  208 bits (530), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 100/135 (74%), Positives = 113/135 (83%), Gaps = 1/135 (0%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           MD +  FNQEL SL D KPPIS+AK+  IT++AI+AIK YKHVVQ VEKFI KCKPEYKV
Sbjct: 1   MDAVNAFNQELFSLMDMKPPISRAKMILITKAAIKAIKLYKHVVQIVEKFIKKCKPEYKV 60

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF  DKDVFGPRF++N+ ATFQ+LY CP EDKSKI+RVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGTDKDVFGPRFSKNITATFQYLYLCPSEDKSKIVRVLNLWQKN 120

Query: 120 EVFTPDIIHPLFDMA 134
            VF  +II PL DMA
Sbjct: 121 GVFKIEIIQPLLDMA 135

May act to physically and functionally link transcription and pre-mRNA processing.

Homo sapiens (taxid: 9606)

>sp|Q63623|SCAF8_RAT Protein SCAF8 OS=Rattus norvegicus GN=Scaf8 PE=1 SV=1

 Score =  206 bits (523), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 99/135 (73%), Positives = 115/135 (85%), Gaps = 1/135 (0%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           M+ +KTFN EL SL D KPPISKAK+T IT++AI+AIKFYKHVVQSVEKFI KCKPEYKV
Sbjct: 1   MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQ  Q+KDV  PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQVGQEKDVCAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 120

Query: 120 EVFTPDIIHPLFDMA 134
            VF  +II PL DMA
Sbjct: 121 NVFKSEIIQPLLDMA 135

May play a role in mRNA processing.

Rattus norvegicus (taxid: 10116)

>sp|Q63627|SFR15_RAT Splicing factor, arginine/serine-rich 15 (Fragment) OS=Rattus norvegicus GN=Scaf4 PE=2 SV=1

 Score =  117 bits (294), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 59/136 (43%), Positives = 92/136 (67%), Gaps = 5/136 (3%)

Query: 148 QARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDA 207
           Q ++   ++CSTTLW+G L K   +++++    E+G + SIN+IPPRGCA++ M  RQDA
Sbjct: 411 QIKSETASVCSTTLWVGQLDKRTTQQDVASLLEEFGPIESINMIPPRGCAYIVMVHRQDA 470

Query: 208 AKALYKLK--NTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDY 265
            +AL KL   N K+  K+I +AWA  KG+K  D+K +W+V+ GV+YIP+D++  E + + 
Sbjct: 471 YRALQKLSRGNYKVNQKSIKIAWALNKGIK-ADFKQYWDVELGVTYIPWDKVKAE-ELES 528

Query: 266 LEDGGVFDEDTV-PLW 280
             +GG+ D DT+ P W
Sbjct: 529 FCEGGMLDSDTLNPDW 544

May act to physically and functionally link transcription and pre-mRNA processing.

Rattus norvegicus (taxid: 10116)

>sp|Q9LEB4|RBP45_NICPL Polyadenylate-binding protein RBP45 OS=Nicotiana plumbaginifolia GN=RBP45 PE=1 SV=1

 Score = 63.5 bits (153), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 40/137 (29%), Positives = 62/137 (45%), Gaps = 5/137 (3%)

Query: 105 DKSKIIRVLNLWQKNEVFT---PDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTL 161
           D+S+ +R +   + N V     P  I P  +      P        QA  G  +  +TT+
Sbjct: 227 DESEQLRAMT--EMNGVLCSTRPMRIGPAANKKPVGTPQKATYQNPQATQGESDPNNTTI 284

Query: 162 WIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQG 221
           ++G L   V EE L   F  YG++V + ++  + C FV    R  A +AL  L  T+L G
Sbjct: 285 FVGGLDPTVAEEHLRQVFSPYGELVHVKIVAGKRCGFVQFGTRASAEQALSSLNGTQLGG 344

Query: 222 KTITLAWAPGKGMKDKD 238
           ++I L+W      K  D
Sbjct: 345 QSIRLSWGRSPSSKQTD 361

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q9SX79|RB47C_ARATH Polyadenylate-binding protein RBP47C OS=Arabidopsis thaliana GN=RBP47C PE=2 SV=1

 Score = 59.7 bits (143), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 54/92 (58%), Gaps = 2/92 (2%)

Query: 155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL 214
           ++ +TT+++G L   V +E+L   F E+G++VS+ +   +GC FV    R +A +AL KL
Sbjct: 300 DIMNTTIFVGGLDSSVTDEDLKQPFNEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKL 359

Query: 215 KNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQ 246
             T +  +T+ L+W  G+   +K  +D +  Q
Sbjct: 360 NGTVIGKQTVRLSW--GRNPANKQPRDKYGNQ 389

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|O60176|YG41_SCHPO Uncharacterized RNA-binding protein C23E6.01c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC23E6.01c PE=1 SV=2

 Score = 58.9 bits (141), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 42/73 (57%)

Query: 157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
            ++T+++G LSK V EEEL   F  +G++V + + P +GC FV    RQ A  A+ +L+ 
Sbjct: 301 ANSTVFVGGLSKFVSEEELKYLFQNFGEIVYVKIPPGKGCGFVQFVNRQSAEIAINQLQG 360

Query: 217 TKLQGKTITLAWA 229
             L    I L+W 
Sbjct: 361 YPLGNSRIRLSWG 373

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q9SX80|R47CP_ARATH Polyadenylate-binding protein RBP47C' OS=Arabidopsis thaliana GN=RBP47C' PE=2 SV=1

 Score = 58.9 bits (141), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           +TT+++G L   V +E+L   F E+G++VS+ +   +GC FV    R +A +AL KL  T
Sbjct: 305 NTTIFVGGLDSSVTDEDLKQPFSEFGEIVSVKIPVGKGCGFVQFVNRPNAEEALEKLNGT 364

Query: 218 KLQGKTITLAWA 229
            +  +T+ L+W 
Sbjct: 365 VIGKQTVRLSWG 376

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q93W34|RP45C_ARATH Polyadenylate-binding protein RBP45C OS=Arabidopsis thaliana GN=RBP45C PE=2 SV=1

 Score = 57.8 bits (138), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 48/83 (57%)

Query: 147 IQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQD 206
            Q  +G  +  +TT+++G + + V E++L   FG++G++V + +   + C FV    R  
Sbjct: 266 TQGNSGESDPTNTTIFVGAVDQSVTEDDLKSVFGQFGELVHVKIPAGKRCGFVQYANRAC 325

Query: 207 AAKALYKLKNTKLQGKTITLAWA 229
           A +AL  L  T+L G++I L+W 
Sbjct: 326 AEQALSVLNGTQLGGQSIRLSWG 348

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	282
321462197	263	hypothetical protein DAPPUDRAFT_14394 [D	0.925	0.992	0.685	1e-107
443715596	274	hypothetical protein CAPTEDRAFT_122321,	0.932	0.959	0.532	1e-82
391327585	657	PREDICTED: uncharacterized protein LOC10	0.971	0.417	0.510	2e-80
260790611	263	hypothetical protein BRAFLDRAFT_264027 [	0.854	0.916	0.546	6e-77
47227869	262	unnamed protein product [Tetraodon nigro	0.907	0.977	0.523	1e-71
91094229	1145	PREDICTED: similar to conserved hypothet	0.539	0.132	0.751	7e-63
242024705	1343	conserved hypothetical protein [Pediculu	0.560	0.117	0.716	3e-62
170050233	1014	conserved hypothetical protein [Culex qu	0.5	0.139	0.760	1e-60
347969782	1392	AGAP003369-PA [Anopheles gambiae str. PE	0.507	0.102	0.736	2e-60
307198209	1633	Putative RNA-binding protein 16 [Harpegn	0.507	0.087	0.75	5e-60

>gi|321462197|gb|EFX73222.1| hypothetical protein DAPPUDRAFT_14394 [Daphnia pulex]

 Score =  393 bits (1009), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 185/270 (68%), Positives = 225/270 (83%), Gaps = 9/270 (3%)

Query: 10  ELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSL 69
           +LSSLYD KPPISKAK+TAIT+ AI+A+KFYKHVVQSVEKF+ KC+PEYK+P LYVIDS+
Sbjct: 1   QLSSLYDMKPPISKAKMTAITKGAIKAVKFYKHVVQSVEKFLQKCRPEYKIPGLYVIDSI 60

Query: 70  VRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIH 128
           VRQSRHQF  DKDVF PRF++N+  TF  +YQC  E+KSK+IRVLNLWQKN VF P++I 
Sbjct: 61  VRQSRHQFGADKDVFAPRFSKNVTYTFYFIYQCTGEEKSKVIRVLNLWQKNAVFPPEVIQ 120

Query: 129 PLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSI 188
           PLFDMAD + P  ++ A         ++CSTTLW+GHLSKLVQ+EELSDTFG+YG+++SI
Sbjct: 121 PLFDMADSSLPPTKKEAL--------SVCSTTLWVGHLSKLVQQEELSDTFGQYGEILSI 172

Query: 189 NLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDG 248
           +LIPPRGCAFVCM+RRQDA +AL KL   KLQGK ITLAWAPGKG+K K+WKDFWEV  G
Sbjct: 173 DLIPPRGCAFVCMHRRQDAYRALTKLAGHKLQGKAITLAWAPGKGVKAKEWKDFWEVDQG 232

Query: 249 VSYIPYDRLSKEIDYDYLEDGGVFDEDTVP 278
           VSY+P+ RLS+  D + LE+GG FDE+T+P
Sbjct: 233 VSYVPWQRLSQMTDLEALEEGGSFDEETLP 262

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443715596|gb|ELU07509.1| hypothetical protein CAPTEDRAFT_122321, partial [Capitella teleta]

 Score =  312 bits (800), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 146/274 (53%), Positives = 197/274 (71%), Gaps = 11/274 (4%)

Query: 10  ELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSL 69
           +LSS+ + +PPIS+AK+ AIT+SAI+ IKFYKH+VQSVEKFI K +PE+KVP LYV+DS+
Sbjct: 1   QLSSVCEARPPISRAKMAAITKSAIKGIKFYKHIVQSVEKFIHKGRPEFKVPGLYVMDSI 60

Query: 70  VRQSRHQFQ-DKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIH 128
           VRQSRHQF  +KDVFGPRF++N+  TFQ L+QC  +D+SK+IRVLNLWQKN VF P +I 
Sbjct: 61  VRQSRHQFSSEKDVFGPRFSKNIVRTFQFLFQCKGDDRSKVIRVLNLWQKNSVFPPAVIQ 120

Query: 129 PLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSI 188
           PL D+A       + +           +CSTT+WIGHLSK   ++ + D    YG+V S+
Sbjct: 121 PLLDLATDPTSTEKHMT----------VCSTTIWIGHLSKNTTQDNIMDEMVNYGEVHSV 170

Query: 189 NLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDG 248
           NL+PPRGCA+VC++ R+DA++AL KLK  KL G T+ +AWA  KG+ +  WK  W+V  G
Sbjct: 171 NLVPPRGCAYVCLSSRKDASRALSKLKGVKLLGNTLKVAWATNKGILESKWKHLWDVDQG 230

Query: 249 VSYIPYDRLSKEIDYDYLEDGGVFDEDTVPLWLK 282
            ++IP+D L   I  D L +GGV D +T+P  L+
Sbjct: 231 STFIPWDDLPDNISLDELTEGGVIDPETIPKRLR 264

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|391327585|ref|XP_003738278.1| PREDICTED: uncharacterized protein LOC100908485 [Metaseiulus occidentalis]

 Score =  305 bits (780), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 146/286 (51%), Positives = 204/286 (71%), Gaps = 12/286 (4%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           M+ +K FN EL +LY+++PP+SKAK+T IT+ A++ +K YKHVV +VEKFI KCKPEYKV
Sbjct: 7   MEEVKAFNAELQTLYESRPPVSKAKMTDITKRAMKGVKLYKHVVHTVEKFIHKCKPEYKV 66

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF  +KDVF PRF +N+K TFQ L +CP + + KI+RVLNLWQKN
Sbjct: 67  PGLYVIDSIVRQSRHQFGSEKDVFAPRFQKNIKNTFQSLMRCPDDQRPKIVRVLNLWQKN 126

Query: 120 EVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTF 179
            VF  ++   L ++      +   L  +  R G   +CS TLW+GH+SK   E +L  +F
Sbjct: 127 GVFPTEVTQMLHEV------VASCLPAV--RRGYITVCSNTLWLGHVSKATTESDLEASF 178

Query: 180 GEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKT--ITLAWAPGKGMKD- 236
           GE+G ++SI+LIPPRGCA++CM+RRQDA + L   +N +L+     I +AWAP KG K+ 
Sbjct: 179 GEHGKILSIDLIPPRGCAYICMDRRQDAYRTLVNKRNIRLKNSPSRIKIAWAPHKGAKNH 238

Query: 237 KDWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFDEDTVPLWLK 282
           K++KD+W+V  G  +IP D++  ++D   LE+GG+ D D++P  LK
Sbjct: 239 KNFKDYWDVDQGCFFIPDDQMPLDVDLAQLEEGGMIDVDSLPDSLK 284

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|260790611|ref|XP_002590335.1| hypothetical protein BRAFLDRAFT_264027 [Branchiostoma floridae] gi|229275527|gb|EEN46346.1| hypothetical protein BRAFLDRAFT_264027 [Branchiostoma floridae]

 Score =  293 bits (750), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 140/256 (54%), Positives = 186/256 (72%), Gaps = 15/256 (5%)

Query: 26  ITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQF-QDKDVFG 84
           +TA+T++AI+AIKFYKHVVQSVEKFI KC+PEYKVP LYVIDS+VRQSRHQF  DKDVF 
Sbjct: 1   MTAVTKAAIKAIKFYKHVVQSVEKFIQKCRPEYKVPGLYVIDSIVRQSRHQFGADKDVFA 60

Query: 85  PRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHREL 144
           PRFA+N+  TFQHL++CPPED+++++RVLNLWQKN VF  ++I PL DMADP        
Sbjct: 61  PRFAKNVTLTFQHLFKCPPEDRARVVRVLNLWQKNHVFKVEVIQPLLDMADP-------- 112

Query: 145 AEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRR 204
              +    ++ +CSTTLW+GHL K   + EL + F   G V SI+LIPPRGCA+VC   R
Sbjct: 113 ---ERAKQMQPVCSTTLWVGHLDKKTTDVELRNIFEAIGPVQSIDLIPPRGCAYVCYETR 169

Query: 205 QDAAKALYKLKNTKLQGKT--ITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEID 262
            DA  AL KLKN ++  +   + +AWAPGKG+K K+ K +W+   G +Y+P+++L  + D
Sbjct: 170 LDAHNALNKLKNLRVGNRQQPVQMAWAPGKGVKGKEHKQYWDDHAGTTYLPWEKLEGK-D 228

Query: 263 YDYLEDGGVFDEDTVP 278
            + L +GG  D +T+P
Sbjct: 229 LESLAEGGYIDNETLP 244

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

>gi|47227869|emb|CAG09032.1| unnamed protein product [Tetraodon nigroviridis]

 Score =  275 bits (704), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 142/271 (52%), Positives = 189/271 (69%), Gaps = 15/271 (5%)

Query: 10  ELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSL 69
           +L S+ D KPPIS+AK+ ++T++AI+AIK YKHVVQ VEKFI KCKPE KVP LYV+DS+
Sbjct: 1   KLFSMIDMKPPISRAKMMSVTKAAIKAIKLYKHVVQIVEKFIKKCKPELKVPGLYVVDSI 60

Query: 70  VRQSRHQFQ-DKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIH 128
           VRQSRHQF  DKDVFGPRF +N   TFQ+LY CP EDK+KI+RVL+LWQKN VF  +++ 
Sbjct: 61  VRQSRHQFGVDKDVFGPRFQKNFTDTFQNLYHCPEEDKNKIVRVLHLWQKNGVFDINLLQ 120

Query: 129 PLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSI 188
            L DMA+ N           + N VE +CSTTLWIG L K  Q+ ++     E+G + SI
Sbjct: 121 SLLDMANGNK---------TSPNIVE-VCSTTLWIGQLDKKTQQSDVVSLLEEFGQIESI 170

Query: 189 NLIPPRGCAFVCMNRRQDAAKALYKLK--NTKLQGKTITLAWAPGKGMKDKDWKDFWEVQ 246
           N+IPPRGCA++ M  RQDA  AL KL   + ++  K + +A A  KG+K    K FW+V+
Sbjct: 171 NMIPPRGCAYIVMVHRQDAYTALNKLSRGSYRVNQKPVKIACALNKGIKSTH-KKFWDVE 229

Query: 247 DGVSYIPYDRLSKEIDYDYLEDGGVFDEDTV 277
            GV+YIP+ ++  E D +  ++GG+ D DT+
Sbjct: 230 QGVTYIPWTKVRVE-DLESYQEGGILDADTL 259

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|91094229|ref|XP_967119.1| PREDICTED: similar to conserved hypothetical protein [Tribolium castaneum] gi|270016224|gb|EFA12670.1| hypothetical protein TcasGA2_TC010693 [Tribolium castaneum]

 Score =  246 bits (629), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 115/153 (75%), Positives = 132/153 (86%), Gaps = 1/153 (0%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           MD +K FN ELSSLY+ KPPISKAK+TAITR AI+AIKFYKHVVQSVEKFI+KCKPEYKV
Sbjct: 1   MDAVKAFNAELSSLYEVKPPISKAKMTAITRGAIKAIKFYKHVVQSVEKFILKCKPEYKV 60

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF  DKDVF PRFA+N++ TF +L+ CP EDKSKIIRVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGADKDVFAPRFAKNMRQTFINLFLCPAEDKSKIIRVLNLWQKN 120

Query: 120 EVFTPDIIHPLFDMADPNHPIHRELAEIQARNG 152
           +VF P++I PLFD+ADPN+PIH+EL      NG
Sbjct: 121 QVFAPEVIQPLFDLADPNNPIHKELGTPMQSNG 153

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242024705|ref|XP_002432767.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212518252|gb|EEB20029.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  244 bits (622), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 116/162 (71%), Positives = 135/162 (83%), Gaps = 4/162 (2%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           MD +K FN ELS+LY+ KPPISKAK+++ITRSAI+AIKFYKHVVQSVEKFI KCKPEYKV
Sbjct: 1   MDAVKAFNNELSALYEVKPPISKAKMSSITRSAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF  DKD+F PRFA+N++ TF +L+ CPPEDK KIIRVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGPDKDLFAPRFAKNMQNTFANLFNCPPEDKGKIIRVLNLWQKN 120

Query: 120 EVFTPDIIHPLFD-MADPNHPIHRELAEIQARNGVENMCSTT 160
            VFTPD+I PLFD +ADPN+PIHRE   + A NG+      T
Sbjct: 121 SVFTPDVIQPLFDQLADPNNPIHRE--NLAASNGLNTSAGHT 160

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170050233|ref|XP_001859912.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167871912|gb|EDS35295.1| conserved hypothetical protein [Culex quinquefasciatus]

 Score =  239 bits (609), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 108/142 (76%), Positives = 125/142 (88%), Gaps = 1/142 (0%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           MD ++ FNQELS LY+ KPPISKAK+ +ITRSA++AIKFYKHVVQSVEKFI KCK EYK+
Sbjct: 1   MDTVRIFNQELSGLYEAKPPISKAKMASITRSAMKAIKFYKHVVQSVEKFISKCKSEYKI 60

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF  +KDVF PRFARN++ATF HL++CPPEDKSKIIRVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGTEKDVFAPRFARNMEATFAHLFRCPPEDKSKIIRVLNLWQKN 120

Query: 120 EVFTPDIIHPLFDMADPNHPIH 141
            VF P+ I PLFD+A+P HPIH
Sbjct: 121 MVFAPETIQPLFDLANPEHPIH 142

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347969782|ref|XP_314272.5| AGAP003369-PA [Anopheles gambiae str. PEST] gi|333469268|gb|EAA09643.5| AGAP003369-PA [Anopheles gambiae str. PEST]

 Score =  238 bits (607), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 106/144 (73%), Positives = 130/144 (90%), Gaps = 1/144 (0%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           M+ ++ FNQELS LY++KPPISKAK+ +ITRSA++AIKFYKHVVQSVEKFI KCK EYK+
Sbjct: 1   METVRVFNQELSGLYESKPPISKAKMASITRSAMKAIKFYKHVVQSVEKFIQKCKCEYKI 60

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF  +KDVF PRFARN+++TF HL++CPPEDKSKIIRVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGPEKDVFAPRFARNMESTFAHLFRCPPEDKSKIIRVLNLWQKN 120

Query: 120 EVFTPDIIHPLFDMADPNHPIHRE 143
            VF P++I PLFD+A+P+HPIH++
Sbjct: 121 MVFLPEVIQPLFDLANPDHPIHQQ 144

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307198209|gb|EFN79224.1| Putative RNA-binding protein 16 [Harpegnathos saltator]

 Score =  237 bits (604), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 108/144 (75%), Positives = 126/144 (87%), Gaps = 1/144 (0%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           MD +K FN ELS+LYD KPPISKAK+ ++TR AI+AIKFYKHVVQSVEKFI KCKPEYKV
Sbjct: 1   MDAVKAFNAELSALYDVKPPISKAKMNSLTRGAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF  +KDVF PRFA+N++ TF +L +CP EDKSK+IRVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGMEKDVFAPRFAKNMQNTFLNLLKCPQEDKSKVIRVLNLWQKN 120

Query: 120 EVFTPDIIHPLFDMADPNHPIHRE 143
            VF P++I PLFD+ADPNHPIH+E
Sbjct: 121 AVFPPEVIQPLFDLADPNHPIHKE 144

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	282
FB|FBgn0034598	1306	CG4266 [Drosophila melanogaste	0.539	0.116	0.594	8.7e-96
ZFIN|ZDB-GENE-030131-4817	1286	wu:fd99c08 "wu:fd99c08" [Danio	0.475	0.104	0.659	2.2e-73
UNIPROTKB|F1LPT8	1267	Rbm16 "Protein Rbm16" [Rattus	0.475	0.105	0.666	4.3e-73
MGI|MGI:1925212	1268	Scaf8 "SR-related CTD-associat	0.475	0.105	0.666	4.3e-73
UNIPROTKB|Q9UPN6	1271	SCAF8 "Protein SCAF8" [Homo sa	0.475	0.105	0.666	5.5e-73
UNIPROTKB|F1SB23	1347	SCAF8 "Uncharacterized protein	0.475	0.099	0.666	6.9e-73
UNIPROTKB|O95104	1147	SCAF4 "Splicing factor, argini	0.475	0.116	0.674	2e-72
UNIPROTKB|F1LSM7	1226	Sfrs15 "Protein Sfrs15" [Rattu	0.475	0.109	0.674	2.1e-72
UNIPROTKB|I3LPZ9	1132	SCAF4 "Uncharacterized protein	0.475	0.118	0.674	2.4e-72
UNIPROTKB|F1P0Y4	1092	SCAF4 "Uncharacterized protein	0.475	0.122	0.659	9.1e-72

FB|FBgn0034598 CG4266 [Drosophila melanogaster (taxid:7227)]

 Score = 504 (182.5 bits), Expect = 8.7e-96, Sum P(2) = 8.7e-96
 Identities = 91/153 (59%), Positives = 111/153 (72%)

Query:     1 MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
             M+ +  FN ELS LYD++PPIS                 YKHVVQSVEKFI+KCKPEYKV
Sbjct:     1 METVVAFNNELSGLYDSRPPISKAKMAAITKSAMRAIKLYKHVVQSVEKFILKCKPEYKV 60

Query:    61 PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
             P LYVIDS+VRQSRHQ+  DKD+F PRF RNL  TF +L++C PEDKS+IIRVLNLWQKN
Sbjct:    61 PGLYVIDSIVRQSRHQYGMDKDLFAPRFQRNLTETFANLFRCAPEDKSRIIRVLNLWQKN 120

Query:   120 EVFTPDIIHPLFDMADPNHPIHRELAEIQARNG 152
              VF  ++I P+FD+ADPNHPI+ ++  +    G
Sbjct:   121 NVFKSEVIQPIFDLADPNHPIYHQMPPVGGSGG 153

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

GO:0003729 "mRNA binding" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-030131-4817 wu:fd99c08 "wu:fd99c08" [Danio rerio (taxid:7955)]

 Score = 462 (167.7 bits), Expect = 2.2e-73, Sum P(2) = 2.2e-73
 Identities = 89/135 (65%), Positives = 101/135 (74%)

Query:     1 MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
             M+ +K FN EL SL + KPPIS                FYKHVVQSVEKFI KCKPEYKV
Sbjct:     1 MEAVKAFNGELYSLNEYKPPISKAKMTQITKSAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query:    61 PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
             P LYVIDS+VRQSRHQF Q+KDVF PRF++N+  TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct:    61 PGLYVIDSIVRQSRHQFGQEKDVFAPRFSKNIIGTFQNLYRCPTDDKSKIVRVLNLWQKN 120

Query:   120 EVFTPDIIHPLFDMA 134
              VF  DII PL DMA
Sbjct:   121 NVFKSDIIQPLLDMA 135

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046660 "female sex differentiation" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|F1LPT8 Rbm16 "Protein Rbm16" [Rattus norvegicus (taxid:10116)]

 Score = 467 (169.5 bits), Expect = 4.3e-73, Sum P(2) = 4.3e-73
 Identities = 90/135 (66%), Positives = 102/135 (75%)

Query:     1 MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
             M+ +KTFN EL SL D KPPIS                FYKHVVQSVEKFI KCKPEYKV
Sbjct:     1 MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query:    61 PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
             P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct:    61 PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 120

Query:   120 EVFTPDIIHPLFDMA 134
              VF  +II PL DMA
Sbjct:   121 NVFKSEIIQPLLDMA 135

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1925212 Scaf8 "SR-related CTD-associated factor 8" [Mus musculus (taxid:10090)]

 Score = 467 (169.5 bits), Expect = 4.3e-73, Sum P(2) = 4.3e-73
 Identities = 90/135 (66%), Positives = 102/135 (75%)

Query:     1 MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
             M+ +KTFN EL SL D KPPIS                FYKHVVQSVEKFI KCKPEYKV
Sbjct:     1 MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query:    61 PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
             P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct:    61 PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 120

Query:   120 EVFTPDIIHPLFDMA 134
              VF  +II PL DMA
Sbjct:   121 NVFKSEIIQPLLDMA 135

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISO

GO:0006397 "mRNA processing" evidence=ISO

GO:0008380 "RNA splicing" evidence=IEA

GO:0016363 "nuclear matrix" evidence=ISO

GO:0019904 "protein domain specific binding" evidence=ISO

GO:0043175 "RNA polymerase core enzyme binding" evidence=ISO

GO:0070063 "RNA polymerase binding" evidence=ISO

UNIPROTKB|Q9UPN6 SCAF8 "Protein SCAF8" [Homo sapiens (taxid:9606)]

 Score = 467 (169.5 bits), Expect = 5.5e-73, Sum P(2) = 5.5e-73
 Identities = 90/135 (66%), Positives = 102/135 (75%)

Query:     1 MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
             M+ +KTFN EL SL D KPPIS                FYKHVVQSVEKFI KCKPEYKV
Sbjct:     1 MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query:    61 PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
             P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct:    61 PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 120

Query:   120 EVFTPDIIHPLFDMA 134
              VF  +II PL DMA
Sbjct:   121 NVFKSEIIQPLLDMA 135

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0043175 "RNA polymerase core enzyme binding" evidence=IPI

GO:0016363 "nuclear matrix" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|F1SB23 SCAF8 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 467 (169.5 bits), Expect = 6.9e-73, Sum P(2) = 6.9e-73
 Identities = 90/135 (66%), Positives = 102/135 (75%)

Query:     1 MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
             M+ +KTFN EL SL D KPPIS                FYKHVVQSVEKFI KCKPEYKV
Sbjct:    79 MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 138

Query:    61 PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
             P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct:   139 PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 198

Query:   120 EVFTPDIIHPLFDMA 134
              VF  +II PL DMA
Sbjct:   199 NVFKSEIIQPLLDMA 213

GO:0043175 "RNA polymerase core enzyme binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|O95104 SCAF4 "Splicing factor, arginine/serine-rich 15" [Homo sapiens (taxid:9606)]

 Score = 464 (168.4 bits), Expect = 2.0e-72, Sum P(2) = 2.0e-72
 Identities = 91/135 (67%), Positives = 99/135 (73%)

Query:     1 MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
             MD +  FNQEL SL D KPPIS                 YKHVVQ VEKFI KCKPEYKV
Sbjct:     1 MDAVNAFNQELFSLMDMKPPISRAKMILITKAAIKAIKLYKHVVQIVEKFIKKCKPEYKV 60

Query:    61 PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
             P LYVIDS+VRQSRHQF  DKDVFGPRF++N+ ATFQ+LY CP EDKSKI+RVLNLWQKN
Sbjct:    61 PGLYVIDSIVRQSRHQFGTDKDVFGPRFSKNITATFQYLYLCPSEDKSKIVRVLNLWQKN 120

Query:   120 EVFTPDIIHPLFDMA 134
              VF  +II PL DMA
Sbjct:   121 GVFKIEIIQPLLDMA 135

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|F1LSM7 Sfrs15 "Protein Sfrs15" [Rattus norvegicus (taxid:10116)]

 Score = 464 (168.4 bits), Expect = 2.1e-72, Sum P(2) = 2.1e-72
 Identities = 91/135 (67%), Positives = 99/135 (73%)

Query:     1 MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
             MD +  FNQEL SL D KPPIS                 YKHVVQ VEKFI KCKPEYKV
Sbjct:     1 MDAVNAFNQELFSLMDMKPPISRAKMILITKAAIKAIKLYKHVVQIVEKFIKKCKPEYKV 60

Query:    61 PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
             P LYVIDS+VRQSRHQF  DKDVFGPRF++N+ ATFQ+LY CP EDKSKI+RVLNLWQKN
Sbjct:    61 PGLYVIDSIVRQSRHQFGTDKDVFGPRFSKNITATFQYLYLCPSEDKSKIVRVLNLWQKN 120

Query:   120 EVFTPDIIHPLFDMA 134
              VF  +II PL DMA
Sbjct:   121 GVFKIEIIQPLLDMA 135

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|I3LPZ9 SCAF4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 464 (168.4 bits), Expect = 2.4e-72, Sum P(2) = 2.4e-72
 Identities = 91/135 (67%), Positives = 99/135 (73%)

Query:     1 MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
             MD +  FNQEL SL D KPPIS                 YKHVVQ VEKFI KCKPEYKV
Sbjct:     1 MDAVNAFNQELFSLMDMKPPISRAKMILITKAAIKAIKLYKHVVQIVEKFIKKCKPEYKV 60

Query:    61 PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
             P LYVIDS+VRQSRHQF  DKDVFGPRF++N+ ATFQ+LY CP EDKSKI+RVLNLWQKN
Sbjct:    61 PGLYVIDSIVRQSRHQFGTDKDVFGPRFSKNITATFQYLYLCPSEDKSKIVRVLNLWQKN 120

Query:   120 EVFTPDIIHPLFDMA 134
              VF  +II PL DMA
Sbjct:   121 GVFKIEIIQPLLDMA 135

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1P0Y4 SCAF4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 456 (165.6 bits), Expect = 9.1e-72, Sum P(2) = 9.1e-72
 Identities = 89/135 (65%), Positives = 99/135 (73%)

Query:     1 MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
             M+ +  FNQEL SL + KPPIS                 YKHVVQ VEKFI KCKPEYKV
Sbjct:     1 MEAVNAFNQELFSLMEMKPPISRAKMILITKAAIKAIKLYKHVVQIVEKFIKKCKPEYKV 60

Query:    61 PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
             P LYVIDS+VRQSRHQF  DKDVFGPRF++N+ ATFQ+LY CP EDKSKI+RVLNLWQKN
Sbjct:    61 PGLYVIDSIVRQSRHQFGTDKDVFGPRFSKNITATFQYLYLCPSEDKSKIVRVLNLWQKN 120

Query:   120 EVFTPDIIHPLFDMA 134
              VF  +II PL DMA
Sbjct:   121 GVFKIEIIQPLLDMA 135

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6DID3	SCAF8_MOUSE	No assigned EC number	0.7481	0.4751	0.1056	yes	N/A
Q9UPN6	SCAF8_HUMAN	No assigned EC number	0.7481	0.4751	0.1054	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	282
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-43
cd03562	114	cd03562, CID, CID (CTD-Interacting Domain) domain	2e-33
smart00582	124	smart00582, RPR, domain present in proteins, which	1e-30
cd12462	79	cd12462, RRM_SCAF8, RNA recognition motif in SR-re	4e-24
cd12461	81	cd12461, RRM_SCAF4, RNA recognition motif found in	2e-23
pfam04818	64	pfam04818, CTD_bind, RNA polymerase II-binding dom	1e-15
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	6e-15
smart00360	73	smart00360, RRM, RNA recognition motif	2e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-14
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	4e-14
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-12
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-12
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-10
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	6e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	6e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-09
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	2e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	9e-09
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	1e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-08
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	1e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-08
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	5e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-07
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	1e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	5e-07
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	8e-07
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	1e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-06
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	4e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	5e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-06
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	6e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	6e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	6e-06
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	7e-06
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	7e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-05
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	2e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-05
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-05
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-05
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	4e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	5e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-05
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	6e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	7e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	7e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	8e-05
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	8e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	8e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	9e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	1e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	1e-04
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	1e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	2e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	3e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	3e-04
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	3e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	4e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	4e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	4e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	4e-04
cd12436	76	cd12436, RRM1_2_MATR3_like, RNA recognition motif	5e-04
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	6e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	6e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	7e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	8e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	9e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.001
cd12435	71	cd12435, RRM_GW182_like, RNA recognition motif in	0.001
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.001
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.002
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.002
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	0.002
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	0.002
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	0.002
cd12443	73	cd12443, RRM_MCM3A_like, RNA recognition motif in	0.002
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.002
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	0.002
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	0.002
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.002
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	0.002
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	0.002
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.002
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.002
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.003
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	0.003
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.003
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.003
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	0.003
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	0.004
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	0.004
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.004
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	0.004

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score =  141 bits (357), Expect = 5e-43
 Identities = 52/77 (67%), Positives = 62/77 (80%)

Query: 157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
           CSTTLWIGHLSK V EE+L + F EYG++ SI++IPPRGCA+VCM  RQDA +AL KL+N
Sbjct: 1   CSTTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRN 60

Query: 217 TKLQGKTITLAWAPGKG 233
            KL GK I +AWAP KG
Sbjct: 61  VKLAGKKIKVAWAPNKG 77

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

 Score =  117 bits (296), Expect = 2e-33
 Identities = 35/121 (28%), Positives = 61/121 (50%), Gaps = 7/121 (5%)

Query: 4   IKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPAL 63
           +  +N  L  L   K   S+  I  +T+ AI   K  K +V+ +EK I KC PE K+P L
Sbjct: 1   VFDYNALLEKLTFNK--NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLL 58

Query: 64  YVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFT 123
           Y++DS+V+    ++  K+ F           ++   +   + + K+ R+LN+W++  VF 
Sbjct: 59  YLLDSIVKNVGRKY--KEFFSEFLVPLFLDAYE---KVDEKTRKKLERLLNIWEERFVFG 113

Query: 124 P 124
            
Sbjct: 114 S 114

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. Length = 114

>gnl|CDD|214731 smart00582, RPR, domain present in proteins, which are involved in regulation of nuclear pre-mRNA

 Score =  111 bits (279), Expect = 1e-30
 Identities = 41/130 (31%), Positives = 68/130 (52%), Gaps = 10/130 (7%)

Query: 6   TFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYV 65
            F Q+L SL       S+  I  +T+ AI      K +V+  EK+I K     K+P LY+
Sbjct: 1   AFEQKLESLN-----NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYL 55

Query: 66  IDSLVRQSRHQF--QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFT 123
           +DS+V+ S+ ++  +  D  GP F   L+       +   E K KI R+LN+W++  +F 
Sbjct: 56  LDSIVQNSKRKYGSEFGDELGPVFQDALRRVLGAAPE---ELKKKIRRLLNIWEERGIFP 112

Query: 124 PDIIHPLFDM 133
           P+++ PL + 
Sbjct: 113 PEVLRPLREK 122

Length = 124

>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 92.8 bits (230), Expect = 4e-24
 Identities = 41/79 (51%), Positives = 56/79 (70%), Gaps = 2/79 (2%)

Query: 157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
           CSTTLW+G + K   +++L++ F E+G + SIN+IPPRGCA+VCM  RQDA +AL KL +
Sbjct: 1   CSTTLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAYRALQKLSS 60

Query: 217 T--KLQGKTITLAWAPGKG 233
              K+  K I +AWA  KG
Sbjct: 61  GSYKIGSKVIKIAWALNKG 79

This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 79

>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins

 Score = 90.9 bits (225), Expect = 2e-23
 Identities = 39/81 (48%), Positives = 56/81 (69%), Gaps = 2/81 (2%)

Query: 155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL 214
           ++CSTTLW+G L K   +++++    E+G + SIN+IPPRGCA++ M  RQDA +AL KL
Sbjct: 1   SVCSTTLWVGQLDKRTTQQDVTSLLEEFGPIESINMIPPRGCAYIVMVHRQDAYRALQKL 60

Query: 215 K--NTKLQGKTITLAWAPGKG 233
              N K+  K+I +AWA  KG
Sbjct: 61  SRGNVKVNQKSIKIAWALNKG 81

The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 81

>gnl|CDD|218279 pfam04818, CTD_bind, RNA polymerase II-binding domain

 Score = 69.6 bits (171), Expect = 1e-15
 Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 3/65 (4%)

Query: 59  KVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQC-PPEDKSKIIRVLNLWQ 117
           K+P LY+ + +V+ S+H+  +KD F   F+  L   F H+Y+    E K KI R+LN+W+
Sbjct: 1   KLPLLYLANDVVQNSKHK--NKDEFVKAFSPVLPDAFAHVYKEGDEEVKKKIRRLLNIWE 58

Query: 118 KNEVF 122
           +  VF
Sbjct: 59  ERNVF 63

This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. Length = 64

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 67.7 bits (166), Expect = 6e-15
 Identities = 26/70 (37%), Positives = 41/70 (58%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
           TT+++G L   V E+EL   FG +G++V + + P +GC FV    R  A  A+ +L+ T 
Sbjct: 2   TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTI 61

Query: 219 LQGKTITLAW 228
           + G  I L+W
Sbjct: 62  IGGSRIRLSW 71

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 66.5 bits (163), Expect = 2e-14
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
           TL++G+L     EEEL + F ++G V S+ L+        +G AFV     +DA KAL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 214 LKNTKLQGKTITL 226
           L   +L G+ + +
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 65.8 bits (161), Expect = 4e-14
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLK 215
           L++G+L     EE+L + F ++G++ S+ ++       +G AFV     +DA KAL  L 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 216 NTKLQGKTITL 226
             +L G+ + +
Sbjct: 61  GKELDGRKLKV 71

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). Length = 72

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 65.4 bits (160), Expect = 4e-14
 Identities = 29/73 (39%), Positives = 45/73 (61%), Gaps = 3/73 (4%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
           TTL++G L + V E++L D F ++G++ SI ++P + CAFV    R+ A KA  +L N K
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERLFN-K 60

Query: 219 L--QGKTITLAWA 229
           L   G+ + L W 
Sbjct: 61  LIINGRRLKLKWG 73

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 9/81 (11%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG---------CAFVCMNRRQDAA 208
           +T L++G+L+  V EE L   FG +G + S+ ++ PR          C FV    R DA 
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 209 KALYKLKNTKLQGKTITLAWA 229
           +AL +L    + G  + L W 
Sbjct: 61  RALDELDGKDVMGYELKLGWG 81

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 60.7 bits (148), Expect = 3e-12
 Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
            L++G+L   V EE+L D FG++G+V S  +I        RG  FV M   ++A  A+ K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 214 LKNTKLQGKTIT 225
           L  T   G+T+T
Sbjct: 61  LNGTDFGGRTLT 72

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 59.9 bits (146), Expect = 5e-12
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLK 215
           L++G+L     EE+L D F ++G + SI ++       +G AFV     +DA KAL  L 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 216 NTKLQGKTIT 225
             +L G+ + 
Sbjct: 61  GKELGGRELR 70

(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 characteristic 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. Length = 70

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 54.9 bits (132), Expect = 4e-10
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALY 212
           T L++ +L + + E+EL   F  YG++V  NL+       PRG AFV  ++R++A  A+ 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 213 KLKNTKLQGKTITLA 227
            L  T   G T+ L+
Sbjct: 61  SLNGTIPPGSTMPLS 75

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 58.9 bits (142), Expect = 6e-10
 Identities = 32/94 (34%), Positives = 53/94 (56%), Gaps = 10/94 (10%)

Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMN 202
           AR G E++  T L++ +L + + +++L   FG+YG +V  N++       PRG AFV  N
Sbjct: 184 ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFN 243

Query: 203 RRQDAAKALYKLKNTKLQGK----TITLAWAPGK 232
           +R++A +A+  L N   +G     T+ LA   GK
Sbjct: 244 KREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK 277

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 54.2 bits (131), Expect = 6e-10
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
           TT+++G+L   + EEEL  TF  +G +  + +   +G AFV  +  + AA A+  +  T 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60

Query: 219 LQGKTITLAWAPGK 232
           + G+T+  +W  GK
Sbjct: 61  INGQTVKCSW--GK 72

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALY 212
             L++  LS    E+EL   F ++G V  + L+        RG  FV     +DA  A+ 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 213 KLKNTKLQGKTITLAWA 229
            L   +L+G+ I +  A
Sbjct: 62  DLNGKELEGRVIKVEKA 78

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 6/71 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGC-AFVCMNRRQDAAKALYKL 214
           LW+  LS   +  +L   F +YG VV   ++     P   C  FV M   ++AAK +  L
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 215 KNTKLQGKTIT 225
             T+L G+ I+
Sbjct: 62  HRTELHGRVIS 72

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 51.3 bits (123), Expect = 9e-09
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKL 214
            L++  L   V +EEL   F ++G V S+ L+      P+G A+V       A++A+ K+
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 215 KNTKLQGKTITLA 227
             T+++ KTI++A
Sbjct: 64  DGTEIKEKTISVA 76

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 50.9 bits (122), Expect = 1e-08
 Identities = 18/70 (25%), Positives = 37/70 (52%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
           TT+++G++     + +L   F  +G ++     P RG AFV ++  + AA A+ +L+   
Sbjct: 1   TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFP 60

Query: 219 LQGKTITLAW 228
           + G+ +   W
Sbjct: 61  VHGRPLRCGW 70

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 9/79 (11%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI---------PPRGCAFVCMNRRQDAAKA 210
            LWIG+L   + E  L   F +YG +   + +          PRG  FV    +++A KA
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 211 LYKLKNTKLQGKTITLAWA 229
           L  L      GK + + WA
Sbjct: 61  LKSLNGKTALGKKLVVRWA 79

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 20/62 (32%), Positives = 37/62 (59%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           S  ++IG++   + EE+L + F +YG++ S+N +  + CAFV      +A KA+  +K+ 
Sbjct: 3   SRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAIDGVKSH 62

Query: 218 KL 219
            L
Sbjct: 63  PL 64

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 7/70 (10%)

Query: 166 LSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKLKNTKL 219
           L     E +L   F  +G V  +  IP       +G AFV    + DA KA+  +   K+
Sbjct: 7   LPFKCTEADLKKLFSPFGFVWEVT-IPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKI 65

Query: 220 QGKTITLAWA 229
           +G+ + + WA
Sbjct: 66  KGRPVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 22/69 (31%), Positives = 40/69 (57%), Gaps = 4/69 (5%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI----PPRGCAFVCMNRRQDAAKALYKLK 215
           ++++G LS  V +EEL++ F  +G ++ +NLI         AF+   R Q AA+A+    
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESEN 64

Query: 216 NTKLQGKTI 224
           ++ L+ KT+
Sbjct: 65  HSMLKNKTM 73

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 49.1 bits (118), Expect = 5e-08
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           L +G L++ V ++ L + F  YG V  ++L        PRG A+V     +DA KA+  +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 215 KNTKLQGKTIT 225
              ++ G+ +T
Sbjct: 61  DGGQIDGQEVT 71

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 48.4 bits (116), Expect = 6e-08
 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
           L++G+L      EEL   F +YG V   +++  +   FV M   +DA  A+  L   +  
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV--KNYGFVHMEEEEDAEDAIKALNGYEFM 59

Query: 221 GKTIT 225
           GK I 
Sbjct: 60  GKRIN 64

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 47.9 bits (115), Expect = 1e-07
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 6/64 (9%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKL 214
           L++G L K   EE++   F EYG++  + +I        +GCAFV  + R++A KA+  L
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 215 KNTK 218
               
Sbjct: 62  HGKV 65

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 51.5 bits (122), Expect = 1e-07
 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 146 EIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFV 199
           E           + TL++G+L   V EE+L + F ++G V  + L+        RG AFV
Sbjct: 103 ESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFV 162

Query: 200 CMNRRQDAAKALYKLKNTKLQGKTI 224
                + A KA+ +L   +L+G+ +
Sbjct: 163 EFESEESAEKAIEELNGKELEGRPL 187

Length = 306

>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 47.3 bits (112), Expect = 1e-07
 Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 2/64 (3%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
           T L +G++S     +EL   F EYG V+  +++  +  AFV M R +DA +A+  L NT+
Sbjct: 1   TKLHVGNISSSCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTE 58

Query: 219 LQGK 222
            QGK
Sbjct: 59  FQGK 62

This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 46.0 bits (110), Expect = 4e-07
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 175 LSDTFGEYGDVVSINLIPPR-GCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
           L   F  +G+V  I L+  + G AFV  +  + A KA+  L      G+ + + ++
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

(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. Length = 56

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 46.0 bits (110), Expect = 4e-07
 Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 4/68 (5%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI----PPRGCAFVCMNRRQDAAKALYKLKN 216
           L++ +L   V EE+L + F  YG V  + L+     PRG AFV     +DA  AL KL  
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 217 TKLQGKTI 224
             L G+T+
Sbjct: 61  LVLDGRTL 68

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 46.3 bits (110), Expect = 5e-07
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T L + +L + + ++E+   F   G++ S  LI  +      G  FV     +DA KA+ 
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 213 KLKNTKLQGKTITLAWA 229
            L   +LQ KTI +++A
Sbjct: 62  TLNGLRLQNKTIKVSYA 78

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 45.7 bits (109), Expect = 5e-07
 Identities = 19/64 (29%), Positives = 36/64 (56%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
           L++G+L   + EEE  + F +YG+V  + L   +G  F+ ++ R +A KA  +L     +
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIMRK 63

Query: 221 GKTI 224
           G+ +
Sbjct: 64  GRQL 67

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 45.4 bits (107), Expect = 8e-07
 Identities = 17/70 (24%), Positives = 37/70 (52%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
           T++ G ++  + E+ +  TF  +G ++ + + P +G +FV  N  + AA A+  +  T +
Sbjct: 2   TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGTTI 61

Query: 220 QGKTITLAWA 229
           +G  +   W 
Sbjct: 62  EGHVVKCYWG 71

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 160 TLWIGHL----SKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK 215
           TL++G +    +    EE L   FGE+GD+  I ++P +G AFV    R  A  A   + 
Sbjct: 3   TLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAEFAKEAMA 62

Query: 216 NTKLQGKT-ITLAWA 229
           +  L G   + + WA
Sbjct: 63  DQSLDGGEVLNVRWA 77

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 8/80 (10%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKAL 211
           T+L++ +++   + ++L   FG+YG +V +  IP       PRG A+V     +DA  AL
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVY-IPLDFYTRRPRGFAYVQFEDVRDAEDAL 59

Query: 212 YKLKNTKLQGKTITLAWAPG 231
           Y L  T+  G+ I + +A G
Sbjct: 60  YYLDRTRFLGREIEIQFAQG 79

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 22/78 (28%), Positives = 31/78 (39%), Gaps = 8/78 (10%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
           TLW+G L   + E  +   F E G+V S+ +I         G  FV     + A +AL  
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 214 LKNTKLQGKTIT--LAWA 229
           L    +        L WA
Sbjct: 61  LNGKPIPNTQQRFRLNWA 78

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALY 212
             L++  L K + ++EL   F +YG +++  ++        RG  F+  ++R +A +A+ 
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 213 KLKNTKLQGKT 223
            L   K +G +
Sbjct: 61  GLNGQKPEGAS 71

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 9/64 (14%)

Query: 173 EELSDTFGEYGDVVSINLIPP-------RGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT 225
           +EL + F  +G V S+ L  P       RG AFV    +Q+A  A+  LK+T L G+ + 
Sbjct: 15  KELRELFSPFGQVKSVRL--PKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLV 72

Query: 226 LAWA 229
           L +A
Sbjct: 73  LEYA 76

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 8/72 (11%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-------RGCAFVCMNRRQDAAKALYK 213
           L++G L++ V E+ L   F  +GD+  I  IP        RG AFV     +DAA A+  
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQ-IPLDYETQKHRGFAFVEFEEPEDAAAAIDN 59

Query: 214 LKNTKLQGKTIT 225
           +  ++L G+TI 
Sbjct: 60  MNESELFGRTIR 71

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 12/77 (15%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR----------GCAFVCMNRRQDAAKA 210
           +++ +L   + E++L   F ++G+V SI  IP +          G AFV       A  A
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIR-IPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 211 LYKLKNTKLQGKTITLA 227
           L +L  T+L G+ I+++
Sbjct: 62  L-QLNGTELGGRKISVS 77

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 43.4 bits (103), Expect = 4e-06
 Identities = 22/72 (30%), Positives = 33/72 (45%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
           T + + +L     EEEL + F ++G +  + L P R  A V      DA KA   L   +
Sbjct: 1   TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTIALVEFLEPSDARKAFKSLAYKR 60

Query: 219 LQGKTITLAWAP 230
            +   + L WAP
Sbjct: 61  FKHVPLYLEWAP 72

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 43.7 bits (104), Expect = 4e-06
 Identities = 18/71 (25%), Positives = 38/71 (53%), Gaps = 5/71 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYK 213
           T +++ +L + + +E+L + FG+YG + S  ++       +G  FV     + A KA+ +
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61

Query: 214 LKNTKLQGKTI 224
           L   ++ GK +
Sbjct: 62  LNGKEVNGKKL 72

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 43.1 bits (102), Expect = 5e-06
 Identities = 29/73 (39%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
           L+IG+LS  V E +L   F E+   VS  L+   G AFV    +  A KA+ KL    LQ
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKLNGKILQ 60

Query: 221 GKTITLAWA-PGK 232
           GK I +  + P K
Sbjct: 61  GKVIEVEHSVPKK 73

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 43.3 bits (103), Expect = 5e-06
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 6/62 (9%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
           T+ + +LS+   E++L + F  +G +  + L         RG AFV  + R+DA +A+ K
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 214 LK 215
           L 
Sbjct: 61  LN 62

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins

 Score = 43.3 bits (102), Expect = 6e-06
 Identities = 24/76 (31%), Positives = 36/76 (47%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           S TL+ G ++  + E +L   FG +G+V S  L   +  AFV M  R+DA  A   ++  
Sbjct: 3   SRTLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKMYNRRDAENAREAMEQY 62

Query: 218 KLQGKTITLAWAPGKG 233
           K     +   W  G G
Sbjct: 63  KSGDMQLRTRWGVGFG 78

This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain). Length = 79

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 43.2 bits (101), Expect = 6e-06
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGC-AFVCMNRRQDAAKAL 211
              LW+  LS   +  +L + F +YG VV   ++     P   C  FV M+  ++A K +
Sbjct: 1   GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60

Query: 212 YKLKNTKLQGKTITL 226
             L  T+L G+ I++
Sbjct: 61  NHLHRTELHGRMISV 75

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 43.1 bits (102), Expect = 6e-06
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
           TL++G+LS  V +E L   F ++G VV   +I        RG  +V     +DA KA+  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 214 LKNTKLQGKTITL 226
           +   +L G+ I +
Sbjct: 61  MDGKELDGRPINV 73

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 42.7 bits (100), Expect = 7e-06
 Identities = 16/70 (22%), Positives = 37/70 (52%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
           T++ G ++  + E+ +  TF  +G ++ I + P +G +F+  +  + AA A+  +  T +
Sbjct: 2   TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGTTI 61

Query: 220 QGKTITLAWA 229
           +G  +   W 
Sbjct: 62  EGHVVKCYWG 71

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 42.6 bits (101), Expect = 7e-06
 Identities = 16/60 (26%), Positives = 34/60 (56%)

Query: 170 VQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
           + EE L   F  +G++++I++   + C FV   + + A +A+ +L  T +QG  + ++ A
Sbjct: 14  LTEEILKKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIAELNGTTVQGVQLKVSLA 73

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. . Length = 75

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 41.8 bits (98), Expect = 1e-05
 Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
             +++G++S     +EL   F E+G VV  + +  +  AFV M R ++A  A+  L   +
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRVVECDKV--KDYAFVHMEREEEALAAIEALNGKE 58

Query: 219 LQGKTI 224
           ++G+ I
Sbjct: 59  VKGRRI 64

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC-AFVCMNRRQDAAKALYKLKNT 217
           TT+ + +       EEL D F  +G +  + L+PP G  A V     Q A  A   L   
Sbjct: 1   TTILVKNFPYGTTAEELRDLFEPHGKLTRV-LMPPAGTIAIVEFANPQQARLAFKALAYR 59

Query: 218 KLQGKTITLAWAP 230
           + +   + L   P
Sbjct: 60  RFKDSILYLEKGP 72

This subgroup corresponds to the RRM3 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
           TL++ +L+  V +E+L+D F +   +    ++        RG  FV     +DA +AL K
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 214 LKNTKLQGKTITLAWA 229
           LKN KL G+ + L  A
Sbjct: 61  LKNKKLHGRILRLDIA 76

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSI----NLIPPR--GCAFVCMNRRQDAAKALYKL 214
           L++G L   V E  L + F   G V+SI    +LI  R  G A+V      DA +AL  L
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 215 KNTKLQGKTITLAW 228
               ++GK I + W
Sbjct: 62  NFDVIKGKPIRIMW 75

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 6/65 (9%)

Query: 171 QEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALYKLKNTKLQGKTI 224
           QEE++ D F E+G++ +++L   R      G A +    +++A  A+  L   +L G+TI
Sbjct: 19  QEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTI 78

Query: 225 TLAWA 229
           ++ WA
Sbjct: 79  SVDWA 83

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 45.2 bits (107), Expect = 2e-05
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINL----IPPR--GCAFVCMNRRQDAAKALYK 213
           +L++G L   V E +L D F  +G V+S+ +    +  R  G  +V      DA +AL  
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 214 LKNTKLQGKTITLAW 228
           +   +L GK I + W
Sbjct: 62  MNFKRLGGKPIRIMW 76

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
           L++ +L     EE+L + F EYG+V  +  I  +  AFV    R DA KA+ ++   +L+
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKI--KDYAFVHFEERDDAVKAMEEMNGKELE 61

Query: 221 GKTITLAWA 229
           G  I ++ A
Sbjct: 62  GSPIEVSLA 70

This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Length = 72

>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 41.0 bits (96), Expect = 4e-05
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 5/67 (7%)

Query: 158 STTLWIGHLS-----KLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALY 212
           S  ++IG++S     + + E+EL     +YG++ SI ++  + CAF+      +A  AL 
Sbjct: 2   SRNVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILREKACAFINFMNIPNAIAALQ 61

Query: 213 KLKNTKL 219
            L   K 
Sbjct: 62  TLNGKKP 68

This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 82

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 171 QEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
           +EE++   F  +G +V  ++   +  AFV     +DA KAL  L  +++ G  +T+ + 
Sbjct: 13  REEDIEKLFEPFGPLVRCDI--RKTFAFVEFEDSEDATKALEALHGSRIDGSVLTVEFV 69

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 40.4 bits (95), Expect = 5e-05
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           L++G+LS    E+ + + FGEYG++ S+ L        P+G  +V  + ++ A  AL  L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 215 KNTKLQGKTITL 226
             T L G+ + L
Sbjct: 61  GGTDLLGRPVRL 72

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 43.8 bits (103), Expect = 5e-05
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T L + +L + + +EE+   F   G++ S  L+  +      G  FV   R +DA KA+ 
Sbjct: 4   TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVN 63

Query: 213 KLKNTKLQGKTITLAWA 229
            L   +LQ KTI +++A
Sbjct: 64  SLNGLRLQNKTIKVSYA 80

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 40.2 bits (95), Expect = 6e-05
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 7/71 (9%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALYK 213
           ++++G+L   ++EEEL   F + GDV ++ ++  R      G  +V    +   A AL K
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-K 59

Query: 214 LKNTKLQGKTI 224
           L   KL+G+ I
Sbjct: 60  LNGIKLKGRKI 70

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 40.2 bits (95), Expect = 6e-05
 Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 6/77 (7%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSI------NLIPPRGCAFVCMNRRQDAAKALYKL 214
           L++G+LS    EE++ + F   GD+  I          P G  FV    R+DA  A+  L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 215 KNTKLQGKTITLAWAPG 231
             TKL  + I + W  G
Sbjct: 61  NGTKLDDRIIRVDWDAG 77

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 40.4 bits (94), Expect = 7e-05
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 8/80 (10%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKAL 211
           T+L++ +++   + E+L   FG YG +V +  +P       PRG A++     +DA  AL
Sbjct: 1   TSLFVRNVADATRPEDLRREFGRYGPIVDV-YVPLDFYTRRPRGFAYIQFEDVRDAEDAL 59

Query: 212 YKLKNTKLQGKTITLAWAPG 231
           Y L    + G+ I + +A G
Sbjct: 60  YNLNRKWVCGRQIEIQFAQG 79

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 40.3 bits (94), Expect = 7e-05
 Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 6/64 (9%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALYKL 214
           L++G + + + E+E+   F E+G+V+ + +I  +      GC FV  + R +A +A+  L
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 215 KNTK 218
            N +
Sbjct: 62  HNQR 65

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 39.9 bits (93), Expect = 8e-05
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
           ++IG LS  V+E+++   FG YG ++ I+L    G  FV     +DA  A+Y+L    L 
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLEIDL--KNGYGFVEFEDSRDADDAVYELNGKDLC 59

Query: 221 GKTITLAWAPG 231
           G+ + +  A G
Sbjct: 60  GERVIVEHARG 70

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 4/62 (6%)

Query: 170 VQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL----QGKTIT 225
           V  EEL   F +YG V  + + P +   FV  +  +DAA A   L   +L    Q K + 
Sbjct: 15  VSREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNGKELELPQQNKPLY 74

Query: 226 LA 227
           L+
Sbjct: 75  LS 76

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. . Length = 80

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 40.0 bits (94), Expect = 8e-05
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 6/70 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKL 214
           L++ +L     EEEL + F  +G++  ++L         +G AFV     + A KA  +L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 215 KNTKLQGKTI 224
             +  QG+ +
Sbjct: 62  DGSIFQGRLL 71

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 40.1 bits (93), Expect = 9e-05
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T L + +L + + +EEL   FG  G++ S  L+  +      G  FV     +DA KA+ 
Sbjct: 5   TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 64

Query: 213 KLKNTKLQGKTITLAWA 229
            L   +LQ KTI +++A
Sbjct: 65  TLNGLRLQTKTIKVSYA 81

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 5/65 (7%)

Query: 173 EELSDTFGEYGDVVSINLIPPR-----GCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA 227
            +L   FG YG V    +   R     G AFV M +R++A  AL      ++ G+ + + 
Sbjct: 16  VKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVD 75

Query: 228 WAPGK 232
           WA  K
Sbjct: 76  WAVQK 80

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T L + +L + + +EE    FG  G++ S  L+  +      G  FV      DA KA+ 
Sbjct: 4   TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAIN 63

Query: 213 KLKNTKLQGKTITLAWA 229
            L   KLQ KTI +++A
Sbjct: 64  TLNGLKLQTKTIKVSYA 80

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSIN-LIPPRGCAFVCMNRRQDAAKALYKLKN 216
           S TL++ +++  V++EEL   F ++GD+ ++      RG   V     + A +A   L+ 
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 217 TKLQGKTI 224
           T+L G+ +
Sbjct: 61  TELGGRKL 68

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 21/55 (38%), Positives = 35/55 (63%), Gaps = 3/55 (5%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINL-IPPR--GCAFVCMNRRQDAAKAL 211
           T+++G+L   ++E E+ D F +YG +V I+L +PPR  G AF+     +DA  A+
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAI 55

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. . Length = 72

>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGC-AFVCMNRRQDAAKALYKL 214
           LW+  LS   +  +L + FG+YG V+S  ++     P   C   V M+   + A+ +  L
Sbjct: 2   LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 215 KNTKLQGKTITL 226
             T+L G+ I++
Sbjct: 62  HRTELHGQQISV 73

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 7/69 (10%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSI----NLIPPRGCAFVCMNRRQDAAKALYKLKN 216
           +++G+L     + EL D F +YG + S+    N  PP G AFV     +DA  A+  L  
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN--PP-GFAFVEFEDPRDAEDAVRALDG 58

Query: 217 TKLQGKTIT 225
            ++ G  + 
Sbjct: 59  RRICGNRVR 67

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           ST L+IG LS    +  L D F  +GDVV   +I        RG  FV  N    A  A+
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93

Query: 212 YKLKNTKLQGKTI 224
            ++   +L G+ I
Sbjct: 94  SEMDGKELNGRHI 106

Length = 144

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 8/66 (12%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PP--RGCAFVCMNRRQDAAKALY 212
           +++G + +   E++L + F +YG V  IN++      PP  +GC FV    R+ A +A  
Sbjct: 4   MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63

Query: 213 KLKNTK 218
            L N K
Sbjct: 64  ALHNMK 69

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
           +++G++ +   +EEL   F  YG V+S  ++  R  AFV +     A +A+ +L   +L 
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM--RQFAFVHLRGEAAADRAIEELNGRELH 60

Query: 221 GKTI 224
           G+ +
Sbjct: 61  GRKL 64

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
            L++G+L      E+L   F   G   S+ L+        +GCAFV  +  +   KAL K
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL-K 60

Query: 214 LKNTKLQGKTI 224
           L +T L+G+ I
Sbjct: 61  LHHTLLKGRKI 71

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 173 EELSDTFGEYGDVVSINLIPPRG-CAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP 230
            EL + F ++G +  + L+PP G  A V      +A  A  KL  +K +   + L WAP
Sbjct: 15  AELRELFSKFGSLGRV-LLPPAGITAIVEFLEPSEAKLAFRKLAYSKFKHVPLYLEWAP 72

This subgroup corresponds to the RRM4 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 38.2 bits (88), Expect = 4e-04
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T L + +L + + +EE    FG  G++ S  L+  +      G  FV     +DA KA+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 213 KLKNTKLQGKTITLAWA 229
            L   +LQ KTI +++A
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 170 VQEEELSDTFGEYGDVVSINLIPPR-----GCAFVCMNRRQDAAKALYKLKNTKLQGKTI 224
           V EE+L + FG  G+V  + +   R     G A V   +R+DA +A+ +     L G+ +
Sbjct: 12  VTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPM 71

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
           TL++ +L     +E+L + F E G +    ++        RG  +V     +DA +AL +
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 214 LKNTKLQGKTITLAWA 229
            K TK  G+ I + +A
Sbjct: 61  KKKTKFGGRKIHVEFA 76

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 21/69 (30%), Positives = 37/69 (53%)

Query: 156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK 215
           M +  +W+  L + V E+ L+  F  YG VV + +   RG A V  ++ + A  A+ ++K
Sbjct: 5   MPTNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQRGQALVFFDKVEAAQAAVNEMK 64

Query: 216 NTKLQGKTI 224
             KL G+ +
Sbjct: 65  GRKLGGRKL 73

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the matrin 3 family of nuclear proteins

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 172 EEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKLKNTKLQGKTITLA 227
           E EL      +G V     +P R  AF+ M   +DA   +  YK     + GK+I +A
Sbjct: 15  EAELLKLAEPFGKVDHYIFLPNRNKAFIEMESPEDAQALVSFYKTYPLTIGGKSIKVA 72

This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region. . Length = 76

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 37.8 bits (87), Expect = 6e-04
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T L + +L + + ++EL   F   G+V S  LI  +      G  FV     +DA +A+ 
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 213 KLKNTKLQGKTITLAWA 229
            L   +LQ KTI +++A
Sbjct: 62  TLNGLRLQSKTIKVSYA 78

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 37.6 bits (87), Expect = 6e-04
 Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 8/80 (10%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKAL 211
           ++L++ +++   + E+L   FG YG +V +  +P       PRG A+V     +DA  AL
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDV-YVPLDFYTRRPRGFAYVQFEDVRDAEDAL 59

Query: 212 YKLKNTKLQGKTITLAWAPG 231
           + L    + G+ I + +A G
Sbjct: 60  HNLDRKWICGRQIEIQFAQG 79

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 37.3 bits (86), Expect = 7e-04
 Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
           L++ +L+  V EE L   FG++G +  +  +  +  AF+  + R  A KA+ ++   +L+
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKELE 61

Query: 221 GKTITLAWA 229
           G+ I + +A
Sbjct: 62  GENIEIVFA 70

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
           ++IG L    +E ++   F  YG +  INL    G  FV     +DA  A+Y+L   +L 
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINL--KNGFGFVEFEDPRDADDAVYELNGKELC 59

Query: 221 GKTITLAWAPG 231
           G+ + +  A G
Sbjct: 60  GERVIVEHARG 70

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 37.2 bits (87), Expect = 9e-04
 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 6/58 (10%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDV--VSINLIP----PRGCAFVCMNRRQDAAKAL 211
           T++I +L     EEEL + F ++G+V    I         +G AFV    ++ A K L
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 6/73 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKAL 211
              +++ +L     E  L   F  +G V ++ +I        +G  FV M   ++A  A+
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 212 YKLKNTKLQGKTI 224
             L   +L G+ +
Sbjct: 61  ASLNGYRLGGRVL 73

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182 family proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 12/44 (27%), Positives = 24/44 (54%)

Query: 181 EYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTI 224
           ++G +++ +L    G A +  + +++AAKA   L N  L   T+
Sbjct: 24  QHGPLLTFHLNLRHGNALIRYSSKEEAAKAQSALNNCVLGNTTL 67

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. . Length = 71

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC---AFVCMNRRQDAAKALYKLKNT 217
           L++G+L + V E+ L++ F + G + S  LI   G    AFV     + AA AL  +   
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60

Query: 218 KLQGKTITLAWA 229
            + G+ I + WA
Sbjct: 61  LILGQEIKVNWA 72

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
           L++G+L     E+E+   F +YG V+  ++I   G  FV M+ +  A +A+  L + KL 
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYG--FVHMDDKTAADEAIRNLHHYKLH 60

Query: 221 GKTITL 226
           G  I +
Sbjct: 61  GVAINV 66

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 6/77 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T L + +L + + +EEL   F   G + S  ++  R      G  FV      DA KA+ 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 213 KLKNTKLQGKTITLAWA 229
            L   +++ K + +++A
Sbjct: 61  TLNGFEIRNKRLKVSYA 77

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLK 215
           L++ +L   + +E L + F  +G + S  ++       +G  FVC +  ++A KA+ ++ 
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63

Query: 216 NTKLQGKTITLAWA 229
              + GK + +A A
Sbjct: 64  GRIIGGKPLYVALA 77

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 5/55 (9%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG-----CAFVCMNRRQDAAKA 210
           LW+G+L + V+EE +S+ F  YG V S+ ++P RG      AFV     + A KA
Sbjct: 2   LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKA 56

This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 75

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 162 WIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLK 215
           ++G++     EE+L + F E G VVS  L+       P+G  F      + AA A+  L 
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 216 NTKLQGKTITLAWA 229
             +  G+ + + +A
Sbjct: 62  GYEFNGRALRVDFA 75

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa MCM3-associated protein (Map80) and similar proteins

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 171 QEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP 230
            ++ L   FG++G V  +   P +  A V       AA A  K K   LQ K I + W  
Sbjct: 14  DKDWLERHFGKFGKVARVYCNPRKKSAVVHFFDHASAALA--KKKGKLLQHKPIQIFWGS 71

Query: 231 GK 232
            K
Sbjct: 72  KK 73

This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 73

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 7/60 (11%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
           TL++  L+    E +L   F EYG +  I L+       PRG AF+     +D  KA YK
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERD-MKAAYK 61

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
            +T+++ +L   +   +L   F +YG VV + ++        +G AF+    R+DA K +
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 212 YKLKNTKLQGKTIT 225
             L N +L G+T+ 
Sbjct: 61  KALNNKELFGRTLK 74

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
           T L + +L   V E+++ + F   G +    L+ P G A V   R+ DA  A+ K  N +
Sbjct: 1   TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVRP-GVAEVVYVRKDDALTAIDKYNNRE 59

Query: 219 LQGKTI 224
           L G+ +
Sbjct: 60  LDGQPM 65

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 8/74 (10%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYK 213
           L + +L+     ++L   F +YG+V  +  IP        RG AFV    ++DA  A+  
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDV-YIPRDRYTRESRGFAFVRFYDKRDAEDAMDA 59

Query: 214 LKNTKLQGKTITLA 227
           +   +L G+ + + 
Sbjct: 60  MDGKELDGRELRVQ 73

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 12/48 (25%), Positives = 20/48 (41%)

Query: 172 EEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
           E ++ D F ++G   S+ +     C FV    R+ A K    +    L
Sbjct: 16  EYKIRDYFEQFGKSKSVIVNHRAKCGFVRFETREAAEKFAAAISENGL 63

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 7/80 (8%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T L I +L + + +EE    F   G V +  ++  +      G  FV     +DA +A+ 
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 213 KLKNTKLQGKTITLAWA-PG 231
            L   +LQ K I +A+A PG
Sbjct: 61  TLNGLQLQNKRIKVAYARPG 80

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL 214
           S  ++IG+L +   EEEL +   ++G +  I ++  +  AFV      +A K +  L
Sbjct: 3   SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTL 59

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 7/73 (9%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
           TL++G+L   V EE L + F + G +  +  IP      P+  AFV          A+  
Sbjct: 3   TLFVGNLDARVTEEILYELFLQAGPLEGVK-IPKDPNGKPKSFAFVTFKHEVSVPYAIQL 61

Query: 214 LKNTKLQGKTITL 226
           L   +L G+ + +
Sbjct: 62  LNGIRLFGRELRI 74

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 7/76 (9%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDA-AKALYK 213
           L++G LS  V E +L + F  +G V  + +I      P RG A++ +   +    K    
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 214 LKNTKLQGKTITLAWA 229
           L  TK +G  + +  A
Sbjct: 62  LNGTKWKGSVLKIEEA 77

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 7/77 (9%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALY 212
           T + + +L     ++++   F  YG + S+  +P       RG AFV  +  ++A  A+ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMN 59

Query: 213 KLKNTKLQGKTITLAWA 229
            LK+T L G+ + L +A
Sbjct: 60  ALKDTHLLGRRLVLQYA 76

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKA 210
           S  L+I +L+    EE+L   F +YG +  ++L P       P+G AFV     + A KA
Sbjct: 2   SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHL-PIDKLTKKPKGFAFVTYMIPEHAVKA 60

Query: 211 LYKLKNTKLQGK 222
             +L  T  QG+
Sbjct: 61  FAELDGTVFQGR 72

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 35.5 bits (81), Expect = 0.003
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC----AFVCMNRRQDAAKALYKLK 215
           TL++G+LS+ V E  +   F + G   S  +I          FV     +DAA AL  + 
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

Query: 216 NTKLQGKTITLAWA 229
             K+ GK + + WA
Sbjct: 61  GRKILGKEVKVNWA 74

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-------PPRGCAFVCMNRRQDAAKALYK 213
           L+IG+L   V E+ L DTF  +G ++    I         +G AF+  +  + +  A+  
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 214 LKNTKLQGKTITLAWA 229
           +    L  + IT+++A
Sbjct: 64  MNGQYLCNRPITVSYA 79

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is 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. . Length = 83

>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL- 219
           ++ G+     ++ E+   FG+YG V  +++    G AFV M   +DA  A+  L N +  
Sbjct: 3   VFCGNFEYDARQSEIERLFGKYGRVDRVDM--KSGFAFVYMEDERDAEDAIRGLDNFEFG 60

Query: 220 -QGKTITLAWA 229
            Q + + + WA
Sbjct: 61  RQRRRLRVEWA 71

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG----CAFVCMNRRQDAAKALYKLK 215
           TL + HL   + E++  D    +G   S+ ++  RG     AF   +  Q A++AL +L 
Sbjct: 1   TLLVRHLPPELSEDDKEDLLKHFG-ASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLH 59

Query: 216 NTKLQGKTITLAWA 229
             K+ GK + + +A
Sbjct: 60  QLKILGKRLVVEYA 73

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKL 214
           +++G LS  +  E L   F  +G++    ++        +G  FV   +++DA  A+  +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 215 KNTKLQGKTITLAW 228
               L G+ I   W
Sbjct: 62  NGQWLGGRAIRTNW 75

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
           TL++G LS    EE L + F  YGD+  + L+        +G AFV     +DA +A   
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 214 LKNTKLQGKTIT 225
                + G  I 
Sbjct: 65  AHKLVIDGSEIF 76

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	282
KOG0132|consensus	894		100.0
cd03562	114	CID CID (CTD-Interacting Domain) domain family; CI	99.86
KOG0148|consensus	321		99.82
smart00582	121	RPR domain present in proteins, which are involved	99.8
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.72
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.67
KOG0148|consensus	321		99.66
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.65
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.63
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.62
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.6
KOG2669|consensus	325		99.58
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.57
KOG0121|consensus	153		99.56
KOG0107|consensus	195		99.56
PLN03120	260	nucleic acid binding protein; Provisional	99.55
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.54
KOG0111|consensus	298		99.53
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.52
KOG0125|consensus	376		99.52
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.5
KOG0122|consensus	270		99.49
PLN03213	759	repressor of silencing 3; Provisional	99.48
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.47
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.47
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.47
KOG0145|consensus	360		99.47
KOG0117|consensus	506		99.46
KOG2071|consensus	579		99.45
KOG0144|consensus	510		99.45
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.44
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.44
KOG0117|consensus	506		99.43
smart00362	72	RRM_2 RNA recognition motif.	99.42
KOG0105|consensus	241		99.42
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.42
KOG0145|consensus	360		99.42
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.42
KOG0113|consensus	335		99.41
KOG0144|consensus	510		99.4
PLN03121	243	nucleic acid binding protein; Provisional	99.39
KOG0149|consensus	247		99.39
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.38
KOG4207|consensus	256		99.37
KOG0114|consensus	124		99.37
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.36
KOG0153|consensus	377		99.34
KOG0109|consensus	346		99.34
KOG0130|consensus	170		99.33
KOG0126|consensus	219		99.32
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.31
KOG0131|consensus	203		99.3
KOG0127|consensus	678		99.25
smart00360	71	RRM RNA recognition motif.	99.25
KOG0131|consensus	203		99.23
KOG0124|consensus	544		99.23
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.22
KOG0123|consensus	369		99.21
KOG0108|consensus	435		99.2
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.18
KOG0146|consensus	371		99.14
KOG0109|consensus	346		99.13
KOG0146|consensus	371		99.12
KOG0110|consensus	725		99.06
KOG4206|consensus	221		99.06
smart00361	70	RRM_1 RNA recognition motif.	99.03
KOG0147|consensus	549		99.01
KOG0110|consensus	725		98.99
PF04818	64	CTD_bind: RNA polymerase II-binding domain.; Inter	98.96
KOG0151|consensus	877		98.95
KOG0127|consensus	678		98.93
KOG4661|consensus	940		98.89
KOG0415|consensus	479		98.81
KOG4212|consensus	608		98.78
KOG4208|consensus	214		98.78
KOG4212|consensus	608		98.78
KOG0123|consensus	369		98.75
KOG0124|consensus	544		98.68
KOG1457|consensus	284		98.64
KOG4660|consensus	549		98.63
KOG4205|consensus	311		98.62
KOG0106|consensus	216		98.57
KOG0116|consensus	419		98.52
KOG0533|consensus	243		98.45
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.44
KOG1190|consensus	492		98.43
KOG4205|consensus	311		98.39
PF12243	139	CTK3: CTD kinase subunit gamma CTK3	98.39
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.32
KOG1548|consensus	382		98.3
KOG4209|consensus	231		98.29
KOG4454|consensus	267		98.21
KOG4206|consensus	221		97.97
KOG0226|consensus	290		97.93
KOG1457|consensus	284		97.9
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.89
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.87
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.83
KOG0106|consensus	216		97.82
KOG4211|consensus	510		97.75
KOG0120|consensus	500		97.75
KOG1456|consensus	494		97.57
KOG1190|consensus	492		97.54
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.4
KOG1548|consensus	382		97.38
KOG0151|consensus	877		97.33
KOG3152|consensus	278		97.31
KOG4210|consensus	285		97.3
KOG0112|consensus	975		97.3
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.26
KOG1855|consensus	484		97.24
KOG2416|consensus	718		97.2
KOG1456|consensus	494		97.18
cd00197	115	VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamil	97.18
KOG0147|consensus	549		97.13
KOG0120|consensus	500		97.11
KOG1995|consensus	351		96.96
KOG4676|consensus	479		96.94
KOG2193|consensus	584		96.78
KOG0129|consensus	520		96.77
KOG2314|consensus	698		96.63
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.61
KOG0129|consensus	520		96.53
KOG4211|consensus	510		96.5
KOG0105|consensus	241		96.48
KOG0112|consensus	975		96.37
KOG4849|consensus	498		96.06
KOG2202|consensus	260		95.99
KOG4307|consensus	944		95.86
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.61
KOG2135|consensus	526		95.24
KOG1996|consensus	378		95.1
KOG4368|consensus	757		94.8
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.76
KOG0128|consensus	881		94.58
KOG4285|consensus	350		94.49
KOG4574|consensus	1007		94.34
KOG0115|consensus	275		93.83
PF00790	140	VHS: VHS domain; InterPro: IPR002014 The VHS domai	93.8
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.39
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	93.29
cd03561	133	VHS VHS domain family; The VHS domain is present i	93.14
KOG1365|consensus	508		93.11
KOG0128|consensus	881		93.0
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.62
KOG2253|consensus	668		92.47
KOG2068|consensus	327		92.43
KOG4210|consensus	285		92.1
KOG4307|consensus	944		89.86
KOG1365|consensus	508		89.82
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	88.28
cd03569	142	VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p s	88.17
smart00288	133	VHS Domain present in VPS-27, Hrs and STAM. Unpubl	87.96
cd03568	144	VHS_STAM VHS domain family, STAM subfamily; member	87.75
KOG4660|consensus	549		87.37
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	86.69
KOG4410|consensus	396		83.49
KOG2591|consensus	684		82.59
cd03567	139	VHS_GGA VHS domain family, GGA subfamily; GGA (Gol	81.76
KOG2193|consensus	584		80.36

>KOG0132|consensus

Probab=100.00  E-value=1e-56  Score=412.57  Aligned_cols=279  Identities=59%  Similarity=0.975  Sum_probs=258.1

Q ss_pred             CchhHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhcc-C
Q psy3994           1 MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQ-D   79 (282)
Q Consensus         1 m~~~~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~-~   79 (282)
                      ||.+++|+.+|.+|.++|.|+|++||..||+.|+++++.|+|+|+.+|+||++|+|+|||++|||||||+|+++++++ +
T Consensus         1 me~v~~Fn~eL~SL~DsK~~IS~sKi~~ITkaAikaIk~ykhVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~   80 (894)
T KOG0132|consen    1 MDAVKEFNGELDSLEDSKPGISGSKILKITKAAIKAIKLYKHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKE   80 (894)
T ss_pred             ChHHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhccc
Confidence            899999999999999999999999999999999999999999999999999999999999999999999999999999 9


Q ss_pred             CCCchhhHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccCcccCCccccccccCCCCCCCCh------------------
Q psy3994          80 KDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIH------------------  141 (282)
Q Consensus        80 ~~~~~~~f~~~l~~~f~~v~~~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~~~~~~~~~~~------------------  141 (282)
                      +++|.++|.++++.+|..++.|..++..++++++|.|+++++|+.++|++++++++..++..                  
T Consensus        81 kd~F~prf~~n~~~tf~~L~~c~~edks~iIrvlNlwqkn~VfK~e~IqpLlDm~~~s~~~~~p~~~~~~~p~~~v~~~~  160 (894)
T KOG0132|consen   81 KDVFGPRFSKNFTGTFQNLYECPQEDKSDIIRVLNLWQKNNVFKSEIIQPLLDMADGSGLSVFPKSPLQALPSPGVLQAP  160 (894)
T ss_pred             ccccCCccchhHHHHHHHHHhcCHHHHHHHHHhhhhhhcccchhHHHHHHHHHHHhccCccccCCCccCCCCCccccCCC
Confidence            99999999999999999999999999999999999999999999999999999887654310                  


Q ss_pred             --hhh----------------------H----------------Hh----------------------------------
Q psy3994         142 --REL----------------------A----------------EI----------------------------------  147 (282)
Q Consensus       142 --~~~----------------------~----------------~~----------------------------------  147 (282)
                        .++                      +                .+                                  
T Consensus       161 ~sda~asvadIs~~~~g~~sqq~~~s~~~~g~d~~~~~~~q~~~~il~~~~~~~~l~~~~~l~~~f~~~~d~e~~~eP~k  240 (894)
T KOG0132|consen  161 SSDALASVADISNDTAGQQSQQLNISGNPSGGDVGSQAALQRSTQILNEEPAEQGLSFNPKLLDRFDYPDDAESSEEPQK  240 (894)
T ss_pred             chhhhhhhcccccCccccchhhccccCCccccchhhhhhhhHHHHHhcccchhhhhhcChhHHhcCCCCcchhhccCCcc
Confidence              000                      0                00                                  


Q ss_pred             -------------h------------------------------------------------------------------
Q psy3994         148 -------------Q------------------------------------------------------------------  148 (282)
Q Consensus       148 -------------~------------------------------------------------------------------  148 (282)
                                   |                                                                  
T Consensus       241 e~a~~~~v~e~Lqq~f~~~~~g~q~q~~~pl~~~~~~~~n~~qs~p~~~~~~q~~lp~~~~~qq~~~~~vq~q~~~~~~~  320 (894)
T KOG0132|consen  241 EQAILPQVAEVLQQHFQATMIGAQQQSALPLGNPMPQFMNVPQSIPSGPPGQQTGLPNDTQVQQITLMNVQAQQNVITEQ  320 (894)
T ss_pred             ccchhhhHHHHhhhhccccccchhhccCCCCCCCCCccccccccCCCCCccccccCCCcccccccceeecccccCCcccc
Confidence                         0                                                                  


Q ss_pred             ----------h---------------------------------------------------------------------
Q psy3994         149 ----------A---------------------------------------------------------------------  149 (282)
Q Consensus       149 ----------~---------------------------------------------------------------------  149 (282)
                                +                                                                     
T Consensus       321 ~d~~e~e~~~~~n~~~r~~~v~~r~r~~~~s~s~~~~~r~~RsrS~sr~~~~~rrs~Srs~~r~~~s~r~~~~er~~re~  400 (894)
T KOG0132|consen  321 QDRIEKEAFRNYNQEARPHGVRSRSRSAPASASRSRRGRLSRSRSRSRRSRSRRRSGSRSRDRIRHSLRDRLGERRDREH  400 (894)
T ss_pred             ccHHHHHHhcccchhhhhhccCCCcCCCCcccccccccccccccCCCcccccccCCCCCcccccCccCchhhcCcccCcc
Confidence                      0                                                                     


Q ss_pred             ------------cCCCCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCC
Q psy3994         150 ------------RNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT  217 (282)
Q Consensus       150 ------------~~~~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~  217 (282)
                                  +++...+.++|||||+|+.+++|.+|..+|+.||+|.+|.++.++|||||++..+.+|++|+.+|++.
T Consensus       401 ereRr~kglP~I~pd~isV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~  480 (894)
T KOG0132|consen  401 ERERRKKGLPTIPPDHISVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQDAEKALQKLSNV  480 (894)
T ss_pred             ccccccccCCCCCCcceeEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhHHHHHHHHHhcc
Confidence                        24566678999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCeeEEEEeecCCCCCCCccccccccCCCeeeecCCCCCcchhhhhhhcCcccccCCCCCCCC
Q psy3994         218 KLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFDEDTVPLWLK  282 (282)
Q Consensus       218 ~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~p~~~~  282 (282)
                      .+.++.|+|.||.++|.+. +|++|||.+.|+++|||++| + .|++.|++|+|+|.+++|+.+|
T Consensus       481 kv~~k~Iki~Wa~g~G~ks-e~k~~wD~~lGVt~IP~~kL-t-~dl~~~~egam~d~~t~~p~~k  542 (894)
T KOG0132|consen  481 KVADKTIKIAWAVGKGPKS-EYKDYWDVELGVTYIPWEKL-T-DDLEAWCEGAMLDGTTGPPEWK  542 (894)
T ss_pred             cccceeeEEeeeccCCcch-hhhhhhhcccCeeEeehHhc-C-HHHHHhhhhceecCccCCcccc
Confidence            9999999999999999998 89999999999999999999 4 4599999999999999988654

>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1

Probab=99.86  E-value=2.8e-21  Score=146.50  Aligned_cols=111  Identities=33%  Similarity=0.547  Sum_probs=100.9

Q ss_pred             HHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCch
Q psy3994           5 KTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFG   84 (282)
Q Consensus         5 ~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~   84 (282)
                      .+|+..|++|..++  +|+++|++||.||++|.++++++|+.|++++++|+|.+||+.|||+|+|+|+.+++      |.
T Consensus         2 ~~~~~~l~~L~~~~--~S~~~I~~lt~~a~~~~~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~------~~   73 (114)
T cd03562           2 FDYNALLEKLTFNK--NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRK------YK   73 (114)
T ss_pred             ccHHHHHHHHHcCc--ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccc------hH
Confidence            57899999998876  79999999999999999999999999999999999999999999999999999444      44


Q ss_pred             hhHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhccCcccC
Q psy3994          85 PRFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKNEVFT  123 (282)
Q Consensus        85 ~~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~~~~~f~  123 (282)
                      ..|+..+.+.|.+++. +++..+.++.+++++|.++++|+
T Consensus        74 ~~~~~~~~~~f~~~~~~~~~~~r~kl~rl~~iW~~~~~f~  113 (114)
T cd03562          74 EFFSEFLVPLFLDAYEKVDEKTRKKLERLLNIWEERFVFG  113 (114)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCCCCC
Confidence            5577777888998887 99999999999999999999875

Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

>KOG0148|consensus

Probab=99.82  E-value=3.1e-20  Score=153.70  Aligned_cols=147  Identities=16%  Similarity=0.359  Sum_probs=113.4

Q ss_pred             CCCCchhhHHHHHH-HHHHHhhc-CChhhHHHHHHHHHhhccCcccCCccccccccCCCCCCCChhhhHHhhh-------
Q psy3994          79 DKDVFGPRFARNLK-ATFQHLYQ-CPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQA-------  149 (282)
Q Consensus        79 ~~~~~~~~f~~~l~-~~f~~v~~-~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~-------  149 (282)
                      .+.+|+++|.+.|+ +.+...|. ..+...+|++|+.++..+.|       +.|+.|.+.. .+.+|..+|..       
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKG-------YgFVSf~~k~-dAEnAI~~MnGqWlG~R~  133 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKG-------YGFVSFPNKE-DAENAIQQMNGQWLGRRT  133 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccc-------eeEEeccchH-HHHHHHHHhCCeeeccce
Confidence            45678888888766 34555554 55555566666666555444       5556555544 33334433311       


Q ss_pred             ----------------------cCCCCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHH
Q psy3994         150 ----------------------RNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDA  207 (282)
Q Consensus       150 ----------------------~~~~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A  207 (282)
                                            --+..++.+|+|||||++..+||+++++.|++||.|.+|++.+.+|||||.|.++|+|
T Consensus       134 IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEaA  213 (321)
T KOG0148|consen  134 IRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEAA  213 (321)
T ss_pred             eeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecccceEEEEecchhhH
Confidence                                  1245567789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         208 AKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       208 ~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ..||..+||+++.|+.++|.|.+...
T Consensus       214 ahAIv~mNntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  214 AHAIVQMNNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             HHHHHHhcCceeCceEEEEeccccCC
Confidence            99999999999999999999998654

>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA

Probab=99.80  E-value=1.8e-19  Score=138.00  Aligned_cols=119  Identities=33%  Similarity=0.604  Sum_probs=106.3

Q ss_pred             HHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchh
Q psy3994           6 TFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGP   85 (282)
Q Consensus         6 ~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~   85 (282)
                      +|++.|++|.     .|+.+|+++|.||++|.++++++|+.|+++++++++.+||+.|||+|+|+++++.+.+.  .|..
T Consensus         1 ~f~~~L~~L~-----~s~~~I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~~--~f~~   73 (121)
T smart00582        1 AFEQKLESLN-----NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYGS--EFGD   73 (121)
T ss_pred             ChHHHHHhcc-----ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccHH--HHHH
Confidence            4889999996     67789999999999999999999999999999999999999999999999999877543  3667


Q ss_pred             hHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhccCcccCCccccccc
Q psy3994          86 RFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKNEVFTPDIIHPLF  131 (282)
Q Consensus        86 ~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~  131 (282)
                      .|.+.+...|..++. ++++.+.++.+++++|.++++|+++.+..+.
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~ki~kll~iW~~~~iF~~~~i~~L~  120 (121)
T smart00582       74 ELGPVFQDALRDVLGAANDETKKKIRRLLNIWEERGIFPPSVLRPLR  120 (121)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhcCCCCCHHHHHHhh
Confidence            788888888888886 6788999999999999999999999877654

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.72  E-value=5.9e-17  Score=127.36  Aligned_cols=81  Identities=32%  Similarity=0.502  Sum_probs=74.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ...+++|||+|||++++|++|+++|++||.|.++.++.      ++|||||+|.+.++|+.|+..||+..+.|++|+|.|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34568999999999999999999999999999999874      689999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy3994         229 APGKGMK  235 (282)
Q Consensus       229 a~~~~~~  235 (282)
                      +..+...
T Consensus       111 a~~~~~~  117 (144)
T PLN03134        111 ANDRPSA  117 (144)
T ss_pred             CCcCCCC
Confidence            9876543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.67  E-value=2.9e-16  Score=140.30  Aligned_cols=115  Identities=21%  Similarity=0.278  Sum_probs=90.6

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      .....++|||+|||+++|+++|+++|+.||.|.+|+++.      ++|||||+|.+.++|++|+..|||..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            344679999999999999999999999999999999974      67999999999999999999999999999999999


Q ss_pred             eecCCCCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccCC
Q psy3994         228 WAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDT  276 (282)
Q Consensus       228 ~a~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~  276 (282)
                      |+++......+.      ..=+..+|.+  .++++|+.+++ .|.+..+.
T Consensus       183 ~a~p~~~~~~~~------~lfV~nLp~~--vtee~L~~~F~~fG~V~~v~  224 (346)
T TIGR01659       183 YARPGGESIKDT------NLYVTNLPRT--ITDDQLDTIFGKYGQIVQKN  224 (346)
T ss_pred             cccccccccccc------eeEEeCCCCc--ccHHHHHHHHHhcCCEEEEE
Confidence            998654322111      1123444444  45788887554 56555443

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG0148|consensus

Probab=99.66  E-value=2.6e-16  Score=130.61  Aligned_cols=175  Identities=19%  Similarity=0.313  Sum_probs=120.0

Q ss_pred             cCCCCchhhHHHHHHHHH-HHhhc-CChhhHHHHHHHHH--hhccCcccCCccccccccCCCCCCCChhhhHHhhhcCCC
Q psy3994          78 QDKDVFGPRFARNLKATF-QHLYQ-CPPEDKSKIIRVLN--LWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGV  153 (282)
Q Consensus        78 ~~~~~~~~~f~~~l~~~f-~~v~~-~~~~~~~k~~~~l~--~w~~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (282)
                      ..+++||+.+...+++.| ..+|+ ..+....|++..--  .|...    +         .+...|              
T Consensus         5 ~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~~v~wa~~----p---------~nQsk~--------------   57 (321)
T KOG0148|consen    5 EPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDELKVNWATA----P---------GNQSKP--------------   57 (321)
T ss_pred             CCceEEeeccChhhHHHHHHHHHHhccccccceeehhhhccccccC----c---------ccCCCC--------------
Confidence            457899999999999865 56666 78888888776511  22110    0         111101              


Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ....---+|||.|.+.++-+.|++.|.+||+|.++++++      +||||||.|-++++|++||..|||..|++|.||..
T Consensus        58 t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTN  137 (321)
T KOG0148|consen   58 TSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTN  137 (321)
T ss_pred             ccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecc
Confidence            111235799999999999999999999999999999996      89999999999999999999999999999999999


Q ss_pred             eecCCCCC----CCccccccccCC----CeeeecCCCCCcchhhhhhhc-Cccccc-CCCCC
Q psy3994         228 WAPGKGMK----DKDWKDFWEVQD----GVSYIPYDRLSKEIDYDYLED-GGVFDE-DTVPL  279 (282)
Q Consensus       228 ~a~~~~~~----~~~~~~~~~~~~----g~~~~p~~~~~~~~~~~~~~~-~~~~~~-~~~p~  279 (282)
                      ||..+...    +..+.+.++...    .+-.=.+....++++++..+. .|.|-+ -+||+
T Consensus       138 WATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~  199 (321)
T KOG0148|consen  138 WATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD  199 (321)
T ss_pred             ccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc
Confidence            99876422    111222222111    111113444337777776444 454444 36665

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.65  E-value=3.4e-17  Score=146.28  Aligned_cols=77  Identities=34%  Similarity=0.677  Sum_probs=70.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCC--eeEEEEe
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQG--KTITLAW  228 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g--~~l~v~~  228 (282)
                      ..++|||+|||..+|+++|+++|++||+|..+++++      ++|||||+|.++++|++|++.||+..+.+  ++|+|.|
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            467899999999999999999999999999999885      46999999999999999999999998865  7899999


Q ss_pred             ecCCC
Q psy3994         229 APGKG  233 (282)
Q Consensus       229 a~~~~  233 (282)
                      |...+
T Consensus       272 a~~~~  276 (346)
T TIGR01659       272 AEEHG  276 (346)
T ss_pred             CCccc
Confidence            98654

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.63  E-value=1.5e-15  Score=137.14  Aligned_cols=107  Identities=24%  Similarity=0.312  Sum_probs=85.5

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||+|||..+++++|+++|+.||+|.+|+++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.|+++
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            58999999999999999999999999999999974      679999999999999999999999999999999999987


Q ss_pred             CCCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-Cccc
Q psy3994         232 KGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVF  272 (282)
Q Consensus       232 ~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~  272 (282)
                      ........        .+.+..+....+.++++.+++ .|.+
T Consensus        83 ~~~~~~~~--------~l~v~~l~~~~~~~~l~~~f~~~G~i  116 (352)
T TIGR01661        83 SSDSIKGA--------NLYVSGLPKTMTQHELESIFSPFGQI  116 (352)
T ss_pred             cccccccc--------eEEECCccccCCHHHHHHHHhccCCE
Confidence            65322211        122333333345778887554 3443

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.62  E-value=2.5e-15  Score=135.67  Aligned_cols=76  Identities=25%  Similarity=0.444  Sum_probs=72.1

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +.+|||+|||+.+++++|+++|++||.|.+++++.      +||||||+|.+.++|.+|+..|||..++|+.|+|.|+.+
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            45799999999999999999999999999999984      689999999999999999999999999999999999998


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      +.
T Consensus       349 ~~  350 (352)
T TIGR01661       349 KA  350 (352)
T ss_pred             CC
Confidence            75

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>PF00076 RRM_1: RNA recognition motif

Probab=99.60  E-value=3.5e-15  Score=102.45  Aligned_cols=65  Identities=40%  Similarity=0.698  Sum_probs=62.1

Q ss_pred             EEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       161 l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      |||+|||+++|+++|+++|++||.+..+.+..     .++||||+|.++++|+.|++.|||..++|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            79999999999999999999999999999886     589999999999999999999999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG2669|consensus

Probab=99.58  E-value=5.9e-15  Score=127.52  Aligned_cols=128  Identities=21%  Similarity=0.365  Sum_probs=111.4

Q ss_pred             HHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCch
Q psy3994           5 KTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFG   84 (282)
Q Consensus         5 ~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~   84 (282)
                      +.|++.|++|..     |+..|++++.|++.|.+++..||++|.+.+++.+..+||..|||+|.|+++++++..+   |+
T Consensus         7 e~l~~kL~~L~~-----TQeSIqtlS~Wli~hkk~a~~IV~~Wl~~~~~~~~~~Kl~llYLaNDVvQnskrk~~e---f~   78 (325)
T KOG2669|consen    7 EALEKKLAELSN-----TQESIQTLSLWLIHHKKHARLIVDVWLKELKKSSVNHKLTLLYLANDVVQNSKRKGPE---FV   78 (325)
T ss_pred             HHHHHHHHhccc-----hHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCCCceeeehhhhHHHHHHhhhcCch---hH
Confidence            568889999864     5559999999999999999999999999999999999999999999999999666555   88


Q ss_pred             hhHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhccCcccCCccccccccCCCCCCCC
Q psy3994          85 PRFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPI  140 (282)
Q Consensus        85 ~~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~~~~~~~~~~  140 (282)
                      ..|.+.+.+.|.+++. ++.....++.|++++|..+++|.++.+..+....+...|+
T Consensus        79 ~ef~~v~~~a~~~i~~~~~~~~k~~l~Rl~nIw~eR~Vf~~~~~~~l~~~l~~e~p~  135 (325)
T KOG2669|consen   79 DEFWPVVLKAFAHIVEETDVKCKKKLGRLINIWEERNVFSPESLVDLEESLGAEKPP  135 (325)
T ss_pred             HHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHHHhccCCHHHHHHHHHHhcccCCc
Confidence            9999999999999998 6666678899999999999999999887776655533333

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.57  E-value=1.1e-15  Score=143.97  Aligned_cols=77  Identities=16%  Similarity=0.317  Sum_probs=72.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||+|||+++++++|+++|+.||.|.++++.+      +||||||+|.+.++|.+|+..|||..++|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            357999999999999999999999999999999984      68999999999999999999999999999999999998


Q ss_pred             CCC
Q psy3994         231 GKG  233 (282)
Q Consensus       231 ~~~  233 (282)
                      .+.
T Consensus       283 ~pP  285 (612)
T TIGR01645       283 TPP  285 (612)
T ss_pred             CCc
Confidence            653

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.

>KOG0121|consensus

Probab=99.56  E-value=6.7e-15  Score=109.13  Aligned_cols=76  Identities=33%  Similarity=0.540  Sum_probs=70.7

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      .++|||||||+..++|++|.++|+.+|+|..|.+-.      +.||+||+|.++++|+.|++.++|+.++.++|++.|.-
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            579999999999999999999999999999997653      67999999999999999999999999999999999987


Q ss_pred             CC
Q psy3994         231 GK  232 (282)
Q Consensus       231 ~~  232 (282)
                      +.
T Consensus       115 GF  116 (153)
T KOG0121|consen  115 GF  116 (153)
T ss_pred             cc
Confidence            53

>KOG0107|consensus

Probab=99.56  E-value=1.3e-14  Score=113.32  Aligned_cols=77  Identities=27%  Similarity=0.494  Sum_probs=72.2

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      .+.||||||+..+++.||+..|..||.+.++.+-. +.|||||+|++..+|+.|+..|+|..+.|..|+|++......
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            58999999999999999999999999999998864 779999999999999999999999999999999999987644

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.55  E-value=3e-14  Score=120.09  Aligned_cols=76  Identities=20%  Similarity=0.296  Sum_probs=70.6

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      .++|||||||+.+|+++|+++|+.||.|.++.++.   .+|||||+|.+.++|+.|+. |||..+.|+.|+|.++.....
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~~~   82 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDYQL   82 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCCCC
Confidence            58999999999999999999999999999999986   47999999999999999995 999999999999999986543

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.54  E-value=4.3e-14  Score=132.60  Aligned_cols=118  Identities=14%  Similarity=0.110  Sum_probs=87.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh--CCCeeCCeeEEEEeecCCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL--KNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l--~g~~~~g~~l~v~~a~~~~~  234 (282)
                      ++++|||+|||+.+++++|+++|++||.|.++.++++|+||||+|.+.++|++|+..+  ++..+.|++|+|.|+..+..
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~   80 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEI   80 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCccc
Confidence            4689999999999999999999999999999999999999999999999999999875  77899999999999976542


Q ss_pred             CCCccccc-cccCC---CeeeecCCCCCcchhhhhhhc-Cccccc
Q psy3994         235 KDKDWKDF-WEVQD---GVSYIPYDRLSKEIDYDYLED-GGVFDE  274 (282)
Q Consensus       235 ~~~~~~~~-~~~~~---g~~~~p~~~~~~~~~~~~~~~-~~~~~~  274 (282)
                      ......+. -....   .+.+.++....++++|..+++ .|.+..
T Consensus        81 ~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~  125 (481)
T TIGR01649        81 KRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLR  125 (481)
T ss_pred             ccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEE
Confidence            21110000 00011   123334443337788887555 444433

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0111|consensus

Probab=99.53  E-value=9.1e-15  Score=118.04  Aligned_cols=87  Identities=31%  Similarity=0.521  Sum_probs=80.2

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++||||+|...++|.-|...|-+||.|..+.++.      +||||||+|...++|.+||..||+.++.||.|+|.+|+|
T Consensus        10 KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP   89 (298)
T KOG0111|consen   10 KRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKP   89 (298)
T ss_pred             ceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCC
Confidence            58999999999999999999999999999999984      899999999999999999999999999999999999999


Q ss_pred             CCCCCCccccccc
Q psy3994         232 KGMKDKDWKDFWE  244 (282)
Q Consensus       232 ~~~~~~~~~~~~~  244 (282)
                      ...+.+..+..|.
T Consensus        90 ~kikegsqkPvWA  102 (298)
T KOG0111|consen   90 EKIKEGSQKPVWA  102 (298)
T ss_pred             ccccCCCCCCccc
Confidence            8877766555544

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.52  E-value=4.5e-14  Score=133.12  Aligned_cols=122  Identities=18%  Similarity=0.221  Sum_probs=88.9

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||||||..+++++|+++|.+||.|.+++++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            458999999999999999999999999999999874      78999999999999999999999999999999999765


Q ss_pred             CCCCCCC--c-cccccccCCCeeeecCCCCCcchhhhhhhc-CcccccCCCC
Q psy3994         231 GKGMKDK--D-WKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDTVP  278 (282)
Q Consensus       231 ~~~~~~~--~-~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~p  278 (282)
                      .......  + ....-.....+-+-.++.-.++++|+.+++ +|.+..+.++
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~  237 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLA  237 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEE
Confidence            4321110  0 000000011122224444446788887554 5666665553

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.

>KOG0125|consensus

Probab=99.52  E-value=2.5e-14  Score=121.78  Aligned_cols=76  Identities=24%  Similarity=0.465  Sum_probs=72.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ..++|+|+|||+...|.||+.+|++||.|.+|.|+.    +||||||+|++.++|++|-.+|||+.+.||+|.|..|..+
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchh
Confidence            347899999999999999999999999999999984    8999999999999999999999999999999999999866

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.50  E-value=9.5e-14  Score=130.68  Aligned_cols=75  Identities=29%  Similarity=0.464  Sum_probs=70.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccC--CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEY--GDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~--G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ..++|||+||+..+++++|+++|++|  |.|++|++++  +||||+|.++++|++|++.|||..+.|+.|+|.||+++.
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~  308 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVD  308 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCC
Confidence            35789999999999999999999999  9999998764  899999999999999999999999999999999998753

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0122|consensus

Probab=99.49  E-value=1.1e-13  Score=113.60  Aligned_cols=76  Identities=25%  Similarity=0.489  Sum_probs=72.3

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ...+|-|.||+.+++|++|+++|.+||.|.++.+.+      +||||||.|.++++|.+||..|||.-++.-.|+|.|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            567899999999999999999999999999998885      79999999999999999999999999999999999999


Q ss_pred             CC
Q psy3994         231 GK  232 (282)
Q Consensus       231 ~~  232 (282)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            86

>PLN03213 repressor of silencing 3; Provisional

Probab=99.48  E-value=1.5e-13  Score=122.73  Aligned_cols=77  Identities=18%  Similarity=0.291  Sum_probs=71.6

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC--CCcEEEEEecCH--HHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--PRGCAFVCMNRR--QDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~--~kg~aFV~f~~~--~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ....+||||||++.+++++|+..|..||.|.++.|++  .||||||+|.+.  .++.+||..|||..++|+.|+|..|++
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            3457999999999999999999999999999999996  789999999987  789999999999999999999999986


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      .
T Consensus        88 ~   88 (759)
T PLN03213         88 H   88 (759)
T ss_pred             H
Confidence            3

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.47  E-value=5.7e-13  Score=125.05  Aligned_cols=77  Identities=23%  Similarity=0.312  Sum_probs=71.8

Q ss_pred             CCCcEEEecCCCc-cCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         156 MCSTTLWIGHLSK-LVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       156 ~~~~~l~V~nl~~-~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .++++|||+|||+ .+|+++|+++|+.||.|.+|+++. .+|||||+|.+.++|..|+..|||..+.|++|+|.+++.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            4678999999997 699999999999999999999986 5799999999999999999999999999999999998654

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.47  E-value=1.8e-14  Score=137.85  Aligned_cols=114  Identities=20%  Similarity=0.264  Sum_probs=85.8

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .++|||+|||.++++++|+++|+.||.|.+|++..     ++|||||+|.+.++|.+|++.+||..+.|+.|.|.....+
T Consensus        88 ~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~  167 (562)
T TIGR01628        88 VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK  167 (562)
T ss_pred             CCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccc
Confidence            46899999999999999999999999999999874     6899999999999999999999999999999999877655


Q ss_pred             CCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-Cccccc
Q psy3994         233 GMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDE  274 (282)
Q Consensus       233 ~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~  274 (282)
                      ..+.....   .....+-+-.+..-.++++|+.+++ .|.+..
T Consensus       168 ~~~~~~~~---~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~  207 (562)
T TIGR01628       168 HEREAAPL---KKFTNLYVKNLDPSVNEDKLRELFAKFGEITS  207 (562)
T ss_pred             cccccccc---cCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEE
Confidence            43311000   0112232333444446788887554 454433

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.47  E-value=2.6e-13  Score=93.38  Aligned_cols=65  Identities=32%  Similarity=0.591  Sum_probs=59.6

Q ss_pred             EEecCCCccCcHHHHHhhhccCCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-----RGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       161 l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~-----kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      |||+|||+++++++|+++|+.||.|..+.+..+     +++|||+|.+.++|.+|++.++|..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999999999864     69999999999999999999999999999875

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0145|consensus

Probab=99.47  E-value=7.6e-14  Score=115.41  Aligned_cols=112  Identities=26%  Similarity=0.505  Sum_probs=91.4

Q ss_pred             CChhhHHHHHHHHH-hhccCcccCCccccccccCCCCCCCChhhhHHhhhcCCCCCCCCcEEEecCCCccCcHHHHHhhh
Q psy3994         101 CPPEDKSKIIRVLN-LWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTF  179 (282)
Q Consensus       101 ~~~~~~~k~~~~l~-~w~~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~te~~l~~~f  179 (282)
                      ..++|+++++..|| ....+++++++.       +.|+               .......+|||.+||..+|..+|+.+|
T Consensus        91 v~p~DAe~AintlNGLrLQ~KTIKVSy-------ARPS---------------s~~Ik~aNLYvSGlPktMtqkelE~iF  148 (360)
T KOG0145|consen   91 VRPKDAEKAINTLNGLRLQNKTIKVSY-------ARPS---------------SDSIKDANLYVSGLPKTMTQKELEQIF  148 (360)
T ss_pred             cChHHHHHHHhhhcceeeccceEEEEe-------ccCC---------------hhhhcccceEEecCCccchHHHHHHHH
Confidence            56888888888888 445677766665       3333               223356789999999999999999999


Q ss_pred             ccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCC--eeEEEEeecCCCC
Q psy3994         180 GEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQG--KTITLAWAPGKGM  234 (282)
Q Consensus       180 ~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g--~~l~v~~a~~~~~  234 (282)
                      ++||.|..-++..      +||.|||.|+.+.+|+.||..|||+...|  .+|.|+||.....
T Consensus       149 s~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq  211 (360)
T KOG0145|consen  149 SPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQ  211 (360)
T ss_pred             HHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCccc
Confidence            9999987766653      89999999999999999999999998866  4899999986643

>KOG0117|consensus

Probab=99.46  E-value=2.5e-13  Score=119.97  Aligned_cols=110  Identities=25%  Similarity=0.429  Sum_probs=87.7

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCee-CCeeEEEEe
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKL-QGKTITLAW  228 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~-~g~~l~v~~  228 (282)
                      .-++.||||.||.++.|++|..+|++.|+|-.++++.      +||||||+|.+.++|+.||+.||+++| .|+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            4579999999999999999999999999999999996      799999999999999999999999998 799999887


Q ss_pred             ecCCCCCCCccccccccCCCeeeecCCCCCcchhhhhhh--cCcccccCCCC
Q psy3994         229 APGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLE--DGGVFDEDTVP  278 (282)
Q Consensus       229 a~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~--~~~~~~~~~~p  278 (282)
                      +...      |+.+      +..||-... .++-|+.+.  .-|++|++..|
T Consensus       161 Svan------~RLF------iG~IPK~k~-keeIlee~~kVteGVvdVivy~  199 (506)
T KOG0117|consen  161 SVAN------CRLF------IGNIPKTKK-KEEILEEMKKVTEGVVDVIVYP  199 (506)
T ss_pred             eeec------ceeE------eccCCcccc-HHHHHHHHHhhCCCeeEEEEec
Confidence            7643      2233      455666665 323333322  25777777664

>KOG2071|consensus

Probab=99.45  E-value=1.6e-13  Score=126.13  Aligned_cols=105  Identities=28%  Similarity=0.519  Sum_probs=97.0

Q ss_pred             hhHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCC
Q psy3994           3 VIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDV   82 (282)
Q Consensus         3 ~~~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~   82 (282)
                      .+.+|++.|.+|..    +|++.|++||.+|.+|..++..||.+||++|.+|+|.+||+++|++|+|++|.      ...
T Consensus         5 ~~~dy~s~ledltf----nskp~i~~lt~la~En~~~a~~iv~~iE~hi~kcpp~~kL~~~y~~dsi~knv------g~p   74 (579)
T KOG2071|consen    5 ACRDYQSSLEDLTF----NSKPIINTLTILAEENLPFAKSIVSAIEAHIAKCPPSQKLPVMYLLDSIVKNV------GSP   74 (579)
T ss_pred             hHHHHHHHHHHHhc----CCcchhHHhhHhhhhcccccHHHHHHHHHHHhhCCcccccchhhhhHHHHhhc------CCc
Confidence            58899999999977    55567999999999999999999999999999999999999999999999999      445


Q ss_pred             chhhHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhc
Q psy3994          83 FGPRFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQ  117 (282)
Q Consensus        83 ~~~~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~  117 (282)
                      |.-.|+.++-.+|.+.|. .++..+.+..+++.+|.
T Consensus        75 y~~~fs~~l~a~f~~~~~~vd~r~r~~l~~~~~tw~  110 (579)
T KOG2071|consen   75 YTTAFSRNLVATFICAFTKVDERTRTSLFKLRATWD  110 (579)
T ss_pred             chhhhhhhHHHHHHHHHhhccccccchhHhhHHhhc
Confidence            666699999999999997 89999999999999998

>KOG0144|consensus

Probab=99.45  E-value=1.3e-13  Score=121.27  Aligned_cols=83  Identities=28%  Similarity=0.542  Sum_probs=74.5

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCe-eCC--eeEEEE
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTK-LQG--KTITLA  227 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~-~~g--~~l~v~  227 (282)
                      +..++||||-|+..+||.+++++|++||.|++|.|.+     +||||||+|.+++-|..||+.|||.. +.|  .+|.|+
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            3468999999999999999999999999999999997     89999999999999999999999985 444  689999


Q ss_pred             eecCCCCCCCc
Q psy3994         228 WAPGKGMKDKD  238 (282)
Q Consensus       228 ~a~~~~~~~~~  238 (282)
                      ||..++.+..+
T Consensus       202 FADtqkdk~~~  212 (510)
T KOG0144|consen  202 FADTQKDKDGK  212 (510)
T ss_pred             ecccCCCchHH
Confidence            99988766443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.44  E-value=9.7e-13  Score=123.93  Aligned_cols=74  Identities=23%  Similarity=0.442  Sum_probs=68.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCee-CCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKL-QGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~-~g~~l~v~~a~  230 (282)
                      ..++|||+|||++++|++|+++|++||.|.++++++     +||||||+|.+.++|++||+.||+..+ .|+.|.|.++.
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc
Confidence            469999999999999999999999999999999874     799999999999999999999999988 47888887664

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.44  E-value=6.1e-13  Score=127.38  Aligned_cols=111  Identities=22%  Similarity=0.296  Sum_probs=83.8

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .+|||||||.++||++|+++|++||.|.+|++.+      ++|||||+|.+.++|++|+..+|+..+.|++|+|.|+...
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            3699999999999999999999999999999974      5789999999999999999999999999999999998644


Q ss_pred             CCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccC
Q psy3994         233 GMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDED  275 (282)
Q Consensus       233 ~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~  275 (282)
                      ....   .   .....+-+-++..-.+.++|..+++ .|.+..+
T Consensus        81 ~~~~---~---~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~  118 (562)
T TIGR01628        81 PSLR---R---SGVGNIFVKNLDKSVDNKALFDTFSKFGNILSC  118 (562)
T ss_pred             cccc---c---cCCCceEEcCCCccCCHHHHHHHHHhcCCccee
Confidence            2111   0   0111222224444435677776554 4444333

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0117|consensus

Probab=99.43  E-value=2.9e-13  Score=119.64  Aligned_cols=78  Identities=28%  Similarity=0.411  Sum_probs=72.3

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKD  236 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~  236 (282)
                      ....|||.||+.++||+.|+++|++||.|++|+.++  .||||.|.++++|-+|++.+||..+.|..|.|.+|++...+.
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~r--DYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPR--DYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeeccc--ceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            457899999999999999999999999999998774  799999999999999999999999999999999999875443

>smart00362 RRM_2 RNA recognition motif

Probab=99.42  E-value=1.2e-12  Score=89.37  Aligned_cols=68  Identities=35%  Similarity=0.615  Sum_probs=63.7

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeCCC----cEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR----GCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~k----g~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      +|||+|||..+++++|+++|.+||.+..+.+...+    |+|||+|.+.++|++|+..++|..+.|++++|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999988754    999999999999999999999999999998874

>KOG0105|consensus

Probab=99.42  E-value=5.2e-13  Score=105.24  Aligned_cols=76  Identities=28%  Similarity=0.497  Sum_probs=70.8

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .+++|||||||.++.+.+++++|.+||.|..|.+..   ..+||||+|++..+|+.||..-+|..++|..|+|+++...
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            468999999999999999999999999999998874   4579999999999999999999999999999999999865

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.42  E-value=6.2e-13  Score=124.23  Aligned_cols=75  Identities=25%  Similarity=0.503  Sum_probs=70.5

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||+|||..+++++|+++|++||.|..+.+..      ++|||||+|.+.++|.+|+..|||..+.|++|+|.||.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            368999999999999999999999999999999883      57999999999999999999999999999999999976


Q ss_pred             C
Q psy3994         231 G  231 (282)
Q Consensus       231 ~  231 (282)
                      .
T Consensus       265 ~  265 (457)
T TIGR01622       265 D  265 (457)
T ss_pred             C
Confidence            3

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0145|consensus

Probab=99.42  E-value=6.9e-13  Score=109.78  Aligned_cols=90  Identities=30%  Similarity=0.416  Sum_probs=80.1

Q ss_pred             CCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEE
Q psy3994         153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL  226 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v  226 (282)
                      ......++|.|..||.++|+++++.+|...|+|++|++++      +-|||||.|-+.++|++|+..|||-.+..++|+|
T Consensus        36 ~t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKV  115 (360)
T KOG0145|consen   36 DTDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKV  115 (360)
T ss_pred             CcCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEE
Confidence            3455678999999999999999999999999999999997      5699999999999999999999999999999999


Q ss_pred             EeecCCCCCCCccccc
Q psy3994         227 AWAPGKGMKDKDWKDF  242 (282)
Q Consensus       227 ~~a~~~~~~~~~~~~~  242 (282)
                      ++|++....-++-+.|
T Consensus       116 SyARPSs~~Ik~aNLY  131 (360)
T KOG0145|consen  116 SYARPSSDSIKDANLY  131 (360)
T ss_pred             EeccCChhhhcccceE
Confidence            9999887655443333

>PF13893 RRM_5: RNA recognition motif

Probab=99.42  E-value=1.5e-12  Score=85.57  Aligned_cols=55  Identities=29%  Similarity=0.592  Sum_probs=51.7

Q ss_pred             HHhhhccCCceEEEEEeCCC-cEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         175 LSDTFGEYGDVVSINLIPPR-GCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       175 l~~~f~~~G~i~~~~~~~~k-g~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      |.++|++||+|.++.+...+ ++|||+|.+.++|+.|++.|||..+.|++|+|.||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999999877 99999999999999999999999999999999996

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0113|consensus

Probab=99.41  E-value=2.2e-12  Score=108.81  Aligned_cols=78  Identities=24%  Similarity=0.433  Sum_probs=73.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      +-+||||+.|+.+++|..|+..|+.||.|..|.+++      ++|||||+|.+..+...|-+..+|..|+|+.|-|.+-.
T Consensus       100 Py~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvER  179 (335)
T KOG0113|consen  100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVER  179 (335)
T ss_pred             ccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecc
Confidence            459999999999999999999999999999999995      79999999999999999999999999999999999988


Q ss_pred             CCCC
Q psy3994         231 GKGM  234 (282)
Q Consensus       231 ~~~~  234 (282)
                      .+.+
T Consensus       180 gRTv  183 (335)
T KOG0113|consen  180 GRTV  183 (335)
T ss_pred             cccc
Confidence            6643

>KOG0144|consensus

Probab=99.40  E-value=6.5e-13  Score=116.96  Aligned_cols=120  Identities=24%  Similarity=0.440  Sum_probs=93.4

Q ss_pred             hcCCCCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCee---
Q psy3994         149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKL---  219 (282)
Q Consensus       149 ~~~~~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~---  219 (282)
                      +.++..+...-++|||-+|+.++|.+|+++|++||.|.+|.+++      ++|||||.|.++++|.+|+.+||+...   
T Consensus        25 ~~~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG  104 (510)
T KOG0144|consen   25 DHTDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPG  104 (510)
T ss_pred             CCCCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCC
Confidence            34455666678999999999999999999999999999999996      789999999999999999999998764   


Q ss_pred             CCeeEEEEeecCCCCCC-CccccccccCCCeeeecCCCCCcchhhhh-hhcCcccccCC
Q psy3994         220 QGKTITLAWAPGKGMKD-KDWKDFWEVQDGVSYIPYDRLSKEIDYDY-LEDGGVFDEDT  276 (282)
Q Consensus       220 ~g~~l~v~~a~~~~~~~-~~~~~~~~~~~g~~~~p~~~~~~~~~~~~-~~~~~~~~~~~  276 (282)
                      .-.++.|++|.....+. .+++.+      +..++-.  .++.+++. |...|.|+++-
T Consensus       105 ~~~pvqvk~Ad~E~er~~~e~KLF------vg~lsK~--~te~evr~iFs~fG~Ied~~  155 (510)
T KOG0144|consen  105 MHHPVQVKYADGERERIVEERKLF------VGMLSKQ--CTENEVREIFSRFGHIEDCY  155 (510)
T ss_pred             CCcceeecccchhhhccccchhhh------hhhcccc--ccHHHHHHHHHhhCccchhh
Confidence            34689999999876552 223333      2223332  35677776 44578888874

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.39  E-value=1.8e-12  Score=107.67  Aligned_cols=75  Identities=16%  Similarity=0.195  Sum_probs=68.8

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .+.+|||+||++.+|+++|+++|+.||+|.+|.+++   .++||||+|.+.++|+.|+ .|+|..+.+++|.|..+...
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~y   81 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQY   81 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCccc
Confidence            358999999999999999999999999999999997   4589999999999999999 59999999999999877644

>KOG0149|consensus

Probab=99.39  E-value=5.3e-13  Score=109.17  Aligned_cols=74  Identities=23%  Similarity=0.403  Sum_probs=65.9

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      .-++||||||++.+..+.|+++|++||+|++..++.      +||||||+|.+.++|.+|++- .+-.|+||+-.|.+|.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            358999999999999999999999999999998884      899999999999999999974 3457899998888875


Q ss_pred             C
Q psy3994         231 G  231 (282)
Q Consensus       231 ~  231 (282)
                      -
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            3

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.38  E-value=4.4e-12  Score=120.06  Aligned_cols=77  Identities=19%  Similarity=0.338  Sum_probs=71.4

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||||||..+++++|+++|+.||.|..+.++.      ++|||||+|.+.++|..|+..|||..+.|+.|.|.+|
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3468999999999999999999999999999998874      6899999999999999999999999999999999999


Q ss_pred             cCC
Q psy3994         230 PGK  232 (282)
Q Consensus       230 ~~~  232 (282)
                      ...
T Consensus       373 ~~~  375 (509)
T TIGR01642       373 CVG  375 (509)
T ss_pred             ccC
Confidence            654

Members of this subfamily are found in plants, metazoa and fungi.

>KOG4207|consensus

Probab=99.37  E-value=6.2e-13  Score=106.60  Aligned_cols=73  Identities=27%  Similarity=0.461  Sum_probs=69.9

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      -++|-|-||...++.++|+.+|++||.|-.|.|++      ++|||||.|.+..+|+.|+++|+|..++|+.|+|++|+
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            36899999999999999999999999999999986      78999999999999999999999999999999999987

>KOG0114|consensus

Probab=99.37  E-value=4.6e-12  Score=90.72  Aligned_cols=76  Identities=28%  Similarity=0.431  Sum_probs=71.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .++-|||.|||..+|.++..++|++||.|..+++-.   -+|-|||.|++..+|.+|+..|+|..+.++.|.|-+-.+.
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            468899999999999999999999999999999975   6899999999999999999999999999999999887754

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.36  E-value=4.7e-12  Score=118.33  Aligned_cols=121  Identities=17%  Similarity=0.155  Sum_probs=87.7

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||..+++++|+++|++||.|..|+++.      ++|||||+|.+.++|++|+. |+|..+.|++|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            34578999999999999999999999999999999974      58999999999999999996 899999999999998


Q ss_pred             ecCCCCCCCcccccc----ccCCCeeeecCCCCCcchhhhhhhc-CcccccCC
Q psy3994         229 APGKGMKDKDWKDFW----EVQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDT  276 (282)
Q Consensus       229 a~~~~~~~~~~~~~~----~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~  276 (282)
                      +..............    .....+-+-++..-.++++|+.+++ .|.+..+.
T Consensus       165 ~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~  217 (457)
T TIGR01622       165 SQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQ  217 (457)
T ss_pred             cchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEE
Confidence            765432211100000    0011122223433346888887655 56554443

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0153|consensus

Probab=99.34  E-value=3.5e-12  Score=109.68  Aligned_cols=80  Identities=34%  Similarity=0.626  Sum_probs=72.4

Q ss_pred             CCCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh-CCCeeCCeeEEEEeec
Q psy3994         152 GVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL-KNTKLQGKTITLAWAP  230 (282)
Q Consensus       152 ~~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l-~g~~~~g~~l~v~~a~  230 (282)
                      +..+...++||||+|.+.++|.+|+++|.+||+|.++.+...++||||+|.++++|+.|.... |...++|.+|+|.|+.
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            344556789999999999999999999999999999999999999999999999999988765 5556799999999999


Q ss_pred             C
Q psy3994         231 G  231 (282)
Q Consensus       231 ~  231 (282)
                      +
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            8

>KOG0109|consensus

Probab=99.34  E-value=2.4e-12  Score=108.20  Aligned_cols=73  Identities=27%  Similarity=0.519  Sum_probs=69.9

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ..|||||||..+++.+|+.+|++||+|.+|.|++  .||||..++...|+.||+.|||..++|..|.|+-++++.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK--NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec--ccceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            4699999999999999999999999999999987  999999999999999999999999999999999999883

>KOG0130|consensus

Probab=99.33  E-value=3.1e-12  Score=95.86  Aligned_cols=83  Identities=23%  Similarity=0.436  Sum_probs=75.8

Q ss_pred             CCCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         152 GVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       152 ~~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      +..+..+.-|||.++....+|+++.+.|..||+|..+.+..      .+|||.|+|.+.++|+.|+..+||..+.|.++.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            44566788999999999999999999999999999998874      689999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q psy3994         226 LAWAPGKGM  234 (282)
Q Consensus       226 v~~a~~~~~  234 (282)
                      |.|+-.++.
T Consensus       146 VDw~Fv~gp  154 (170)
T KOG0130|consen  146 VDWCFVKGP  154 (170)
T ss_pred             EEEEEecCC
Confidence            999976554

>KOG0126|consensus

Probab=99.32  E-value=3.5e-13  Score=105.92  Aligned_cols=76  Identities=30%  Similarity=0.561  Sum_probs=70.9

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +.-|||||||...||.+|..+|++||+|+.|.+++      ++||||..|++..+...|+..|||..+.||.|+|.....
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            57899999999999999999999999999999996      899999999999999999999999999999999987754


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      ..
T Consensus       115 Yk  116 (219)
T KOG0126|consen  115 YK  116 (219)
T ss_pred             cc
Confidence            43

>cd00590 RRM RRM (RNA recognition motif), 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

Probab=99.31  E-value=1.8e-11  Score=83.82  Aligned_cols=69  Identities=35%  Similarity=0.651  Sum_probs=64.6

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-----RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~-----kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      +|+|+|||..+++++|+++|+.||.|..+.+...     +|+|||+|.+.++|..|+..+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999998863     79999999999999999999999999999999875

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).

>KOG0131|consensus

Probab=99.30  E-value=4.7e-12  Score=99.75  Aligned_cols=74  Identities=31%  Similarity=0.439  Sum_probs=70.6

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ...|||||||+..++++.|.++|-+.|.|.++.+++      ++||||++|.++++|+-|++.||...+.|++|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            458999999999999999999999999999999986      78999999999999999999999999999999999988

>KOG0127|consensus

Probab=99.25  E-value=3.1e-11  Score=109.36  Aligned_cols=79  Identities=29%  Similarity=0.492  Sum_probs=73.5

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ..+...|.|.|||+.+...+|+.+|+.||.|..+.|++     -.|||||+|....+|..|+..+||..+.||++-|.||
T Consensus       114 ~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWA  193 (678)
T KOG0127|consen  114 DLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWA  193 (678)
T ss_pred             cCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeee
Confidence            44478999999999999999999999999999999996     3599999999999999999999999999999999999


Q ss_pred             cCCC
Q psy3994         230 PGKG  233 (282)
Q Consensus       230 ~~~~  233 (282)
                      .++.
T Consensus       194 V~Kd  197 (678)
T KOG0127|consen  194 VDKD  197 (678)
T ss_pred             cccc
Confidence            8764

>smart00360 RRM RNA recognition motif

Probab=99.25  E-value=3.2e-11  Score=81.78  Aligned_cols=65  Identities=35%  Similarity=0.639  Sum_probs=60.1

Q ss_pred             ecCCCccCcHHHHHhhhccCCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         163 IGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       163 V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~------kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      |+|||..+++++|+++|++||.|..+.+...      +|+|||+|.+.++|.+|+..+++..+.|+.++|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            6899999999999999999999999988763      6799999999999999999999999999998873

>KOG0131|consensus

Probab=99.23  E-value=2.8e-11  Score=95.39  Aligned_cols=116  Identities=22%  Similarity=0.337  Sum_probs=89.6

Q ss_pred             CChhhHHHHHHHHH-hhccCcccCCccccccccCCCCCCCChhhhHHhhhcCCCCCCCCcEEEecCCCccCcHHHHHhhh
Q psy3994         101 CPPEDKSKIIRVLN-LWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTF  179 (282)
Q Consensus       101 ~~~~~~~k~~~~l~-~w~~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~te~~l~~~f  179 (282)
                      ..+++++-+++++| +..-++.+.......     .                ..+...+.++|||||.+.++|..|.+.|
T Consensus        59 ~~eedadYAikiln~VkLYgrpIrv~kas~-----~----------------~~nl~vganlfvgNLd~~vDe~~L~dtF  117 (203)
T KOG0131|consen   59 RTEEDADYAIKILNMVKLYGRPIRVNKASA-----H----------------QKNLDVGANLFVGNLDPEVDEKLLYDTF  117 (203)
T ss_pred             echhhhHHHHHHHHHHHhcCceeEEEeccc-----c----------------cccccccccccccccCcchhHHHHHHHH
Confidence            35788888888888 333455444443220     0                1122235889999999999999999999


Q ss_pred             ccCCceEEE-EEe------CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCCCCC
Q psy3994         180 GEYGDVVSI-NLI------PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDK  237 (282)
Q Consensus       180 ~~~G~i~~~-~~~------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~  237 (282)
                      +.||.+.+. +++      .++|||||.|.+.+.+.+|+..|||+.+..++++|.++..+..++.
T Consensus       118 safG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg~  182 (203)
T KOG0131|consen  118 SAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKGE  182 (203)
T ss_pred             HhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCcc
Confidence            999987663 333      2689999999999999999999999999999999999998876653

>KOG0124|consensus

Probab=99.23  E-value=8.6e-12  Score=107.84  Aligned_cols=114  Identities=21%  Similarity=0.312  Sum_probs=85.6

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      |+||||.+...+.|+.||..|.+||.|.++.+.+      +||||||+|+-.+.|+.|++.|||..++||.|+|..-..-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            7899999999999999999999999999999875      8999999999999999999999999999999999843322


Q ss_pred             CCCC-------CccccccccCCCeeeec-CCCCCcchhhhhhhc-CcccccCCC
Q psy3994         233 GMKD-------KDWKDFWEVQDGVSYIP-YDRLSKEIDYDYLED-GGVFDEDTV  277 (282)
Q Consensus       233 ~~~~-------~~~~~~~~~~~g~~~~p-~~~~~~~~~~~~~~~-~~~~~~~~~  277 (282)
                      +.-.       ++-+.|   ++ +.+-. -.+| .++|++.-++ .|.|-.|.|
T Consensus       194 pQAQpiID~vqeeAk~f---nR-iYVaSvHpDL-Se~DiKSVFEAFG~I~~C~L  242 (544)
T KOG0124|consen  194 PQAQPIIDMVQEEAKKF---NR-IYVASVHPDL-SETDIKSVFEAFGEIVKCQL  242 (544)
T ss_pred             cccchHHHHHHHHHHhh---he-EEeeecCCCc-cHHHHHHHHHhhcceeeEEe
Confidence            1110       011111   11 11222 3344 6788886444 677766655

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.22  E-value=4.4e-11  Score=102.96  Aligned_cols=73  Identities=33%  Similarity=0.584  Sum_probs=69.3

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      .++|||||||..+++++|+++|..||.+..+.+..      .+|||||+|.+.++|..|+..++|..+.|++|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            69999999999999999999999999998888874      67999999999999999999999999999999999965

>KOG0123|consensus

Probab=99.21  E-value=6.6e-11  Score=106.64  Aligned_cols=109  Identities=26%  Similarity=0.443  Sum_probs=87.9

Q ss_pred             CChhhHHHHHHHHHhhccCcccCCccccccccCCCCCCCChhhhHHhhhcCCCCCCCCcEEEecCCCccCcHHHHHhhhc
Q psy3994         101 CPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFG  180 (282)
Q Consensus       101 ~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~te~~l~~~f~  180 (282)
                      ..+.++.+++..+|.-.-.+       .+++-++....|                   +.+||.||++.++..+|.++|+
T Consensus        45 ~~~~da~~A~~~~n~~~~~~-------~~~rim~s~rd~-------------------~~~~i~nl~~~~~~~~~~d~f~   98 (369)
T KOG0123|consen   45 QQPADAERALDTMNFDVLKG-------KPIRIMWSQRDP-------------------SLVFIKNLDESIDNKSLYDTFS   98 (369)
T ss_pred             CCHHHHHHHHHHcCCcccCC-------cEEEeehhccCC-------------------ceeeecCCCcccCcHHHHHHHH
Confidence            56788888888877433222       234444433311                   2399999999999999999999


Q ss_pred             cCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCCCC
Q psy3994         181 EYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKD  236 (282)
Q Consensus       181 ~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~  236 (282)
                      .||+|.+|++..    ++|| ||+|.+.++|.+|+..+||..+.|+.|.|.....+..+.
T Consensus        99 ~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~  157 (369)
T KOG0123|consen   99 EFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEERE  157 (369)
T ss_pred             hhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhc
Confidence            999999999985    7899 999999999999999999999999999999988765543

>KOG0108|consensus

Probab=99.20  E-value=4.9e-11  Score=108.55  Aligned_cols=77  Identities=22%  Similarity=0.488  Sum_probs=72.9

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      +.+||||+|..+++++|..+|+..|.|.+++++.      .+||||++|.+.+.|..|++.|||.++.||+|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            8999999999999999999999999999999984      7899999999999999999999999999999999999876


Q ss_pred             CCC
Q psy3994         233 GMK  235 (282)
Q Consensus       233 ~~~  235 (282)
                      ..+
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            544

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.18  E-value=1.3e-10  Score=110.01  Aligned_cols=76  Identities=18%  Similarity=0.280  Sum_probs=66.5

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccC------------CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEY------------GDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQG  221 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~------------G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g  221 (282)
                      .....++|||||||+.+|+++|+++|..+            +.|..+.+...+|||||+|.+.++|..|+ .|+|..+.|
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al-~l~g~~~~g  249 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAM-ALDSIIYSN  249 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhh-cCCCeEeeC
Confidence            34557899999999999999999999864            45677777789999999999999999999 499999999


Q ss_pred             eeEEEEeec
Q psy3994         222 KTITLAWAP  230 (282)
Q Consensus       222 ~~l~v~~a~  230 (282)
                      +.|+|....
T Consensus       250 ~~l~v~r~~  258 (509)
T TIGR01642       250 VFLKIRRPH  258 (509)
T ss_pred             ceeEecCcc
Confidence            999997554

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0146|consensus

Probab=99.14  E-value=4.7e-11  Score=99.41  Aligned_cols=82  Identities=21%  Similarity=0.298  Sum_probs=75.7

Q ss_pred             CCCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         152 GVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       152 ~~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      ....+.+|+|||-.||...++.||..+|-+||.|.+.++..      +|+||||.|++..+|+.||..|||..|+-++|+
T Consensus       279 qreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLK  358 (371)
T KOG0146|consen  279 QREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLK  358 (371)
T ss_pred             hhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhh
Confidence            34567789999999999999999999999999999988763      899999999999999999999999999999999


Q ss_pred             EEeecCCC
Q psy3994         226 LAWAPGKG  233 (282)
Q Consensus       226 v~~a~~~~  233 (282)
                      |.+.+++.
T Consensus       359 VQLKRPkd  366 (371)
T KOG0146|consen  359 VQLKRPKD  366 (371)
T ss_pred             hhhcCccc
Confidence            99988875

>KOG0109|consensus

Probab=99.13  E-value=7.4e-11  Score=99.33  Aligned_cols=75  Identities=32%  Similarity=0.579  Sum_probs=71.4

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ..+++++||||.+.++..+|+..|++||.+.+|++++  +|+||.|+-.++|..|++.|+|+++.|+++.|+.+.++
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeec--ceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence            3569999999999999999999999999999999987  99999999999999999999999999999999999865

>KOG0146|consensus

Probab=99.12  E-value=6.9e-11  Score=98.40  Aligned_cols=79  Identities=20%  Similarity=0.466  Sum_probs=71.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCee---CCeeEEEEe
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKL---QGKTITLAW  228 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~---~g~~l~v~~  228 (282)
                      ..++||||-|...-+|+|++++|..||.|.+|.+.+     +||||||.|.++.+|+.||..|||...   ....|.|++
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            568999999999999999999999999999999986     899999999999999999999999864   346799999


Q ss_pred             ecCCCCC
Q psy3994         229 APGKGMK  235 (282)
Q Consensus       229 a~~~~~~  235 (282)
                      |...+.+
T Consensus        98 ADTdkER  104 (371)
T KOG0146|consen   98 ADTDKER  104 (371)
T ss_pred             ccchHHH
Confidence            9866544

>KOG0110|consensus

Probab=99.06  E-value=1.3e-10  Score=108.43  Aligned_cols=127  Identities=20%  Similarity=0.363  Sum_probs=94.4

Q ss_pred             HHHHhhcCChhhHHHHHHHHH-hhccCcccCCccccccccCCCCCCCChhhhHHhhhcCCCCCCCCcEEEecCCCccCcH
Q psy3994          94 TFQHLYQCPPEDKSKIIRVLN-LWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQE  172 (282)
Q Consensus        94 ~f~~v~~~~~~~~~k~~~~l~-~w~~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~te  172 (282)
                      .|.++-...+++++.+++.++ +-..+..+...+       +. +.|... .    ++........+.|+|.|||...+-
T Consensus       561 GfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~-------S~-~k~~~~-~----gK~~~~kk~~tKIlVRNipFeAt~  627 (725)
T KOG0110|consen  561 GFGFVEFAKPESAQAALKALQGTVLDGHKLELKI-------SE-NKPAST-V----GKKKSKKKKGTKILVRNIPFEATK  627 (725)
T ss_pred             ceeEEEecCHHHHHHHHHHhcCceecCceEEEEe-------cc-Cccccc-c----ccccccccccceeeeeccchHHHH
Confidence            444444456788888888887 333444333222       11 101110 0    011222233689999999999999


Q ss_pred             HHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         173 EELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       173 ~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .+++.+|..||.+.+|+++.      ++|||||.|-+..+|.+|+.+|.++-+.||+|.+.||....
T Consensus       628 rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  628 REVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             HHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            99999999999999999996      69999999999999999999999999999999999998763

>KOG4206|consensus

Probab=99.06  E-value=4e-10  Score=92.10  Aligned_cols=76  Identities=28%  Similarity=0.533  Sum_probs=70.1

Q ss_pred             CcEEEecCCCccCcHHHHHh----hhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         158 STTLWIGHLSKLVQEEELSD----TFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~----~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      +.||||.||++.+..++|++    +|++||.|..|...+   .||-|||.|.+.+.|..|+..|+|..+.|+++++.+|+
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            45999999999999998888    999999999987764   78999999999999999999999999999999999998


Q ss_pred             CCC
Q psy3994         231 GKG  233 (282)
Q Consensus       231 ~~~  233 (282)
                      .+.
T Consensus        89 s~s   91 (221)
T KOG4206|consen   89 SDS   91 (221)
T ss_pred             Ccc
Confidence            763

>smart00361 RRM_1 RNA recognition motif

Probab=99.03  E-value=9.4e-10  Score=75.63  Aligned_cols=56  Identities=29%  Similarity=0.600  Sum_probs=49.2

Q ss_pred             HHHHHhhhc----cCCceEEEE-Ee--------CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         172 EEELSDTFG----EYGDVVSIN-LI--------PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       172 e~~l~~~f~----~~G~i~~~~-~~--------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      +++|+++|+    .||.|.++. +.        +++|||||+|.+.++|.+|+..|||..+.|+.|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            567888888    999999884 32        158999999999999999999999999999999863

>KOG0147|consensus

Probab=99.01  E-value=4.3e-10  Score=102.21  Aligned_cols=73  Identities=26%  Similarity=0.522  Sum_probs=68.1

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .||||||.+++++++|+.+|++||.|..|.+..      .+|||||+|.+.+.|.+|+..|||..+.|+.|+|.....+
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            399999999999999999999999999998875      6899999999999999999999999999999999877644

>KOG0110|consensus

Probab=98.99  E-value=1.1e-09  Score=102.21  Aligned_cols=119  Identities=24%  Similarity=0.310  Sum_probs=90.5

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ++|||.||++.+|.+++...|...|.|.++.|..         +.|||||+|.+.++|++|++.|+|+.++|+.|.|+++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            3399999999999999999999999999998875         3399999999999999999999999999999999999


Q ss_pred             cCCCC-CCCccccccccCCC--eeeecCCCCCcchhhhh-hhcCcccccCCCCC
Q psy3994         230 PGKGM-KDKDWKDFWEVQDG--VSYIPYDRLSKEIDYDY-LEDGGVFDEDTVPL  279 (282)
Q Consensus       230 ~~~~~-~~~~~~~~~~~~~g--~~~~p~~~~~~~~~~~~-~~~~~~~~~~~~p~  279 (282)
                      ..+.. ..+.-...|..-+-  +.+||+.-.  ..+++. |...|.+..+.+|-
T Consensus       596 ~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt--~rEVr~LF~aFGqlksvRlPK  647 (725)
T KOG0110|consen  596 ENKPASTVGKKKSKKKKGTKILVRNIPFEAT--KREVRKLFTAFGQLKSVRLPK  647 (725)
T ss_pred             cCccccccccccccccccceeeeeccchHHH--HHHHHHHHhcccceeeeccch
Confidence            83311 11112233333111  456677665  445554 55578887777774

>PF04818 CTD_bind: RNA polymerase II-binding domain

Probab=98.96  E-value=3.2e-10  Score=76.52  Aligned_cols=63  Identities=32%  Similarity=0.734  Sum_probs=55.6

Q ss_pred             ccceeehhhHHHHHhhhhccCCCCchhhHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhccCcccC
Q psy3994          59 KVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKNEVFT  123 (282)
Q Consensus        59 kl~~lYv~Dsi~r~~~~~~~~~~~~~~~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~~~~~f~  123 (282)
                      ||+.|||+|+|+++++++..  +.|...|.+.+..+|.+++. .+++.+.++.+++++|.++++|+
T Consensus         1 KL~~lYl~ndI~q~sk~k~~--~~f~~~F~~~l~~~~~~~~~~~~~~~~~kv~rll~iW~~r~if~   64 (64)
T PF04818_consen    1 KLALLYLANDILQNSKRKNP--DEFAPAFSPVLPDAFAHAYKNVDPEVRKKVQRLLNIWEERNIFS   64 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT--HCHHHHHHCCHHHHHHHHCCCS-HHHHHHHHHHHHHHHHCTSS-
T ss_pred             CcceeehHHHHHHHhhhcCh--HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhCCCCCC
Confidence            68899999999999988843  36999999999999999998 68999999999999999999874

; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....

>KOG0151|consensus

Probab=98.95  E-value=1.4e-09  Score=101.33  Aligned_cols=79  Identities=30%  Similarity=0.553  Sum_probs=73.8

Q ss_pred             CCCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhCCCeeCCe
Q psy3994         152 GVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---------PRGCAFVCMNRRQDAAKALYKLKNTKLQGK  222 (282)
Q Consensus       152 ~~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~  222 (282)
                      +..++..+++|||||++.++++.|-..|+.||.|.+++++.         .+.||||-|.++.+|++|+..|+|..+.+.
T Consensus       168 DdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~  247 (877)
T KOG0151|consen  168 DDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEY  247 (877)
T ss_pred             CCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeee
Confidence            44567789999999999999999999999999999999985         578999999999999999999999999999


Q ss_pred             eEEEEeec
Q psy3994         223 TITLAWAP  230 (282)
Q Consensus       223 ~l~v~~a~  230 (282)
                      .+++.|++
T Consensus       248 e~K~gWgk  255 (877)
T KOG0151|consen  248 EMKLGWGK  255 (877)
T ss_pred             eeeecccc
Confidence            99999995

>KOG0127|consensus

Probab=98.93  E-value=1.6e-09  Score=98.39  Aligned_cols=120  Identities=19%  Similarity=0.278  Sum_probs=91.4

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +.||||++||+.++.++|.++|+.+|+|..+.++.      +||||||+|.-.+++++|+...++..+.|+.|+|..|..
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            38999999999999999999999999999998885      689999999999999999999999999999999999986


Q ss_pred             CCCCC----Cccc-------------cccc---cCCCeeeecCCCCCcchhhhhhhc-CcccccCCCCC
Q psy3994         232 KGMKD----KDWK-------------DFWE---VQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDTVPL  279 (282)
Q Consensus       232 ~~~~~----~~~~-------------~~~~---~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~p~  279 (282)
                      +....    ...+             ..-+   -..=+.++||.--  +.+|+..++ .|-+-+..+|.
T Consensus        85 R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k--~~dLk~vFs~~G~V~Ei~IP~  151 (678)
T KOG0127|consen   85 RARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCK--KPDLKNVFSNFGKVVEIVIPR  151 (678)
T ss_pred             cccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccC--cHHHHHHHhhcceEEEEEccc
Confidence            53221    0000             0000   0011456677766  558887555 45555556663

>KOG4661|consensus

Probab=98.89  E-value=3.7e-09  Score=96.47  Aligned_cols=78  Identities=28%  Similarity=0.543  Sum_probs=72.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ...+++|||.+|+..+...+|+.+|++||.|+-.+++.      -++|+||++.+.++|.+||..||.+.+.|+.|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            45678999999999999999999999999999988885      478999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3994         229 APGK  232 (282)
Q Consensus       229 a~~~  232 (282)
                      ++..
T Consensus       482 aKNE  485 (940)
T KOG4661|consen  482 AKNE  485 (940)
T ss_pred             cccC
Confidence            9865

>KOG0415|consensus

Probab=98.81  E-value=7.2e-09  Score=89.64  Aligned_cols=82  Identities=18%  Similarity=0.399  Sum_probs=74.7

Q ss_pred             CCCCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeE
Q psy3994         151 NGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTI  224 (282)
Q Consensus       151 ~~~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l  224 (282)
                      .....++...|||.-|.+-+++++|.-+|+.||.|.+|.+++      +-.||||+|++.++.++|.-.|++..|++++|
T Consensus       232 dAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRI  311 (479)
T KOG0415|consen  232 DADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRI  311 (479)
T ss_pred             ccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceE
Confidence            345567788999999999999999999999999999999997      45799999999999999999999999999999


Q ss_pred             EEEeecCC
Q psy3994         225 TLAWAPGK  232 (282)
Q Consensus       225 ~v~~a~~~  232 (282)
                      .|.|+.+-
T Consensus       312 HVDFSQSV  319 (479)
T KOG0415|consen  312 HVDFSQSV  319 (479)
T ss_pred             Eeehhhhh
Confidence            99998753

>KOG4212|consensus

Probab=98.78  E-value=2e-08  Score=89.18  Aligned_cols=74  Identities=23%  Similarity=0.397  Sum_probs=67.9

Q ss_pred             CcEEEecCCCccCcHHHHHhhhc-cCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFG-EYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~-~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .+.+||.|||.+..+.+|+++|. +.|+|..|.+..     .||||.|+|.+++.+++|++.||.+.+.||+|.|+....
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            46699999999999999999996 579999999884     799999999999999999999999999999999987654

>KOG4208|consensus

Probab=98.78  E-value=2.7e-08  Score=80.30  Aligned_cols=78  Identities=21%  Similarity=0.302  Sum_probs=70.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccC-CceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEY-GDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~-G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ......+|++.+|..+.+.++..+|.+| |.+..+++.+      +||||||+|++.+.|+-|-+.||+..+.|+.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3445789999999999999999999998 7777888754      89999999999999999999999999999999999


Q ss_pred             eecCC
Q psy3994         228 WAPGK  232 (282)
Q Consensus       228 ~a~~~  232 (282)
                      +-.+.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            98876

>KOG4212|consensus

Probab=98.78  E-value=1.2e-08  Score=90.56  Aligned_cols=77  Identities=19%  Similarity=0.268  Sum_probs=68.2

Q ss_pred             CCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...+..++|+|.|||.++|+..|++-|..||.|....|+. .+.-+-|.|.+.++|++|+..|+|..+.||.|+|.+.
T Consensus       531 gaarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  531 GAARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cccccccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            3445678999999999999999999999999999998853 3344589999999999999999999999999999873

>KOG0123|consensus

Probab=98.75  E-value=4.1e-08  Score=88.62  Aligned_cols=72  Identities=32%  Similarity=0.515  Sum_probs=66.5

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ..||||   +++||.+|.+.|+++|.+.++++.+   +-|||||.|.+..+|++|+..||...+.|+++++-|+....
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            469999   8999999999999999999998875   67999999999999999999999999999999999987554

>KOG0124|consensus

Probab=98.68  E-value=3.5e-08  Score=85.80  Aligned_cols=75  Identities=16%  Similarity=0.345  Sum_probs=69.6

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      -.+|||..+.++.+|++|+..|+.||+|.+|.+-+      +|||||++|.+..+...|+..||-..++|.-|+|..+..
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            46799999999999999999999999999999985      899999999999999999999999999999999987764


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      .
T Consensus       290 P  290 (544)
T KOG0124|consen  290 P  290 (544)
T ss_pred             C
Confidence            4

>KOG1457|consensus

Probab=98.64  E-value=1.7e-07  Score=76.55  Aligned_cols=77  Identities=21%  Similarity=0.299  Sum_probs=64.7

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe-CC------CcEEEEEecCHHHHHHHHHHhCCCee---CCeeEEE
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-PP------RGCAFVCMNRRQDAAKALYKLKNTKL---QGKTITL  226 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~-~~------kg~aFV~f~~~~~A~~Ai~~l~g~~~---~g~~l~v  226 (282)
                      ..+||||.+||.++...+|..+|..|-.-+.+.+. .+      +.+||++|.++.+|..|+.+|||..+   .+.+|++
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            46999999999999999999999998544444333 12      36999999999999999999999998   5789999


Q ss_pred             EeecCCC
Q psy3994         227 AWAPGKG  233 (282)
Q Consensus       227 ~~a~~~~  233 (282)
                      ++|++..
T Consensus       113 ElAKSNt  119 (284)
T KOG1457|consen  113 ELAKSNT  119 (284)
T ss_pred             eehhcCc
Confidence            9998653

>KOG4660|consensus

Probab=98.63  E-value=2e-08  Score=91.74  Aligned_cols=71  Identities=34%  Similarity=0.531  Sum_probs=66.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      +...++|+|-|||..+++++|+++|+.||+|..++..+ .+|..||+|.|..+|++|+++|++..+.|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            45678999999999999999999999999999987765 789999999999999999999999999999988

>KOG4205|consensus

Probab=98.62  E-value=3.8e-08  Score=86.20  Aligned_cols=79  Identities=27%  Similarity=0.429  Sum_probs=69.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..+++|||+|++.++++.|+..|.+||+|..|.+++      +|||+||+|.+.+...+++.. .-+.+.|+.+.+.-|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            468999999999999999999999999999999885      789999999998888888753 4567899999999998


Q ss_pred             CCCCCC
Q psy3994         231 GKGMKD  236 (282)
Q Consensus       231 ~~~~~~  236 (282)
                      ++....
T Consensus        84 ~r~~~~   89 (311)
T KOG4205|consen   84 SREDQT   89 (311)
T ss_pred             Cccccc
Confidence            886543

>KOG0106|consensus

Probab=98.57  E-value=4.9e-08  Score=80.56  Aligned_cols=71  Identities=25%  Similarity=0.477  Sum_probs=67.2

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ..+|||+||+.+.+.++.++|..||.+..+.+..  ||+||.|.+..+|..|+..+||..+.|-.+.|.|+++
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--ccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            3589999999999999999999999999998876  9999999999999999999999999998899999995

>KOG0116|consensus

Probab=98.52  E-value=2.5e-07  Score=84.08  Aligned_cols=74  Identities=12%  Similarity=0.216  Sum_probs=64.6

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ..+|||+|||.++++.+|+++|..||.|+...|..      ..+||||+|.+.++++.|+.+ +-..++++++.|+.-++
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            45699999999999999999999999999887764      228999999999999999986 56678999999988776


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      .
T Consensus       367 ~  367 (419)
T KOG0116|consen  367 G  367 (419)
T ss_pred             c
Confidence            4

>KOG0533|consensus

Probab=98.45  E-value=6.6e-07  Score=75.51  Aligned_cols=77  Identities=26%  Similarity=0.415  Sum_probs=69.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      -+++|+|.|||..+++++|+++|..||.+..+-+..     +.|.|=|.|...++|.+|++.+||..++|+++++....+
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            348899999999999999999999999888887663     679999999999999999999999999999999888765


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      ..
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            53

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.44  E-value=1e-06  Score=61.13  Aligned_cols=70  Identities=19%  Similarity=0.378  Sum_probs=49.2

Q ss_pred             cEEEecCCCccCcHH----HHHhhhccCC-ceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         159 TTLWIGHLSKLVQEE----ELSDTFGEYG-DVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       159 ~~l~V~nl~~~~te~----~l~~~f~~~G-~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      +.|||.|||.+.+..    -|++++..+| .|.++    ..+.|+|.|.+.+.|++|.+.|+|..+.|++|.|++....
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~   77 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKN   77 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCc
Confidence            579999999887764    4677777885 56666    4589999999999999999999999999999999998543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1190|consensus

Probab=98.43  E-value=1.4e-06  Score=76.98  Aligned_cols=75  Identities=27%  Similarity=0.431  Sum_probs=68.8

Q ss_pred             CcEEEecCCCc-cCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         158 STTLWIGHLSK-LVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       158 ~~~l~V~nl~~-~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      +..|.|.||.. .+|.+.|..+|+.||.|.+|+|.. .+.-|.|+|.+...|+.|+..|+|+.+.|++|+|.+++..
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCc
Confidence            58899999984 579999999999999999999986 5578999999999999999999999999999999999854

>KOG4205|consensus

Probab=98.39  E-value=4e-07  Score=79.79  Aligned_cols=78  Identities=24%  Similarity=0.457  Sum_probs=69.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ....+|||+||.++++.++++.|.+||.|..+.++.      ++||+||.|.++++..+++. ...+.+.|+.+.|..|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            356999999999999999999999999888877763      78999999999999999886 57889999999999999


Q ss_pred             CCCCC
Q psy3994         231 GKGMK  235 (282)
Q Consensus       231 ~~~~~  235 (282)
                      ++...
T Consensus       175 pk~~~  179 (311)
T KOG4205|consen  175 PKEVM  179 (311)
T ss_pred             chhhc
Confidence            87544

>PF12243 CTK3: CTD kinase subunit gamma CTK3

Probab=98.39  E-value=1.7e-06  Score=67.00  Aligned_cols=120  Identities=18%  Similarity=0.261  Sum_probs=99.6

Q ss_pred             HHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCch
Q psy3994           5 KTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFG   84 (282)
Q Consensus         5 ~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~   84 (282)
                      -.|.+.|+.|+.     |..+|++.+..|++|......+..+|-..+.+..=..++.++|.+|+++..+....+....|+
T Consensus         8 ~~F~~~L~~L~a-----S~qSi~kaa~fAlk~~~~~edL~~cIle~le~~~lN~R~nI~~fID~l~e~~~~~~~~~~~Yv   82 (139)
T PF12243_consen    8 MQFTQLLRRLNA-----SQQSIQKAAQFALKNRDMEEDLWSCILEQLEKENLNTRINIFYFIDSLCESSQKSKKYNYPYV   82 (139)
T ss_pred             HHHHHHHHHcch-----hHHHHHHHHHHHHHccccHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhcccccchhH
Confidence            356777777754     445999999999999999999999999999888778899999999999999877776677899


Q ss_pred             hhHHHHHHHHHHHhhc-CCh--hhHHHHHHHHHhhccCcccCCccccc
Q psy3994          85 PRFARNLKATFQHLYQ-CPP--EDKSKIIRVLNLWQKNEVFTPDIIHP  129 (282)
Q Consensus        85 ~~f~~~l~~~f~~v~~-~~~--~~~~k~~~~l~~w~~~~~f~~~~i~~  129 (282)
                      .....+|...+..+.+ -+.  .-...+.++|..|..++.++++.+..
T Consensus        83 ~~l~~dL~~Iv~~V~P~~~~g~~N~~~~~kvL~~~~~k~~l~~~~~~~  130 (139)
T PF12243_consen   83 SMLQRDLPRIVDAVAPPDNSGAANLKSVRKVLKNWSKKKILDPEEYEE  130 (139)
T ss_pred             HHHHHHHHHHHHHhCCCCCccchHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence            9999999999988887 222  46677889999999999888765443

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.32  E-value=3.4e-06  Score=61.20  Aligned_cols=75  Identities=24%  Similarity=0.248  Sum_probs=63.2

Q ss_pred             cEEEecCCCccCcHHHHHhhhccC--CceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeC----CeeEEE
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEY--GDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQ----GKTITL  226 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~--G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~----g~~l~v  226 (282)
                      +||-+.|||...|.++|.+++...  |....+-++.      +.|||||.|.+.+.|.+-.+.++|..+.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            789999999999999999988653  6655555552      7899999999999999999999999873    567889


Q ss_pred             EeecCCC
Q psy3994         227 AWAPGKG  233 (282)
Q Consensus       227 ~~a~~~~  233 (282)
                      .||+-+|
T Consensus        82 ~yAriQG   88 (97)
T PF04059_consen   82 SYARIQG   88 (97)
T ss_pred             ehhHhhC
Confidence            9998665

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG1548|consensus

Probab=98.30  E-value=1.7e-06  Score=74.94  Aligned_cols=75  Identities=20%  Similarity=0.390  Sum_probs=67.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEE--------EEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCee
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVS--------INLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKT  223 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~--------~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~  223 (282)
                      .++.|||.|||.++|.+++.++|++||-|.+        |++.+     .+|=|.+.|.-+++...|+..|++..+.|+.
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            4678999999999999999999999998754        45543     5899999999999999999999999999999


Q ss_pred             EEEEeecC
Q psy3994         224 ITLAWAPG  231 (282)
Q Consensus       224 l~v~~a~~  231 (282)
                      |+|+.|+-
T Consensus       213 ~rVerAkf  220 (382)
T KOG1548|consen  213 LRVERAKF  220 (382)
T ss_pred             EEEehhhh
Confidence            99999973

>KOG4209|consensus

Probab=98.29  E-value=1.4e-06  Score=73.50  Aligned_cols=76  Identities=18%  Similarity=0.402  Sum_probs=68.6

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...+.+||||+...+|.+++...|+.||.+..+.+..      ++||+||.|.+.+.++.|+. |+|..+.|+.+.|.+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            3458899999999999999999999999998777774      68999999999999999999 9999999999999888


Q ss_pred             cCC
Q psy3994         230 PGK  232 (282)
Q Consensus       230 ~~~  232 (282)
                      +-.
T Consensus       178 r~~  180 (231)
T KOG4209|consen  178 RTN  180 (231)
T ss_pred             eee
Confidence            644

>KOG4454|consensus

Probab=98.21  E-value=5.6e-07  Score=73.33  Aligned_cols=75  Identities=20%  Similarity=0.184  Sum_probs=67.5

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ..+||||+|+...++|+-|.++|-+-|.|..+.|+.    ...||||.|.++.+..-|++.+||..+.++.+++.+-.+
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            458999999999999999999999999999999885    234999999999999999999999999999888877653

>KOG4206|consensus

Probab=97.97  E-value=3.3e-05  Score=63.59  Aligned_cols=77  Identities=26%  Similarity=0.373  Sum_probs=69.5

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeC-CeeEEEEeec
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQ-GKTITLAWAP  230 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~-g~~l~v~~a~  230 (282)
                      ..+++..+|+.|||..++.+.+..+|.+|+....++++. .++.|||+|.+...|..|.+.++|..+. ...++|.+|+
T Consensus       142 ~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  142 MAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             CCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            356778999999999999999999999999999999987 6789999999999999999999999885 7888888775

>KOG0226|consensus

Probab=97.93  E-value=7.8e-06  Score=68.22  Aligned_cols=75  Identities=19%  Similarity=0.362  Sum_probs=65.3

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEe------CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ...||.|.|...++++.|-+.|.+|-.....+++      .++||+||.|.+..++.+|+.+|+|..++.++|+++-...
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~w  269 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEW  269 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhH
Confidence            4789999999999999999999999665555554      3899999999999999999999999999999998876655


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      +
T Consensus       270 k  270 (290)
T KOG0226|consen  270 K  270 (290)
T ss_pred             H
Confidence            4

>KOG1457|consensus

Probab=97.90  E-value=1.2e-05  Score=65.84  Aligned_cols=68  Identities=21%  Similarity=0.291  Sum_probs=57.2

Q ss_pred             CCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3994         153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--PRGCAFVCMNRRQDAAKALYKLKNTKLQ  220 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~--~kg~aFV~f~~~~~A~~Ai~~l~g~~~~  220 (282)
                      .......||||.||.+++||++|+.+|+.|.....+++..  .-..||++|++.+.|..|+..|+|..+.
T Consensus       205 ~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  205 SGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             ccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhcceec
Confidence            3344567999999999999999999999997766666653  4468999999999999999999998773

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.89  E-value=3.1e-05  Score=57.36  Aligned_cols=70  Identities=27%  Similarity=0.450  Sum_probs=44.9

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCC-----eeCCeeEEEEe
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT-----KLQGKTITLAW  228 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~-----~~~g~~l~v~~  228 (282)
                      +.|.+.+++..++.++|++.|+.||.|..|.+...-.-|+|.|.+.++|+.|+..+...     .+.+..+.++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            56888889999999999999999999999999988889999999999999999877543     34555544443

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.87  E-value=3.3e-05  Score=49.70  Aligned_cols=52  Identities=25%  Similarity=0.424  Sum_probs=44.6

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHH
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL  211 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai  211 (282)
                      +.|-|.+.++... +.+...|..||+|..+.+.....+.+|+|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            5788888887765 446668999999999999877899999999999999985

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.83  E-value=3.5e-05  Score=66.80  Aligned_cols=75  Identities=17%  Similarity=0.414  Sum_probs=62.0

Q ss_pred             CCcEEEecCCCccCcHHH------HHhhhccCCceEEEEEeCC-------Cc-E-EEEEecCHHHHHHHHHHhCCCeeCC
Q psy3994         157 CSTTLWIGHLSKLVQEEE------LSDTFGEYGDVVSINLIPP-------RG-C-AFVCMNRRQDAAKALYKLKNTKLQG  221 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~------l~~~f~~~G~i~~~~~~~~-------kg-~-aFV~f~~~~~A~~Ai~~l~g~~~~g  221 (282)
                      ...-+||-+||+.+..++      -.++|++||.|..+.+.+.       .+ + .||+|.+.++|.+||...+|..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            446789999998775554      3578999999999988751       12 2 3999999999999999999999999


Q ss_pred             eeEEEEeecC
Q psy3994         222 KTITLAWAPG  231 (282)
Q Consensus       222 ~~l~v~~a~~  231 (282)
                      |.|+..++.-
T Consensus       193 r~lkatYGTT  202 (480)
T COG5175         193 RVLKATYGTT  202 (480)
T ss_pred             ceEeeecCch
Confidence            9999999874

>KOG0106|consensus

Probab=97.82  E-value=1.4e-05  Score=66.26  Aligned_cols=73  Identities=32%  Similarity=0.435  Sum_probs=64.8

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ....+.+.|.+++..+.+.+|.+.|.++|.+.....  .++++||+|.+.++|.+|+..++|..+.|+.|.+...
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            445688999999999999999999999999965555  5699999999999999999999999999999999444

>KOG4211|consensus

Probab=97.75  E-value=0.0002  Score=65.22  Aligned_cols=113  Identities=19%  Similarity=0.154  Sum_probs=80.5

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      -.|-+.+||+.+|+++|.++|+.+ .|+++.+++    ..|-|||+|.+.+++++|++ .+...+..|-|.|--+.+...
T Consensus        11 ~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~e~   88 (510)
T KOG4211|consen   11 FEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGAEA   88 (510)
T ss_pred             eEEEecCCCccccHHHHHHHHhcC-ceeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCccc
Confidence            456678999999999999999999 478877775    67899999999999999998 476777888899987765533


Q ss_pred             CCC-----ccccccccCCCeeeecCCCCCcchhhhhhhcCcccccC
Q psy3994         235 KDK-----DWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFDED  275 (282)
Q Consensus       235 ~~~-----~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~  275 (282)
                      .-.     ....-.+.--.+.-+||.-  |++|+..|+.|-+|-..
T Consensus        89 d~~~~~~g~~s~~~d~vVRLRGLPfsc--te~dI~~FFaGL~Iv~~  132 (510)
T KOG4211|consen   89 DWVMRPGGPNSSANDGVVRLRGLPFSC--TEEDIVEFFAGLEIVPD  132 (510)
T ss_pred             cccccCCCCCCCCCCceEEecCCCccC--cHHHHHHHhcCCccccc
Confidence            210     0000011111123457764  48999999988555443

>KOG0120|consensus

Probab=97.75  E-value=2.1e-05  Score=72.69  Aligned_cols=79  Identities=16%  Similarity=0.311  Sum_probs=71.5

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .....+|||+||-..++.+++++...||.+....+..      ++||||.+|.+......|+..|||..+++++|.|+.|
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            3457899999999999999999999999998877764      7999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy3994         230 PGKGM  234 (282)
Q Consensus       230 ~~~~~  234 (282)
                      -....
T Consensus       367 ~~g~~  371 (500)
T KOG0120|consen  367 IVGAS  371 (500)
T ss_pred             hccch
Confidence            76543

>KOG1456|consensus

Probab=97.57  E-value=0.00044  Score=60.93  Aligned_cols=86  Identities=16%  Similarity=0.167  Sum_probs=69.5

Q ss_pred             hcCCCCCCCCcEEEecCCC--ccCcHHHHHhhhccCCceEEEEEeCCC-cEEEEEecCHHHHHHHHHHhCCCee-CC-ee
Q psy3994         149 ARNGVENMCSTTLWIGHLS--KLVQEEELSDTFGEYGDVVSINLIPPR-GCAFVCMNRRQDAAKALYKLKNTKL-QG-KT  223 (282)
Q Consensus       149 ~~~~~~~~~~~~l~V~nl~--~~~te~~l~~~f~~~G~i~~~~~~~~k-g~aFV~f~~~~~A~~Ai~~l~g~~~-~g-~~  223 (282)
                      +..+....++..|.+.=|.  ..+|-+-|..+....|.|.+|.+.+.. --|.|+|++.+.|++|...|||..| .| .+
T Consensus       111 R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCT  190 (494)
T KOG1456|consen  111 RPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCT  190 (494)
T ss_pred             cCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhccccccccccee
Confidence            3445555566777776555  457889999999999999999888644 4699999999999999999999987 34 58


Q ss_pred             EEEEeecCCCC
Q psy3994         224 ITLAWAPGKGM  234 (282)
Q Consensus       224 l~v~~a~~~~~  234 (282)
                      |+|++|++...
T Consensus       191 LKIeyAkP~rl  201 (494)
T KOG1456|consen  191 LKIEYAKPTRL  201 (494)
T ss_pred             EEEEecCccee
Confidence            99999998754

>KOG1190|consensus

Probab=97.54  E-value=0.00029  Score=62.73  Aligned_cols=77  Identities=25%  Similarity=0.335  Sum_probs=66.2

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEE-EEe-CCCcEEEEEecCHHHHHHHHHHhCCCeeCCe-eEEEEeecC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSI-NLI-PPRGCAFVCMNRRQDAAKALYKLKNTKLQGK-TITLAWAPG  231 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~-~~~-~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~-~l~v~~a~~  231 (282)
                      -+++.++...|+|+.++|++++..|..-|...+. +.. .++.+|.+.+.+.++|..|+..++.+.+++. .|||+|+++
T Consensus       411 ~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  411 FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             CCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            3567899999999999999999999998776544 333 4789999999999999999999999999655 899999875

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.40  E-value=0.0011  Score=48.54  Aligned_cols=71  Identities=11%  Similarity=0.142  Sum_probs=53.4

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEE-------------EeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCe-e
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSIN-------------LIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGK-T  223 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~-------------~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~-~  223 (282)
                      .+.|.|-+.|+..+ ..+.+.|++||.|.+..             .......--|+|.++.+|.+|+. -||..+.|. .
T Consensus         6 ~~wVtVFGfp~~~~-~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPSAS-NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GGGH-HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHHHH-HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            46788888998854 66788999999998875             45577899999999999999998 599999886 5


Q ss_pred             EEEEeec
Q psy3994         224 ITLAWAP  230 (282)
Q Consensus       224 l~v~~a~  230 (282)
                      +-|.+.+
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            5677764

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1548|consensus

Probab=97.38  E-value=0.00067  Score=59.24  Aligned_cols=80  Identities=16%  Similarity=0.333  Sum_probs=65.5

Q ss_pred             CCCCCCcEEEecCCCc----cCc-------HHHHHhhhccCCceEEEEEe--CCCcEEEEEecCHHHHHHHHHHhCCCee
Q psy3994         153 VENMCSTTLWIGHLSK----LVQ-------EEELSDTFGEYGDVVSINLI--PPRGCAFVCMNRRQDAAKALYKLKNTKL  219 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~----~~t-------e~~l~~~f~~~G~i~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~l~g~~~  219 (282)
                      ......++|.+.|+=.    ..+       .++|++-..+||.|.+|.+.  ++.|.+-|.|.+.++|..||+.|+|..+
T Consensus       260 sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~f  339 (382)
T KOG1548|consen  260 SKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWF  339 (382)
T ss_pred             ccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeee
Confidence            3345568888888742    122       24566778899999999888  6899999999999999999999999999


Q ss_pred             CCeeEEEEeecCC
Q psy3994         220 QGKTITLAWAPGK  232 (282)
Q Consensus       220 ~g~~l~v~~a~~~  232 (282)
                      +||.|......++
T Consensus       340 dgRql~A~i~DG~  352 (382)
T KOG1548|consen  340 DGRQLTASIWDGK  352 (382)
T ss_pred             cceEEEEEEeCCc
Confidence            9999998877655

>KOG0151|consensus

Probab=97.33  E-value=0.00024  Score=67.23  Aligned_cols=121  Identities=16%  Similarity=0.336  Sum_probs=88.2

Q ss_pred             HHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHH--HhcCCCCccceeehhhHHHHHhhhhccCCCC
Q psy3994           5 KTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFI--IKCKPEYKVPALYVIDSLVRQSRHQFQDKDV   82 (282)
Q Consensus         5 ~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~--~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~   82 (282)
                      ..||..|..|+-     .+++|..+-.+|++|++++..||.++...+  +..+...|+.-|||+.+|+-|.-..-.....
T Consensus       434 dklE~liR~LTp-----Ek~sIg~aM~FalenA~aa~EI~eci~eSlt~~~t~~~kKiarLyLvsDIL~N~sarv~nas~  508 (877)
T KOG0151|consen  434 DKLEDLIRGLTP-----EKSSIGDAMVFALENADAAGEIVECITESLTNKETPLPKKIARLYLVSDILHNSSARVANASA  508 (877)
T ss_pred             HHHHHHHHhcCc-----ccchHHHHHHHHHhhhhhHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHhhhhhhhhHHHH
Confidence            468888888844     455999999999999999999999998766  3445688999999999999886444333334


Q ss_pred             chhhHHHHHHHHHHHhhc----C-----ChhhHHHHHHHHHhhccCcccCCcccccc
Q psy3994          83 FGPRFARNLKATFQHLYQ----C-----PPEDKSKIIRVLNLWQKNEVFTPDIIHPL  130 (282)
Q Consensus        83 ~~~~f~~~l~~~f~~v~~----~-----~~~~~~k~~~~l~~w~~~~~f~~~~i~~~  130 (282)
                      |-..|...|...|..++.    .     .+.-.+++++++..|..=-+|+.+.+..+
T Consensus       509 YR~~FEa~L~~Ifd~l~~~yr~I~gRIkaE~fkqRV~kVirvWedW~ifpe~~l~~l  565 (877)
T KOG0151|consen  509 YRKSFEATLEDIFDDLNDLYRSIGGRIKAEAFKQRVMKVIRVWEDWAIFPEDFLIGL  565 (877)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHhCcHHHHHHH
Confidence            555566667766654432    2     24556788889988886666666655443

>KOG3152|consensus

Probab=97.31  E-value=0.00013  Score=61.14  Aligned_cols=67  Identities=19%  Similarity=0.345  Sum_probs=58.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC--------------C----cEEEEEecCHHHHHHHHHHhCCCe
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP--------------R----GCAFVCMNRRQDAAKALYKLKNTK  218 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~--------------k----g~aFV~f~~~~~A~~Ai~~l~g~~  218 (282)
                      ..-.||+++||+.++..-|+++|+.||+|-+|.+.+.              +    .-|.|+|.+...|.+....|||..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4568999999999999999999999999999988751              1    125789999999999999999999


Q ss_pred             eCCee
Q psy3994         219 LQGKT  223 (282)
Q Consensus       219 ~~g~~  223 (282)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99875

>KOG4210|consensus

Probab=97.30  E-value=0.0002  Score=62.66  Aligned_cols=77  Identities=21%  Similarity=0.377  Sum_probs=68.6

Q ss_pred             CCcEEE-ecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         157 CSTTLW-IGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       157 ~~~~l~-V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++| |++++..+++++|+..|..+|.|..++++.      .+|||+|.|.+...+..++.. +...+.++++.+...
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            445666 999999999999999999999999999885      689999999999999999886 788899999999999


Q ss_pred             cCCCC
Q psy3994         230 PGKGM  234 (282)
Q Consensus       230 ~~~~~  234 (282)
                      .+.+.
T Consensus       262 ~~~~~  266 (285)
T KOG4210|consen  262 EPRPK  266 (285)
T ss_pred             CCCcc
Confidence            87753

>KOG0112|consensus

Probab=97.30  E-value=0.00033  Score=68.01  Aligned_cols=83  Identities=18%  Similarity=0.267  Sum_probs=75.2

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCC--eeEEEEeecC
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQG--KTITLAWAPG  231 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g--~~l~v~~a~~  231 (282)
                      .....+.+|+|+|..++....|...|..||.|..|.+-+...||+|.|.+...|+.|+..|-|..++|  ++++|.+|..
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~  530 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASP  530 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccC
Confidence            55678999999999999999999999999999999998888999999999999999999999999965  6799999987


Q ss_pred             CCCCC
Q psy3994         232 KGMKD  236 (282)
Q Consensus       232 ~~~~~  236 (282)
                      .+..+
T Consensus       531 ~~~~P  535 (975)
T KOG0112|consen  531 PGATP  535 (975)
T ss_pred             CCCCh
Confidence            65443

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.26  E-value=0.0016  Score=50.47  Aligned_cols=74  Identities=24%  Similarity=0.408  Sum_probs=53.2

Q ss_pred             cEEEecCCC------ccCcH---HHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         159 TTLWIGHLS------KLVQE---EELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       159 ~~l~V~nl~------~~~te---~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .||.|.-+.      ...++   .+|-+.|..||++.-+++..  +.-.|+|.+-++|-+|+. ++|.++.|+.|+|+..
T Consensus        28 aTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~--~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LK  104 (146)
T PF08952_consen   28 ATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVG--DTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLK  104 (146)
T ss_dssp             -EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEET--TCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE-
T ss_pred             ceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeC--CeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeC
Confidence            667665444      12332   36888899999999999987  678999999999999997 8999999999999998


Q ss_pred             cCCCCC
Q psy3994         230 PGKGMK  235 (282)
Q Consensus       230 ~~~~~~  235 (282)
                      .+....
T Consensus       105 tpdW~~  110 (146)
T PF08952_consen  105 TPDWLK  110 (146)
T ss_dssp             ------
T ss_pred             CccHHH
Confidence            876543

; PDB: 1UFW_A 2DNR_A.

>KOG1855|consensus

Probab=97.24  E-value=0.00022  Score=63.80  Aligned_cols=62  Identities=31%  Similarity=0.364  Sum_probs=54.5

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC-------------------CcEEEEEecCHHHHHHHHHHhCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-------------------RGCAFVCMNRRQDAAKALYKLKN  216 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~-------------------kg~aFV~f~~~~~A~~Ai~~l~g  216 (282)
                      .++++|.+-|||.+-.-+-|.++|+.+|.|..|+|..+                   +-||+|+|+..+.|.+|.+.|+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            45789999999988777889999999999999999852                   56999999999999999998754


Q ss_pred             C
Q psy3994         217 T  217 (282)
Q Consensus       217 ~  217 (282)
                      .
T Consensus       309 e  309 (484)
T KOG1855|consen  309 E  309 (484)
T ss_pred             h
Confidence            3

>KOG2416|consensus

Probab=97.20  E-value=0.00029  Score=65.48  Aligned_cols=80  Identities=18%  Similarity=0.205  Sum_probs=69.4

Q ss_pred             CCCCCCCcEEEecCCCccCcHHHHHhhhc-cCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCee---CCeeEEEE
Q psy3994         152 GVENMCSTTLWIGHLSKLVQEEELSDTFG-EYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL---QGKTITLA  227 (282)
Q Consensus       152 ~~~~~~~~~l~V~nl~~~~te~~l~~~f~-~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~---~g~~l~v~  227 (282)
                      +.....+..|||.||-.-+|.-+|+.+++ ..|.|....|-+-|..|||.|.+.++|.+...+|||..+   +++.|.+.
T Consensus       438 PsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~ad  517 (718)
T KOG2416|consen  438 PSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIAD  517 (718)
T ss_pred             CCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEee
Confidence            44556788999999999999999999998 567777776667889999999999999999999999987   67789999


Q ss_pred             eecC
Q psy3994         228 WAPG  231 (282)
Q Consensus       228 ~a~~  231 (282)
                      |+..
T Consensus       518 f~~~  521 (718)
T KOG2416|consen  518 FVRA  521 (718)
T ss_pred             ecch
Confidence            9874

>KOG1456|consensus

Probab=97.18  E-value=0.0024  Score=56.45  Aligned_cols=79  Identities=19%  Similarity=0.258  Sum_probs=69.6

Q ss_pred             CCCCCCcEEEecCCCc-cCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         153 VENMCSTTLWIGHLSK-LVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~-~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ....+++.+-|-+|.. .++-+.|-.+|-.||.|.+|++++ ..|-|.|++.+..+.++|+..||+..+.|.+|.|..++
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~Sk  361 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSK  361 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeecc
Confidence            4445678899999985 467788999999999999999997 55899999999999999999999999999999998887


Q ss_pred             C
Q psy3994         231 G  231 (282)
Q Consensus       231 ~  231 (282)
                      -
T Consensus       362 Q  362 (494)
T KOG1456|consen  362 Q  362 (494)
T ss_pred             c
Confidence            3

>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain

Probab=97.18  E-value=0.00087  Score=50.48  Aligned_cols=105  Identities=18%  Similarity=0.198  Sum_probs=76.3

Q ss_pred             HHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchh
Q psy3994           7 FNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGP   85 (282)
Q Consensus         7 f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~   85 (282)
                      |+..+.+.+....+ -+..-|..++.........+..++..+.+.+.+.+|..++.+|+|+|++++|.      ...|..
T Consensus         1 ~~~~v~~AT~~~~~~p~~~~i~~i~d~~~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~------g~~f~~   74 (115)
T cd00197           1 FEKTVEKATSNENMGPDWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNC------GERFHQ   74 (115)
T ss_pred             ChHHHHHHcCCCCCCCCHHHHHHHHHHHHCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHc------cHHHHH
Confidence            45566666554444 67778999999887766778899999999999999999999999999999998      334444


Q ss_pred             hHHHHHH--HHHHH-----hhc-CChhhHHHHHHHHHhhc
Q psy3994          86 RFARNLK--ATFQH-----LYQ-CPPEDKSKIIRVLNLWQ  117 (282)
Q Consensus        86 ~f~~~l~--~~f~~-----v~~-~~~~~~~k~~~~l~~w~  117 (282)
                      .++.+..  +.+.+     ... .+...+.++..++..|.
T Consensus        75 ~i~~~~~~~~l~~~~~~~~~~~~~~~~Vr~k~~~l~~~w~  114 (115)
T cd00197          75 EVASNDFAVELLKFDKSKLLGDDVSTNVREKAIELVQLWA  114 (115)
T ss_pred             HHHHhHHHHHHHHhhccccccCCCChHHHHHHHHHHHHHh
Confidence            4444321  12111     111 36778899999999985

The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra

>KOG0147|consensus

Probab=97.13  E-value=0.00088  Score=61.85  Aligned_cols=59  Identities=25%  Similarity=0.408  Sum_probs=52.1

Q ss_pred             HHHHhhhccCCceEEEEEeCCC-cEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         173 EELSDTFGEYGDVVSINLIPPR-GCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       173 ~~l~~~f~~~G~i~~~~~~~~k-g~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +++.+-.++||.|..|.+.++. ||-||.|.+.+.|..|+.+|||.++.|+.|...|-.-
T Consensus       468 edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~  527 (549)
T KOG0147|consen  468 EDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPL  527 (549)
T ss_pred             HHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeeh
Confidence            4556666999999999988744 9999999999999999999999999999999988753

>KOG0120|consensus

Probab=97.11  E-value=0.0014  Score=60.86  Aligned_cols=60  Identities=20%  Similarity=0.389  Sum_probs=51.5

Q ss_pred             HHHHhhhccCCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         173 EELSDTFGEYGDVVSINLIP---------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       173 ~~l~~~f~~~G~i~~~~~~~---------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ++++.-+++||.|.+|.+++         .-|.-||+|.+.+++++|+.+|+|.++.||.+...|-...
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence            34666678999999999986         3577899999999999999999999999999988886543

>KOG1995|consensus

Probab=96.96  E-value=0.00078  Score=59.17  Aligned_cols=78  Identities=21%  Similarity=0.241  Sum_probs=67.5

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEE--------Ee------CCCcEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSIN--------LI------PPRGCAFVCMNRRQDAAKALYKLKNTKLQG  221 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~--------~~------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g  221 (282)
                      ....+|||-+||..++++++.++|.++|.|..=+        +-      .+|+=|-|.|.+..+|+.|+..+++..+.+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            3457899999999999999999999999875321        11      178999999999999999999999999999


Q ss_pred             eeEEEEeecCCC
Q psy3994         222 KTITLAWAPGKG  233 (282)
Q Consensus       222 ~~l~v~~a~~~~  233 (282)
                      .+|+|..|..+.
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999999998664

>KOG4676|consensus

Probab=96.94  E-value=0.0024  Score=56.73  Aligned_cols=71  Identities=17%  Similarity=0.290  Sum_probs=60.3

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ..|-|.||.+.+|.++++.+|+..|.|..+++.+         ....|||.|.+...+..|. .|.++.+-++.|.|...
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEec
Confidence            4799999999999999999999999999998875         3578999999999988885 47778877777766555


Q ss_pred             c
Q psy3994         230 P  230 (282)
Q Consensus       230 ~  230 (282)
                      -
T Consensus        87 ~   87 (479)
T KOG4676|consen   87 G   87 (479)
T ss_pred             C
Confidence            4

>KOG2193|consensus

Probab=96.78  E-value=0.00078  Score=60.32  Aligned_cols=79  Identities=30%  Similarity=0.364  Sum_probs=63.8

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCC-eeCCeeEEEEeecCCCCCCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT-KLQGKTITLAWAPGKGMKDK  237 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~-~~~g~~l~v~~a~~~~~~~~  237 (282)
                      ..+|+|||.+..+..+|+.+|....--.+-.++...||+||.+.+..-|.+|++.++|. ++.|.++.|....++..+.+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqrsr   81 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQRSR   81 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHHhh
Confidence            35899999999999999999986522122223335599999999999999999999988 58999999999988865543

>KOG0129|consensus

Probab=96.77  E-value=0.0038  Score=57.42  Aligned_cols=64  Identities=20%  Similarity=0.445  Sum_probs=50.5

Q ss_pred             CCCCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe---------CCCc---EEEEEecCHHHHHHHHHHhC
Q psy3994         151 NGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI---------PPRG---CAFVCMNRRQDAAKALYKLK  215 (282)
Q Consensus       151 ~~~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~---------~~kg---~aFV~f~~~~~A~~Ai~~l~  215 (282)
                      .......++.||||+||++++|+.|...|..||.+. +..+         .++|   |+|+.|+++.+.+.-+.+..
T Consensus       252 ~~~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  252 GYRSPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             CCCccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            345556789999999999999999999999999743 2223         2567   99999999888887766543

>KOG2314|consensus

Probab=96.63  E-value=0.0086  Score=55.71  Aligned_cols=74  Identities=19%  Similarity=0.263  Sum_probs=59.5

Q ss_pred             CCCcEEEecCCCccCc------HHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCee-CCee
Q psy3994         156 MCSTTLWIGHLSKLVQ------EEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKL-QGKT  223 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~t------e~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~-~g~~  223 (282)
                      .....|+|.|+|---.      ..-|..+|+++|++....++.     .+||.|++|.+...|+.|++.|||..+ ..++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            3457889999985322      134778899999999998873     689999999999999999999999998 5677


Q ss_pred             EEEEee
Q psy3994         224 ITLAWA  229 (282)
Q Consensus       224 l~v~~a  229 (282)
                      ..|..-
T Consensus       136 f~v~~f  141 (698)
T KOG2314|consen  136 FFVRLF  141 (698)
T ss_pred             EEeehh
Confidence            777543

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.61  E-value=0.012  Score=45.36  Aligned_cols=75  Identities=21%  Similarity=0.338  Sum_probs=58.3

Q ss_pred             CCCCcEEEecCCCccCc-HH---HHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         155 NMCSTTLWIGHLSKLVQ-EE---ELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~t-e~---~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      .++-.||.|.=|..++. .+   .+...++.||+|.++... .+.-|.|.|.+..+|.+|+.+++. ...|..+++.|-.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWqq  160 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQQ  160 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeeccc
Confidence            33457888887776653 23   455567889999999754 567899999999999999999886 5678889999976


Q ss_pred             C
Q psy3994         231 G  231 (282)
Q Consensus       231 ~  231 (282)
                      .
T Consensus       161 r  161 (166)
T PF15023_consen  161 R  161 (166)
T ss_pred             c
Confidence            4

>KOG0129|consensus

Probab=96.53  E-value=0.0054  Score=56.43  Aligned_cols=57  Identities=25%  Similarity=0.417  Sum_probs=51.8

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhc-cCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHH
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFG-EYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK  213 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~-~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~  213 (282)
                      +.+|||||+||.-++.++|-.+|. -||.|..+-|-.      ++|=|=|+|.+..+-.+||.+
T Consensus       369 prrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  369 PRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            568999999999999999999998 699999987764      689999999999999999974

>KOG4211|consensus

Probab=96.50  E-value=0.0084  Score=54.90  Aligned_cols=74  Identities=22%  Similarity=0.242  Sum_probs=56.8

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEE-EEEe-----CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVS-INLI-----PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~-~~~~-----~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .....|-+.+||+.+|+++|.++|+..-.+.. +.++     ++.|-|||+|++.+.|+.|+.. |...|+-|-|.|..+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            34578889999999999999999998744333 2223     2568899999999999999975 556677777777555


Q ss_pred             c
Q psy3994         230 P  230 (282)
Q Consensus       230 ~  230 (282)
                      .
T Consensus       180 s  180 (510)
T KOG4211|consen  180 S  180 (510)
T ss_pred             H
Confidence            3

>KOG0105|consensus

Probab=96.48  E-value=0.011  Score=47.55  Aligned_cols=67  Identities=22%  Similarity=0.257  Sum_probs=58.6

Q ss_pred             CCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3994         153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ  220 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~  220 (282)
                      ......-.|.|.+||+..++++|+++..+-|.|....+.+. |.+.|+|...++.+-|+..|..+.+.
T Consensus       110 psrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  110 PSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-cceeeeeeehhhHHHHHHhhcccccc
Confidence            33445568899999999999999999999999999888765 69999999999999999999887763

>KOG0112|consensus

Probab=96.37  E-value=0.0011  Score=64.57  Aligned_cols=80  Identities=20%  Similarity=0.312  Sum_probs=68.4

Q ss_pred             CCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      .....++|||+|||+..+++.+++..|..+|.+.+|.+-.     ...||||.|.+...+-.|...+.+..|....++..
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            3445689999999999999999999999999999998864     35799999999999999999999998866667777


Q ss_pred             eecCC
Q psy3994         228 WAPGK  232 (282)
Q Consensus       228 ~a~~~  232 (282)
                      +..++
T Consensus       447 lG~~k  451 (975)
T KOG0112|consen  447 LGQPK  451 (975)
T ss_pred             ccccc
Confidence            76543

>KOG4849|consensus

Probab=96.06  E-value=0.0052  Score=53.86  Aligned_cols=69  Identities=14%  Similarity=0.325  Sum_probs=55.1

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCc--eEEEEEe------CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEE
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGD--VVSINLI------PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL  226 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~--i~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v  226 (282)
                      .-.+|||||-|++|+++|.+.+...|-  +..+++.      .+||||.|...+..+.++.++.|-...+.|..=.|
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            357899999999999999999887763  3333333      28999999999999999999998888888865433

>KOG2202|consensus

Probab=95.99  E-value=0.003  Score=53.19  Aligned_cols=58  Identities=24%  Similarity=0.417  Sum_probs=48.3

Q ss_pred             HHHhhhc-cCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         174 ELSDTFG-EYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       174 ~l~~~f~-~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ++...|+ +||+|+++.+-.     -+|-.+|.|...++|++|+..|||..+.|++|...+..-
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            3444444 899999986653     467899999999999999999999999999999888753

>KOG4307|consensus

Probab=95.86  E-value=0.028  Score=53.72  Aligned_cols=70  Identities=21%  Similarity=0.358  Sum_probs=58.9

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceE-EEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVV-SINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~-~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      +.|-+.|.|.+++-+|+-++|..|-.+- +|.+-.     ..|-|.|.|++.++|.+|..-|+++.|..+.+.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            4788899999999999999999995433 333322     568899999999999999999999999999988764

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.61  E-value=0.041  Score=44.96  Aligned_cols=61  Identities=20%  Similarity=0.260  Sum_probs=48.8

Q ss_pred             HHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhC--CCeeCCeeEEEEeecCC
Q psy3994         172 EEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK--NTKLQGKTITLAWAPGK  232 (282)
Q Consensus       172 e~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~--g~~~~g~~l~v~~a~~~  232 (282)
                      .+.|+++|..|+.+..+...++-+-..|.|.+.++|.+|...|+  +..+.|..++|.++...
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             HHHHHHHHHhcCCceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            47899999999999999888877888999999999999999999  99999999999999644

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG2135|consensus

Probab=95.24  E-value=0.013  Score=53.50  Aligned_cols=77  Identities=18%  Similarity=0.247  Sum_probs=62.8

Q ss_pred             CCCcEEEecCCCccC-cHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         156 MCSTTLWIGHLSKLV-QEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~-te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ...+.+-+.-.|... +-++|...|.+||+|..|.+--+.-.|.|+|.++.+|-.|-. .++..+++|.|+|.|-.+.+
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            344556666566655 558899999999999999887666789999999999977764 68999999999999998754

>KOG1996|consensus

Probab=95.10  E-value=0.059  Score=46.41  Aligned_cols=59  Identities=22%  Similarity=0.361  Sum_probs=48.5

Q ss_pred             HHHHHhhhccCCceEEEEEeC------C-CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         172 EEELSDTFGEYGDVVSINLIP------P-RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       172 e~~l~~~f~~~G~i~~~~~~~------~-kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ++++++-.++||.|..|.+..      + ----||+|+..++|.+|+--|||..++||.++..|-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            356788889999999987663      2 2346999999999999999999999999998766643

>KOG4368|consensus

Probab=94.80  E-value=0.072  Score=49.95  Aligned_cols=125  Identities=19%  Similarity=0.320  Sum_probs=78.6

Q ss_pred             hHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHH---HHHHHHHHHhc--CCCCccceeehhhHHHHHhhhhcc
Q psy3994           4 IKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHV---VQSVEKFIIKC--KPEYKVPALYVIDSLVRQSRHQFQ   78 (282)
Q Consensus         4 ~~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~---v~~~~~~~~~~--~p~~kl~~lYv~Dsi~r~~~~~~~   78 (282)
                      |.+|+..|+.+.+ +  -|+.-|..-.+|...|.+.-.+.   +..+.+.|+.-  .-..+|-++|+|+++.---+++..
T Consensus       103 ~~~~~~~l~~~~~-~--c~kd~is~~k~w~f~~~~s~~~~e~~~~~l~n~~~~~~~~~~lrlh~~ylind~~~hcqrk~~  179 (757)
T KOG4368|consen  103 MNEFDNLLQPIID-T--CTKDAISAGKNWMFSNAKSPPHCELMAGHLRNRITADGAHFELRLHLIYLINDVLHHCQRKQA  179 (757)
T ss_pred             HHHHHHHHHHHHH-H--HhHHHHHHhhhhhhhcCCCchHHHHHHHHHHhhhcccccchhhhhhhHHHHHHHHHHHHHHHH
Confidence            7899999999976 2  46667777778888887654332   22233333332  346789999999998655444333


Q ss_pred             CCCCchhhHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhccCcccCCccccccccC
Q psy3994          79 DKDVFGPRFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDM  133 (282)
Q Consensus        79 ~~~~~~~~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~~~  133 (282)
                      ..  -...+++-+.-.++.-+. +.+...+++.++|-.|++++.|..++++.+..-
T Consensus       180 ~~--~~~~l~~~v~~~yc~~~~~~~e~~~~~~~~ll~~we~~~yf~ds~~~ql~~~  233 (757)
T KOG4368|consen  180 RE--LLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQSP  233 (757)
T ss_pred             HH--HHHHHHHHhHHHHHhhhhhhHhHHHHHHHHHHHHHhhcCchhHHHHHHhhhh
Confidence            21  111233333333333333 334455668889999999999999988776653

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.76  E-value=0.16  Score=35.60  Aligned_cols=54  Identities=19%  Similarity=0.338  Sum_probs=40.7

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK  215 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~  215 (282)
                      +..+|+ .|..+...||.++|+.||.|.---+.  -.-|||...+++.|..++..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~--dTSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIN--DTSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEEEEEEC--TTEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEEEEEEc--CCcEEEEeecHHHHHHHHHHhc
Confidence            556666 99999999999999999986544333  3669999999999999998876

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG0128|consensus

Probab=94.58  E-value=0.019  Score=55.90  Aligned_cols=76  Identities=20%  Similarity=0.199  Sum_probs=66.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ....++|.|.|+..|.++++.++..+|.+.+++++.     ++|.|||.|.+..+|.+++....+..+..+.+.|..+.+
T Consensus       735 gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  735 GKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            356899999999999999999999999999988774     789999999999999999988888777777777777655


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      .
T Consensus       815 ~  815 (881)
T KOG0128|consen  815 E  815 (881)
T ss_pred             c
Confidence            3

>KOG4285|consensus

Probab=94.49  E-value=0.15  Score=44.24  Aligned_cols=74  Identities=19%  Similarity=0.135  Sum_probs=57.5

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCee-EEEEeecCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKT-ITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~-l~v~~a~~~  232 (282)
                      ...-|-|-+.|+.-. ..+..+|++||+|++........+-.|.|.++.+|++|+. .||..|+|.. |-|.-...+
T Consensus       196 ~D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  196 ADTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             ccceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCCH
Confidence            345566667777544 5677899999999998777677899999999999999998 4999998764 456654444

>KOG4574|consensus

Probab=94.34  E-value=0.057  Score=52.72  Aligned_cols=114  Identities=15%  Similarity=0.163  Sum_probs=81.4

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCee--CCeeEEEEeecCCCCCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL--QGKTITLAWAPGKGMKD  236 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~--~g~~l~v~~a~~~~~~~  236 (282)
                      .+.++.|.+-+.+-..|..++..||.+.+.+..++-..|.|.|.+.+.|..|..+++|..+  .|-+.+|.+|+.-.+-.
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~~~e  378 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLPMYE  378 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheecccccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccccccc
Confidence            4455666666777788999999999999999988888999999999999999999999976  68889999998654321


Q ss_pred             CccccccccCCCeeeecCCCCCcchhhhh----hhcCcccccCCCC
Q psy3994         237 KDWKDFWEVQDGVSYIPYDRLSKEIDYDY----LEDGGVFDEDTVP  278 (282)
Q Consensus       237 ~~~~~~~~~~~g~~~~p~~~~~~~~~~~~----~~~~~~~~~~~~p  278 (282)
                      ..+     .-.|+..++-+++ --++|..    +..+|-+..-+++
T Consensus       379 p~l-----n~~g~nn~~~~~~-l~e~ln~g~~n~q~~gsl~~p~f~  418 (1007)
T KOG4574|consen  379 PPL-----NLTGYNNFNHQPL-LQEQLNTGLFNTQSQGSLKSPVFE  418 (1007)
T ss_pred             CCc-----CcccccCCCCCcc-hhhhhccccceeccCCcccccccc
Confidence            111     2344555555555 3334432    3345555544443

>KOG0115|consensus

Probab=93.83  E-value=0.1  Score=44.18  Aligned_cols=57  Identities=18%  Similarity=0.286  Sum_probs=49.5

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLK  215 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~  215 (282)
                      ..|||.||+..++.+.+...|+.||.|....+..     ..+=++|.|...-.|.+|...++
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhc
Confidence            6799999999999999999999999998765542     55678999999999999998774

>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM

Probab=93.80  E-value=0.14  Score=39.95  Aligned_cols=113  Identities=19%  Similarity=0.269  Sum_probs=75.0

Q ss_pred             HHHHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCc
Q psy3994           5 KTFNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVF   83 (282)
Q Consensus         5 ~~f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~   83 (282)
                      .+|+..+...+....+ ..-..|..++...-..-...+..+..+.+.|++.+|...+..|.|+|..++|--..+... +-
T Consensus         4 ~~~~~li~kATs~~~~~~Dw~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~e-v~   82 (140)
T PF00790_consen    4 SSITELIEKATSESLPSPDWSLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHRE-VA   82 (140)
T ss_dssp             SHHHHHHHHHT-TTSSS--HHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHH-HT
T ss_pred             ChHHHHHHHHhCcCCCCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHH-Hh
Confidence            3567777777665554 445667777776666656778999999999999999999999999999999974333210 00


Q ss_pred             hhhHHHHHHHHHHHhhcCChh--hHHHHHHHHHhhccC
Q psy3994          84 GPRFARNLKATFQHLYQCPPE--DKSKIIRVLNLWQKN  119 (282)
Q Consensus        84 ~~~f~~~l~~~f~~v~~~~~~--~~~k~~~~l~~w~~~  119 (282)
                      ...|...+.+.+..-.. ++.  .+.+++.++..|...
T Consensus        83 ~~~fl~~l~~l~~~~~~-~~~~~Vk~k~l~ll~~W~~~  119 (140)
T PF00790_consen   83 SKEFLDELVKLIKSKKT-DPETPVKEKILELLQEWAEA  119 (140)
T ss_dssp             SHHHHHHHHHHHHHTTT-HHHSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCCC-CchhHHHHHHHHHHHHHHHH
Confidence            11344444444433332 122  789999999999743

Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=93.39  E-value=0.53  Score=32.27  Aligned_cols=67  Identities=19%  Similarity=0.304  Sum_probs=40.3

Q ss_pred             EEEec-CCCccCcHHHHHhhhccCCc-----eEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         160 TLWIG-HLSKLVQEEELSDTFGEYGD-----VVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       160 ~l~V~-nl~~~~te~~l~~~f~~~G~-----i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ++|+. +=-..++..+|..++..-+.     |-.+.+..  .|+||+-.. +.|..++..|++..+.|++++|+.|
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD--NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S--S-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEee--eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45553 33356788888888877654     45666655  899999875 4789999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=93.29  E-value=0.4  Score=31.69  Aligned_cols=54  Identities=22%  Similarity=0.335  Sum_probs=41.2

Q ss_pred             cEEEecCCCccCcHHHHHhhhccC---CceEEEEEeCCCcEEEEEecCHHHHHHHHHHh
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEY---GDVVSINLIPPRGCAFVCMNRRQDAAKALYKL  214 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~---G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l  214 (282)
                      ..|+|.|+. +++.++++.+|..|   ....++..+.. .-|-|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD-tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD-TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC-CcEEEEECCHHHHHHHHHcC
Confidence            579999985 47778899999998   12456666544 33678999999999999764

>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule)

Probab=93.14  E-value=0.31  Score=37.58  Aligned_cols=96  Identities=16%  Similarity=0.159  Sum_probs=65.4

Q ss_pred             CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchh-hHHHHHHHHHHHhh
Q psy3994          21 ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGP-RFARNLKATFQHLY   99 (282)
Q Consensus        21 ~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~-~f~~~l~~~f~~v~   99 (282)
                      ..-.-|.+++...-..-...+..+..+.+.|+..+|...+..|.|+|..++|.-..+..  .++. .|...+.+.+..-.
T Consensus        16 ~D~~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~--~i~s~~fl~~l~~l~~~~~   93 (133)
T cd03561          16 PDWALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHL--QVADKEFLLELVKIAKNSP   93 (133)
T ss_pred             ccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHH--HHhhHHHHHHHHHHhCCCC
Confidence            44556777777665444577888999999999999999999999999999997332221  0111 22223333332211


Q ss_pred             cCChhhHHHHHHHHHhhcc
Q psy3994         100 QCPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus       100 ~~~~~~~~k~~~~l~~w~~  118 (282)
                      ..++..+.+++.++..|..
T Consensus        94 ~~~~~Vk~kil~ll~~W~~  112 (133)
T cd03561          94 KYDPKVREKALELILAWSE  112 (133)
T ss_pred             CCCHHHHHHHHHHHHHHHH
Confidence            2467899999999999975

It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me

>KOG1365|consensus

Probab=93.11  E-value=0.078  Score=47.31  Aligned_cols=73  Identities=18%  Similarity=0.308  Sum_probs=59.5

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEE---EEEe-----CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVS---INLI-----PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~---~~~~-----~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...|-+.+||...+-++|-++|..|..-..   +.++     ++.|-|||+|.+.+.|..|....+.+...+|-|.|--+
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeec
Confidence            456888999999999999999998864322   3333     26789999999999999999999988888898888665


Q ss_pred             c
Q psy3994         230 P  230 (282)
Q Consensus       230 ~  230 (282)
                      .
T Consensus       360 S  360 (508)
T KOG1365|consen  360 S  360 (508)
T ss_pred             c
Confidence            4

>KOG0128|consensus

Probab=93.00  E-value=0.013  Score=57.11  Aligned_cols=64  Identities=22%  Similarity=0.327  Sum_probs=53.8

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe------CCCcEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLKNTKLQ  220 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~  220 (282)
                      ...++||.||+..+.+.+|...|..+|.+..+++.      .-||+|++.|...+.+.+|+....+..++
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            34688999999999999999999999988877665      26899999999999999999865554444

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=92.62  E-value=0.39  Score=38.95  Aligned_cols=77  Identities=16%  Similarity=0.158  Sum_probs=50.9

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhcc-CCce---EEEEEe--C------CCcEEEEEecCHHHHHHHHHHhCCCeeC---C
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGE-YGDV---VSINLI--P------PRGCAFVCMNRRQDAAKALYKLKNTKLQ---G  221 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~-~G~i---~~~~~~--~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~---g  221 (282)
                      ....|.|.+||+++||+++.+.+.. +|.-   ..+.-.  .      .-.-|||.|.+.++...-...++|+.+.   |
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            3578999999999999999998887 6655   333311  1      2346899999999999999999998762   2


Q ss_pred             --eeEEEEeecCCC
Q psy3994         222 --KTITLAWAPGKG  233 (282)
Q Consensus       222 --~~l~v~~a~~~~  233 (282)
                        .+-.|.+|.-+.
T Consensus        86 ~~~~~~VE~Apyqk   99 (176)
T PF03467_consen   86 NEYPAVVEFAPYQK   99 (176)
T ss_dssp             -EEEEEEEE-SS--
T ss_pred             CCcceeEEEcchhc
Confidence              245778876543

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG2253|consensus

Probab=92.47  E-value=0.13  Score=49.05  Aligned_cols=72  Identities=17%  Similarity=0.136  Sum_probs=62.3

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .++.-++||||+...+..+-++.+...+|-|.++....   |||..|..+..+.+|+..++-..++|..+.+.-.
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            34557999999999999999999999999998887654   9999999999999999998888888887766553

>KOG2068|consensus

Probab=92.43  E-value=0.058  Score=47.39  Aligned_cols=75  Identities=16%  Similarity=0.299  Sum_probs=59.0

Q ss_pred             CcEEEecCCCccCc-HHHHH--hhhccCCceEEEEEeCC---------CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         158 STTLWIGHLSKLVQ-EEELS--DTFGEYGDVVSINLIPP---------RGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       158 ~~~l~V~nl~~~~t-e~~l~--~~f~~~G~i~~~~~~~~---------kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      ..-+||-+|+.... +..|+  ..|.+||.|.++.+...         ..-++|+|...++|..||...+|..++|+.++
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            46688989987664 44443  46899999999887651         12379999999999999999999999999988


Q ss_pred             EEeecCC
Q psy3994         226 LAWAPGK  232 (282)
Q Consensus       226 v~~a~~~  232 (282)
                      ..++..+
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            7777643

>KOG4210|consensus

Probab=92.10  E-value=0.22  Score=43.72  Aligned_cols=123  Identities=17%  Similarity=0.107  Sum_probs=78.6

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++.|+|++..++.+.+...++..+|......+..      ++|++.+.|...+.+..|+.........++.+.....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            3568999999999999998888899998766655442      7899999999999999999854445666666666555


Q ss_pred             cCCCCCC---CccccccccCCCeeeecCCCCCcchhhhh-hhcCcccccCCCC
Q psy3994         230 PGKGMKD---KDWKDFWEVQDGVSYIPYDRLSKEIDYDY-LEDGGVFDEDTVP  278 (282)
Q Consensus       230 ~~~~~~~---~~~~~~~~~~~g~~~~p~~~~~~~~~~~~-~~~~~~~~~~~~p  278 (282)
                      ...+.+.   ...........++..+.++--.+.++|+. +...|.+-..-+|
T Consensus       166 ~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~  218 (285)
T KOG4210|consen  166 TRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLP  218 (285)
T ss_pred             ccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccC
Confidence            5444221   11112222333344444444445667663 3333444333333

>KOG4307|consensus

Probab=89.86  E-value=0.25  Score=47.46  Aligned_cols=81  Identities=16%  Similarity=0.077  Sum_probs=63.7

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEE-EEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVS-INLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~-~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      .......|||..||..+++.++-+.|..-..|++ |.+..     -++-|||.|...+++..|...-+.+.++-+.|+|.
T Consensus       430 P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  430 PGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             CCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            3456789999999999999999999988777776 55443     46899999999999988887666666677888997


Q ss_pred             eecCCCC
Q psy3994         228 WAPGKGM  234 (282)
Q Consensus       228 ~a~~~~~  234 (282)
                      -...+++
T Consensus       510 si~~~~m  516 (944)
T KOG4307|consen  510 SIADYAM  516 (944)
T ss_pred             chhhHHH
Confidence            6655443

>KOG1365|consensus

Probab=89.82  E-value=0.92  Score=40.74  Aligned_cols=64  Identities=23%  Similarity=0.317  Sum_probs=46.1

Q ss_pred             EEEecCCCccCcHHHHHhhhccC----CceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeE
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEY----GDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTI  224 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~----G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l  224 (282)
                      -|-..+||.++++.++.++|.+-    |..+.+-+++     ..|-|||.|...+.|+.|+.. |...++-|-|
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYI  235 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYI  235 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHH
Confidence            45568999999999999999732    2344444442     568999999999999999975 4444444433

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=88.28  E-value=4.8  Score=29.92  Aligned_cols=63  Identities=13%  Similarity=0.128  Sum_probs=45.1

Q ss_pred             CcEEEecCCC-ccCcHHHHHhhhccC-CceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3994         158 STTLWIGHLS-KLVQEEELSDTFGEY-GDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQ  220 (282)
Q Consensus       158 ~~~l~V~nl~-~~~te~~l~~~f~~~-G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~  220 (282)
                      ++++.+=-.| ..++-++|..+.+.+ ..|..+++.+    ++--+.++|.+.+.|..-...+||..+.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            3455554444 455556676655555 4577788886    4456889999999999999999999874

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting)

Probab=88.17  E-value=2.5  Score=32.98  Aligned_cols=111  Identities=19%  Similarity=0.262  Sum_probs=73.9

Q ss_pred             HHHHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCc
Q psy3994           5 KTFNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVF   83 (282)
Q Consensus         5 ~~f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~   83 (282)
                      ..|++.+...+..... ..=.-|..++...-..-...+..+.++.+.++.-.|...+-.|-|+|..++|--..+... +-
T Consensus         3 ~~~~~~I~kATs~~l~~~dw~~ileicD~In~~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~e-va   81 (142)
T cd03569           3 SEFDELIEKATSELLGEPDLASILEICDMIRSKDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDE-VA   81 (142)
T ss_pred             chHHHHHHHHcCcccCccCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHH-Hh
Confidence            3566666666553333 445556667776654445678888999999999889999999999999999963322210 00


Q ss_pred             hhhHHHHHHHHHHHhhcCChhhHHHHHHHHHhhcc
Q psy3994          84 GPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        84 ~~~f~~~l~~~f~~v~~~~~~~~~k~~~~l~~w~~  118 (282)
                      ...|...+...+..  ..++..+.+++.++..|..
T Consensus        82 s~~fl~~l~~l~~~--~~~~~Vk~kil~li~~W~~  114 (142)
T cd03569          82 SREFMDELKDLIKT--TKNEEVRQKILELIQAWAL  114 (142)
T ss_pred             hHHHHHHHHHHHcc--cCCHHHHHHHHHHHHHHHH
Confidence            11344444443332  3567889999999999974

The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.

>smart00288 VHS Domain present in VPS-27, Hrs and STAM

Probab=87.96  E-value=1.8  Score=33.32  Aligned_cols=105  Identities=16%  Similarity=0.176  Sum_probs=68.4

Q ss_pred             HHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchhh
Q psy3994           8 NQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGPR   86 (282)
Q Consensus         8 ~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~~   86 (282)
                      ++.+...++...+ ..-..|..++...-..-...+..+..+.+.|+.-+|...+-.|-|+|..++|--..+.      ..
T Consensus         2 ~~~i~kATs~~l~~~dw~~~l~icD~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~------~e   75 (133)
T smart00288        2 ERLIDKATSPSLLEEDWELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFH------LE   75 (133)
T ss_pred             hhHHHHHcCcCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHH------HH
Confidence            3444445443333 4555677777766555456788889999999988999999999999999999733332      22


Q ss_pred             HHH-HHHHHHHHhhc---CChhhHHHHHHHHHhhcc
Q psy3994          87 FAR-NLKATFQHLYQ---CPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        87 f~~-~l~~~f~~v~~---~~~~~~~k~~~~l~~w~~  118 (282)
                      ++. .+.+.+..+..   ..+..+.++..++..|..
T Consensus        76 v~s~~fl~~L~~l~~~~~~~~~Vk~kil~li~~W~~  111 (133)
T smart00288       76 VASKEFLNELVKLIKPKYPLPLVKKRILELIQEWAD  111 (133)
T ss_pred             HHhHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHH
Confidence            222 22223333332   123378999999999974

Unpublished observations. Domain of unknown function.

>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein)

Probab=87.75  E-value=1.9  Score=33.81  Aligned_cols=109  Identities=17%  Similarity=0.249  Sum_probs=68.5

Q ss_pred             HHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchhh
Q psy3994           8 NQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGPR   86 (282)
Q Consensus         8 ~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~~   86 (282)
                      |+.+...+....+ ..=.-|..++-..-..-...+..+.+|.+.++.-+|.-.+-.|-|+|..++|--..+-.. +-...
T Consensus         2 e~~iekATse~l~~~dw~~il~icD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~e-vask~   80 (144)
T cd03568           2 DDLVEKATDEKLTSENWGLILDVCDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQE-VASRD   80 (144)
T ss_pred             hHHHHHHcCccCCCcCHHHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHH-HhhHH
Confidence            3344444332322 344556667666555556778888899999998889999999999999999973322210 00012


Q ss_pred             HHHHHHHHHHHhhcCChhhHHHHHHHHHhhccC
Q psy3994          87 FARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN  119 (282)
Q Consensus        87 f~~~l~~~f~~v~~~~~~~~~k~~~~l~~w~~~  119 (282)
                      |...+.+.+..-  .+...+.++..++..|...
T Consensus        81 Fl~eL~kl~~~~--~~~~Vk~kil~li~~W~~~  111 (144)
T cd03568          81 FTQELKKLINDR--VHPTVKEKLREVVKQWADE  111 (144)
T ss_pred             HHHHHHHHhccc--CCHHHHHHHHHHHHHHHHH
Confidence            333333322221  5688999999999999743

Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.

>KOG4660|consensus

Probab=87.37  E-value=1  Score=42.35  Aligned_cols=41  Identities=20%  Similarity=0.297  Sum_probs=34.7

Q ss_pred             CCcEEEEEecCHHHHHHHHHHhCCCee----CCeeEEEEeecCCC
Q psy3994         193 PRGCAFVCMNRRQDAAKALYKLKNTKL----QGKTITLAWAPGKG  233 (282)
Q Consensus       193 ~kg~aFV~f~~~~~A~~Ai~~l~g~~~----~g~~l~v~~a~~~~  233 (282)
                      +.|||||.|.+.+++..+.+++||+..    ..+.+.+.||+-++
T Consensus       430 NvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQG  474 (549)
T KOG4660|consen  430 NVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQG  474 (549)
T ss_pred             ccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhhc
Confidence            679999999999999999999999964    34566888888665

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=86.69  E-value=4.5  Score=27.08  Aligned_cols=55  Identities=15%  Similarity=0.187  Sum_probs=42.9

Q ss_pred             cCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEE
Q psy3994         169 LVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL  226 (282)
Q Consensus       169 ~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v  226 (282)
                      .++-++++..+..|+ ...|..  ++.-=||.|.+..+|+++....+|..+.+.++..
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~~--d~tGfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIRD--DRTGFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEEe--cCCEEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            456789999999995 344443  3344589999999999999999999888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4410|consensus

Probab=83.49  E-value=1.6  Score=37.69  Aligned_cols=51  Identities=18%  Similarity=0.228  Sum_probs=41.3

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCce-EEEEEeCCCcEEEEEecCHHH
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDV-VSINLIPPRGCAFVCMNRRQD  206 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i-~~~~~~~~kg~aFV~f~~~~~  206 (282)
                      ...+-||++|||.++.-.+|+..+.+.|.+ .++....++|-||..|.++..
T Consensus       328 ~~~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswkg~~~k~flh~~~~~~  379 (396)
T KOG4410|consen  328 GAKTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWKGHFGKCFLHFGNRKG  379 (396)
T ss_pred             ccccceeeccCccccchHHHHHHHHhcCCCceeEeeecCCcceeEecCCccC
Confidence            445789999999999999999999988764 355555588899999998643

>KOG2591|consensus

Probab=82.59  E-value=2.2  Score=40.19  Aligned_cols=67  Identities=18%  Similarity=0.253  Sum_probs=51.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhcc--CCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCC--eeCCeeE
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGE--YGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT--KLQGKTI  224 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~--~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~--~~~g~~l  224 (282)
                      ..|-+.+.-||.++..++++.+|..  +-.+.+|.+-.+-+ =||+|++..+|+.|.+.|...  .+.|++|
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-WyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-WYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-eEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            3467788999999999999999975  66788887765433 599999999999998766422  3455544

>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins

Probab=81.76  E-value=5.7  Score=30.88  Aligned_cols=95  Identities=20%  Similarity=0.219  Sum_probs=63.2

Q ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchhhHHHHHHHHHHHhh--c
Q psy3994          23 KAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLY--Q  100 (282)
Q Consensus        23 ~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~~f~~~l~~~f~~v~--~  100 (282)
                      =.-|..++...-..-...+..+..+.+.++.-+|.-.|-.|.++|+.++|--..+... +--..|..++.+.+..-+  .
T Consensus        19 w~~ileicD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~e-vas~~Fl~el~kl~~~k~~~~   97 (139)
T cd03567          19 WEAIQAFCEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSE-VGKFRFLNELIKLVSPKYLGS   97 (139)
T ss_pred             HHHHHHHHHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHH-HHhHHHHHHHHHHhccccCCC
Confidence            3445566665533334556777888888888888889999999999999974333210 111235555555554333  1


Q ss_pred             -CChhhHHHHHHHHHhhcc
Q psy3994         101 -CPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus       101 -~~~~~~~k~~~~l~~w~~  118 (282)
                       .+...+.++..++..|..
T Consensus        98 ~~~~~Vk~kil~li~~W~~  116 (139)
T cd03567          98 RTSEKVKTKIIELLYSWTL  116 (139)
T ss_pred             CCCHHHHHHHHHHHHHHHH
Confidence             467899999999999984

The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.

>KOG2193|consensus

Probab=80.36  E-value=0.076  Score=47.97  Aligned_cols=73  Identities=21%  Similarity=0.348  Sum_probs=62.1

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ++.+-+.|+|+...++.|..++..||.++.|..+.   ....--|+|.+.+.+..|+..++|..+....++|.|-.
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            46688999999999999999999999999886653   22333578999999999999999999999999998764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	282
2diw_A	152	Solution Structure Of The Rpr Domain Of Putative Rn		4e-48
3d9i_A	145	Snapshots Of The Rna Processing Factor Scaf8 Bound		9e-48
3d9j_A	145	Snapshots Of The Rna Processing Factor Scaf8 Bound		2e-47
3d9p_A	145	Snapshots Of The Rna Processing Factor Scaf8 Bound		1e-46
3d9o_A	145	Snapshots Of The Rna Processing Factor Scaf8 Bound		5e-46
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		4e-08
1sxl_A	97	Resonance Assignments And Solution Structure Of The		5e-08
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		8e-08
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		2e-06
2la4_A	101	Nmr Structure Of The C-Terminal Rrm Domain Of Poly(		4e-05
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-04
2ytc_A	85	Solution Structure Of Rna Binding Domain In Pre-Mrn		2e-04
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		2e-04
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		2e-04
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		3e-04
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		9e-04

>pdb|2DIW|A Chain A, Solution Structure Of The Rpr Domain Of Putative Rna- Binding Protein 16 Length = 152

Iteration: 1
 Score =  187 bits (476), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 91/140 (65%), Positives = 104/140 (74%), Gaps = 1/140 (0%)
Query: 1   MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
           M+ +KTFN EL SL D KPPIS                FYKHVVQSVEKFI KCKPEYKV
Sbjct: 10  MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 69
Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct: 70  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 129
Query: 120 EVFTPDIIHPLFDMADPNHP 139
            VF  +II PL DMA  + P
Sbjct: 130 NVFKSEIIQPLLDMAAGSGP 149

>pdb|3D9I|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To Different Phosphorylated Forms Of The Carboxy-Terminal Domain Of Rna-Polymerase Ii Length = 145

Iteration: 1
 Score =  186 bits (473), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 90/135 (66%), Positives = 102/135 (75%), Gaps = 1/135 (0%)
Query: 1   MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
           M+ +KTFN EL SL D KPPIS                FYKHVVQSVEKFI KCKPEYKV
Sbjct: 1   MEAVKTFNSELYSLMDMKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60
Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 120
Query: 120 EVFTPDIIHPLFDMA 134
            VF  +II PL DMA
Sbjct: 121 NVFKSEIIQPLLDMA 135

>pdb|3D9J|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To Different Phosphorylated Forms Of The Carboxy-Terminal Domain Of Rna-Polymerase Ii Length = 145

Iteration: 1
 Score =  185 bits (470), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 90/135 (66%), Positives = 102/135 (75%), Gaps = 1/135 (0%)
Query: 1   MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
           M+ +KTFN EL SL D KPPIS                FYKHVVQSVEKFI KCKPEYKV
Sbjct: 1   MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60
Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 120
Query: 120 EVFTPDIIHPLFDMA 134
            VF  +II PL DMA
Sbjct: 121 NVFKSEIIQPLLDMA 135

>pdb|3D9P|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To Different Phosphorylated Forms Of The Carboxy-Terminal Domain Of Rna-Polymerase Ii Length = 145

Iteration: 1
 Score =  182 bits (463), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 89/135 (65%), Positives = 101/135 (74%), Gaps = 1/135 (0%)
Query: 1   MDVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKV 60
           M+ +KTFN EL SL D KPPIS                FYKHVVQSVEKFI KCKPEYKV
Sbjct: 1   MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60
Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+ VLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVTVLNLWQKN 120
Query: 120 EVFTPDIIHPLFDMA 134
            VF  +II PL DMA
Sbjct: 121 NVFKSEIIQPLLDMA 135

>pdb|3D9O|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To Different Phosphorylated Forms Of The Carboxy-Terminal Domain Of Rna-Polymerase Ii Length = 145

Iteration: 1
 Score =  181 bits (458), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 89/134 (66%), Positives = 101/134 (75%), Gaps = 1/134 (0%)
Query: 2   DVIKTFNQELSSLYDTKPPISXXXXXXXXXXXXXXXXFYKHVVQSVEKFIIKCKPEYKVP 61
           + +KTFN EL SL D KPPIS                FYKHVVQSVEKFI KCKPEYKVP
Sbjct: 2   EAVKTFNSELYSLXDXKPPISKAKXTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVP 61
Query: 62  ALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNE 120
            LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN 
Sbjct: 62  GLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNN 121
Query: 121 VFTPDIIHPLFDMA 134
           VF  +II PL D A
Sbjct: 122 VFKSEIIQPLLDXA 135

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 55.1 bits (131), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 10/94 (10%)
Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMN 202
           AR G E++  T L++ +L + + +++L   FG+YG +V  N++       PRG AFV  N
Sbjct: 91  ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 150
Query: 203 RRQDAAKALYKLKNTKLQGK----TITLAWAPGK 232
           +R++A +A+  L N   +G     ++ LA   GK
Sbjct: 151 KREEAQEAISALNNVIPEGGSQPLSVRLAEEHGK 184

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 54.7 bits (130), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 10/94 (10%)
Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMN 202
           AR G E++  T L++ +L + + +++L   FG+YG +V  N++       PRG AFV  N
Sbjct: 4   ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 63
Query: 203 RRQDAAKALYKLKNTKLQGK----TITLAWAPGK 232
           +R++A +A+  L N   +G     ++ LA   GK
Sbjct: 64  KREEAQEAISALNNVIPEGGSQPLSVRLAEEHGK 97

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 54.3 bits (129), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 50/85 (58%), Gaps = 6/85 (7%)
Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMN 202
           AR G E++  T L++ +L + + +++L   FG+YG +V  N++       PRG AFV  N
Sbjct: 80  ARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYN 139
Query: 203 RRQDAAKALYKLKNTKLQGKTITLA 227
           +R++A +A+  L N   +G +  L+
Sbjct: 140 KREEAQEAISALNNVIPEGGSQPLS 164

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           ST L +G++S     +EL   F EYG V+  +++  +  AFV M R +DA +A+  L NT
Sbjct: 10  STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNT 67
Query: 218 KLQGK 222
           + QGK
Sbjct: 68  EFQGK 72

>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U) Binding 1 Length = 101

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 33/71 (46%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
           TT +IG++     E +L   F  +G ++     P +GC F+  +  + AA  +  L N  
Sbjct: 28  TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFP 87
Query: 219 LQGKTITLAWA 229
            QG+ +   W 
Sbjct: 88  FQGRNLRTGWG 98

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/125 (26%), Positives = 57/125 (45%), Gaps = 12/125 (9%)
Query: 100 QCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCST 159
           Q PP+ K     V    +K  +   + +H +  +   +HPI  + A+ +  N VE+    
Sbjct: 41  QNPPQSKGCCF-VTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVED---R 96
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRR---QDAAKAL 211
            L+IG +SK   E ++   F  +G +    ++       RGCAFV    R   Q A KA+
Sbjct: 97  KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 212 YKLKN 216
           ++ + 
Sbjct: 157 HQAQT 161

>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna- Splicing Factor Rbm22 Length = 85

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYK 213
           E+   TTL++G L   + E +L + F ++G++ +I ++  + CAF+    RQ A  A  K
Sbjct: 8   EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEK 67
Query: 214 LKNTKL-QGKTITLAWA 229
             N  +  G+ + + W 
Sbjct: 68  SFNKLIVNGRRLNVKWG 84

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 16/70 (22%), Positives = 37/70 (52%)
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
           T++ G ++  + ++ +  TF  +G ++ I + P +G +FV  +  + AA A+  +  T +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTI 86
Query: 220 QGKTITLAWA 229
           +G  +   W 
Sbjct: 87  EGHVVKCYWG 96

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/138 (24%), Positives = 62/138 (44%), Gaps = 12/138 (8%)
Query: 100 QCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCST 159
           Q PP+ K     V    +K  +   + +H +  +   +HPI  + A+ +  N VE+    
Sbjct: 53  QNPPQSKGCCF-VTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVED---R 108
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRR---QDAAKAL 211
            L+IG +SK   E ++   F  +G +    ++       RGCAFV    R   Q A KA+
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 168
Query: 212 YKLKNTKLQGKTITLAWA 229
           ++ +  +     + + +A
Sbjct: 169 HQAQTMEGCSSPMVVKFA 186

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/117 (26%), Positives = 51/117 (43%), Gaps = 9/117 (7%)
Query: 100 QCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCST 159
           Q PP+ K     V    +K  +   + +H    +   +HPI  + A+ +  N VE+    
Sbjct: 41  QNPPQSKGCCF-VTFYTRKAALEAQNALHNXKVLPGXHHPIQXKPADSEKNNAVEDR--- 96
Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKAL 211
            L+IG +SK   E ++   F  +G +    ++       RGCAFV    R  A  A+
Sbjct: 97  KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T L + +L + + ++E    FG  GD+ S  L+  +      G  FV  +   DA KA+ 
Sbjct: 5   TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 213 KLKNTKLQGKTITLAWA 229
            L   KLQ KTI +++A
Sbjct: 65  TLNGLKLQTKTIKVSYA 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	282
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	2e-48
3clj_A	157	Protein NRD1; CTD-interacting domain, nucleus, pho	3e-38
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	9e-28
4fld_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	1e-25
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	3e-24
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-23
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	9e-23
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	2e-21
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	9e-21
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-20
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	8e-20
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-19
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-19
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-19
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	6e-19
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-18
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-17
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-14
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-17
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	9e-17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	9e-12
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	9e-17
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-16
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-16
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-16
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-16
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-15
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-15
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-15
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-15
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-15
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-15
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-15
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-15
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-10
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-15
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	8e-15
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-15
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	9e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-14
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-14
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-14
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-14
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-14
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-14
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-14
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-14
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-14
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-14
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-14
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-14
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-14
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-14
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-14
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	7e-14
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-14
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-13
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-13
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-13
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-13
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-13
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-13
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-10
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-13
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	5e-13
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	8e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	8e-13
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-11
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-12
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-12
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-12
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-12
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-12
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-12
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-12
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	5e-12
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-11
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-11
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-11
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-09
2div_A	99	TRNA selenocysteine associated protein; structural	4e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-11
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	7e-11
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	8e-11
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-10
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-10
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-10
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-10
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	3e-10
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-10
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-10
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-09
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-07
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	4e-07
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	6e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-06
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-06
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-05
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-06
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-06
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-05
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-05
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	9e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-04
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	5e-04
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	6e-04

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A Length = 145

 Score =  156 bits (396), Expect = 2e-48
 Identities = 103/143 (72%), Positives = 119/143 (83%), Gaps = 2/143 (1%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
           M+ +KTFN EL SL D KPPISKAK+T IT++AI+AIKFYKHVVQSVEKFI KCKPEYKV
Sbjct: 1   MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60

Query: 61  PALYVIDSLVRQSRHQF-QDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKN 119
           P LYVIDS+VRQSRHQF Q+KDVF PRF+ N+ +TFQ+LY+CP +DKSKI+RVLNLWQKN
Sbjct: 61  PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKN 120

Query: 120 EVFTPDIIHPLFDMAD-PNHPIH 141
            VF  +II PL DMA    H  H
Sbjct: 121 NVFKSEIIQPLLDMAAALEHHHH 143

>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae} Length = 157

 Score =  131 bits (330), Expect = 3e-38
 Identities = 25/141 (17%), Positives = 53/141 (37%), Gaps = 12/141 (8%)

Query: 4   IKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPAL 63
            + F   L S  D K  IS ++I  +T  A+  I     ++  +  +   C   +K+ +L
Sbjct: 3   FQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSL 62

Query: 64  YVIDSLVRQSRHQFQDKDVFGP-----------RFARNLKATFQHLYQC-PPEDKSKIIR 111
           Y+IDS+ R    + +                       ++            + K KI  
Sbjct: 63  YIIDSIGRAYLDETRSNSNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEKIRM 122

Query: 112 VLNLWQKNEVFTPDIIHPLFD 132
           +L++W ++ +F    ++ +  
Sbjct: 123 LLDIWDRSGLFQKSYLNAIRS 143

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X Length = 144

 Score =  103 bits (258), Expect = 9e-28
 Identities = 33/136 (24%), Positives = 57/136 (41%), Gaps = 16/136 (11%)

Query: 1   MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKV 60
             ++K FN  L  L     PI    IT +T+ A   I   ++ V ++E  I KC P+ K+
Sbjct: 6   EVIVKDFNSILEELTFNSRPI----ITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKL 61

Query: 61  PALYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPE-DKSKIIRVLNLWQKN 119
            A Y +DS+ +           +   F+RNL   ++  Y       ++K+I +  LW   
Sbjct: 62  YAFYALDSICKNVGSP------YTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNP 115

Query: 120 -----EVFTPDIIHPL 130
                 +F    +  +
Sbjct: 116 NDTGLPLFEGSALEKI 131

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens} Length = 132

 Score = 93.9 bits (233), Expect = 3e-24
 Identities = 18/126 (14%), Positives = 49/126 (38%), Gaps = 9/126 (7%)

Query: 5   KTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALY 64
            + +++  S+ +T   I       I        K +  +V    K++ +    +++   Y
Sbjct: 8   SSLDRKFQSVTNTMESIQGLSSWCIENK-----KHHSTIVYHWMKWLRRSAYPHRLNLFY 62

Query: 65  VIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTP 124
           + + +++  +   ++  +F   FA  L      +    P     + R+  +W+   V+  
Sbjct: 63  LANDVIQNCKR--KNAIIFRESFADVLPEAAALVK--DPSVSKSVERIFKIWEDRNVYPE 118

Query: 125 DIIHPL 130
           ++I  L
Sbjct: 119 EMIVAL 124

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 90.1 bits (224), Expect = 4e-23
 Identities = 19/72 (26%), Positives = 33/72 (45%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
            TT +IG++     E +L   F  +G ++     P +GC F+  +  + AA  +  L N 
Sbjct: 27  VTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANF 86

Query: 218 KLQGKTITLAWA 229
             QG+ +   W 
Sbjct: 87  PFQGRNLRTGWG 98

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 88.5 bits (220), Expect = 9e-23
 Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 151 NGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKA 210
           +  E+   TTL++G L   + E +L + F ++G++ +I ++  + CAF+    RQ A  A
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVA 64

Query: 211 LYKLKN-TKLQGKTITLAWA 229
             K  N   + G+ + + W 
Sbjct: 65  AEKSFNKLIVNGRRLNVKWG 84

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A* Length = 142

 Score = 86.6 bits (214), Expect = 2e-21
 Identities = 26/141 (18%), Positives = 63/141 (44%), Gaps = 11/141 (7%)

Query: 6   TFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFII--KCKPEYKVPAL 63
            F  +L++L D++  IS A      +  +   +    V +  +++++        K+  L
Sbjct: 7   QFTTKLNTLEDSQESISSAS-----KWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGL 61

Query: 64  YVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKNEVF 122
           Y+++ +V+Q++ Q      F   F +        + Q  P + K K+ RV+N+ ++  +F
Sbjct: 62  YLMNHVVQQAKGQK--IIQFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIF 119

Query: 123 TPDIIHPLFD-MADPNHPIHR 142
           +  +++ +   +A      H 
Sbjct: 120 SKQVVNDIERSLAAALEHHHH 140

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 83.9 bits (208), Expect = 9e-21
 Identities = 16/72 (22%), Positives = 38/72 (52%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           + T++ G ++  + ++ +  TF  +G ++ I + P +G +FV  +  + AA A+  +  T
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84

Query: 218 KLQGKTITLAWA 229
            ++G  +   W 
Sbjct: 85  TIEGHVVKCYWG 96

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 82.3 bits (204), Expect = 2e-20
 Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
            TL++      +    L   F  +G+++ +++ PPR CAFV   + + A +A+ +L  T+
Sbjct: 16  NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQ 73

Query: 219 LQGKTITLAWAPGKGMKD 236
           ++   + +  A  + M D
Sbjct: 74  VESVQLKVNIARKQPMLD 91

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 81.2 bits (201), Expect = 8e-20
 Identities = 20/75 (26%), Positives = 37/75 (49%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
            + L++G+L   + EEE+   F +YG    + +   +G  F+ +  R  A  A  +L N 
Sbjct: 15  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNM 74

Query: 218 KLQGKTITLAWAPGK 232
            L+GK + + +A   
Sbjct: 75  PLRGKQLRVRFACHS 89

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 81.4 bits (201), Expect = 1e-19
 Identities = 19/84 (22%), Positives = 29/84 (34%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
            T +   +L       E+ +TF  +G +  + L      A V      +A KA   L  +
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69

Query: 218 KLQGKTITLAWAPGKGMKDKDWKD 241
           K     + L WAP         K 
Sbjct: 70  KFHHVPLYLEWAPIGVFGAAPQKK 93

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 79.3 bits (196), Expect = 5e-19
 Identities = 21/110 (19%), Positives = 43/110 (39%), Gaps = 7/110 (6%)

Query: 133 MADPNHPIHRE-----LAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVS 187
           M   +H  H                   + +T L++      VQE EL++ FG +G +  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60

Query: 188 INLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDK 237
           + +    G AFV     + AAKA+ ++       + + + ++     + +
Sbjct: 61  VKI--LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 78.9 bits (195), Expect = 6e-19
 Identities = 18/72 (25%), Positives = 28/72 (38%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
              L++ +L     EE +   F          +   R  AFV  + R+DA +A+  L   
Sbjct: 15  VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGK 74

Query: 218 KLQGKTITLAWA 229
            L G  I +  A
Sbjct: 75  VLDGSPIEVTLA 86

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 78.1 bits (193), Expect = 1e-18
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK 218
             L++ +L+  V EE L   F ++G +  +  +  +  AF+  + R  A KA+ ++    
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKD 69

Query: 219 LQGKTITLAWAPGKGMKDKD 238
           L+G+ I + +A     K K+
Sbjct: 70  LEGENIEIVFAKPPDQKRKE 89

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 74.6 bits (184), Expect = 2e-17
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL-KNT 217
             L+IG+LS  V  ++L   FG+    ++  ++   G AFV    +  A +A+  L    
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 68

Query: 218 KLQGKTITLAWAPGKGMK 235
           +L GK + + ++  K ++
Sbjct: 69  ELHGKIMEVDYSVSKKLR 86

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 74.2 bits (183), Expect = 3e-17
 Identities = 16/69 (23%), Positives = 28/69 (40%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           +T LW+G L        L+  F  +G + +I+ +     A++       A  A  K++  
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF 76

Query: 218 KLQGKTITL 226
            L G    L
Sbjct: 77  PLGGPDRRL 85

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 76.1 bits (188), Expect = 4e-17
 Identities = 24/117 (20%), Positives = 47/117 (40%), Gaps = 17/117 (14%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +T L + +L + + + EL   F   G + +  ++         G AFV      D+ +A+
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED 268
             L    ++ K + +++A   G   KD   +  V +         L + I  D L+ 
Sbjct: 63  KVLNGITVRNKRLKVSYARPGGESIKDTNLY--VTN---------LPRTITDDQLDT 108

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 67.2 bits (165), Expect = 7e-14
 Identities = 28/90 (31%), Positives = 52/90 (57%), Gaps = 8/90 (8%)

Query: 148 QARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCM 201
            AR G E++  T L++ +L + + +++L   FG+YG +V  N++       PRG AFV  
Sbjct: 79  YARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 138

Query: 202 NRRQDAAKALYKLKNTKLQG--KTITLAWA 229
           N+R++A +A+  L N   +G  + +++  A
Sbjct: 139 NKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 73.0 bits (180), Expect = 8e-17
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 2/84 (2%)

Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAA 208
             +G     ST L +G++S     +EL   F EYG V+  +++  +  AFV M R +DA 
Sbjct: 1   GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAV 58

Query: 209 KALYKLKNTKLQGKTITLAWAPGK 232
           +A+  L NT+ QGK + +  +  +
Sbjct: 59  EAIRGLDNTEFQGKRMHVQLSTSR 82

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 73.5 bits (181), Expect = 8e-17
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 8/88 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-------PPRGCAFVCMNRRQDAAKA 210
           ++ + + ++     + E+ + F  +G++ ++ L          RG  FV    +QDA KA
Sbjct: 15  TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74

Query: 211 LYKLKN-TKLQGKTITLAWAPGKGMKDK 237
              L + T L G+ + L WA  +     
Sbjct: 75  FNALCHSTHLYGRRLVLEWADSEVTVQS 102

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 74.9 bits (185), Expect = 9e-17
 Identities = 30/117 (25%), Positives = 47/117 (40%), Gaps = 17/117 (14%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
            T L + +L + + +EE    FG  G++ S  L+         G  FV     +DA KA+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED 268
             L   +LQ KTI +++A       +D   +  V           L K +    LE 
Sbjct: 62  NTLNGLRLQTKTIKVSYARPSSASIRDANLY--VSG---------LPKTMTQKELEQ 107

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 61.0 bits (149), Expect = 9e-12
 Identities = 22/90 (24%), Positives = 44/90 (48%), Gaps = 8/90 (8%)

Query: 148 QARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCM 201
            AR    ++    L++  L K + ++EL   F +YG +++  ++        RG  F+  
Sbjct: 78  YARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 137

Query: 202 NRRQDAAKALYKLKNTKLQG--KTITLAWA 229
           ++R +A +A+  L   K  G  + IT+ +A
Sbjct: 138 DKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 76.8 bits (188), Expect = 9e-17
 Identities = 19/126 (15%), Positives = 38/126 (30%), Gaps = 11/126 (8%)

Query: 117 QKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLS--------- 167
            + ++    +   + D          +  E     G     + TL++G +          
Sbjct: 95  DEEDIGKLALRTEVLD--CFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLK 152

Query: 168 KLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA 227
               E  +   F   GD+  I  +  + C FV    + +A  A   + N  L   +    
Sbjct: 153 PAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEW 212

Query: 228 WAPGKG 233
               +G
Sbjct: 213 DDRREG 218

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 71.9 bits (177), Expect = 2e-16
 Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 4/85 (4%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP----RGCAFVCMNRRQDAAKALYK 213
             TL++G+LS+ V E  +   F + G   S  +I          FV     +DAA AL  
Sbjct: 15  PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAA 74

Query: 214 LKNTKLQGKTITLAWAPGKGMKDKD 238
           +   K+ GK + + WA     +   
Sbjct: 75  MNGRKILGKEVKVNWATTPSSQKSG 99

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 71.1 bits (175), Expect = 3e-16
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           +  +++G++S     +EL   F   G V+  +++  +  AFV M +  DA  A+ +L   
Sbjct: 9   TWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNGK 66

Query: 218 KLQGKTITLAWAPGK 232
           +++GK I +  +   
Sbjct: 67  EVKGKRINVELSTKG 81

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 71.6 bits (176), Expect = 4e-16
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +  L++ +LS  V E +L   F  + +     +         RG AF+    ++ A +AL
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84

Query: 212 YKLKNTKLQGKTITLAWA 229
           + +   KL GK + + + 
Sbjct: 85  HLVNGYKLYGKILVIEFG 102

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 72.9 bits (179), Expect = 4e-16
 Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 6/81 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           S TL++G+LS    EE++ + F + GD+  I +          G  FV    R DA  A+
Sbjct: 39  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98

Query: 212 YKLKNTKLQGKTITLAWAPGK 232
             +  T+L  + I   W  G 
Sbjct: 99  RYINGTRLDDRIIRTDWDAGF 119

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 69.9 bits (172), Expect = 1e-15
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKAL 211
             TL + +L+     + L   F +YG V  + +        PRG AFV  + R+DA  A 
Sbjct: 13  MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAE 72

Query: 212 YKLKNTKLQGKTITLAWA 229
             +   +L G+ + +  A
Sbjct: 73  AAMDGAELDGRELRVQVA 90

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 69.5 bits (171), Expect = 1e-15
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL 214
           +     L+IG+L +   E+E+   F +YG V+  ++I  +   FV +  +  A  A+  L
Sbjct: 5   SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNL 62

Query: 215 KNTKLQGKTITLAWAPGK 232
            + KL G  I +  +  K
Sbjct: 63  HHYKLHGVNINVEASKNK 80

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 69.7 bits (171), Expect = 2e-15
 Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 158 STTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
           ++ ++IG+L+  LV++ ++   F +YG V   ++   +G AFV  +  + A  A+     
Sbjct: 27  NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLGENG 84

Query: 217 TKLQGKTITLAWA 229
             L G+T+ +  A
Sbjct: 85  RVLAGQTLDINMA 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 69.1 bits (169), Expect = 3e-15
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDV-VSINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
           +  +++G+L +  +  +L     E G V + +    PR  AF+       A +A+  L+ 
Sbjct: 19  AADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQG 78

Query: 217 TKLQGKTITLAWAPGKGMKDK 237
            +L   T+ +A A  +  +DK
Sbjct: 79  LRLGTDTLRVALA--RQQRDK 97

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 69.2 bits (170), Expect = 3e-15
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           + T+ + +LS+  +E +L + F  +G +  I L         +G AF+  +RR+DAA+A+
Sbjct: 15  NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74

Query: 212 YKLKNTKLQGKTITLAWA 229
             +         + + WA
Sbjct: 75  AGVSGFGYDHLILNVEWA 92

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 68.8 bits (169), Expect = 3e-15
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L++G L++ V ++ L   F  +GD+  I +         RG AFV     +DAA A+
Sbjct: 12  KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71

Query: 212 YKLKNTKLQGKTITLAWA 229
             +  ++L G+TI +  A
Sbjct: 72  DNMNESELFGRTIRVNLA 89

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 72.0 bits (177), Expect = 5e-15
 Identities = 18/88 (20%), Positives = 36/88 (40%)

Query: 143 ELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMN 202
           ++                L++G+L   + EE+    F  YG+   + +   RG  F+ + 
Sbjct: 7   DIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLE 66

Query: 203 RRQDAAKALYKLKNTKLQGKTITLAWAP 230
            R  A  A  +L  T L+ + + + +A 
Sbjct: 67  SRTLAEIAKAELDGTILKSRPLRIRFAT 94

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 56.2 bits (136), Expect = 1e-09
 Identities = 17/89 (19%), Positives = 31/89 (34%), Gaps = 9/89 (10%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALY 212
              L + +LS +V  E L   F ++G V    ++        G  FV    +  A KAL 
Sbjct: 96  GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE 155

Query: 213 KLKNTKL----QGKTITLAWAPGKGMKDK 237
           +  +         + + +        +D 
Sbjct: 156 RCGDGAFLLTTTPRPVIVEPMEQFDDEDG 184

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 68.4 bits (168), Expect = 5e-15
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
             T+++G L + V E  L + F + G VV+ ++         +G  FV     +DA  A+
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74

Query: 212 YKLKNTKLQGKTITLAWA 229
             +   KL GK I +  A
Sbjct: 75  KIMDMIKLYGKPIRVNKA 92

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 69.9 bits (172), Expect = 6e-15
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKL 214
            L++G+L K + E+ L   F   G + +I ++          AFV  ++  DA  AL  L
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 215 KNTKLQGKTITLAWAPGKGMKDKD 238
              +++   + + WA        D
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSD 85

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 57.2 bits (139), Expect = 3e-10
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
            L++G L+  V +E L + F ++   +S +++        RG  FV    + DA  A+  
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 214 LKNTKLQGKTITLAWA 229
           ++   L G+ + + WA
Sbjct: 149 MQGQDLNGRPLRINWA 164

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 67.9 bits (166), Expect = 6e-15
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI---PPRGCAFVCMNRRQDAAKALYKL 214
              L I ++   +Q E L     +YG V S   +          V  + +  A +AL KL
Sbjct: 15  IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKL 74

Query: 215 KNTKLQGKTITLAWAPGK 232
              +L+  T+ +A+ P +
Sbjct: 75  NGFQLENFTLKVAYIPDE 92

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 68.6 bits (168), Expect = 7e-15
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L++  + +   EE++ D F EYG++ +I+L         +G   V     ++A  A+
Sbjct: 22  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81

Query: 212 YKLKNTKLQGKTITLAWA 229
             L    L G+ I++ W 
Sbjct: 82  EGLNGQDLMGQPISVDWC 99

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 69.0 bits (169), Expect = 8e-15
 Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 6/88 (6%)

Query: 148 QARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCM 201
              +G        L++G L++ V ++ L   F  +GD+  I +         RG AFV  
Sbjct: 53  SGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 112

Query: 202 NRRQDAAKALYKLKNTKLQGKTITLAWA 229
              +DAA A+  +  ++L G+TI +  A
Sbjct: 113 ELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 68.1 bits (167), Expect = 8e-15
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 4/81 (4%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI----PPRGCAFVCMNRRQDAAKALYK 213
              L + ++    ++ +L   FG++G ++ + +I      +G  FV      DA +A  K
Sbjct: 29  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK 88

Query: 214 LKNTKLQGKTITLAWAPGKGM 234
           L  T ++G+ I +  A  + M
Sbjct: 89  LHGTVVEGRKIEVNNATARVM 109

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 67.2 bits (165), Expect = 8e-15
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L++G L++ V ++ L   F  +GD+  I +         RG AFV     +DAA A+
Sbjct: 7   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66

Query: 212 YKLKNTKLQGKTITLAWA 229
             +  ++L G+TI +  A
Sbjct: 67  DNMNESELFGRTIRVNLA 84

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 67.8 bits (166), Expect = 9e-15
 Identities = 16/79 (20%), Positives = 28/79 (35%), Gaps = 6/79 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              +    L+  V+E  L D   +YG+V  + ++         G A V     + A + +
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 212 YKLKNTKLQGKTITLAWAP 230
             L  T + G  I      
Sbjct: 66  KNLHLTSVMGNIIHAQLDI 84

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 69.1 bits (169), Expect = 1e-14
 Identities = 24/108 (22%), Positives = 41/108 (37%), Gaps = 8/108 (7%)

Query: 128 HPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVS 187
              +D A     +            VE M S  L + +L+     + L   F +YG V  
Sbjct: 42  EWTYDDATKTFTVTEGSHHHHHHMDVEGMTS--LKVDNLTYRTSPDTLRRVFEKYGRVGD 99

Query: 188 INLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
           + +         RG AFV  + ++DA  A+  +    L G+ + +  A
Sbjct: 100 VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 67.3 bits (165), Expect = 1e-14
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 4/84 (4%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYK 213
              L + ++    ++ +L   FG++G ++ + +I      +G  FV      DA +A  K
Sbjct: 15  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK 74

Query: 214 LKNTKLQGKTITLAWAPGKGMKDK 237
           L  T ++G+ I +  A  + M + 
Sbjct: 75  LHGTVVEGRKIEVNNATARVMTNS 98

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 67.3 bits (165), Expect = 1e-14
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L++  + +   EE++ D F EYG++ +I+L         +G   V     ++A  A+
Sbjct: 23  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82

Query: 212 YKLKNTKLQGKTITLAWA 229
             L    L G+ I++ W 
Sbjct: 83  EGLNGQDLMGQPISVDWC 100

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 66.9 bits (164), Expect = 1e-14
 Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALY 212
             T+++G+L   V+EE L + F + G +  + +       P+   FVC    +  + A+ 
Sbjct: 16  DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIA 75

Query: 213 KLKNTKLQGKTITLAWA 229
            L   +L G+ I ++  
Sbjct: 76  LLNGIRLYGRPINVSGP 92

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 66.4 bits (163), Expect = 2e-14
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 7/77 (9%)

Query: 156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-------PPRGCAFVCMNRRQDAA 208
           M  T + IG L++ V ++ + + F  YG +  I++          +G A+V      +A 
Sbjct: 2   MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61

Query: 209 KALYKLKNTKLQGKTIT 225
           KAL  +   ++ G+ IT
Sbjct: 62  KALKHMDGGQIDGQEIT 78

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 67.4 bits (165), Expect = 2e-14
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +  L +  LS    E +L + F +YG +  ++++        RG AFV      DA +A 
Sbjct: 46  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105

Query: 212 YKLKNTKLQGKTITLAWA 229
            +    +L G+ I + ++
Sbjct: 106 ERANGMELDGRRIRVDFS 123

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 66.4 bits (163), Expect = 2e-14
 Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           S+ L++G L   + E+ L   F  +G + +I L+        +G  F+  +  + A +AL
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64

Query: 212 YKLKNTKLQGKTITLAWA 229
            +L   +L G+ + +   
Sbjct: 65  EQLNGFELAGRPMRVGHV 82

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 66.6 bits (163), Expect = 3e-14
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKL 214
              +++G+L   ++ +++ D F +YG +  I+L         AFV     +DA  A+Y  
Sbjct: 22  DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGR 81

Query: 215 KNTKLQGKTITLAWA 229
                 G  + + + 
Sbjct: 82  DGYDYDGYRLRVEFP 96

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 67.5 bits (165), Expect = 3e-14
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
            T+L + +L+     + L   F +YG V  + +         RG AFV  + ++DA  A+
Sbjct: 47  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106

Query: 212 YKLKNTKLQGKTITLAWA 229
             +    L G+ + +  A
Sbjct: 107 DAMDGAVLDGRELRVQMA 124

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 66.1 bits (162), Expect = 3e-14
 Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
            +T+++ +L   +   +L   F +YG VV + ++        +G AF+    +  A    
Sbjct: 16  KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75

Query: 212 YKLKNTKLQGKTITLAWA 229
             + N +L G+ I  + A
Sbjct: 76  RAINNKQLFGRVIKASIA 93

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 66.1 bits (162), Expect = 3e-14
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 8/84 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALY 212
              L+I  L     +EEL +    +G V  + L+      P+G A+V       A++A+ 
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76

Query: 213 KLKNTKLQGKTITLAWA---PGKG 233
           K+    ++   I +A +   P  G
Sbjct: 77  KMDGMTIKENIIKVAISNSGPSSG 100

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 67.9 bits (166), Expect = 4e-14
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 6/84 (7%)

Query: 156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAK 209
           +    L++  + +  QE+E+ + F +YG++ +I+L         +G A V     + A  
Sbjct: 70  VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 129

Query: 210 ALYKLKNTKLQGKTITLAWAPGKG 233
           A   L   ++ G+TI + W   KG
Sbjct: 130 AKEALNGAEIMGQTIQVDWCFVKG 153

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 65.7 bits (161), Expect = 5e-14
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +  L +  LS    E +L + F +YG +  ++++        RG AFV      DA +A 
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74

Query: 212 YKLKNTKLQGKTITLAWA 229
            +    +L G+ I ++  
Sbjct: 75  ERANGMELDGRRIRVSGP 92

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 65.8 bits (161), Expect = 5e-14
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L++  + +  QE+E+ + F +YG++ +I+L         +G A V     + A  A 
Sbjct: 26  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85

Query: 212 YKLKNTKLQGKTITLAWA 229
             L   ++ G+TI + W 
Sbjct: 86  EALNGAEIMGQTIQVDWC 103

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 66.2 bits (162), Expect = 5e-14
 Identities = 23/105 (21%), Positives = 41/105 (39%), Gaps = 6/105 (5%)

Query: 133 MADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP 192
             DP+   H +L +     G        L + +L   V + ++ + F E+G +    +  
Sbjct: 11  GRDPDKWQH-DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDY 69

Query: 193 -----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK 232
                  G A V   RR DA KA+ + K   L G+ + +     +
Sbjct: 70  DRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 65.8 bits (161), Expect = 6e-14
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALY 212
            +T+++ +L   V  ++L + F   G VV  +++       RG   V   +  +A +A+ 
Sbjct: 15  GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74

Query: 213 KLKNTKLQGKTITLAWA 229
                 L  + + +   
Sbjct: 75  MFNGQLLFDRPMHVKMD 91

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 65.3 bits (160), Expect = 7e-14
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           S  L++ +LS    EE+L   F  YG +  ++         P+G AFV     + A KA 
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67

Query: 212 YKLKNTKLQGKTITLAWA 229
            ++     QG+ + +  +
Sbjct: 68  AEVDGQVFQGRMLHVLPS 85

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 65.8 bits (161), Expect = 7e-14
 Identities = 26/104 (25%), Positives = 39/104 (37%), Gaps = 5/104 (4%)

Query: 153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDA 207
           VE      L+IG L++   E+ L   FG++G +  + LI       RG AF+      DA
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61

Query: 208 AKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSY 251
             A   +    L GK I +  A     +    +         S 
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSP 105

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 65.0 bits (159), Expect = 7e-14
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 9/81 (11%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI---------PPRGCAFVCMNRRQDAA 208
           S+ L+I +L+    EE L   F + G + S  +             G  FV   + + A 
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64

Query: 209 KALYKLKNTKLQGKTITLAWA 229
           KAL +L+   + G  + +  +
Sbjct: 65  KALKQLQGHTVDGHKLEVRIS 85

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 64.9 bits (159), Expect = 8e-14
 Identities = 14/78 (17%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           S  +++G +     EE++ D     G V+++ ++        +G AF+     + +A A+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 212 YKLKNTKLQGKTITLAWA 229
             L   +L  + +   ++
Sbjct: 62  RNLNGYQLGSRFLKCGYS 79

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 65.9 bits (161), Expect = 1e-13
 Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 6/87 (6%)

Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMN 202
            +   E      L + ++   V E +L   F  YG + S+ ++        RG  FV   
Sbjct: 33  TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92

Query: 203 RRQDAAKALYKLKNTKLQGKTITLAWA 229
               A +A+  L    +  K + +A A
Sbjct: 93  SGSSAQQAIAGLNGFNILNKRLKVALA 119

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 64.6 bits (158), Expect = 1e-13
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKL 219
           +++G+L     + EL   F  YG + ++ +   P G AFV     +DA  A+  L    +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62

Query: 220 QGKTITLAWAPGKG 233
            G  + +  + G  
Sbjct: 63  CGSRVRVELSTGMP 76

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 64.2 bits (157), Expect = 1e-13
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 10/85 (11%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           S TL + +LS    EE L + F +   +     +P       +G AF+     +DA +AL
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEAL 70

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKD 236
                 +++G+ I L     +G  +
Sbjct: 71  NSCNKREIEGRAIRLELQGPRGSPN 95

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDT----FGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKA 210
           + T++I +L++ ++++EL  +    F  +G ++ I +      RG AFV       A  A
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67

Query: 211 LYKLKNTKLQGKTITLAWA 229
           L  ++      K + + +A
Sbjct: 68  LRSMQGFPFYDKPMRIQYA 86

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 63.8 bits (156), Expect = 2e-13
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L++G LS    E+ L   F +YG +  + ++        RG  FV      DA  A+
Sbjct: 12  EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71

Query: 212 YKLKNTKLQGKTITLAWA 229
             +    + G+ I +  A
Sbjct: 72  MAMNGKSVDGRQIRVDQA 89

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 64.3 bits (157), Expect = 2e-13
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKL 214
           +  L+I +L   +  EE+ D FG+YG +  I +      RG A+V      DA  A+  L
Sbjct: 8   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 215 KNTKLQGKTITLAWAPGKGMKDK 237
               +  + + + +        K
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQK 90

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 63.8 bits (156), Expect = 3e-13
 Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 8/80 (10%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALY 212
              L++G L+K   EE++   F  +G +    ++       +GCAFV  +   +A  A++
Sbjct: 15  DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74

Query: 213 KLKNTKL---QGKTITLAWA 229
            L  ++       ++ + +A
Sbjct: 75  ALHGSQTMPGASSSLVVKFA 94

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 63.4 bits (155), Expect = 3e-13
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
             ++++G++     EE+L D F E G VVS  L+       P+G  F     ++ A  A+
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKDKD 238
             L   +  G+ + +  A  +  K++ 
Sbjct: 68  RNLNGREFSGRALRVDNAASEKNKEEL 94

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 63.8 bits (156), Expect = 3e-13
 Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 5/77 (6%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALY 212
            T L+I +L   + E+EL +    +G V+S  ++       RG  F  M   +     + 
Sbjct: 25  PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIG 84

Query: 213 KLKNTKLQGKTITLAWA 229
                 ++      A  
Sbjct: 85  HFNGKFIKTPPGVSAPT 101

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 66.9 bits (164), Expect = 4e-13
 Identities = 13/81 (16%), Positives = 30/81 (37%), Gaps = 6/81 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L + +L   + +++  +    +G +    L+        +G  F    ++  AA+A 
Sbjct: 95  DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154

Query: 212 YKLKNTKLQGKTITLAWAPGK 232
             L    L  +T+ + W    
Sbjct: 155 SDLLGKPLGPRTLYVHWTDAG 175

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 66.9 bits (164), Expect = 5e-13
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
              + I  L   V  +E+ D   +Y  +    +   +G AFV +   + A  A+     +
Sbjct: 22  RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQS 80

Query: 218 KLQGKTITLAWAP 230
           +L+ + +++   P
Sbjct: 81  RLRERELSVQLQP 93

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 64.2 bits (157), Expect = 3e-12
 Identities = 11/78 (14%), Positives = 22/78 (28%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLV-QEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKAL 211
           S  L +  L       + L              L        +G A +     + A +A 
Sbjct: 184 SRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQ 243

Query: 212 YKLKNTKLQGKTITLAWA 229
            +     L G  + +++ 
Sbjct: 244 QQADGLSLGGSHLRVSFC 261

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 64.9 bits (159), Expect = 5e-13
 Identities = 19/87 (21%), Positives = 44/87 (50%), Gaps = 1/87 (1%)

Query: 148 QARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-PPRGCAFVCMNRRQD 206
           + R+  +   + TL   +LS  + E+EL + F +  ++  ++     +G A++      D
Sbjct: 89  KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEAD 148

Query: 207 AAKALYKLKNTKLQGKTITLAWAPGKG 233
           A K L + +  ++ G++++L +   KG
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 61.9 bits (151), Expect = 6e-12
 Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 6/86 (6%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-----RGCAFVCMNRRQDAAKALY 212
              L+IG+L+      EL     E      + ++       R   +V     +D  KAL 
Sbjct: 13  PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL- 71

Query: 213 KLKNTKLQGKTITLAWAPGKGMKDKD 238
           +L   K+ G  I L    G+  K   
Sbjct: 72  ELTGLKVFGNEIKLEKPKGRDSKKVR 97

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 63.1 bits (154), Expect = 5e-13
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 5/78 (6%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALY 212
              L + +L   V + ++ + F E+G +    +         G A V   R+ DA KA+ 
Sbjct: 29  GGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMK 88

Query: 213 KLKNTKLQGKTITLAWAP 230
           +     L G+ + +    
Sbjct: 89  QYNGVPLDGRPMNIQLVT 106

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 65.8 bits (161), Expect = 5e-13
 Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 148 QARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCM 201
                  +    +L++G L   V E  L + F   G ++SI +          G A+V  
Sbjct: 5   SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNF 64

Query: 202 NRRQDAAKALYKLKNTKLQGKTITLAWA 229
            +  DA +AL  +    ++GK + + W+
Sbjct: 65  QQPADAERALDTMNFDVIKGKPVRIMWS 92

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 58.8 bits (143), Expect = 1e-10
 Identities = 16/90 (17%), Positives = 41/90 (45%), Gaps = 4/90 (4%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKL 214
             ++I +L K +  + L DTF  +G+++S  ++      +G  FV    ++ A +A+ K+
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 163

Query: 215 KNTKLQGKTITLAWAPGKGMKDKDWKDFWE 244
               L  + + +     +  ++ +     +
Sbjct: 164 NGMLLNDRKVFVGRFKSRKEREAELGARAK 193

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 63.0 bits (154), Expect = 5e-13
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 4/76 (5%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI----PPRGCAFVCMNRRQDAAKALYK 213
              L++ +L   + +E L   F  +G + S  ++      +G  FVC +  ++A KA+ +
Sbjct: 15  VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTE 74

Query: 214 LKNTKLQGKTITLAWA 229
           +    +  K + +A A
Sbjct: 75  MNGRIVATKPLYVALA 90

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 63.8 bits (155), Expect = 5e-13
 Identities = 14/91 (15%), Positives = 37/91 (40%), Gaps = 9/91 (9%)

Query: 158 STTLWIGHLSKLVQEEEL----SDTFGEYGDVVSINLI---PPRGCAFVCMNRRQDAAKA 210
           S  + I +++  V +E+L           GD++ I +       G A++    ++ A   
Sbjct: 29  SQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAF 88

Query: 211 LYKLKNTKLQGKTITLAWAPGKGMKDKDWKD 241
           +   +    QG  + + ++  +  + +  +D
Sbjct: 89  VEAFQGYPFQGNPLVITFS--ETPQSQVAED 117

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 62.2 bits (152), Expect = 6e-13
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYK 213
           +  +++ +L      + L D F E G V+  ++       +GC  V     + A +A   
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRM 67

Query: 214 LKNTKLQGKTIT 225
           +   KL G+ I 
Sbjct: 68  MNGMKLSGREID 79

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 66.5 bits (163), Expect = 7e-13
 Identities = 16/83 (19%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQD 206
           V ++   TLW+ +      +  + D   +   V     +P       R  A++ +  ++D
Sbjct: 112 VSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKED 171

Query: 207 AAKALYKLKNTKLQGKTITLAWA 229
           A   + KL   K++G T+    +
Sbjct: 172 ARYCVEKLNGLKIEGYTLVTKVS 194

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 65.4 bits (160), Expect = 1e-12
 Identities = 22/107 (20%), Positives = 47/107 (43%), Gaps = 12/107 (11%)

Query: 137 NHPIHRELA---EIQARNGVENMCSTTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIP 192
            + +  +++   E   R     +    + I +LS +L+ E  L ++F  +G +  IN+  
Sbjct: 186 GYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPA 245

Query: 193 -------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK 232
                     CAF+    +  A +AL ++  + L  + I+++ A  K
Sbjct: 246 GQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK 291

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 54.6 bits (132), Expect = 6e-09
 Identities = 12/75 (16%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP----RGCAFVCMNRRQDAAKALYKL 214
           TT+ + +L K   + ++   F   G ++ +++          A +   R   A  A+ K 
Sbjct: 42  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 101

Query: 215 KNTKLQGKTITLAWA 229
            +  +    I ++  
Sbjct: 102 -HKVVGQNEIIVSHL 115

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 62.0 bits (151), Expect = 7e-13
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           S+ + + +L +    +E+ D   +Y  +    +   +  AFV +   + A  A+      
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 218 KLQGKTITLAWAPGKGM 234
             +GK + +   P   +
Sbjct: 64  SFRGKDLIVQLQPTDAL 80

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 62.7 bits (153), Expect = 7e-13
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 12/84 (14%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
             T++I +LS   +EE L +   ++GD+  + ++        +GCAF     ++ A K L
Sbjct: 15  GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74

Query: 212 ------YKLKNTKLQGKTITLAWA 229
                  +    KL G+ + +  A
Sbjct: 75  AAASLEAEGGGLKLDGRQLKVDLA 98

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 64.5 bits (157), Expect = 8e-13
 Identities = 20/96 (20%), Positives = 37/96 (38%), Gaps = 5/96 (5%)

Query: 142 RELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGC 196
            +L +     G        L + +L   V + ++ + F E+G +    +         G 
Sbjct: 72  HDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGT 131

Query: 197 AFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK 232
           A V   RR DA KA+ + K   L G+ + +     +
Sbjct: 132 ADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 167

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 62.5 bits (152), Expect = 8e-13
 Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 10/91 (10%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP--------RGCAFVCMNRRQDAAK 209
           +  L+IG + K+ + EE+ +   +  + V   ++          RG AFV     + AA 
Sbjct: 8   NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 67

Query: 210 ALYKL--KNTKLQGKTITLAWAPGKGMKDKD 238
           A  KL     +L G  I + WA  +   D+D
Sbjct: 68  ARRKLMPGRIQLWGHQIAVDWAEPEIDVDED 98

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 61.7 bits (151), Expect = 9e-13
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 6/81 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +  L++G L+  V +E L + F ++   +S +++        RG  FV    + DA  A+
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

Query: 212 YKLKNTKLQGKTITLAWAPGK 232
             ++   L G+ + + WA   
Sbjct: 61  DSMQGQDLNGRPLRINWAAKL 81

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 65.0 bits (158), Expect = 1e-12
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 2/92 (2%)

Query: 148 QARNGVENMCSTTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQ 205
            A  G+    ++ L + +L+ + V  + L   FG YGDV  + ++   +  A V M    
Sbjct: 24  IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGN 83

Query: 206 DAAKALYKLKNTKLQGKTITLAWAPGKGMKDK 237
            A  A+  L   KL GK I +  +  + ++  
Sbjct: 84  QAQLAMSHLNGHKLHGKPIRITLSKHQNVQLP 115

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 61.6 bits (149), Expect = 2e-11
 Identities = 24/96 (25%), Positives = 39/96 (40%), Gaps = 3/96 (3%)

Query: 137 NHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP--R 194
           N P+HR               S TL + ++   V EE+L   F   G VV         R
Sbjct: 130 NSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR 189

Query: 195 GCAFVCMNRRQDAAKALYKLKNTKL-QGKTITLAWA 229
             A + M   ++A +AL  L N  L +   + ++++
Sbjct: 190 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 225

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 64.1 bits (156), Expect = 1e-12
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 158 STTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLK 215
           ++ L + +L+ + V  + L   FG YGDV  + ++   +  A V M     A  A+  L 
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62

Query: 216 NTKLQGKTITLAWAPGKG 233
             KL GK I +  +  + 
Sbjct: 63  GHKLHGKPIRITLSKHQN 80

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 60.3 bits (146), Expect = 3e-11
 Identities = 24/96 (25%), Positives = 39/96 (40%), Gaps = 3/96 (3%)

Query: 137 NHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP--R 194
           N P+HR               S TL + ++   V EE+L   F   G VV         R
Sbjct: 99  NSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR 158

Query: 195 GCAFVCMNRRQDAAKALYKLKNTKL-QGKTITLAWA 229
             A + M   ++A +AL  L N  L +   + ++++
Sbjct: 159 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 194

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 63.0 bits (153), Expect = 1e-12
 Identities = 27/103 (26%), Positives = 46/103 (44%), Gaps = 7/103 (6%)

Query: 131 FDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINL 190
           F + + +H  H        R+     C   +++G+L     + EL   FG YG + S+ +
Sbjct: 52  FTVTEGSHHHHHH----MHRDSCPLDCK--VYVGNLGNNGNKTELERAFGYYGPLRSVWV 105

Query: 191 IP-PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK 232
              P G AFV     +DAA A+ +L    L G  + +  + G+
Sbjct: 106 ARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 148

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 62.3 bits (151), Expect = 1e-12
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 7/86 (8%)

Query: 151 NGVENMCSTT--LWI--GHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQD 206
            G+E +   T  L +  G L   V   +L     + G V ++ + P +  +F      ++
Sbjct: 16  EGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEE 75

Query: 207 AAKALYKLKNTKL---QGKTITLAWA 229
           + +A   L   ++    G+ ITL   
Sbjct: 76  SKRAYVTLNGKEVVDDLGQKITLYLN 101

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 61.0 bits (149), Expect = 1e-12
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 6/73 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           S+ L+I  L     +++L      YG +VS   I        +G  FV  +    A KA+
Sbjct: 5   SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64

Query: 212 YKLKNTKLQGKTI 224
             LK + +Q +  
Sbjct: 65  TALKASGVQAQMA 77

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L++G L   + E+ L   F  +G + SI L+        +G  F+  +  + A KAL
Sbjct: 26  PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85

Query: 212 YKLKNTKLQGKTITLAWA 229
            +L   +L G+ + +   
Sbjct: 86  EQLNGFELAGRPMKVGHV 103

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 61.2 bits (149), Expect = 2e-12
 Identities = 21/95 (22%), Positives = 43/95 (45%), Gaps = 9/95 (9%)

Query: 148 QARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCM 201
              +G+++  +  L+IG + + + E++L   F E+G +  + ++        +GCAF+  
Sbjct: 3   SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62

Query: 202 NRRQDAAKALYKLKNTKL---QGKTITLAWAPGKG 233
             R+ A KA   L   K      + I +  A  + 
Sbjct: 63  CERESALKAQSALHEQKTLPGMNRPIQVKPADSES 97

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 63.9 bits (156), Expect = 2e-12
 Identities = 15/107 (14%), Positives = 39/107 (36%), Gaps = 7/107 (6%)

Query: 135 DPNHPIHR-ELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP- 192
               P +  +   I  +   E      +++  + + + ++++   F  +G + S  L   
Sbjct: 101 KVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARD 160

Query: 193 -----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM 234
                 +G  F+   + Q +  A+  +    L G+ + +  A    M
Sbjct: 161 PTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPM 207

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 63.1 bits (154), Expect = 4e-12
 Identities = 23/137 (16%), Positives = 52/137 (37%), Gaps = 18/137 (13%)

Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMN 202
           A+        + +++G +   + E+ +   F  +G + SI++         +G AFV   
Sbjct: 19  AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYE 78

Query: 203 RRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDR-----L 257
             + A  AL ++ +  L G+ I +      G          E         ++R     +
Sbjct: 79  VPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEAR-----AFNRIYVASV 133

Query: 258 SKEIDYDYLEDGGVFDE 274
            +++  D ++   VF+ 
Sbjct: 134 HQDLSDDDIKS--VFEA 148

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 60.7 bits (148), Expect = 3e-12
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 3/82 (3%)

Query: 158 STTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
            + L+IG+L  K V +E+L   F  YG ++ IN+       F+  +  Q    A+     
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECESQ 67

Query: 217 TKLQGKTITLAWAPGKGMKDKD 238
               GK + L  +        D
Sbjct: 68  EMNFGKKLILEVSSSNARPQFD 89

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 62.6 bits (153), Expect = 3e-12
 Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 9/93 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP--------RGCAFVCMNRRQDAAK 209
           +  +++G + +   E++L + F +YG V  IN++          +GC FV    R+ A +
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 210 ALYKLKNTKLQGKTITLAWA-PGKGMKDKDWKD 241
           A   L N K+           P    K+   +D
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVED 95

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 59.5 bits (145), Expect = 4e-11
 Identities = 25/101 (24%), Positives = 44/101 (43%), Gaps = 11/101 (10%)

Query: 137 NHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI----- 191
           +HPI  + A+ +  N VE+     L+IG +SK   E ++   F  +G +    ++     
Sbjct: 77  HHPIQMKPADSEKNNAVED---RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDG 133

Query: 192 PPRGCAFVCMNRRQDAAKALYKLKNTKL---QGKTITLAWA 229
             RGCAFV    R  A  A+  +   +        + + +A
Sbjct: 134 LSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 61.0 bits (148), Expect = 3e-12
 Identities = 11/74 (14%), Positives = 29/74 (39%), Gaps = 2/74 (2%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKLK 215
           S  + +  L + V E +L +   ++G +  + ++P +  A V       A + +      
Sbjct: 15  SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADV 74

Query: 216 NTKLQGKTITLAWA 229
              + G+     ++
Sbjct: 75  PVYIAGQQAFFNYS 88

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 61.0 bits (148), Expect = 3e-12
 Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
            + +  L      ++L D   E GDV   + +   G   V   R++D   A+ KL NTK 
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYAD-VYRDGTGVVEFVRKEDMTYAVRKLDNTKF 75

Query: 220 QGKTITLAWA 229
           +      A+ 
Sbjct: 76  RSHEGETAYI 85

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 60.4 bits (147), Expect = 3e-12
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 155 NMCSTTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYK 213
           +   + L+IG+L  K V +E+L   F  YG ++ IN+       F+  +  Q    A+  
Sbjct: 19  SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIEX 76

Query: 214 LKNTKLQGKTITLAWAPGK 232
                  GK + L  +   
Sbjct: 77  ESQEMNFGKKLILEVSSSN 95

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 60.4 bits (147), Expect = 4e-12
 Identities = 18/77 (23%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSIN-LIPPRGCAFVCMNRRQDAAKALYKLKN 216
           + TL   +LS  + E+EL + F +  ++  ++     +G A++      DA K L + + 
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 75

Query: 217 TKLQGKTITLAWAPGKG 233
            ++ G++++L +   KG
Sbjct: 76  AEIDGRSVSLYYTGEKG 92

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 60.4 bits (147), Expect = 5e-12
 Identities = 22/100 (22%), Positives = 39/100 (39%), Gaps = 6/100 (6%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              +++G LS  +  E++   F  +G +    ++        +G  FV    + DA  A+
Sbjct: 15  HFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 74

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSY 251
            ++    L G+ I   WA  K    K   +    Q G S 
Sbjct: 75  QQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSS 114

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 60.4 bits (147), Expect = 5e-12
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           L+I HL +   +++L   F  +G+VVS  +         +   FV  +    A  A+  +
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 215 KNTKLQGKTITLAWAPGKG 233
              ++  K + +     K 
Sbjct: 88  NGFQIGMKRLKVQLKRSKN 106

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 62.4 bits (152), Expect = 5e-12
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +  L+IG L   + ++++ +    +G + + NL+        +G AF          +A+
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173

Query: 212 YKLKNTKLQGKTITLAWA 229
             L   +L  K + +  A
Sbjct: 174 AGLNGMQLGDKKLLVQRA 191

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 50.0 bits (120), Expect = 1e-07
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 12/83 (14%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-----------RGCAFVCMNRRQD 206
           +  L++G++   + EE + D F     +  +   P            +  AF+      +
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 207 AAKALYKLKNTKLQGKTITLAWA 229
             +A+        QG+++ +   
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRP 85

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 59.9 bits (145), Expect = 8e-12
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKLK 215
           S  + I  L   V E E+      +G V ++ ++  +  AF+ MN  + A   +  Y   
Sbjct: 31  SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSV 90

Query: 216 NTKLQGKTITLAWA 229
              L+G+ I + ++
Sbjct: 91  TPVLRGQPIYIQFS 104

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 17/85 (20%), Positives = 41/85 (48%), Gaps = 4/85 (4%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYK 213
           S  ++I +L K +  + L DTF  +G+++S  ++      +G  FV    ++ A +A+ K
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 64

Query: 214 LKNTKLQGKTITLAWAPGKGMKDKD 238
           +    L  + + +     +  ++ +
Sbjct: 65  MNGMLLNDRKVFVGRFKSRKEREAE 89

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 59.1 bits (143), Expect = 1e-11
 Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 2/83 (2%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKLK 215
           S  + I  L   V E E+      +G V ++ ++  +  AF+ MN  + A   +  Y   
Sbjct: 16  SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSV 75

Query: 216 NTKLQGKTITLAWAPGKGMKDKD 238
              L+G+ I + ++  K +K   
Sbjct: 76  TPVLRGQPIYIQFSNHKELKTDS 98

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 9/82 (10%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           S TL++  LS+   EE L ++F      V   ++        +G  FV  N  +DA  A 
Sbjct: 15  SKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71

Query: 212 YKLKNTKLQGKTITLAWAPGKG 233
             +++ ++ G  +TL WA  KG
Sbjct: 72  EAMEDGEIDGNKVTLDWAKPKG 93

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 58.6 bits (142), Expect = 2e-11
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKLK 215
           S  + I  L   V E +L +   E+G +  + ++P +  A V       A  A+      
Sbjct: 21  SPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADN 80

Query: 216 NTKLQGKTITLAWA 229
              + G    + ++
Sbjct: 81  QIYIAGHPAFVNYS 94

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L+I HL +   + +L+ TF  +G+V+S  +         +   FV  +    A  A+
Sbjct: 40  GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99

Query: 212 YKLKNTKLQGKTITLAWA 229
             +   ++  K + +   
Sbjct: 100 KAMNGFQVGTKRLKVQLK 117

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 60.3 bits (147), Expect = 2e-11
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +  L+IG L   + ++++ +    +G + + NL+        +G AF          +A+
Sbjct: 94  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153

Query: 212 YKLKNTKLQGKTITLAWA 229
             L   +L  K + +  A
Sbjct: 154 AGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 50.7 bits (122), Expect = 5e-08
 Identities = 15/106 (14%), Positives = 34/106 (32%), Gaps = 17/106 (16%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-----------RGCAFVCMNRRQD 206
           +  L++G++   + EE + D F     +  +   P            +  AF+      +
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 207 AAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDF-----WEVQD 247
             +A+        QG+++ +             K F       + D
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLND 108

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 58.3 bits (141), Expect = 3e-11
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 2/74 (2%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKLK 215
           S  L I  L   V E E+      +G V +I ++  +  AF+ +   + A   +  Y   
Sbjct: 15  SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAV 74

Query: 216 NTKLQGKTITLAWA 229
              L+ + I + ++
Sbjct: 75  TPHLRNQPIYIQYS 88

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 61.8 bits (149), Expect = 3e-11
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 158 STTLWIGHLSKLVQEEEL----SDTFGEYGDVVSINLI---PPRGCAFVCMNRRQDAAKA 210
           + T++I +L++ ++++EL       F ++G ++ I +      RG AFV       A  A
Sbjct: 9   NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68

Query: 211 LYKLKNTKLQGKTITLAWA 229
           L  ++      K + + +A
Sbjct: 69  LRSMQGFPFYDKPMRIQYA 87

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 55.3 bits (132), Expect = 5e-09
 Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR-GCAFVCMNRRQDAAKALYKLKNTK 218
            L++ +L +   E  LS  F ++     + L+P R   AFV  +    A  A   L+  K
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFK 268

Query: 219 L-QGKTITLAWA 229
           + Q   + +++A
Sbjct: 269 ITQNNAMKISFA 280

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 58.3 bits (141), Expect = 3e-11
 Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL 219
            + +  L      ++L D   E GDV   + +   G   V   R++D   A+ KL NTK 
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYAD-VYRDGTGVVEFVRKEDMTYAVRKLDNTKF 76

Query: 220 QGKTITLAWA 229
           +      A+ 
Sbjct: 77  RSHEGETAYI 86

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 60.5 bits (146), Expect = 4e-11
 Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 2/88 (2%)

Query: 158 STTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIPP-RGCAFVCMNRRQDAAKALYKLK 215
           S  L +  L    +  + + + F  YG+V  +  +    G A V M       +A+  L 
Sbjct: 4   SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLN 63

Query: 216 NTKLQGKTITLAWAPGKGMKDKDWKDFW 243
           N  + G+ + +  +    +         
Sbjct: 64  NNFMFGQKMNVCVSKQPAIMPGQSYGLE 91

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 53.6 bits (128), Expect = 8e-09
 Identities = 14/97 (14%), Positives = 27/97 (27%), Gaps = 6/97 (6%)

Query: 136 PNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--- 192
                +R     QA        S  L   +    V EE   +   E G     ++     
Sbjct: 101 SESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSG 160

Query: 193 ---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL 226
                    +  + + DA + L  L + +++      
Sbjct: 161 KSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPY 197

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 57.3 bits (139), Expect = 4e-11
 Identities = 25/87 (28%), Positives = 36/87 (41%), Gaps = 11/87 (12%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYG-DVVSINLIP------PRGCAFVCMNRRQDAAKA 210
           + +LW+G L   + E  +S  F   G  V+S+ +I       P G  FV       A K 
Sbjct: 9   AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68

Query: 211 LYKLKNTKLQG----KTITLAWAPGKG 233
           L+K+    L G    K   L +A   G
Sbjct: 69  LHKINGKPLPGATPAKRFKLNYATYSG 95

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 56.8 bits (138), Expect = 6e-11
 Identities = 16/84 (19%), Positives = 37/84 (44%), Gaps = 11/84 (13%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           + ++++G++      EEL   F   G V  + ++       P+G A++  + ++    +L
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65

Query: 212 YKLKNTKLQGKTITLAWA----PG 231
             L  +  +G+ I +       PG
Sbjct: 66  -ALDESLFRGRQIKVIPKRTNRPG 88

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 56.8 bits (138), Expect = 7e-11
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKA 210
           S+ ++IG+L   + E+ L DTF  +G ++    I         +G AF+       +  A
Sbjct: 5   SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64

Query: 211 LYKLKNTKLQGKTITLAWA 229
           +  +    L  + IT+++A
Sbjct: 65  IEAMNGQYLCNRPITVSYA 83

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 58.4 bits (141), Expect = 7e-11
 Identities = 18/104 (17%), Positives = 34/104 (32%), Gaps = 8/104 (7%)

Query: 134 ADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYG--DVVSINLI 191
            +P+   + +   I             +++G  S    +++L       G  DVV +   
Sbjct: 31  QEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFA 90

Query: 192 P------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
                   +G A V +       K L  L    L G+ + +  A
Sbjct: 91  ENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA 134

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 57.9 bits (140), Expect = 8e-11
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 11/83 (13%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-----------RGCAFVCMNRRQD 206
           +  +++ +L+K VQE++L   FG Y D  S                 +G AF+ +   + 
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 207 AAKALYKLKNTKLQGKTITLAWA 229
           AAKAL +     L GK + + +A
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFA 127

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 7/72 (9%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
            +++G+L      E++ + F ++G V ++ LI       P+G  FV M   +  ++A+ K
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61

Query: 214 LKNTKLQGKTIT 225
           L NT   G+TI 
Sbjct: 62  LDNTDFMGRTIR 73

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 56.2 bits (136), Expect = 1e-10
 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 12/84 (14%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYG--DVVSINLIP------PRGCAFVCMNRRQDAAK 209
             T+ + +++     + +      Y    V +I LI        RG AFV ++   DA++
Sbjct: 9   MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQ 68

Query: 210 ALYKLKNT----KLQGKTITLAWA 229
            L  L++     K+ GKTI + +A
Sbjct: 69  LLQILQSLHPPLKIDGKTIGVDFA 92

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 57.0 bits (138), Expect = 1e-10
 Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 11/90 (12%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
             ++++G++      ++L   F   G +  I ++       P+G A++    R     A+
Sbjct: 36  KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95

Query: 212 YKLKNTKLQGKTITLAWA----PGKGMKDK 237
             +  T  +G+TI +       PG    D+
Sbjct: 96  -AMDETVFRGRTIKVLPKRTNMPGISSTDR 124

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 56.1 bits (136), Expect = 1e-10
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 8/77 (10%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYG--DVVSINLIP------PRGCAFVCMNRRQDAAKALY 212
           L+IG+L+    +E+L++     G  D++ I           +G A V +     + K + 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 213 KLKNTKLQGKTITLAWA 229
            L   +L G+   +  +
Sbjct: 64  LLPKRELHGQNPVVTPS 80

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 14/86 (16%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVS--------INLIP------PRGCAFVCMNR 203
           + T+++  L + V  E ++D F + G + +        INL         +G A V  + 
Sbjct: 13  NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72

Query: 204 RQDAAKALYKLKNTKLQGKTITLAWA 229
              A  A+      +  G  I +++A
Sbjct: 73  PPSAKAAIDWFDGKEFSGNPIKVSFA 98

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 58.2 bits (140), Expect = 3e-10
 Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 8/86 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYG--DVVSINLIP------PRGCAFVCMNRRQDAAK 209
              L+IG+L+    +E+L++     G  D++ I           +G A V +     + K
Sbjct: 68  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 127

Query: 210 ALYKLKNTKLQGKTITLAWAPGKGMK 235
            +  L   +L G+   +     + + 
Sbjct: 128 LMDLLPKRELHGQNPVVTPVNKQFLS 153

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 21/90 (23%), Positives = 33/90 (36%), Gaps = 6/90 (6%)

Query: 148 QARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMN 202
               G E+     L+IG+L+      EL     E      + ++       R   +V   
Sbjct: 7   DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 66

Query: 203 RRQDAAKALYKLKNTKLQGKTITLAWAPGK 232
             +D  KAL +L   K+ G  I L    G+
Sbjct: 67  SAEDLEKAL-ELTGLKVFGNEIKLEKPKGR 95

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 55.5 bits (134), Expect = 3e-10
 Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 14/91 (15%)

Query: 153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDV--------VSINLIP------PRGCAF 198
            +N  + T+++  L + V  E ++D F + G +          INL         +G A 
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 199 VCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
           V  +    A  A+      +  G  I +++A
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 55.5 bits (134), Expect = 4e-10
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 14/86 (16%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDV--------VSINLIP------PRGCAFVCMNR 203
           ++ +++  L+  V  ++L+D F + G V          I++        P+G A V    
Sbjct: 15  NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74

Query: 204 RQDAAKALYKLKNTKLQGKTITLAWA 229
              A  A+        QG  + ++ A
Sbjct: 75  PPTAKAAVEWFDGKDFQGSKLKVSLA 100

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 54.5 bits (132), Expect = 4e-10
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 6/75 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           +++G LS  +    ++  F  +G +    ++        +G  FV    + DA  A+ ++
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 215 KNTKLQGKTITLAWA 229
               L G+ I   WA
Sbjct: 69  GGQWLGGRQIRTNWA 83

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
            T + + ++   V  +E+ D F  Y  +     +       P G A V    R +A  A+
Sbjct: 15  PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74

Query: 212 YKLKNTKLQGKTITLAWA 229
             L +  +  + + L   
Sbjct: 75  IDLNDRPIGSRKVKLVLG 92

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 18/88 (20%), Positives = 29/88 (32%), Gaps = 9/88 (10%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKA 210
             T ++G+L   V EE + + F     + ++ L          +G  +           A
Sbjct: 15  PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

Query: 211 LYKLKNTKLQGKTITLAWAPGKGMKDKD 238
           L  L    L  K I +  A     KD  
Sbjct: 74  L-SLNEESLGNKRIRVDVADQAQDKDSG 100

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 7/77 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALY 212
             T+++G +   + E E+   F  YG V  + +I       +G  FV      D  K + 
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68

Query: 213 KLKNTKLQGKTITLAWA 229
              N    GK + L  A
Sbjct: 69  SQIN--FHGKKLKLGPA 83

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 7/74 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           + T++   L+  ++  +L D F   G V  + +I        +G A+V     Q    A+
Sbjct: 25  ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 84

Query: 212 YKLKNTKLQGKTIT 225
             L   +L G  I 
Sbjct: 85  -GLTGQRLLGVPII 97

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
            T + + ++   V  +E+ D F  Y  +     +       P G A V    R +A  A+
Sbjct: 15  PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74

Query: 212 YKLKNTKLQGKTITLAWA 229
             L +  +  + + L+  
Sbjct: 75  IDLNDRPIGSRKVKLSGP 92

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 52.9 bits (127), Expect = 3e-09
 Identities = 16/99 (16%), Positives = 37/99 (37%), Gaps = 5/99 (5%)

Query: 133 MADPNHPIHRELAEIQARNGVENMCST--TLWIGHLSKLVQEEELSDTFGEYGDVVS--- 187
           M   +H  H     +   + +  + +    + + +L +    ++L D   E     +   
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSS 60

Query: 188 INLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL 226
           +N     G   +     +   +AL +L N + +G  IT+
Sbjct: 61  VNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 52.9 bits (127), Expect = 3e-09
 Identities = 17/90 (18%), Positives = 40/90 (44%), Gaps = 12/90 (13%)

Query: 152 GVENMCSTTLWIGHLSKLVQEEEL---SDTFGEYGDVVSINLIP---------PRGCAFV 199
            V  +    +++  LS+ + + E+    + FG++G +  + +           P   A+V
Sbjct: 9   SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYV 68

Query: 200 CMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
              R +DA +A+  + N  + G+T+  +  
Sbjct: 69  TYIRSEDALRAIQCVNNVVVDGRTLKASLG 98

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 51.1 bits (123), Expect = 8e-09
 Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 9/79 (11%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-------PPRGCAFVCMNRRQDAAKA 210
             T ++G+L   V EE + + F     + ++ L          +G  +           A
Sbjct: 19  PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 77

Query: 211 LYKLKNTKLQGKTITLAWA 229
           L  L    L  + I +  A
Sbjct: 78  L-SLNEESLGNRRIRVDVA 95

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 8/81 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKAL 211
             T ++G+L     + ++   F +   + S+ L+        +G  +V  +      +AL
Sbjct: 15  PYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73

Query: 212 YKLKNTKLQGKTITLAWAPGK 232
                  L  +++ +  A G+
Sbjct: 74  -TYDGALLGDRSLRVDIAEGR 93

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 51.0 bits (121), Expect = 2e-07
 Identities = 22/117 (18%), Positives = 41/117 (35%), Gaps = 6/117 (5%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
           TL++  ++    E +L   F  YG +  I+++       PRG AF+     +D   A   
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163

Query: 214 LKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGG 270
               K+ G+ + +    G+ +K    +       G      D   +    D      
Sbjct: 164 ADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYD 220

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 10/78 (12%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALY 212
           + +++I         +++ +   + G V++I +        +G  FV  +  + A K + 
Sbjct: 11  NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV- 69

Query: 213 KLKNTKLQGKTITLAWAP 230
           +    K +   + + +  
Sbjct: 70  ETPGQKYKETDLLILFKD 87

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 46.2 bits (109), Expect = 4e-07
 Identities = 19/73 (26%), Positives = 31/73 (42%)

Query: 152 GVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL 211
           G     S+ L + +L+  +    L     ++G +VS +    +G A      R++A KA 
Sbjct: 1   GAMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQ 60

Query: 212 YKLKNTKLQGKTI 224
             L N  L   TI
Sbjct: 61  MALNNCVLANTTI 73

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 45.8 bits (108), Expect = 6e-07
 Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 172 EEELSDTFGEYGDVVSINLIPP---RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW 228
           ++ L + F  +G V S+ L P    +  A V M   QDA  A+  L   K+  K I ++ 
Sbjct: 27  QQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL 86

Query: 229 APGKGMK 235
           A G    
Sbjct: 87  ATGASGP 93

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 46.4 bits (110), Expect = 7e-07
 Identities = 16/86 (18%), Positives = 27/86 (31%), Gaps = 7/86 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              +++  L    + + + D F +   V     I         G  FV      D   AL
Sbjct: 25  GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL 84

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKDK 237
                  +  + I +     KGM +K
Sbjct: 85  -CRHKQYMGNRFIQVHPITKKGMLEK 109

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 14/94 (14%), Positives = 30/94 (31%), Gaps = 7/94 (7%)

Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMN 202
           +  G  N       I ++   + + ++           +   +         G A V   
Sbjct: 6   SGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFK 65

Query: 203 RRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKD 236
              DA K+  +L   KL G+   +     + M++
Sbjct: 66  NEDDARKSE-RLHRKKLNGREAFVHVVTLEDMRE 98

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 48.3 bits (114), Expect = 1e-06
 Identities = 40/342 (11%), Positives = 90/342 (26%), Gaps = 117/342 (34%)

Query: 5   KTFNQELSSLYDTKPPISK------AKITAITRSAIRAIKFYKHVV-------------- 44
           + + ++   LY+     +K           + R A+  ++  K+V+              
Sbjct: 110 RMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL-RQALLELRPAKNVLIDGVLGSGKTWVAL 168

Query: 45  QSVEKFIIKCKPEYKV------------PALYVIDSLVRQSRHQFQ---DKDVFGPRFAR 89
                + ++CK ++K+              L ++  L+ Q    +    D          
Sbjct: 169 DVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIH 228

Query: 90  NLKATFQHLYQCPPEDKSKIIRVLNLWQKN--EVF---------TPDIIHPLFDMADPNH 138
           +++A  + L +  P +   ++ +LN+        F         T      + D      
Sbjct: 229 SIQAELRRLLKSKPYENCLLV-LLNVQNAKAWNAFNLSCKILLTTRFK--QVTDFLSAAT 285

Query: 139 PIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAF 198
             H  L                    H S  +  +E+     +Y D      +P      
Sbjct: 286 TTHISL-------------------DHHSMTLTPDEVKSLLLKYLDC-RPQDLPREVL-- 323

Query: 199 VCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLS 258
                                    +++          +D    W   D   ++  D+L+
Sbjct: 324 ----------------TTNPR---RLSIIAE-----SIRDGLATW---DNWKHVNCDKLT 356

Query: 259 KEID-----------YDYLEDGGVFDEDT-VP------LWLK 282
             I+               +   VF     +P      +W  
Sbjct: 357 TIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFD 398

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.0 bits (108), Expect = 8e-06
 Identities = 50/292 (17%), Positives = 88/292 (30%), Gaps = 87/292 (29%)

Query: 9   QELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKF--IIKCKPEYKVPALYVI 66
           Q+L     T  P   + I    R  +     +KHV  + +K   II+       PA Y  
Sbjct: 316 QDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV--NCDKLTTIIESSLNVLEPAEY-- 371

Query: 67  DSLVRQSRHQFQDKDVFGPRFARNLKATFQHL--------YQCPPEDKSKIIR--VLNLW 116
                  R  F    VF P    +       L                +K+ +  ++   
Sbjct: 372 -------RKMFDRLSVF-PP---SAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ 420

Query: 117 QKNEVFTPDIIHPL-FDM---ADPNHPIHRELAEIQARNGVENMCSTTL----------- 161
            K    +   I  +  ++    +  + +HR +  +   N  +   S  L           
Sbjct: 421 PKESTIS---IPSIYLELKVKLENEYALHRSI--VDHYNIPKTFDSDDLIPPYLDQYFYS 475

Query: 162 WIG-HLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ 220
            IG HL  +   E +   F      V ++        F+     Q       K+++    
Sbjct: 476 HIGHHLKNIEHPERM-TLFRM----VFLDF------RFL----EQ-------KIRHD--- 510

Query: 221 GKTITLAWAPGKGMKD-----KDWKDFWEVQDGVSYIPYDRLSKEIDYDYLE 267
               + AW     + +     K +K +    D      Y+RL   I  D+L 
Sbjct: 511 ----STAWNASGSILNTLQQLKFYKPYICDNDPK----YERLVNAIL-DFLP 553

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 46.1 bits (110), Expect = 3e-06
 Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 11/96 (11%)

Query: 135 DPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI--- 191
           +P   + RE     ++    ++    +++G + +  +E  L D F +YG +  I ++   
Sbjct: 85  EPKRAVSRE----DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR 140

Query: 192 ---PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTI 224
                RG AFV  +      K +   K   + G   
Sbjct: 141 GSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNC 175

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 41.9 bits (99), Expect = 7e-05
 Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 7/84 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           L+IG LS    +E L   F ++G +    ++        RG  FV     ++   A+   
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 74

Query: 215 KNTKLQGKTITLAWAPGKGMKDKD 238
           +  K+ G+ +    A  +    + 
Sbjct: 75  RPHKVDGRVVEPKRAVSREDSQRP 98

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 6/66 (9%)

Query: 163 IGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKN 216
           I      V ++ L+  F + G VV++           +G  FV      DA K +     
Sbjct: 17  IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76

Query: 217 TKLQGK 222
            +L  K
Sbjct: 77  KRLDLK 82

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 2/66 (3%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC-AFVCMNRRQDAAKALYKLKNTK 218
           ++++    + V   +LS+ F  +G V S+ +   +G  A V M         L       
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVL-SQSQHS 68

Query: 219 LQGKTI 224
           L G  +
Sbjct: 69  LGGHRL 74

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 43.2 bits (102), Expect = 5e-06
 Identities = 12/75 (16%), Positives = 30/75 (40%), Gaps = 12/75 (16%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGD-----------VVSINLIPPRGCAFVCMNRRQDAAK 209
           L++G++   + EE + D F                V+++ +   +  AF+      +  +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 210 ALYKLKNTKLQGKTI 224
           A+        QG+++
Sbjct: 69  AM-AFDGIIFQGQSL 82

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDA 207
           ++   T +++G L     +  L   F  +GD+    +I        RG  FV M  R  A
Sbjct: 13  KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72

Query: 208 AKALYKLKNTKLQGKTIT 225
            +A  K  N  + G+   
Sbjct: 73  ERAC-KDPNPIIDGRKAN 89

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 7/71 (9%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           +++G +     E EL + F ++G V  + +I       PRG  F+     Q   +A+  +
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71

Query: 215 KNTKLQGKTIT 225
               + GK + 
Sbjct: 72  HFHDIMGKKVE 82

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 42.7 bits (101), Expect = 7e-06
 Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 7/83 (8%)

Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNR 203
             +G       T+ +      V E+ + +        V+I ++        G  FV  + 
Sbjct: 1   GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSN 59

Query: 204 RQDAAKALYKLKNTKLQGKTITL 226
            ++  +AL K     + G+ I +
Sbjct: 60  EEEVKQAL-KCNREYMGGRYIEV 81

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 8/55 (14%), Positives = 18/55 (32%), Gaps = 4/55 (7%)

Query: 172 EEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGK 222
           +  +   F ++G + +          +G  F+       A  A+      KL  +
Sbjct: 35  KNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 16/109 (14%), Positives = 32/109 (29%), Gaps = 7/109 (6%)

Query: 132 DMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI 191
            MA              +   V++     + +  L     E ++ + F      V +++ 
Sbjct: 20  HMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIE 78

Query: 192 P-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMK 235
                   G A V     ++A  A+       +Q + I L      G  
Sbjct: 79  IGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGAS 126

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 43.3 bits (103), Expect = 1e-05
 Identities = 14/73 (19%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKAL 211
           +  +++G +   V+ +E  + F ++G ++   L+        RG  FV  +   DA   +
Sbjct: 87  TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD-SADAVDRV 145

Query: 212 YKLKNTKLQGKTI 224
            + K    + + I
Sbjct: 146 CQNKFIDFKDRKI 158

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 39.4 bits (93), Expect = 4e-04
 Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 8/91 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           S  ++IG L+    E+ L + FG+YG V  + ++        RG  F+   +     + +
Sbjct: 3   SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKDKDWKDF 242
                  L GK I    A  +  +DK  K F
Sbjct: 63  KTQH--ILDGKVIDPKRAIPRDEQDKTGKIF 91

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 3/70 (4%)

Query: 158 STTLWIGHL-SKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKL 214
              + + +L      +  +      YG + +  L+  +  AF+ M  R+DA   +     
Sbjct: 25  GRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLK 84

Query: 215 KNTKLQGKTI 224
           K    QG+ +
Sbjct: 85  KALWFQGRCV 94

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 7/77 (9%)

Query: 160 TLWIGHLSKLVQEEELSDTFGE-YGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYK 213
           +L++G L+  V +  L + F + Y       ++       +G  FV      +  +AL +
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 214 LKN-TKLQGKTITLAWA 229
            +    L  K + L+ A
Sbjct: 71  CQGAVGLGSKPVRLSVA 87

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 8/55 (14%), Positives = 18/55 (32%), Gaps = 4/55 (7%)

Query: 172 EEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGK 222
           +  +   F ++G + +          +G  F+       A  A+      KL  +
Sbjct: 21  KNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 163 IGHLSKLVQEEELSDTFGEYGDVVSINLI-PPRGCAFVCMNRRQDAAKALYKLKNTKLQG 221
           +G  +  + E+EL + F +YGDV+ + +  P R  AFV     Q A       ++  ++G
Sbjct: 10  VGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLC--GEDLIIKG 67

Query: 222 KTI 224
            ++
Sbjct: 68  ISV 70

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 7/75 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              + +  L     +EE+   F     V +   +P        G AFV    ++ A KAL
Sbjct: 42  DGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL 101

Query: 212 YKLKNTKLQGKTITL 226
                 ++  + I +
Sbjct: 102 -GKHKERIGHRYIEV 115

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 40.1 bits (94), Expect = 9e-05
 Identities = 13/83 (15%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALY 212
              + +  +     E ++ D F     V +++L+        G   V     QD  +AL 
Sbjct: 16  DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL- 73

Query: 213 KLKNTKLQGKTITLAWAPGKGMK 235
           K     +  + + ++ A  +   
Sbjct: 74  KRNRMLMIQRYVEVSPATERQWV 96

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 7/83 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALY 212
              + +  L     E ++ + F      + +++         G A V     +DA  A+ 
Sbjct: 15  GHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM- 72

Query: 213 KLKNTKLQGKTITLAWAPGKGMK 235
                 +Q + + L      G  
Sbjct: 73  AKDKANMQHRYVELFLNSTAGTS 95

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-PPRGCAFVCMNRRQDAAKALY 212
            +   + +++G  ++ +  EEL   F +YG+VV + +  P R  AFV     + A     
Sbjct: 7   HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLC- 65

Query: 213 KLKNTKLQGKTI 224
             ++  ++G ++
Sbjct: 66  -GEDLIIKGISV 76

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 17/91 (18%), Positives = 33/91 (36%), Gaps = 7/91 (7%)

Query: 151 NGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRR 204
           N  +      + +  L     +EE+   F     V +   +P        G AFV    +
Sbjct: 8   NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQ 67

Query: 205 QDAAKALYKLKNTKLQGKTITLAWAPGKGMK 235
           + A KAL K    ++  + I +  +    ++
Sbjct: 68  EIAEKAL-KKHKERIGHRYIEIFKSSRAEVR 97

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 9/97 (9%)

Query: 134 ADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP- 192
           +  +H  H      +  +   +     ++IG LS    +E L + FG++G+V    ++  
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGSS--GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD 60

Query: 193 -----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTI 224
                 RG  FV    +    K L      +L  KTI
Sbjct: 61  PLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTI 96

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 38.2 bits (90), Expect = 2e-04
 Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 7/68 (10%)

Query: 163 IGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKN 216
           +G LS     E++   F ++G V    L+        RG  FV         K   ++  
Sbjct: 4   VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHF 62

Query: 217 TKLQGKTI 224
            ++  K +
Sbjct: 63  HEINNKMV 70

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 12/66 (18%), Positives = 24/66 (36%), Gaps = 6/66 (9%)

Query: 165 HLSKL----VQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKLKNTK 218
           H+           +L      +G + +  ++     AF+ M   +DA  A+  Y      
Sbjct: 19  HIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPAL 78

Query: 219 LQGKTI 224
           + GK +
Sbjct: 79  VFGKPV 84

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 7/70 (10%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           +++G LS    +++L D F ++G+VV   +         RG  F+         K L   
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVL-DQ 72

Query: 215 KNTKLQGKTI 224
           K  +L G+ I
Sbjct: 73  KEHRLDGRVI 82

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 7/70 (10%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           L++G L     +E L   F +YG+VV   ++        RG  FV           L   
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-AS 77

Query: 215 KNTKLQGKTI 224
           +   L G+ I
Sbjct: 78  RPHTLDGRNI 87

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 37.5 bits (88), Expect = 4e-04
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 7/68 (10%)

Query: 163 IGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKN 216
           +G LS    EE++ + FG +G+V SI L         RG  F+     +   K + + K 
Sbjct: 4   VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKY 62

Query: 217 TKLQGKTI 224
             +     
Sbjct: 63  HNVGLSKC 70

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 12/70 (17%), Positives = 28/70 (40%), Gaps = 8/70 (11%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           L +  L     E++L + F  +G+V+ + +         +G  FV     +   K +   
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM-SQ 76

Query: 215 KNTKLQGKTI 224
           ++  + G+  
Sbjct: 77  RHM-IDGRWC 85

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 7/70 (10%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           L+IG LS    EE L + + ++G +    ++        RG  FV  +   +   A+   
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AA 88

Query: 215 KNTKLQGKTI 224
           +   + G+ +
Sbjct: 89  RPHSIDGRVV 98

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 39.4 bits (91), Expect = 5e-04
 Identities = 10/97 (10%), Positives = 34/97 (35%), Gaps = 6/97 (6%)

Query: 138 HPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP---- 193
                +           ++ + +++I         +++ +   + G V++I +       
Sbjct: 89  RRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKA 148

Query: 194 -RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
            +G  FV  +  + A K + +    K +   + + + 
Sbjct: 149 FKGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFK 184

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 36.7 bits (86), Expect = 6e-04
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 7/70 (10%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKL 214
           ++IG LS    +E L + FG++G+V    ++        RG  FV    +    K L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 215 KNTKLQGKTI 224
              +L  KTI
Sbjct: 62  SRHELDSKTI 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	282
3d9j_A	145	RNA-binding protein 16; SCAF8, RNA polymerase II C	99.97
3clj_A	157	Protein NRD1; CTD-interacting domain, nucleus, pho	99.97
1sz9_A	144	PCF11 protein; RNA polymerase II CTD interacting d	99.91
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.83
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.83
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.82
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.82
4fu3_A	135	Regulation of nuclear PRE-mRNA domain-containing 1	99.82
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.81
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.81
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.8
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.8
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.8
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.8
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.8
4flb_A	132	Regulation of nuclear PRE-mRNA domain-containing;	99.79
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.79
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.79
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.78
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.78
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.78
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.78
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.78
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.78
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.77
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.77
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.77
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.77
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.77
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.77
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.77
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.77
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.77
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.77
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.77
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.77
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.77
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.76
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.76
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.76
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.76
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.76
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.76
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.76
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.76
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.76
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.76
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.76
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.76
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.76
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.76
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.75
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.75
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.75
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.75
1x5p_A	97	Negative elongation factor E; structure genomics,	99.75
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.75
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.75
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.75
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.75
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.75
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.75
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.75
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.75
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.75
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.74
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.74
2div_A	99	TRNA selenocysteine associated protein; structural	99.74
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.74
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.74
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.74
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.74
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.74
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.74
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.74
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.74
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.74
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.73
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.73
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.73
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.73
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.73
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.73
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.73
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.73
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.73
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.73
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.73
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.73
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.73
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.73
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.73
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.72
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.72
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.72
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.72
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.72
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.72
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.72
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.72
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.72
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.71
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.71
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.71
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.71
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.71
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.71
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.71
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.71
2km4_A	142	Regulator of TY1 transposition protein 103; CTD-in	99.71
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.71
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.7
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.7
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.7
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.7
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.7
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.7
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.7
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.7
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.7
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.7
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.7
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.7
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.69
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.69
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.69
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.69
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.69
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.69
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.69
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.69
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.69
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.69
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.69
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.69
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.68
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.68
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.68
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.68
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.68
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.68
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.67
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.67
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.67
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.66
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.66
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.66
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.66
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.65
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.65
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.65
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.65
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.65
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.45
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.64
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.64
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.64
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.63
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.62
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.62
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.62
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.62
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.62
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.61
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.61
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.61
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.6
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.59
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.59
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.59
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.59
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.59
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.59
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.59
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.59
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.59
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.58
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.58
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.58
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.58
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.57
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.57
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.57
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.56
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.56
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.56
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.56
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.56
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.55
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.55
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.55
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.54
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.54
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.54
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.53
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.52
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.47
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.46
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.46
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.44
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.43
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.41
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.37
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.36
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.28
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.15
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.05
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.81
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.66
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.05
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.53
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.2
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.05
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.98
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.94
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.56
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.46
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.29
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.47
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.46
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	91.71
1x5b_A	163	Signal transducing adaptor molecule 2; VHS domain,	89.12
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	88.47
3zyq_A	226	Hepatocyte growth factor-regulated tyrosine kinas	88.22
1mhq_A	148	ADP-ribosylation factor binding protein GGA2; supe	87.62
1juq_A	171	ADP-ribosylation factor binding protein GGA3; prot	86.28
3g2s_A	149	C-terminal fragment of sortilin-related receptor;	84.31
1elk_A	157	Target of MYB1; superhelix of helices, endocytosis	84.21
3ldz_A	140	STAM-1, signal transducing adapter molecule 1; ubi	84.07

>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting domain, arm repeats phospho-CTD, phosphoprotein, transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A* 3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A

Probab=99.97  E-value=1.7e-31  Score=208.78  Aligned_cols=134  Identities=75%  Similarity=1.200  Sum_probs=126.4

Q ss_pred             CchhHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhcc-C
Q psy3994           1 MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQ-D   79 (282)
Q Consensus         1 m~~~~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~-~   79 (282)
                      |+++++|++.|++|.++++|+|+++|++||.||++|++++++||+.|+++|++|+|.+||++|||+|||+|+++++.+ +
T Consensus         1 m~~v~~f~~~L~~L~~~k~~~S~~~I~~LT~~a~~~~~~~~~IV~~~~~~i~k~~~~~KL~~LYL~DsIvrn~~~k~~~~   80 (145)
T 3d9j_A            1 MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQE   80 (145)
T ss_dssp             -CHHHHHHHHHHGGGGSCSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             CcHHHHHHHHHHHHHhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceeehhhhhHHHHHHhhhhcCCc
Confidence            999999999999999999779999999999999999999999999999999999999999999999999999999875 4


Q ss_pred             CCCchhhHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccCcccCCccccccccCC
Q psy3994          80 KDVFGPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMA  134 (282)
Q Consensus        80 ~~~~~~~f~~~l~~~f~~v~~~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~~~~  134 (282)
                      .+.|++.|+..|.++|..++.+++..+.++.+++++|+++++|+++.++.+.+..
T Consensus        81 ~~~f~~~F~~~L~~~f~~~~~~~~~~r~kl~rLl~iW~~r~vF~~~~l~~l~~~l  135 (145)
T 3d9j_A           81 KDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMA  135 (145)
T ss_dssp             TCSHHHHHHHHHHHHHHHHTSSCGGGHHHHHHHHHHHHHTTSSCHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHh
Confidence            5689999999999999999998899999999999999999999999998887643

>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae}

Probab=99.97  E-value=8.2e-31  Score=204.33  Aligned_cols=133  Identities=20%  Similarity=0.369  Sum_probs=118.8

Q ss_pred             CchhHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccC-
Q psy3994           1 MDVIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQD-   79 (282)
Q Consensus         1 m~~~~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~-   79 (282)
                      |+ +++|++.|++|.++++++|++||.+||.+|++|+++|+++|+.++++|++|+|+|||++|||+|||+|+++++.+. 
T Consensus         1 Ms-v~ef~~~L~sL~~lkp~iS~skI~~LT~~A~~nv~~~~~iv~~l~~~ikk~p~~hKL~~LYVvDSIvR~~~~~~~k~   79 (157)
T 3clj_A            1 MD-FQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSIGRAYLDETRSN   79 (157)
T ss_dssp             CC-HHHHHHHHHGGGGCSSSCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CC-HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhCCCcceeeeeeehHHHHHHHHHHHHhc
Confidence            88 9999999999999995699999999999999999999999999999999999999999999999999999887621 


Q ss_pred             -------CCCchh---hHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhccCcccCCccccccccCC
Q psy3994          80 -------KDVFGP---RFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMA  134 (282)
Q Consensus        80 -------~~~~~~---~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~~~~  134 (282)
                             .+.|+.   ++...+..+|..++. ++++++.|+.+++++|+++++|++++++++.+..
T Consensus        80 g~~~~a~~gt~a~~v~~~~e~i~~l~~~~~~~~~~~~k~Ki~klldiW~k~~~Fp~e~i~~i~~~~  145 (157)
T 3clj_A           80 SNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEKIRMLLDIWDRSGLFQKSYLNAIRSKC  145 (157)
T ss_dssp             CC----STTSHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTTTTSCCTTTTSHH
T ss_pred             CCccCCCCccHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHccCCCCCHHHHHHHHHHh
Confidence                   134653   555566777788787 8999999999999999999999999999987643

>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm repeats, transcription; 2.10A {Saccharomyces cerevisiae} SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X

Probab=99.91  E-value=1.6e-25  Score=174.52  Aligned_cols=122  Identities=26%  Similarity=0.442  Sum_probs=112.5

Q ss_pred             hhHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCC
Q psy3994           3 VIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDV   82 (282)
Q Consensus         3 ~~~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~   82 (282)
                      ++++|.+.|++|.    .+|+++|++||.||++|++++++||++|+++|++|+|.+||+.|||+|||+||.      ...
T Consensus         8 ~~~~f~~~L~~L~----~nSk~~I~~LT~~a~~~~~~a~~Iv~~i~~~i~k~~p~~KL~~LYL~DsIvkN~------g~~   77 (144)
T 1sz9_A            8 IVKDFNSILEELT----FNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNV------GSP   77 (144)
T ss_dssp             HHHHHHHHHTTCS----SCCHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHT------CTT
T ss_pred             HHHHHHHHHHHhc----cccHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHhhHHHHHHHHHHHHHhc------cch
Confidence            5889999999883    279999999999999999999999999999999999999999999999999998      456


Q ss_pred             chhhHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhccC-----cccCCccccccccCC
Q psy3994          83 FGPRFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKN-----EVFTPDIIHPLFDMA  134 (282)
Q Consensus        83 ~~~~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~~~-----~~f~~~~i~~~~~~~  134 (282)
                      |.+.|++++.++|.++|. +++..+.++.+++++|..+     ++|+.+.++++..+-
T Consensus        78 y~~~F~~~l~~~f~~~~~~~d~~~r~k~~rL~~~W~~~~~~~~~vF~~~~l~~i~~~l  135 (144)
T 1sz9_A           78 YTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFL  135 (144)
T ss_dssp             HHHHHHTTHHHHHHHHHHTSCHHHHHHHHHHHHHHTSGGGCSSCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhCcccCCCCCCCHHHHHHHHHHH
Confidence            999999999999999998 8999999999999999999     999999888876643

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.5e-20  Score=138.30  Aligned_cols=82  Identities=22%  Similarity=0.293  Sum_probs=75.7

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCC--CeeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN--TKLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g--~~~~g~~l~v~~a~~~  232 (282)
                      ..++++|||+|||+++|+++|+++|++||.|.++++++.||||||+|.+.++|+.|++.|++  ..+.|++|+|.||+++
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~   92 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK   92 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCC
Confidence            34579999999999999999999999999999999999999999999999999999998864  7899999999999988


Q ss_pred             CCCC
Q psy3994         233 GMKD  236 (282)
Q Consensus       233 ~~~~  236 (282)
                      ..+.
T Consensus        93 ~~~~   96 (105)
T 1sjq_A           93 ELKT   96 (105)
T ss_dssp             SCCC
T ss_pred             CCCc
Confidence            6554

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.83  E-value=1.3e-20  Score=138.14  Aligned_cols=75  Identities=32%  Similarity=0.458  Sum_probs=71.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      .+++|||+|||+++|+++|+++|++||.|.++++++      ++|||||+|.+.++|++|++.|||..+.|++|+|.||+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            468999999999999999999999999999999874      57899999999999999999999999999999999997


Q ss_pred             C
Q psy3994         231 G  231 (282)
Q Consensus       231 ~  231 (282)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.82  E-value=3.3e-20  Score=130.75  Aligned_cols=75  Identities=24%  Similarity=0.228  Sum_probs=72.2

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..+..||||||++.+||++|+++|.+||+|.++.+..+||||||+|.+.++|.+|++.|||..+.|++|+|++|.
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            357899999999999999999999999999999999999999999999999999999999999999999999993

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.82  E-value=4.9e-20  Score=134.30  Aligned_cols=79  Identities=18%  Similarity=0.291  Sum_probs=73.9

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCe--eCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTK--LQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~--~~g~~l~v~~a~~~  232 (282)
                      ..++++|||+|||+.+|+++|+++|++||.|.+++++++||||||+|.+.++|.+|+..|+|..  +.|++|+|.|++++
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecccc
Confidence            3467999999999999999999999999999999999999999999999999999999999885  78999999999876


Q ss_pred             C
Q psy3994         233 G  233 (282)
Q Consensus       233 ~  233 (282)
                      .
T Consensus        98 ~   98 (100)
T 3r27_A           98 K   98 (100)
T ss_dssp             C
T ss_pred             c
Confidence            4

>4fu3_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural genomics consortium, SGC, domain swapping, transc; HET: MSE; 1.90A {Homo sapiens} PDB: 4fld_A*

Probab=99.82  E-value=5.4e-21  Score=148.17  Aligned_cols=123  Identities=21%  Similarity=0.334  Sum_probs=111.2

Q ss_pred             hHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCc
Q psy3994           4 IKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVF   83 (282)
Q Consensus         4 ~~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~   83 (282)
                      -..|++.|++|..++     .+|++++.||++|.++++++|++|+++++++++.+||+.|||+|+|+++++++..   .|
T Consensus         6 ~~~l~~~L~~L~~s~-----~sI~~~s~w~l~~~~~a~~iv~~i~~~l~~~~~~~KL~~LYLindIl~ns~~~~~---~y   77 (135)
T 4fu3_A            6 ESALEKKLSELSNSQ-----QSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGP---EF   77 (135)
T ss_dssp             HHHHHHHHHHCCSST-----THHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCTTTHHHHHHHHHHHHHHHTTTCS---HH
T ss_pred             HHHHHHHHHHccccH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHhcCH---HH
Confidence            467999999996554     4999999999999999999999999999999999999999999999999976643   49


Q ss_pred             hhhHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhccCcccCCccccccccCC
Q psy3994          84 GPRFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFDMA  134 (282)
Q Consensus        84 ~~~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~~~~  134 (282)
                      ...|.+.|...|.+++. ++++.+.++.+++++|..+++|+++.+..+...-
T Consensus        78 ~~~f~~~l~~~~~~~~~~~~~~~k~kl~kll~iW~~r~vf~~~~i~~L~~~l  129 (135)
T 4fu3_A           78 TREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSM  129 (135)
T ss_dssp             HHHHHTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHTTSSCHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCCcCHHHHHHHHHHH
Confidence            99999999999999987 7788999999999999999999999988876643

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.81  E-value=8.3e-20  Score=137.59  Aligned_cols=79  Identities=22%  Similarity=0.449  Sum_probs=72.8

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .+++|||||||+++|+++|+++|++||.|.+++++.    +||||||+|.+.++|++|++.|||..+.|++|+|.++.++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            367899999999999999999999999999999985    5799999999999999999999999999999999999877


Q ss_pred             CCC
Q psy3994         233 GMK  235 (282)
Q Consensus       233 ~~~  235 (282)
                      ..+
T Consensus        84 ~~~   86 (115)
T 4f25_A           84 KER   86 (115)
T ss_dssp             CC-
T ss_pred             ccc
Confidence            544

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=3.8e-19  Score=130.60  Aligned_cols=82  Identities=21%  Similarity=0.249  Sum_probs=75.2

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh--CCCeeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL--KNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l--~g~~~~g~~l~v~~a~~~  232 (282)
                      ..++++|||+|||+.+++++|+++|++||.|.++.+++.||||||+|.+.++|+.|+..|  ++..+.|++|+|.||+++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   91 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   91 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcc
Confidence            346789999999999999999999999999999999999999999999999999999987  467899999999999987


Q ss_pred             CCCC
Q psy3994         233 GMKD  236 (282)
Q Consensus       233 ~~~~  236 (282)
                      ..+.
T Consensus        92 ~~~~   95 (101)
T 2cq1_A           92 ELKT   95 (101)
T ss_dssp             SCCC
T ss_pred             cCcC
Confidence            6543

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=1.2e-19  Score=133.36  Aligned_cols=78  Identities=15%  Similarity=0.147  Sum_probs=72.7

Q ss_pred             CCCcEEEecCCCc-cCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCC--eeCCeeEEEEeecCC
Q psy3994         156 MCSTTLWIGHLSK-LVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT--KLQGKTITLAWAPGK  232 (282)
Q Consensus       156 ~~~~~l~V~nl~~-~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~--~~~g~~l~v~~a~~~  232 (282)
                      .++++|||+|||+ .+|+++|+++|++||.|.++.+++.+|||||+|.+.++|+.|+..||+.  .+.|++|+|.||+..
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   92 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   92 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCC
Confidence            3579999999999 9999999999999999999999999999999999999999999999865  599999999999865


Q ss_pred             C
Q psy3994         233 G  233 (282)
Q Consensus       233 ~  233 (282)
                      .
T Consensus        93 ~   93 (102)
T 1x4d_A           93 K   93 (102)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.1e-19  Score=135.41  Aligned_cols=82  Identities=22%  Similarity=0.293  Sum_probs=75.7

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCC--CeeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN--TKLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g--~~~~g~~l~v~~a~~~  232 (282)
                      ..++++|||+|||+++|+++|+++|++||.|.++++++.||||||+|.+.++|++|+..|++  ..+.|++|+|.||+++
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k  107 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK  107 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCC
Confidence            34579999999999999999999999999999999999999999999999999999999874  6899999999999988


Q ss_pred             CCCC
Q psy3994         233 GMKD  236 (282)
Q Consensus       233 ~~~~  236 (282)
                      ..+.
T Consensus       108 ~~~~  111 (119)
T 2ad9_A          108 ELKT  111 (119)
T ss_dssp             SCCC
T ss_pred             CCCc
Confidence            7654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.80  E-value=5.5e-20  Score=132.71  Aligned_cols=79  Identities=19%  Similarity=0.350  Sum_probs=71.2

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCC-ceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhC-CCeeCCeeEEEEee
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYG-DVVSINLIP------PRGCAFVCMNRRQDAAKALYKLK-NTKLQGKTITLAWA  229 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G-~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~-g~~~~g~~l~v~~a  229 (282)
                      +++|||+|||+++|+++|+++|++|| .|.++++++      +||||||+|.+.++|++|++.++ +..++|++|+|.||
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            47899999999999999999999999 899998874      68999999999999999999874 56799999999999


Q ss_pred             cCCCCCC
Q psy3994         230 PGKGMKD  236 (282)
Q Consensus       230 ~~~~~~~  236 (282)
                      .++....
T Consensus        81 ~~~~~~~   87 (91)
T 2lxi_A           81 DPKPKIN   87 (91)
T ss_dssp             CSCCCCS
T ss_pred             CCCCCCC
Confidence            9876443

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=3.3e-19  Score=131.67  Aligned_cols=81  Identities=15%  Similarity=0.281  Sum_probs=74.2

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCC--eeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT--KLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~--~~~g~~l~v~~a~~~  232 (282)
                      ..++++|||+|||+.+++++|+++|++||.|.++.+++.||||||+|.+.++|.+|+..|++.  .+.|++|+|.|++++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            345799999999999999999999999999999999999999999999999999999998765  489999999999987


Q ss_pred             CCC
Q psy3994         233 GMK  235 (282)
Q Consensus       233 ~~~  235 (282)
                      ..+
T Consensus        92 ~~~   94 (104)
T 1wex_A           92 RIT   94 (104)
T ss_dssp             SCC
T ss_pred             ccc
Confidence            544

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=4.3e-19  Score=129.42  Aligned_cols=79  Identities=19%  Similarity=0.339  Sum_probs=75.0

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeC--CeeEEEEeecCCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQ--GKTITLAWAPGKG  233 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~--g~~l~v~~a~~~~  233 (282)
                      .++++|||+|||.++++++|+++|++||.|.++.+...+|||||+|.+.++|++|+..|||..+.  |++|+|.||+++.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            35689999999999999999999999999999999999999999999999999999999999999  9999999999875


Q ss_pred             C
Q psy3994         234 M  234 (282)
Q Consensus       234 ~  234 (282)
                      .
T Consensus        95 ~   95 (97)
T 1why_A           95 S   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural genomics consortium, SGC, protein binding; 1.80A {Homo sapiens}

Probab=99.79  E-value=1.8e-20  Score=144.59  Aligned_cols=119  Identities=14%  Similarity=0.318  Sum_probs=102.2

Q ss_pred             HHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCch
Q psy3994           5 KTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFG   84 (282)
Q Consensus         5 ~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~   84 (282)
                      ++|+..|+.|+     .|+.+|++++.||++|.++++++|++|+++|++++|.+||+.|||+|+|++++++++..  .|.
T Consensus         8 ~~l~~~L~~L~-----~s~~sI~~~s~w~l~h~~~a~~Iv~~i~~~l~~~~~~~KL~~LYL~ndIl~ns~~~~~~--~f~   80 (132)
T 4flb_A            8 SSLDRKFQSVT-----NTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAI--IFR   80 (132)
T ss_dssp             HHHHHHHHHCC-----SSHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTTTTCT--HHH
T ss_pred             HHHHHHHHHCc-----ccHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHhcccChH--HHH
Confidence            56777777773     57779999999999999999999999999999999999999999999999999777654  477


Q ss_pred             hhHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccCcccCCcccccccc
Q psy3994          85 PRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFD  132 (282)
Q Consensus        85 ~~f~~~l~~~f~~v~~~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~~  132 (282)
                      ..|.+.+.++|..+.  +++.+.++.+++++|..+++|+++.+..+..
T Consensus        81 ~~f~~~l~~~~~~~~--~~~~~~kl~~ll~iW~~r~vf~~~~i~~L~~  126 (132)
T 4flb_A           81 ESFADVLPEAAALVK--DPSVSKSVERIFKIWEDRNVYPEEMIVALRE  126 (132)
T ss_dssp             HHHHTTHHHHHHTTC--STTTHHHHHHHHHHHHHHTSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC--CHHHHHHHHHHHHHhccCCCcCHHHHHHHHH
Confidence            777777777666554  5889999999999999999999998877654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.79  E-value=5.7e-19  Score=131.87  Aligned_cols=78  Identities=21%  Similarity=0.241  Sum_probs=72.6

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ++.++|||+|||+++++++|+++|++||.|.+++++.      ++|||||+|.+.++|++|++.|||..+.|+.|+|.+|
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3568999999999999999999999999999999873      6799999999999999999999999999999999999


Q ss_pred             cCCC
Q psy3994         230 PGKG  233 (282)
Q Consensus       230 ~~~~  233 (282)
                      ....
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            7553

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=5.2e-19  Score=125.64  Aligned_cols=76  Identities=26%  Similarity=0.559  Sum_probs=72.3

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh-CCCeeCCeeEEEEeec
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL-KNTKLQGKTITLAWAP  230 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l-~g~~~~g~~l~v~~a~  230 (282)
                      ....++|||+|||.++++++|+++|++||.|.++.+.+++|||||+|.+.++|++|+..| +|..+.|++|+|+||+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            345689999999999999999999999999999999999999999999999999999999 9999999999999985

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.78  E-value=4.1e-19  Score=130.49  Aligned_cols=78  Identities=24%  Similarity=0.543  Sum_probs=74.1

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ...+++|||||||.++++++|+++|++||.|.++++.+++|||||+|.+.++|++|+..|||..+.|++|+|.||+++
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            345689999999999999999999999999999999999999999999999999999999999999999999999864

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=3.4e-19  Score=132.80  Aligned_cols=79  Identities=15%  Similarity=0.228  Sum_probs=72.9

Q ss_pred             CCCCcEEEecCCCcc-CcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCC--CeeCCeeEEEEeecC
Q psy3994         155 NMCSTTLWIGHLSKL-VQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN--TKLQGKTITLAWAPG  231 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~-~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g--~~~~g~~l~v~~a~~  231 (282)
                      ..++++|||+|||++ +++++|+++|++||.|.++.++++||||||+|.+.++|+.|+..||+  ..+.|++|+|.||+.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~  101 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK  101 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECcc
Confidence            345799999999998 99999999999999999999999999999999999999999998864  568999999999987


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      +.
T Consensus       102 ~~  103 (112)
T 1x4f_A          102 YK  103 (112)
T ss_dssp             CS
T ss_pred             cc
Confidence            64

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=8.2e-19  Score=128.41  Aligned_cols=80  Identities=25%  Similarity=0.402  Sum_probs=75.6

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.+.+++|||||+|.+.++|++|+..|||..+.|++|+|.|++++..
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS   91 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCC
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999988753

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.7e-18  Score=124.41  Aligned_cols=79  Identities=27%  Similarity=0.485  Sum_probs=73.8

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      ..+.++|||+|||.++++++|+++|++||.|.++.+.  +|||||+|.+.++|++|+..|||..+.|++|+|.|++++..
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            3457999999999999999999999999999999998  69999999999999999999999999999999999998764


Q ss_pred             C
Q psy3994         235 K  235 (282)
Q Consensus       235 ~  235 (282)
                      .
T Consensus        83 ~   83 (90)
T 2dnq_A           83 A   83 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.2e-18  Score=126.89  Aligned_cols=79  Identities=27%  Similarity=0.337  Sum_probs=73.7

Q ss_pred             CCcEEEecCCCccCcHHHHH----hhhccCCceEEEEEeCC---CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         157 CSTTLWIGHLSKLVQEEELS----DTFGEYGDVVSINLIPP---RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~----~~f~~~G~i~~~~~~~~---kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ..++|||+|||.++++++|+    ++|++||.|.+++++..   +|||||+|.+.++|++|+..|||..+.|++|+|.||
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   87 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA   87 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            46899999999999999999    99999999999999854   899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy3994         230 PGKGMK  235 (282)
Q Consensus       230 ~~~~~~  235 (282)
                      +++..+
T Consensus        88 ~~~~~~   93 (96)
T 2dgx_A           88 TGASGP   93 (96)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            877543

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.78  E-value=1.3e-18  Score=122.88  Aligned_cols=76  Identities=25%  Similarity=0.528  Sum_probs=71.5

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +.+|||+|||.++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.||++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999985      389999999999999999999999999999999999987


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=2.4e-18  Score=126.79  Aligned_cols=81  Identities=28%  Similarity=0.434  Sum_probs=75.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ....++|||+|||+.+++++|+++|++||.|.+++++.    ++|||||+|.+.++|++|+..|||..+.|++|+|.|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   91 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECC
Confidence            34579999999999999999999999999999999986    67999999999999999999999999999999999999


Q ss_pred             CCCCC
Q psy3994         231 GKGMK  235 (282)
Q Consensus       231 ~~~~~  235 (282)
                      ++..+
T Consensus        92 ~~~~~   96 (103)
T 2cqi_A           92 TPSSQ   96 (103)
T ss_dssp             CTTCC
T ss_pred             CCccc
Confidence            87644

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=3.6e-18  Score=125.82  Aligned_cols=83  Identities=23%  Similarity=0.470  Sum_probs=76.2

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .....++|||+|||.++++++|+++|++||.|..++++.    ++|||||+|.+.++|++|+..|||..+.|++|+|.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            344579999999999999999999999999999999986    4899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q psy3994         230 PGKGMKD  236 (282)
Q Consensus       230 ~~~~~~~  236 (282)
                      .++..+.
T Consensus        91 ~~~~~~~   97 (103)
T 2cq3_A           91 TARVMTN   97 (103)
T ss_dssp             CSSCCCC
T ss_pred             ccCCCCC
Confidence            9886543

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.77  E-value=1.5e-18  Score=124.02  Aligned_cols=77  Identities=25%  Similarity=0.436  Sum_probs=72.3

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .+++|||+|||.++++++|+++|++||.|.++.++.       ++|||||+|.+.++|++|+..|||..+.|+.|+|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            468999999999999999999999999999999863       6799999999999999999999999999999999999


Q ss_pred             cCCC
Q psy3994         230 PGKG  233 (282)
Q Consensus       230 ~~~~  233 (282)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8765

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.5e-18  Score=129.28  Aligned_cols=80  Identities=20%  Similarity=0.469  Sum_probs=75.7

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMK  235 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~  235 (282)
                      ...++|||+|||..+++++|+++|++||.|.++++...+|||||+|.+.++|++|+..|||..+.|++|+|.|++++...
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  102 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM  102 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCCC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999987643

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.77  E-value=1.5e-18  Score=129.19  Aligned_cols=81  Identities=22%  Similarity=0.447  Sum_probs=73.5

Q ss_pred             CCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .....+++|||||||.++++++|+++|++||.|..+.+.  +|||||+|.+.++|++|+..|||..+.|++|+|.|++++
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            334567999999999999999999999999999999998  799999999999999999999999999999999999987


Q ss_pred             CCC
Q psy3994         233 GMK  235 (282)
Q Consensus       233 ~~~  235 (282)
                      ..+
T Consensus       104 ~~r  106 (108)
T 2jvo_A          104 AKR  106 (108)
T ss_dssp             C--
T ss_pred             CCC
Confidence            644

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.77  E-value=1.2e-18  Score=124.23  Aligned_cols=76  Identities=22%  Similarity=0.490  Sum_probs=70.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      +.++|||+|||.++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+..|||..+.|+.|+|.||+
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            468999999999999999999999999999999975      47999999999999999999999999999999999998


Q ss_pred             CC
Q psy3994         231 GK  232 (282)
Q Consensus       231 ~~  232 (282)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            75

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=2.7e-18  Score=124.52  Aligned_cols=79  Identities=23%  Similarity=0.412  Sum_probs=74.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ++++|||+|||..+++++|+++|++||.|..+.+..      ++|||||+|.+.++|++|+..|||..+.|++|+|.|+.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            568999999999999999999999999999999986      47899999999999999999999999999999999999


Q ss_pred             CCCCC
Q psy3994         231 GKGMK  235 (282)
Q Consensus       231 ~~~~~  235 (282)
                      ++...
T Consensus        84 ~~~~~   88 (95)
T 2dnz_A           84 ERLDG   88 (95)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            87644

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.77  E-value=1.3e-18  Score=123.54  Aligned_cols=75  Identities=31%  Similarity=0.505  Sum_probs=70.6

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .+.++|||+|||+++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|++.|||..+.|++|+|+||
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4579999999999999999999999999999999864      5899999999999999999999999999999999998


Q ss_pred             c
Q psy3994         230 P  230 (282)
Q Consensus       230 ~  230 (282)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2.5e-18  Score=126.75  Aligned_cols=81  Identities=25%  Similarity=0.434  Sum_probs=74.9

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||.++++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            44579999999999999999999999999999999985      468999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy3994         229 APGKGMK  235 (282)
Q Consensus       229 a~~~~~~  235 (282)
                      ++++..+
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9987644

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2.4e-18  Score=126.77  Aligned_cols=82  Identities=22%  Similarity=0.458  Sum_probs=75.7

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ....++|||+|||+.+++++|+++|++||.|..+.+..    ++|||||+|.+.++|++|+..|||..+.|++|+|.|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ   91 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEec
Confidence            34679999999999999999999999999999999984    58999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q psy3994         231 GKGMKD  236 (282)
Q Consensus       231 ~~~~~~  236 (282)
                      ++..+.
T Consensus        92 ~~~~~~   97 (103)
T 2d9p_A           92 RKEERQ   97 (103)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.7e-18  Score=125.85  Aligned_cols=80  Identities=25%  Similarity=0.438  Sum_probs=74.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEE-EEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSI-NLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~-~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ++++|||+|||.++++++|+++|++||.|..+ +++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.||
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            56899999999999999999999999999999 8875      4899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q psy3994         230 PGKGMKD  236 (282)
Q Consensus       230 ~~~~~~~  236 (282)
                      .++..++
T Consensus        84 ~~~~~~~   90 (96)
T 1x5t_A           84 FKKDSKG   90 (96)
T ss_dssp             CCCCCCC
T ss_pred             cccCCCC
Confidence            9876554

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=4.2e-18  Score=124.56  Aligned_cols=81  Identities=23%  Similarity=0.443  Sum_probs=74.5

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      .....++|||+|||.++++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+. |||..+.|++|+|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            344679999999999999999999999999999999975      58999999999999999998 99999999999999


Q ss_pred             eecCCCCC
Q psy3994         228 WAPGKGMK  235 (282)
Q Consensus       228 ~a~~~~~~  235 (282)
                      |+.++..+
T Consensus        85 ~a~~~~~~   92 (99)
T 2dgs_A           85 RAEPRDSK   92 (99)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCccc
Confidence            99987654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=3.4e-18  Score=125.32  Aligned_cols=80  Identities=23%  Similarity=0.367  Sum_probs=74.2

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ....++|||+|||.++++++|+++|++||.|.++.+..     ++|||||+|.+.++|++|+..|||..+.|++|+|.|+
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            34578999999999999999999999999999999985     4599999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy3994         230 PGKGM  234 (282)
Q Consensus       230 ~~~~~  234 (282)
                      +++..
T Consensus        94 ~~~~~   98 (100)
T 2do4_A           94 NSGPS   98 (100)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            98764

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=3.5e-18  Score=127.24  Aligned_cols=81  Identities=20%  Similarity=0.363  Sum_probs=74.7

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ....++|||+|||.++++++|+++|++||.|..+.+..   ++|||||+|.+.++|++|++.|||..+.|+.|+|.|+++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   98 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   98 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEccc
Confidence            34578999999999999999999999999999999975   578999999999999999999999999999999999988


Q ss_pred             CCCC
Q psy3994         232 KGMK  235 (282)
Q Consensus       232 ~~~~  235 (282)
                      +...
T Consensus        99 ~~~~  102 (109)
T 1x4a_A           99 GRGT  102 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.77  E-value=2.4e-18  Score=125.14  Aligned_cols=78  Identities=18%  Similarity=0.372  Sum_probs=73.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ++++|||+|||..+++++|+++|++||.|.++++..      ++|||||+|.+.++|++|+..|||..+.|+.|+|.||.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            358999999999999999999999999999999975      47999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy3994         231 GKGM  234 (282)
Q Consensus       231 ~~~~  234 (282)
                      +++.
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            8753

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=2.2e-18  Score=125.82  Aligned_cols=80  Identities=24%  Similarity=0.341  Sum_probs=73.7

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEE
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL  226 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v  226 (282)
                      .++++|||+|||.++++++|+++|++||.|..+.+..         ++|||||+|.+.++|++|+..|||..+.|++|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3568999999999999999999999999999999873         4689999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q psy3994         227 AWAPGKGMK  235 (282)
Q Consensus       227 ~~a~~~~~~  235 (282)
                      .|++++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999887543

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=4.1e-18  Score=124.59  Aligned_cols=81  Identities=26%  Similarity=0.361  Sum_probs=75.0

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ..++++|||+|||.++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34579999999999999999999999999999999975      569999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy3994         229 APGKGMK  235 (282)
Q Consensus       229 a~~~~~~  235 (282)
                      ++++..+
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9987644

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.76  E-value=1.9e-18  Score=124.54  Aligned_cols=80  Identities=20%  Similarity=0.309  Sum_probs=74.5

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..+.++|||+|||.++++++|+++|++||.|..+.+..    ++|||||+|.+.++|++|+..|||..+.|+.|+|.|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            34579999999999999999999999999999999885    57999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy3994         231 GKGM  234 (282)
Q Consensus       231 ~~~~  234 (282)
                      +...
T Consensus        85 ~~~~   88 (92)
T 2dgv_A           85 NASG   88 (92)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            8754

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=7.6e-19  Score=131.42  Aligned_cols=77  Identities=23%  Similarity=0.279  Sum_probs=73.6

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ..++|||+|||..+++++|+++|++||.|.++.++.++|||||+|.+.++|++|+..|||..+.|++|+|.||....
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999998654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=4.4e-18  Score=126.16  Aligned_cols=82  Identities=24%  Similarity=0.481  Sum_probs=75.5

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC-------CcEEEEEecCHHHHHHHHHHh-CCCeeCCeeEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-------RGCAFVCMNRRQDAAKALYKL-KNTKLQGKTIT  225 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~-------kg~aFV~f~~~~~A~~Ai~~l-~g~~~~g~~l~  225 (282)
                      .....++|||+|||..+++++|+++|++||.|..+.++..       +|||||+|.+.++|++|+..| ||..+.|++|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3446799999999999999999999999999999999764       799999999999999999999 99999999999


Q ss_pred             EEeecCCCCC
Q psy3994         226 LAWAPGKGMK  235 (282)
Q Consensus       226 v~~a~~~~~~  235 (282)
                      |.||+++...
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999987644

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=4.8e-18  Score=122.59  Aligned_cols=79  Identities=33%  Similarity=0.542  Sum_probs=73.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      ....++|||+|||.++++++|+++|++||.|..+.+.+  +||||+|.+.++|++|+..|||..+.|+.|+|.|++++..
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   84 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR   84 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCC
Confidence            44579999999999999999999999999999999975  7999999999999999999999999999999999988754


Q ss_pred             C
Q psy3994         235 K  235 (282)
Q Consensus       235 ~  235 (282)
                      .
T Consensus        85 ~   85 (92)
T 2dgt_A           85 T   85 (92)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.76  E-value=6.6e-18  Score=126.96  Aligned_cols=82  Identities=22%  Similarity=0.440  Sum_probs=75.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~------kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||..+++++|+++|+.||.|..++++..      +|||||+|.+.++|++|+..|||..+.|+.|+|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345799999999999999999999999999999999853      68999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q psy3994         229 APGKGMKD  236 (282)
Q Consensus       229 a~~~~~~~  236 (282)
                      ++++....
T Consensus        92 a~~~~~~~   99 (115)
T 2dgo_A           92 ATRKPPAP   99 (115)
T ss_dssp             SSCCCCCS
T ss_pred             ccCCCCCC
Confidence            99876543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=3.1e-18  Score=125.93  Aligned_cols=81  Identities=30%  Similarity=0.486  Sum_probs=75.0

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .+.++|||+|||..+++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.|+
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            4579999999999999999999999999999999875      5899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q psy3994         230 PGKGMKD  236 (282)
Q Consensus       230 ~~~~~~~  236 (282)
                      +++..+.
T Consensus        90 ~~~~~~~   96 (102)
T 2cqb_A           90 KPMRIKE   96 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.76  E-value=5e-18  Score=123.84  Aligned_cols=78  Identities=23%  Similarity=0.379  Sum_probs=72.2

Q ss_pred             CCCCCcEEEecCCCc-cCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         154 ENMCSTTLWIGHLSK-LVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~-~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ...++++|||||||. ++++++|+++|++||.|.++++.  +|||||+|.+.++|++|+..|||..+.|++|+|.|++++
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            344679999999998 99999999999999999999984  799999999999999999999999999999999999876


Q ss_pred             C
Q psy3994         233 G  233 (282)
Q Consensus       233 ~  233 (282)
                      +
T Consensus        96 ~   96 (97)
T 2xnq_A           96 A   96 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=4.3e-18  Score=127.31  Aligned_cols=79  Identities=22%  Similarity=0.392  Sum_probs=73.2

Q ss_pred             CCCCcEEEecCCCccCcHHHHH---hhhccCCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhCCCeeCCe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELS---DTFGEYGDVVSINLIP---------PRGCAFVCMNRRQDAAKALYKLKNTKLQGK  222 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~---~~f~~~G~i~~~~~~~---------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~  222 (282)
                      ....++|||+|||+++++++|+   ++|++||.|..+.+++         ++|||||+|.+.++|++|+..|||..+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3456899999999999999999   9999999999999985         347999999999999999999999999999


Q ss_pred             eEEEEeecCCC
Q psy3994         223 TITLAWAPGKG  233 (282)
Q Consensus       223 ~l~v~~a~~~~  233 (282)
                      +|+|.||.++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999999875

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=4.2e-18  Score=123.25  Aligned_cols=76  Identities=22%  Similarity=0.449  Sum_probs=71.2

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ..+.++|||+|||..+++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|++.|||..+.|++|+|.|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            34568999999999999999999999999999999975      578999999999999999999999999999999999


Q ss_pred             ec
Q psy3994         229 AP  230 (282)
Q Consensus       229 a~  230 (282)
                      |+
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.76  E-value=4.6e-18  Score=125.66  Aligned_cols=80  Identities=21%  Similarity=0.387  Sum_probs=74.3

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC-----CcEEEEEecCHHHHHHHHHHhCCCeeCC---eeEEEE
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-----RGCAFVCMNRRQDAAKALYKLKNTKLQG---KTITLA  227 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~-----kg~aFV~f~~~~~A~~Ai~~l~g~~~~g---~~l~v~  227 (282)
                      ..+++|||+|||.++++++|+++|++||.|.++.+...     +|||||+|.+.++|++|+..|||..+.|   ++|+|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            45799999999999999999999999999999999864     7999999999999999999999999988   999999


Q ss_pred             eecCCCCC
Q psy3994         228 WAPGKGMK  235 (282)
Q Consensus       228 ~a~~~~~~  235 (282)
                      ||+++..+
T Consensus        93 ~a~~~~~~  100 (105)
T 2dnh_A           93 FADTDKES  100 (105)
T ss_dssp             ESCSSCCC
T ss_pred             ECccCccc
Confidence            99987644

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.4e-18  Score=126.75  Aligned_cols=81  Identities=26%  Similarity=0.354  Sum_probs=74.5

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||.++++++|+++|++||.|..+.+..      ++|||||+|.+.++|++|+..|||..+.|+.|+|.|
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34579999999999999999999999999999999874      479999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy3994         229 APGKGMK  235 (282)
Q Consensus       229 a~~~~~~  235 (282)
                      |++....
T Consensus        90 a~~~~~~   96 (103)
T 2dnm_A           90 ARYGRRD   96 (103)
T ss_dssp             CSSCCSC
T ss_pred             CCcCCCC
Confidence            9976543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=4.3e-18  Score=122.30  Aligned_cols=79  Identities=24%  Similarity=0.423  Sum_probs=73.3

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      ....++|||+|||.++|+++|+++|++||.|..+.+.+  +||||+|.+.++|++|+..|||..+.|++|+|.|++++..
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence            34568999999999999999999999999999999975  7999999999999999999999999999999999998754


Q ss_pred             C
Q psy3994         235 K  235 (282)
Q Consensus       235 ~  235 (282)
                      +
T Consensus        84 ~   84 (90)
T 2dnp_A           84 K   84 (90)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=7.6e-18  Score=125.31  Aligned_cols=79  Identities=23%  Similarity=0.265  Sum_probs=74.2

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCC-----eeEEEEeec
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQG-----KTITLAWAP  230 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g-----~~l~v~~a~  230 (282)
                      ...++|||+|||+++++++|+++|++||.|..+.++.. |||||+|.+.++|++|++.|||..+.|     +.|+|.+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~   91 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   91 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCC
Confidence            35689999999999999999999999999999999887 999999999999999999999999999     999999999


Q ss_pred             CCCCC
Q psy3994         231 GKGMK  235 (282)
Q Consensus       231 ~~~~~  235 (282)
                      ++...
T Consensus        92 ~~~~~   96 (108)
T 1x4c_A           92 PRSPS   96 (108)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.75  E-value=2.1e-18  Score=125.19  Aligned_cols=74  Identities=28%  Similarity=0.441  Sum_probs=67.7

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCc--eEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCC----eeCCeeEE
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGD--VVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNT----KLQGKTIT  225 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~--i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~----~~~g~~l~  225 (282)
                      -.||||+|||+.+|+++|+++|++||.  +.+|++++      +||||||+|.+.++|++|++.|||.    .++|++|+
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~   88 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIG   88 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEE
Confidence            468999999999999999999999995  66888874      6899999999999999999999997    48999999


Q ss_pred             EEeecC
Q psy3994         226 LAWAPG  231 (282)
Q Consensus       226 v~~a~~  231 (282)
                      |+||++
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999985

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.75  E-value=2.8e-18  Score=127.94  Aligned_cols=81  Identities=26%  Similarity=0.461  Sum_probs=74.7

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ....+++|||+|||..+++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            345678999999999999999999999999999999974      47999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy3994         228 WAPGKGM  234 (282)
Q Consensus       228 ~a~~~~~  234 (282)
                      |+.+++.
T Consensus       102 ~a~~~~~  108 (110)
T 1oo0_B          102 WCFVKGP  108 (110)
T ss_dssp             ESEESSC
T ss_pred             EcccCCC
Confidence            9987763

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.5e-18  Score=125.45  Aligned_cols=80  Identities=26%  Similarity=0.397  Sum_probs=71.8

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCc-eEEEEEeCCCcEEEEEecCHHHHHHHHHHhCC-CeeCCeeEEEEeecCCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGD-VVSINLIPPRGCAFVCMNRRQDAAKALYKLKN-TKLQGKTITLAWAPGKG  233 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~-i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g-~~~~g~~l~v~~a~~~~  233 (282)
                      ...++|||+|||.++|+++|+++|++||. |..+.+ .++|||||+|.+.++|++|+..||| ..+.|++|+|.|++++.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~   84 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   84 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcc
Confidence            35689999999999999999999999999 555544 5789999999999999999999999 99999999999999876


Q ss_pred             CCC
Q psy3994         234 MKD  236 (282)
Q Consensus       234 ~~~  236 (282)
                      .++
T Consensus        85 ~~~   87 (93)
T 2cqh_A           85 LRS   87 (93)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.9e-18  Score=127.09  Aligned_cols=81  Identities=22%  Similarity=0.442  Sum_probs=74.8

Q ss_pred             CCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ......++|||+|||.++++++|+++|++||.|.++++..    ++|||||+|.+.++|++|+..|||..+.|++|+|.|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3445679999999999999999999999999999999985    489999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy3994         229 APGKG  233 (282)
Q Consensus       229 a~~~~  233 (282)
                      |+++.
T Consensus       104 a~~~~  108 (109)
T 2err_A          104 ATARV  108 (109)
T ss_dssp             CCCSC
T ss_pred             CCCCc
Confidence            98764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.4e-17  Score=121.33  Aligned_cols=79  Identities=23%  Similarity=0.428  Sum_probs=73.7

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      ..+.++|||+|+  ++++++|+++|++||.|.++.+..++|||||+|.+.++|++|+..|||..+.|++|+|.||+++..
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            345789999996  899999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             C
Q psy3994         235 K  235 (282)
Q Consensus       235 ~  235 (282)
                      .
T Consensus        90 ~   90 (97)
T 1x5p_A           90 L   90 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=4.5e-18  Score=125.71  Aligned_cols=81  Identities=28%  Similarity=0.346  Sum_probs=74.7

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      .....++|||+|||.++++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            344679999999999999999999999999999999875      56899999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy3994         228 WAPGKGM  234 (282)
Q Consensus       228 ~a~~~~~  234 (282)
                      ||.++..
T Consensus        91 ~a~~~~~   97 (105)
T 1x5u_A           91 KASAHNK   97 (105)
T ss_dssp             ETTTTSC
T ss_pred             ECCCCCc
Confidence            9988754

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.75  E-value=8.4e-18  Score=123.93  Aligned_cols=79  Identities=24%  Similarity=0.479  Sum_probs=73.4

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMK  235 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~  235 (282)
                      .+.++|||+|||+++|+++|+++|++||.|..+.++  ++||||+|.+.++|++|+..|||..+.|++|+|.|++++..+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            356899999999999999999999999999999987  489999999999999999999999999999999999987654


Q ss_pred             C
Q psy3994         236 D  236 (282)
Q Consensus       236 ~  236 (282)
                      .
T Consensus        87 ~   87 (103)
T 2dgu_A           87 R   87 (103)
T ss_dssp             C
T ss_pred             c
Confidence            3

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.9e-18  Score=127.01  Aligned_cols=80  Identities=25%  Similarity=0.471  Sum_probs=74.0

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ....+++|||+|||..+++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            344578999999999999999999999999999999974      47999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy3994         228 WAPGKG  233 (282)
Q Consensus       228 ~a~~~~  233 (282)
                      ||.+++
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            998765

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.75  E-value=2.1e-18  Score=128.69  Aligned_cols=77  Identities=16%  Similarity=0.132  Sum_probs=71.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCC-ceEEEEEe--CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYG-DVVSINLI--PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G-~i~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ..++|||+|||+++++++|+++|++|| .|..+.+.  .++|||||+|.+.++|++|++.|||..+.|++|+|.+++++.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC--
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            358999999999999999999999999 99999986  378999999999999999999999999999999999998664

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=4.2e-18  Score=125.21  Aligned_cols=81  Identities=23%  Similarity=0.425  Sum_probs=74.8

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||+++++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.|
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34569999999999999999999999999999999985      578999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy3994         229 APGKGMK  235 (282)
Q Consensus       229 a~~~~~~  235 (282)
                      ++++...
T Consensus        89 a~~~~~~   95 (102)
T 1x5s_A           89 AGKSSDN   95 (102)
T ss_dssp             EECCCCC
T ss_pred             CCCCCCC
Confidence            9987643

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=7.8e-18  Score=125.65  Aligned_cols=81  Identities=25%  Similarity=0.416  Sum_probs=74.8

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhC------CCeeCCe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLK------NTKLQGK  222 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~------g~~~~g~  222 (282)
                      ..+.++|||+|||+++++++|+++|++||.|..|.++.      ++|||||+|.+.++|++|+..||      |..+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            34578999999999999999999999999999999983      58999999999999999999999      9999999


Q ss_pred             eEEEEeecCCCCC
Q psy3994         223 TITLAWAPGKGMK  235 (282)
Q Consensus       223 ~l~v~~a~~~~~~  235 (282)
                      +|+|.|+.++...
T Consensus        92 ~l~v~~a~~~~~~  104 (111)
T 1x4h_A           92 QLKVDLAVTRDEA  104 (111)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCccC
Confidence            9999999987644

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.75  E-value=4.6e-18  Score=126.52  Aligned_cols=79  Identities=24%  Similarity=0.447  Sum_probs=73.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ...+++|||+|||..+++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999984      479999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy3994         229 APGKG  233 (282)
Q Consensus       229 a~~~~  233 (282)
                      ++++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            98774

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.75  E-value=8.8e-18  Score=126.61  Aligned_cols=79  Identities=29%  Similarity=0.480  Sum_probs=73.7

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ..++|||+|||.++++++|+++|++||.|.++.+..     ++|||||+|.+.++|++|+..|||..+.|+.|+|.||++
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   85 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK   85 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            468999999999999999999999999999999986     469999999999999999999999999999999999987


Q ss_pred             CCCC
Q psy3994         232 KGMK  235 (282)
Q Consensus       232 ~~~~  235 (282)
                      +...
T Consensus        86 ~~~~   89 (116)
T 2fy1_A           86 PSFQ   89 (116)
T ss_dssp             SSCS
T ss_pred             CCCC
Confidence            7543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.75  E-value=4e-18  Score=130.32  Aligned_cols=78  Identities=17%  Similarity=0.270  Sum_probs=71.8

Q ss_pred             CCCcEEEecCCCccCcHHHHH----hhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         156 MCSTTLWIGHLSKLVQEEELS----DTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~----~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      .++++|||||||+.+++++|+    ++|++||.|.+|.+..   ++|||||+|.+.++|..|+..|||..+.|++|+|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~  106 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF  106 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEE
Confidence            457899999999999998876    6999999999998863   789999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy3994         229 APGKG  233 (282)
Q Consensus       229 a~~~~  233 (282)
                      |+++.
T Consensus       107 a~~~~  111 (127)
T 2a3j_A          107 SETPQ  111 (127)
T ss_dssp             CCCCC
T ss_pred             ccCcc
Confidence            99775

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5.6e-18  Score=122.80  Aligned_cols=77  Identities=25%  Similarity=0.395  Sum_probs=71.7

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ..++++|||+|||..+++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34568999999999999999999999999999999974      478999999999999999999999999999999999


Q ss_pred             ecC
Q psy3994         229 APG  231 (282)
Q Consensus       229 a~~  231 (282)
                      |++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            975

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.74  E-value=4.3e-18  Score=123.91  Aligned_cols=78  Identities=23%  Similarity=0.346  Sum_probs=71.9

Q ss_pred             CCCcEEEecCCCc-cCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         156 MCSTTLWIGHLSK-LVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       156 ~~~~~l~V~nl~~-~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      .++++|||+|||+ .+++++|+++|++||.|.++.+.  +|||||+|.+.++|++|+..|||..+.|++|+|.|++++..
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   85 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR   85 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCC
Confidence            3579999999998 99999999999999999999996  69999999999999999999999999999999999987754


Q ss_pred             C
Q psy3994         235 K  235 (282)
Q Consensus       235 ~  235 (282)
                      .
T Consensus        86 ~   86 (96)
T 2kvi_A           86 P   86 (96)
T ss_dssp             -
T ss_pred             C
Confidence            3

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=6.7e-18  Score=123.44  Aligned_cols=80  Identities=31%  Similarity=0.541  Sum_probs=73.5

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceE-EEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCee----
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVV-SINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKT----  223 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~-~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~----  223 (282)
                      ..++++|||+|||+++++++|+++|++||.|. +++++.      ++|||||+|.+.++|++|+..|||..+.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34579999999999999999999999999999 999885      4599999999999999999999999999999    


Q ss_pred             EEEEeecCCCC
Q psy3994         224 ITLAWAPGKGM  234 (282)
Q Consensus       224 l~v~~a~~~~~  234 (282)
                      |+|.||++.+.
T Consensus        86 l~v~~a~~~~~   96 (99)
T 2div_A           86 FKLNYATYSGP   96 (99)
T ss_dssp             CCEEETTCCSS
T ss_pred             EEEeecCCCCC
Confidence            99999987753

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=2.3e-17  Score=123.75  Aligned_cols=81  Identities=19%  Similarity=0.265  Sum_probs=74.0

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...+++|||+|||.++++++|+++|++||.|.+++++.     ++|||||+|.+.++|++|+..|||..+.|+.|+|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            34568999999999999999999999999999999886     3799999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy3994         230 PGKGMK  235 (282)
Q Consensus       230 ~~~~~~  235 (282)
                      +....+
T Consensus        92 ~~~~~~   97 (114)
T 2do0_A           92 ERALPK   97 (114)
T ss_dssp             SCCCCC
T ss_pred             ccCCCC
Confidence            865433

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.74  E-value=9.2e-18  Score=126.19  Aligned_cols=81  Identities=20%  Similarity=0.302  Sum_probs=74.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||.++++++|+++|++||.|.+++++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999885      458999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy3994         229 APGKGMK  235 (282)
Q Consensus       229 a~~~~~~  235 (282)
                      ++++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9987643

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=4.6e-18  Score=126.84  Aligned_cols=77  Identities=18%  Similarity=0.284  Sum_probs=72.1

Q ss_pred             CCCcEEEe--cCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCee-----CCeeEEEEe
Q psy3994         156 MCSTTLWI--GHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL-----QGKTITLAW  228 (282)
Q Consensus       156 ~~~~~l~V--~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~-----~g~~l~v~~  228 (282)
                      .++++|||  |||+.++++++|+++|++||.|.++.++.+||||||+|.+.++|++|++.|||..+     .|++|.|.+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~  102 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF  102 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEe
Confidence            35689999  88999999999999999999999999998999999999999999999999999998     789999999


Q ss_pred             ecCC
Q psy3994         229 APGK  232 (282)
Q Consensus       229 a~~~  232 (282)
                      +...
T Consensus       103 a~~~  106 (114)
T 2cq2_A          103 VEKV  106 (114)
T ss_dssp             ESCC
T ss_pred             cccC
Confidence            9854

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2e-17  Score=120.98  Aligned_cols=78  Identities=27%  Similarity=0.381  Sum_probs=72.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccC--CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEY--GDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~--G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ....++|||+|||+++++++|+++|++|  |.|.++.+.  +|||||+|.+.++|++|+..|||..+.|++|+|.||+++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   89 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            3457899999999999999999999999  999999875  599999999999999999999999999999999999987


Q ss_pred             CC
Q psy3994         233 GM  234 (282)
Q Consensus       233 ~~  234 (282)
                      ..
T Consensus        90 ~~   91 (99)
T 2cpd_A           90 DK   91 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.74  E-value=5.5e-18  Score=123.37  Aligned_cols=78  Identities=23%  Similarity=0.431  Sum_probs=73.3

Q ss_pred             CCCcEEEecCCCccCcHHHHH----hhhccCCceEEEEEe---CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         156 MCSTTLWIGHLSKLVQEEELS----DTFGEYGDVVSINLI---PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~----~~f~~~G~i~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      .++++|||+|||.++++++|+    ++|++||.|.++.+.   .++|||||+|.+.++|++|+..|||..+.|++|+|.|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   85 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   85 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            457999999999999999999    999999999999987   3689999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy3994         229 APGKG  233 (282)
Q Consensus       229 a~~~~  233 (282)
                      ++++.
T Consensus        86 a~~~~   90 (97)
T 1nu4_A           86 AKTDS   90 (97)
T ss_dssp             CSSCC
T ss_pred             ccCCC
Confidence            99875

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.74  E-value=6.1e-18  Score=125.21  Aligned_cols=82  Identities=24%  Similarity=0.469  Sum_probs=75.0

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCee---CCeeE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKL---QGKTI  224 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~---~g~~l  224 (282)
                      .....++|||+|||.++++++|+++|++||.|.+++++.      ++|||||+|.+.++|++|+..|||..+   .|++|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            344579999999999999999999999999999999985      579999999999999999999999987   89999


Q ss_pred             EEEeecCCCCC
Q psy3994         225 TLAWAPGKGMK  235 (282)
Q Consensus       225 ~v~~a~~~~~~  235 (282)
                      +|.|+.++..+
T Consensus        89 ~v~~a~~~~~~   99 (106)
T 2dgp_A           89 QVKPADSESRG   99 (106)
T ss_dssp             EEEECCCCSCC
T ss_pred             EEEECCccccc
Confidence            99999987643

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.74  E-value=6.6e-18  Score=122.46  Aligned_cols=76  Identities=24%  Similarity=0.469  Sum_probs=71.4

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ...++|||+|||+.+++++|+++|++||.|.++.++.     ++|||||+|.+.++|++|+..|||..+.|++|+|.||+
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            3568999999999999999999999999999999985     37999999999999999999999999999999999987


Q ss_pred             C
Q psy3994         231 G  231 (282)
Q Consensus       231 ~  231 (282)
                      .
T Consensus        94 ~   94 (95)
T 2ywk_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.74  E-value=1.3e-17  Score=123.57  Aligned_cols=78  Identities=21%  Similarity=0.337  Sum_probs=72.3

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ...+.++|||+|||+.+++++|+++|++||.|.++.++.     ++|||||+|.+.++|++|+..|||..+.|+.|+|.|
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            334579999999999999999999999999999999984     589999999999999999999999999999999999


Q ss_pred             ecC
Q psy3994         229 APG  231 (282)
Q Consensus       229 a~~  231 (282)
                      |.+
T Consensus       105 a~s  107 (107)
T 3ulh_A          105 VTS  107 (107)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            863

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=122.44  Aligned_cols=77  Identities=23%  Similarity=0.358  Sum_probs=71.0

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEE--------EEEeC------CCcEEEEEecCHHHHHHHHHHhCCCee
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVS--------INLIP------PRGCAFVCMNRRQDAAKALYKLKNTKL  219 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~--------~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~  219 (282)
                      .....++|||+|||.++++++|+++|++||.|..        ++++.      ++|||||+|.+.++|++|++.|||..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3445799999999999999999999999999999        88874      478999999999999999999999999


Q ss_pred             CCeeEEEEeec
Q psy3994         220 QGKTITLAWAP  230 (282)
Q Consensus       220 ~g~~l~v~~a~  230 (282)
                      .|++|+|++|+
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999985

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=6.9e-18  Score=125.59  Aligned_cols=80  Identities=28%  Similarity=0.396  Sum_probs=73.6

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCc-eEEEEEe-------CCCcEEEEEecCHHHHHHHHHHhC--CCeeCCeeEE
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGD-VVSINLI-------PPRGCAFVCMNRRQDAAKALYKLK--NTKLQGKTIT  225 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~-i~~~~~~-------~~kg~aFV~f~~~~~A~~Ai~~l~--g~~~~g~~l~  225 (282)
                      .+.++|||+|||.++++++|+++|++||. |.++.++       .++|||||+|.+.++|++|+..||  +..+.|++|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45689999999999999999999999998 9999998       478999999999999999999996  5899999999


Q ss_pred             EEeecCCCCC
Q psy3994         226 LAWAPGKGMK  235 (282)
Q Consensus       226 v~~a~~~~~~  235 (282)
                      |.||+++...
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999987643

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.3e-17  Score=121.50  Aligned_cols=78  Identities=23%  Similarity=0.352  Sum_probs=71.0

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe--CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI--PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ...+++|||+|||+++++++|+++|++||.|. +.++  .++|||||+|.+.++|++|+..|||..+.|++|+|.|++++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            34578999999999999999999999999986 4444  57899999999999999999999999999999999999887


Q ss_pred             C
Q psy3994         233 G  233 (282)
Q Consensus       233 ~  233 (282)
                      .
T Consensus        95 ~   95 (97)
T 2e5j_A           95 R   95 (97)
T ss_dssp             C
T ss_pred             C
Confidence            5

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.73  E-value=2.4e-18  Score=126.20  Aligned_cols=76  Identities=18%  Similarity=0.231  Sum_probs=71.2

Q ss_pred             CCcEEEecCCCc------cCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCC-ee
Q psy3994         157 CSTTLWIGHLSK------LVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQG-KT  223 (282)
Q Consensus       157 ~~~~l~V~nl~~------~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g-~~  223 (282)
                      .+++|||+|||.      ++++++|+++|++||.|.+++++.      ++|||||+|.+.++|++|+..|||..+.| ++
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            358999999999      999999999999999999999873      67999999999999999999999999999 99


Q ss_pred             EEEEeecCC
Q psy3994         224 ITLAWAPGK  232 (282)
Q Consensus       224 l~v~~a~~~  232 (282)
                      |+|.+|.++
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999999764

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.6e-17  Score=122.62  Aligned_cols=80  Identities=23%  Similarity=0.289  Sum_probs=72.9

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ..+.++|||+|||.++++++|+++|+.|| |.++.++.       ++|||||+|.+.++|++|+ .|||..+.|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            34569999999999999999999999999 99999874       3789999999999999999 999999999999999


Q ss_pred             eecCCCCCC
Q psy3994         228 WAPGKGMKD  236 (282)
Q Consensus       228 ~a~~~~~~~  236 (282)
                      ++.++..+.
T Consensus        90 ~a~~~~~~~   98 (104)
T 1wi8_A           90 VADQAQDKD   98 (104)
T ss_dssp             ECCCCCCCC
T ss_pred             EccCCCCCC
Confidence            999876543

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.73  E-value=7.6e-18  Score=120.56  Aligned_cols=76  Identities=18%  Similarity=0.301  Sum_probs=72.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .+++|||+|||+++++++|+++|++| .|.++++..++|||||+|.+.++|++|+..|||..+.|++|+|.||....
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            46899999999999999999999999 99999998899999999999999999999999999999999999997654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.73  E-value=4.2e-18  Score=125.03  Aligned_cols=76  Identities=22%  Similarity=0.383  Sum_probs=72.4

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~-kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      ++|||+|||+++|+++|+++|++||.|.++.++.. +|||||+|.+.++|++|+..|||..+.|++|+|.|++++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   77 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR   77 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCC
Confidence            58999999999999999999999999999999985 99999999999999999999999999999999999988753

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.73  E-value=1.4e-17  Score=124.26  Aligned_cols=75  Identities=24%  Similarity=0.446  Sum_probs=70.9

Q ss_pred             CCcEEEecCCCcc-CcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKL-VQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~-~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .+++|||+|||++ +++++|+++|++||.|..+.+  ++|||||+|.+.++|++|+..|||..+.|++|+|.|++++.
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            4689999999999 999999999999999999998  67999999999999999999999999999999999998654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=5.4e-18  Score=124.97  Aligned_cols=74  Identities=14%  Similarity=0.265  Sum_probs=70.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ..++|||||||+++|+++|+++|++||.|.+|+++.     ++|||||+|.+.++|++|+. ++|..+.|+.|.|.|+..
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            458999999999999999999999999999999985     68999999999999999999 899999999999999875

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.73  E-value=9.6e-18  Score=128.77  Aligned_cols=80  Identities=25%  Similarity=0.404  Sum_probs=74.3

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ...++++|||+|||.++++++|+++|++||.|..++++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            344678999999999999999999999999999999984      68999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy3994         228 WAPGKG  233 (282)
Q Consensus       228 ~a~~~~  233 (282)
                      |+.++.
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            998765

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.9e-17  Score=124.01  Aligned_cols=81  Identities=22%  Similarity=0.313  Sum_probs=74.0

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceE--------EEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVV--------SINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQ  220 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~--------~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~  220 (282)
                      ....++|||+|||..+++++|+++|++||.|.        .+++..      ++|||||+|.+.++|++|+..|||..+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            44579999999999999999999999999998        588774      4789999999999999999999999999


Q ss_pred             CeeEEEEeecCCCCC
Q psy3994         221 GKTITLAWAPGKGMK  235 (282)
Q Consensus       221 g~~l~v~~a~~~~~~  235 (282)
                      |++|+|.|++++...
T Consensus        92 g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           92 GSKLKVSLARKKPPM  106 (113)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CCEEEEEECCCCCCC
Confidence            999999999987644

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.73  E-value=1.4e-17  Score=125.79  Aligned_cols=77  Identities=21%  Similarity=0.356  Sum_probs=71.3

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      .....++|||+|||+++++++|+++|++||.|.+++++.      ++|||||+|.+.++|++|++.|||..+.|++|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345679999999999999999999999999999999975      47999999999999999999999999999999999


Q ss_pred             eec
Q psy3994         228 WAP  230 (282)
Q Consensus       228 ~a~  230 (282)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            985

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.73  E-value=4.2e-17  Score=135.14  Aligned_cols=77  Identities=19%  Similarity=0.294  Sum_probs=72.4

Q ss_pred             CCcEEEecCCC-ccCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~-~~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ++++|||+||| ..+++++|+++|++||.|.++++++ ++|||||+|.+.++|++|++.|||..+.|++|+|.+++.+.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCc
Confidence            46899999999 8999999999999999999999987 58999999999999999999999999999999999997543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=3.7e-17  Score=123.05  Aligned_cols=80  Identities=23%  Similarity=0.353  Sum_probs=72.9

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      .....++|||+|||..+++++|+++|++||.|..++++.      ++|||||+|.+.++|++|+..+++ .+.|++|+|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            344579999999999999999999999999999999985      578999999999999999999998 8999999999


Q ss_pred             eecCCCC
Q psy3994         228 WAPGKGM  234 (282)
Q Consensus       228 ~a~~~~~  234 (282)
                      ||.....
T Consensus        92 ~a~~~~~   98 (116)
T 2cqd_A           92 LAYLGAK   98 (116)
T ss_dssp             ESTTTCC
T ss_pred             EcccCCC
Confidence            9986543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=9.9e-18  Score=123.64  Aligned_cols=81  Identities=21%  Similarity=0.280  Sum_probs=74.7

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhcc-CCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCe-eCCeeEEEEe
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGE-YGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTK-LQGKTITLAW  228 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~-~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~-~~g~~l~v~~  228 (282)
                      .+.++|||+|||+++|+++|+++|++ ||.|.++.++.     ++|||||+|.+.++|++|+..|||.. +.|++|+|.|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~   86 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSV   86 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEE
Confidence            35689999999999999999999999 99999999985     48999999999999999999999999 9999999999


Q ss_pred             ecCCCCCC
Q psy3994         229 APGKGMKD  236 (282)
Q Consensus       229 a~~~~~~~  236 (282)
                      +.++..+.
T Consensus        87 a~~~~~~~   94 (104)
T 2dhg_A           87 AIPKASRV   94 (104)
T ss_dssp             CCCCCSCC
T ss_pred             ccCCCcCC
Confidence            98776443

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.73  E-value=1.7e-18  Score=124.54  Aligned_cols=76  Identities=21%  Similarity=0.388  Sum_probs=65.4

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCC--ceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYG--DVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G--~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      .+|||||||.++|+++|+++|++||  .|.+++++.      ++|||||+|.+.++|++|++.|||..+.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  999999874      57999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy3994         231 GKGM  234 (282)
Q Consensus       231 ~~~~  234 (282)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7753

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=2.4e-17  Score=121.39  Aligned_cols=79  Identities=16%  Similarity=0.312  Sum_probs=72.2

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ..+.++|||+|||..+++++|+++|++|| |.+++++.      ++|||||+|.+.++|++|+ .|||..+.|++|+|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            34579999999999999999999999997 99999984      4789999999999999999 8999999999999999


Q ss_pred             ecCCCCC
Q psy3994         229 APGKGMK  235 (282)
Q Consensus       229 a~~~~~~  235 (282)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2dng_A           90 AEGRKQD   96 (103)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            9987644

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.72  E-value=1.2e-17  Score=123.54  Aligned_cols=78  Identities=12%  Similarity=0.197  Sum_probs=71.8

Q ss_pred             CCCCcEEEecCCCccC------cHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCe-e
Q psy3994         155 NMCSTTLWIGHLSKLV------QEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGK-T  223 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~------te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~-~  223 (282)
                      ...+++|||||||..+      ++++|+++|++||.|.++.+++    ++|||||+|.+.++|++|+..|||..+.|+ +
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            3456899999999999      7899999999999999999884    689999999999999999999999999998 9


Q ss_pred             EEEEeecCC
Q psy3994         224 ITLAWAPGK  232 (282)
Q Consensus       224 l~v~~a~~~  232 (282)
                      |+|.||...
T Consensus        92 l~V~~a~~~  100 (105)
T 2nlw_A           92 FRVNLFTDF  100 (105)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEEcchH
Confidence            999999754

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.72  E-value=1.3e-17  Score=127.38  Aligned_cols=82  Identities=24%  Similarity=0.447  Sum_probs=75.0

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ....+++|||+|||..+|+++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            344578999999999999999999999999999999975      38999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q psy3994         228 WAPGKGMK  235 (282)
Q Consensus       228 ~a~~~~~~  235 (282)
                      ||.++..+
T Consensus        98 ~a~~~~~~  105 (126)
T 3ex7_B           98 WCFVRGPP  105 (126)
T ss_dssp             ESEESSSC
T ss_pred             EecCCCCC
Confidence            99876543

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.72  E-value=1.3e-17  Score=131.39  Aligned_cols=80  Identities=26%  Similarity=0.407  Sum_probs=74.8

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP-RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~-kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .....++|||||||+++|+++|+++|++||.|.+++++.. +|||||+|.+.++|.+|+..|||..+.|++|+|.|++++
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            3445799999999999999999999999999999999874 999999999999999999999999999999999999876


Q ss_pred             C
Q psy3994         233 G  233 (282)
Q Consensus       233 ~  233 (282)
                      .
T Consensus       149 ~  149 (150)
T 2i2y_A          149 K  149 (150)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.72  E-value=2.6e-17  Score=127.90  Aligned_cols=83  Identities=23%  Similarity=0.358  Sum_probs=75.9

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      .....++|||+|||.++++++|+++|+.||.|.+++++.      ++|||||+|.+.++|++|+..|||..+.|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            345678999999999999999999999999999999974      47999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q psy3994         228 WAPGKGMKD  236 (282)
Q Consensus       228 ~a~~~~~~~  236 (282)
                      ||+++..++
T Consensus       118 ~a~~~~~~~  126 (139)
T 1u6f_A          118 LAASGHQRP  126 (139)
T ss_dssp             ESSCCCCCC
T ss_pred             ECCCCCCCC
Confidence            999876553

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.72  E-value=2e-17  Score=124.26  Aligned_cols=78  Identities=24%  Similarity=0.403  Sum_probs=73.0

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .++++|||+|||.++++++|+++|++||.|.++.++.   ++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   85 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNAN   85 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            3568999999999999999999999999999999975   6799999999999999999999999999999999999865


Q ss_pred             C
Q psy3994         233 G  233 (282)
Q Consensus       233 ~  233 (282)
                      .
T Consensus        86 ~   86 (115)
T 3lqv_A           86 R   86 (115)
T ss_dssp             H
T ss_pred             h
Confidence            4

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=4.9e-18  Score=120.61  Aligned_cols=76  Identities=25%  Similarity=0.316  Sum_probs=70.4

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .++++|||+|||+++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+..|||..+.|+.|+|.|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            3568999999999999999999999999999999885      4799999999999999999999999999999998886


Q ss_pred             cC
Q psy3994         230 PG  231 (282)
Q Consensus       230 ~~  231 (282)
                      ++
T Consensus        83 ~s   84 (85)
T 1x4e_A           83 SS   84 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.72  E-value=2.7e-17  Score=117.71  Aligned_cols=74  Identities=19%  Similarity=0.436  Sum_probs=70.0

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||+|||+++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+ .|||..+.|+.|+|.++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            48999999999999999999999999999999874      4899999999999999999 8999999999999999986


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            5

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.72  E-value=3.1e-17  Score=122.23  Aligned_cols=79  Identities=27%  Similarity=0.389  Sum_probs=70.6

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||.++++++|+++|+.||.|.+++++.      ++|||||+|.+.++|++|+..+ |..+.|+.|+|.++
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVA  101 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEc
Confidence            3568999999999999999999999999999999975      4799999999999999999976 58999999999999


Q ss_pred             cCCCCC
Q psy3994         230 PGKGMK  235 (282)
Q Consensus       230 ~~~~~~  235 (282)
                      .++..+
T Consensus       102 ~~~~~~  107 (109)
T 2rs2_A          102 FPRRAQ  107 (109)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.72  E-value=4.9e-17  Score=123.89  Aligned_cols=82  Identities=22%  Similarity=0.305  Sum_probs=75.6

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....+++|||+|||..+++++|+++|++||.|.++++..     ++|||||+|.+.++|++|+..|||..+.|++|+|.|
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            445679999999999999999999999999999999986     679999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy3994         229 APGKGMK  235 (282)
Q Consensus       229 a~~~~~~  235 (282)
                      |.+....
T Consensus       111 a~~~~~~  117 (124)
T 2kt5_A          111 VASQIDL  117 (124)
T ss_dssp             ECCTTCC
T ss_pred             eCCCCCC
Confidence            9876543

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=3.8e-17  Score=122.70  Aligned_cols=81  Identities=23%  Similarity=0.403  Sum_probs=72.9

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCce----EEEEEeC--CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDV----VSINLIP--PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i----~~~~~~~--~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .++++|||+|||.++|+++|+++|++||.|    ..+++..  ++|||||+|.+.++|++|+..|||..+.|++|+|.||
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            357999999999999999999999999998    5666553  6899999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q psy3994         230 PGKGMKD  236 (282)
Q Consensus       230 ~~~~~~~  236 (282)
                      +++..+.
T Consensus       103 ~~~~~~~  109 (115)
T 2cpx_A          103 KNKKQRS  109 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCCC
Confidence            9876543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=6.9e-17  Score=116.17  Aligned_cols=77  Identities=16%  Similarity=0.210  Sum_probs=71.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ....++|||+|||.++++++|+++|+.| .|.+++++.     ++|||||+|.+.++|++|+. |||..+.|+.|+|.+|
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            3457899999999999999999999999 999999885     47899999999999999999 9999999999999999


Q ss_pred             cCCC
Q psy3994         230 PGKG  233 (282)
Q Consensus       230 ~~~~  233 (282)
                      .++.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            8774

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.71  E-value=6.8e-17  Score=123.20  Aligned_cols=77  Identities=16%  Similarity=0.217  Sum_probs=70.7

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-CCcE-EEEEecCHHHHHHHHHHhCCCeeCC--eeEEEEeecCCCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGC-AFVCMNRRQDAAKALYKLKNTKLQG--KTITLAWAPGKGM  234 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-~kg~-aFV~f~~~~~A~~Ai~~l~g~~~~g--~~l~v~~a~~~~~  234 (282)
                      -.|||+||+..+|+++|+++|++||.|.+|.+.. ++|| |||+|.+.++|+.|++.|||..+.|  ++|+|+||+++..
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            5688999999999999999999999999998875 6788 9999999999999999999999988  8999999998754


Q ss_pred             C
Q psy3994         235 K  235 (282)
Q Consensus       235 ~  235 (282)
                      .
T Consensus       109 ~  109 (130)
T 3zzy_A          109 N  109 (130)
T ss_dssp             C
T ss_pred             e
Confidence            3

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1.8e-17  Score=122.56  Aligned_cols=81  Identities=25%  Similarity=0.391  Sum_probs=74.0

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||+.+++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+.. ||..+.|+.|+|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            34579999999999999999999999999999999985      468999999999999999998 99999999999999


Q ss_pred             ecCCCCCC
Q psy3994         229 APGKGMKD  236 (282)
Q Consensus       229 a~~~~~~~  236 (282)
                      +.++...+
T Consensus        92 a~~~~~~~   99 (105)
T 2dh8_A           92 CTPRGMQP   99 (105)
T ss_dssp             SCCSSCCT
T ss_pred             ccCCCCCC
Confidence            99876543

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.71  E-value=3.8e-17  Score=116.47  Aligned_cols=74  Identities=26%  Similarity=0.423  Sum_probs=67.8

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||+++++++|+++|++||.|.+++++.      ++|||||+|.+.++|++|+. +++..+.|+.|+|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            34568999999999999999999999999999999974      47899999999999999996 588899999999998


Q ss_pred             e
Q psy3994         229 A  229 (282)
Q Consensus       229 a  229 (282)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.71  E-value=4.3e-17  Score=130.00  Aligned_cols=111  Identities=21%  Similarity=0.308  Sum_probs=88.7

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ++++|||+|||+++++++|+++|++||.|.++++..      ++|||||+|.+.++|++|+..|+|..+.|++|+|.|+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            368999999999999999999999999999999874      46899999999999999999999999999999999998


Q ss_pred             CCCCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccC
Q psy3994         231 GKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDED  275 (282)
Q Consensus       231 ~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~  275 (282)
                      +.........-+      +..+|.+  .++++|..+++ .|.+...
T Consensus        82 ~~~~~~~~~~l~------v~nl~~~--~t~~~l~~~f~~~G~i~~~  119 (168)
T 1b7f_A           82 PGGESIKDTNLY------VTNLPRT--ITDDQLDTIFGKYGSIVQK  119 (168)
T ss_dssp             CCSSTTTTCEEE------EESCCTT--CCHHHHHHHHTSSSCEEEE
T ss_pred             CCcccCCCCCEE------EeCCCCC--CCHHHHHHhhhcCCcEEEE
Confidence            776433222111      3445543  35788887665 4544433

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.71  E-value=1e-17  Score=129.61  Aligned_cols=80  Identities=25%  Similarity=0.378  Sum_probs=74.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||+|||.++|+++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.|++
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~  125 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR  125 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            568999999999999999999999999999999874      57899999999999999999999999999999999999


Q ss_pred             CCCCCC
Q psy3994         231 GKGMKD  236 (282)
Q Consensus       231 ~~~~~~  236 (282)
                      ++..+.
T Consensus       126 ~~~~~~  131 (135)
T 2lea_A          126 YGRPPD  131 (135)
T ss_dssp             CCCCCT
T ss_pred             CCCCCc
Confidence            876443

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=1.5e-17  Score=121.33  Aligned_cols=78  Identities=21%  Similarity=0.323  Sum_probs=70.5

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||.++++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            3468999999999999999999999999997665552      5799999999999999999999999999999999999


Q ss_pred             cCCC
Q psy3994         230 PGKG  233 (282)
Q Consensus       230 ~~~~  233 (282)
                      ..+.
T Consensus        93 ~~~~   96 (98)
T 2cqp_A           93 SGPS   96 (98)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            8654

>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain, RNA polymerase II binding protein, phosphoprotein; NMR {Saccharomyces cerevisiae} PDB: 2l0i_A*

Probab=99.71  E-value=2.4e-18  Score=133.92  Aligned_cols=125  Identities=19%  Similarity=0.356  Sum_probs=111.5

Q ss_pred             Cc-hhHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhc--CCCCccceeehhhHHHHHhhhhc
Q psy3994           1 MD-VIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKC--KPEYKVPALYVIDSLVRQSRHQF   77 (282)
Q Consensus         1 m~-~~~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~--~p~~kl~~lYv~Dsi~r~~~~~~   77 (282)
                      |+ ..++|++.|++|.+     |+.+|++++.|++.|.++++.+|+.|.+++++.  ++.+||+.|||+|+|+++++++.
T Consensus         1 m~fs~~~l~~kL~~L~~-----sq~sIq~~s~W~l~h~~~a~~iv~~~~~~l~~~~~~~~kKL~~lYL~NDVlqnsk~k~   75 (142)
T 2km4_A            1 MAFSSEQFTTKLNTLED-----SQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLMNHVVQQAKGQK   75 (142)
T ss_dssp             -CCCHHHHHHHHHTCCS-----CHHHHHHHHHHHHTCGGGHHHHHHHHHHHHTSSSSCHHHHHHHHHHHHHHHHHHGGGT
T ss_pred             CCCCHHHHHHHHHhccc-----cHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcCCCccceehhhhhHHHHHHHHhhcC
Confidence            44 36789999999954     666999999999999999999999999999997  77999999999999999998876


Q ss_pred             cCCCCchhhHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhccCcccCCcccccccc
Q psy3994          78 QDKDVFGPRFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKNEVFTPDIIHPLFD  132 (282)
Q Consensus        78 ~~~~~~~~~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~~~~~f~~~~i~~~~~  132 (282)
                      +.  .|+..|.+.|.+.|..++. ++++.+.++.+++++|+++++|+.+.+..+..
T Consensus        76 ~~--~f~~~F~~~L~~~~~~~~~~~~~~~~~kv~rvl~iWeer~vf~~~~i~~L~~  129 (142)
T 2km4_A           76 II--QFQDSFGKVAAEVLGRINQEFPRDLKKKLSRVVNILKERNIFSKQVVNDIER  129 (142)
T ss_dssp             CC--HHHHHHHHTHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTCSCHHHHHHHHH
T ss_pred             ch--HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhccCCcCHHHHHHHHH
Confidence            53  6999999999999999998 88999999999999999999999988776543

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.71  E-value=4.3e-17  Score=129.37  Aligned_cols=81  Identities=25%  Similarity=0.365  Sum_probs=74.8

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||+++++++|+++|++||.|.+++++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.||
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            4568999999999999999999999999999999875      6799999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q psy3994         230 PGKGMKD  236 (282)
Q Consensus       230 ~~~~~~~  236 (282)
                      +++..++
T Consensus       148 ~~~~~~~  154 (158)
T 2kn4_A          148 RYGRPPD  154 (158)
T ss_dssp             CCSSCCC
T ss_pred             CCCCCCC
Confidence            9875443

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=7.6e-17  Score=118.26  Aligned_cols=80  Identities=25%  Similarity=0.302  Sum_probs=69.8

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe--CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI--PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ....++|||+|||.++++++|+++|++||.|.-+...  .++|||||+|.+.++|++|+..|||..+.|+.|+|.|++++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   91 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPR   91 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEEECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCC
Confidence            3457999999999999999999999999988322211  26899999999999999999999999999999999999987


Q ss_pred             CC
Q psy3994         233 GM  234 (282)
Q Consensus       233 ~~  234 (282)
                      ..
T Consensus        92 ~~   93 (101)
T 2fc9_A           92 GS   93 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.8e-17  Score=122.23  Aligned_cols=78  Identities=26%  Similarity=0.474  Sum_probs=72.8

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||+|||..+++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+..|||..+.|+.|+|.||.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            358999999999999999999999999999999885      37999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy3994         231 GKGM  234 (282)
Q Consensus       231 ~~~~  234 (282)
                      ++..
T Consensus        87 ~~~~   90 (104)
T 1p1t_A           87 SEKN   90 (104)
T ss_dssp             CTTH
T ss_pred             Cccc
Confidence            8753

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.70  E-value=6.6e-17  Score=128.10  Aligned_cols=79  Identities=30%  Similarity=0.450  Sum_probs=73.3

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||..+|+++|+++|++||.|..|.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.||
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3579999999999999999999999999999999974      4689999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy3994         230 PGKGM  234 (282)
Q Consensus       230 ~~~~~  234 (282)
                      ++...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87643

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.70  E-value=3.4e-17  Score=118.98  Aligned_cols=80  Identities=23%  Similarity=0.371  Sum_probs=71.3

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe-CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      .+.++|||+|||..+++++|+++|++||.|..+... .++|||||+|.+.++|++|+..|||..+.|++|+|.|+.+++.
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            356899999999999999999999999998877211 2689999999999999999999999999999999999988764


Q ss_pred             C
Q psy3994         235 K  235 (282)
Q Consensus       235 ~  235 (282)
                      .
T Consensus        94 ~   94 (96)
T 1fjc_A           94 T   94 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.70  E-value=6.7e-17  Score=128.53  Aligned_cols=110  Identities=27%  Similarity=0.331  Sum_probs=87.3

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~------kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +++|||+|||+++++++|+++|+.||.|.++.+...      +|||||+|.+.++|++|+..|||..+.|++|+|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            589999999999999999999999999999999863      49999999999999999999999999999999999987


Q ss_pred             CCCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccC
Q psy3994         232 KGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDED  275 (282)
Q Consensus       232 ~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~  275 (282)
                      .........-      -+..+|.+  .++++|..+++ .|.+...
T Consensus        82 ~~~~~~~~~l------~v~nl~~~--~t~~~l~~~f~~~G~i~~~  118 (167)
T 1fxl_A           82 SSASIRDANL------YVSGLPKT--MTQKELEQLFSQYGRIITS  118 (167)
T ss_dssp             CCGGGTTCEE------EEESCCTT--CCHHHHHHHHGGGSCEEEE
T ss_pred             CcccCCCCcE------EECCCCCc--CCHHHHHHHHHhcCCEeEE
Confidence            6532211111      13444443  35788887665 3544433

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.70  E-value=1.5e-17  Score=117.08  Aligned_cols=69  Identities=13%  Similarity=0.265  Sum_probs=64.5

Q ss_pred             CcEEEecCCCccC------cHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCe-eEEE
Q psy3994         158 STTLWIGHLSKLV------QEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGK-TITL  226 (282)
Q Consensus       158 ~~~l~V~nl~~~~------te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~-~l~v  226 (282)
                      +++|||||||..+      ++++|+++|++||.|.++.+++    ++|||||+|.+.++|++|+..|||..+.|+ +|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            3789999999999      7799999999999999999884    689999999999999999999999999999 8876

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.70  E-value=5.3e-17  Score=129.94  Aligned_cols=83  Identities=27%  Similarity=0.456  Sum_probs=74.4

Q ss_pred             CCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEE
Q psy3994         153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL  226 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v  226 (282)
                      ....++++|||+|||+.+++++|+.+|++||.|..|.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  146 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  146 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3455678999999999999999999999999999999985      3799999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q psy3994         227 AWAPGKGMK  235 (282)
Q Consensus       227 ~~a~~~~~~  235 (282)
                      .||.+++.+
T Consensus       147 ~~a~~~~~~  155 (165)
T 1rk8_A          147 DWCFVKGPK  155 (165)
T ss_dssp             EESEECC--
T ss_pred             EEecCCCCC
Confidence            999877644

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=7.3e-17  Score=118.53  Aligned_cols=82  Identities=28%  Similarity=0.404  Sum_probs=70.1

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe---CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI---PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~---~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ...+.++|||+|||.++++++|+++|+.|+.+.-+...   .++|||||+|.+.++|++|+..|||..+.|+.|+|.||+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   90 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK   90 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEec
Confidence            34467999999999999999999999998654433322   146999999999999999999999999999999999999


Q ss_pred             CCCCC
Q psy3994         231 GKGMK  235 (282)
Q Consensus       231 ~~~~~  235 (282)
                      ++...
T Consensus        91 ~~~~~   95 (102)
T 2fc8_A           91 PKGEG   95 (102)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            87654

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.70  E-value=2.3e-17  Score=120.89  Aligned_cols=77  Identities=19%  Similarity=0.277  Sum_probs=68.9

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ....++|||||||.++++++|+++|+.|| |.+++++.       ++|||||+|.+.++|++|+ .|||..+.|+.|+|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            34579999999999999999999999999 99999875       4789999999999999999 899999999999999


Q ss_pred             eecCCC
Q psy3994         228 WAPGKG  233 (282)
Q Consensus       228 ~a~~~~  233 (282)
                      +|+++.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            998763

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=8.5e-17  Score=120.64  Aligned_cols=78  Identities=18%  Similarity=0.362  Sum_probs=71.8

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCee--------CCe
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKL--------QGK  222 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~--------~g~  222 (282)
                      ...++|||+|||+++++++|+++|++||.|.+++++.     ++|||||+|.+.++|++|+..|||..+        .++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~  102 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE  102 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCC
Confidence            4568999999999999999999999999999999985     479999999999999999999999999        578


Q ss_pred             eEEEEeecCCC
Q psy3994         223 TITLAWAPGKG  233 (282)
Q Consensus       223 ~l~v~~a~~~~  233 (282)
                      +|+|.||.+++
T Consensus       103 ~l~v~~a~p~~  113 (114)
T 1x5o_A          103 PLLCKFSGPSS  113 (114)
T ss_dssp             CBEEEECCCSC
T ss_pred             ceeEEccCCCC
Confidence            89999998664

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.70  E-value=6.9e-17  Score=115.82  Aligned_cols=74  Identities=26%  Similarity=0.397  Sum_probs=63.1

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCee--CCeeEEEEeecCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKL--QGKTITLAWAPGK  232 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~--~g~~l~v~~a~~~  232 (282)
                      .+.++|||||||+++|+++|+++|++||.|.+++++. +||||||+|.+.++|++    ++|..+  .|++|.|.+|.++
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCC
Confidence            3568999999999999999999999999999999986 79999999999999883    566654  6999999999877


Q ss_pred             C
Q psy3994         233 G  233 (282)
Q Consensus       233 ~  233 (282)
                      .
T Consensus        85 ~   85 (89)
T 3d2w_A           85 H   85 (89)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.69  E-value=1.9e-17  Score=114.65  Aligned_cols=69  Identities=22%  Similarity=0.332  Sum_probs=65.1

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      +|||+|||+++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|++ +||..+.|++|+|+||
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            489999999999999999999999999999874      47999999999999999998 9999999999999986

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.69  E-value=5.1e-17  Score=128.74  Aligned_cols=76  Identities=21%  Similarity=0.339  Sum_probs=70.5

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCC--ceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYG--DVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G--~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ..++|||||||+++|+++|+++|+.||  .|.+++++.      ++|||||+|.+.++|++|+..|||..+.|+.|+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            458999999999999999999999999  999999974      579999999999999999999999999999999999


Q ss_pred             ecCC
Q psy3994         229 APGK  232 (282)
Q Consensus       229 a~~~  232 (282)
                      |.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9865

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.69  E-value=2.3e-17  Score=119.63  Aligned_cols=75  Identities=20%  Similarity=0.311  Sum_probs=68.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||+|||+++++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+..|||..+.|++|+|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            458999999999999999999999999998766653      57999999999999999999999999999999999986


Q ss_pred             C
Q psy3994         231 G  231 (282)
Q Consensus       231 ~  231 (282)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            4

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.69  E-value=4.5e-17  Score=137.04  Aligned_cols=80  Identities=23%  Similarity=0.420  Sum_probs=72.7

Q ss_pred             CCCCcEEEecCCCccC---------cHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCee------
Q psy3994         155 NMCSTTLWIGHLSKLV---------QEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL------  219 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~---------te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~------  219 (282)
                      ...+++||||||+..+         ++++|+.+|++||+|.+|+++.+||||||+|.++++|+.|++.|+|..+      
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~  210 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDK  210 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTST
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHHHHHHHHHhCCCEEeccccc
Confidence            4467999999999998         7999999999999999999999999999999999999999999999999      


Q ss_pred             ------CCeeEEEEeecCCCC
Q psy3994         220 ------QGKTITLAWAPGKGM  234 (282)
Q Consensus       220 ------~g~~l~v~~a~~~~~  234 (282)
                            .|+.|.|+||+....
T Consensus       211 e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          211 EWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             TGGGGGGSCCCEEEECC----
T ss_pred             cccccCCCCEEEEEEccCCCC
Confidence                  899999999987654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=9.4e-17  Score=120.80  Aligned_cols=78  Identities=21%  Similarity=0.358  Sum_probs=72.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||+|||.++++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+.. +|..+.|+.|+|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            358999999999999999999999999999999986      478999999999999999997 9999999999999999


Q ss_pred             CCCCC
Q psy3994         231 GKGMK  235 (282)
Q Consensus       231 ~~~~~  235 (282)
                      ++...
T Consensus       105 ~~~~~  109 (116)
T 1x4b_A          105 AREES  109 (116)
T ss_dssp             SCCCC
T ss_pred             CCccC
Confidence            88644

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.69  E-value=1.1e-17  Score=120.06  Aligned_cols=75  Identities=31%  Similarity=0.558  Sum_probs=67.2

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ++|||+|||.++++++|+++|++||.|.++.+..      ++|||||+|.+.+ |.+|+..|||..+.|++|+|.+|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            6899999999999999999999999999999974      5899999999999 99999999999999999999999876


Q ss_pred             CC
Q psy3994         233 GM  234 (282)
Q Consensus       233 ~~  234 (282)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            53

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.69  E-value=1.5e-17  Score=127.99  Aligned_cols=79  Identities=24%  Similarity=0.405  Sum_probs=72.3

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEE--EEEeC------CCcEEEEEecCHHHHHHHHHHhCCC----eeCC
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVS--INLIP------PRGCAFVCMNRRQDAAKALYKLKNT----KLQG  221 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~--~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~----~~~g  221 (282)
                      ....+++|||||||+++|+++|+++|++||.|..  |+++.      +||||||+|.+. +|.+|+..|||.    .+.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456789999999999999999999999999976  88874      579999999999 999999999999    9999


Q ss_pred             eeEEEEeecCCC
Q psy3994         222 KTITLAWAPGKG  233 (282)
Q Consensus       222 ~~l~v~~a~~~~  233 (282)
                      ++|+|.||+++.
T Consensus        98 r~l~V~~a~~~~  109 (131)
T 2m2b_A           98 KTINVEFAKGSK  109 (131)
T ss_dssp             CCCCCEECCCSC
T ss_pred             EEEEEEECCCCC
Confidence            999999998764

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.6e-16  Score=116.89  Aligned_cols=79  Identities=16%  Similarity=0.291  Sum_probs=71.3

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||..+++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+.  +++.+.|+.|+|.|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            34568999999999999999999999999999999875      46899999999999999998  57899999999999


Q ss_pred             ecCCCCC
Q psy3994         229 APGKGMK  235 (282)
Q Consensus       229 a~~~~~~  235 (282)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqg_A           90 PNSKQSQ   96 (103)
T ss_dssp             CCTTCCC
T ss_pred             cCCCCcC
Confidence            9987543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.69  E-value=7.1e-17  Score=134.46  Aligned_cols=114  Identities=19%  Similarity=0.215  Sum_probs=87.4

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .+.++|||||||+++|+++|+++|++||.|.+|++++      ++|||||+|.+.++|++|+..+||..+.|+.|++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            3568999999999999999999999999999999974      5799999999999999999999999999999999999


Q ss_pred             cCCCCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccC
Q psy3994         230 PGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDED  275 (282)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~  275 (282)
                      ........  ..  ....-+..+|.  -.++++|+.+++ .|.+..+
T Consensus        93 ~~~~~~~~--~~--~~~l~v~nl~~--~~t~~~l~~~F~~~G~i~~~  133 (213)
T 4f02_A           93 QRDPSLRK--SG--VGNIFIKNLDK--SIDNKALYDTFSAFGNILSC  133 (213)
T ss_dssp             CCCTHHHH--HC--TTEEEEESCCT--TCCHHHHHHHHGGGSCEEEE
T ss_pred             cccccccc--cc--cccceECCccc--ccHHHHHHHHHhhcCCeEEE
Confidence            76542210  00  00111334444  346888887665 4555444

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=2.5e-17  Score=114.57  Aligned_cols=70  Identities=30%  Similarity=0.468  Sum_probs=66.3

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ++|||+|||+++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+..++ ..+.|++|+|+||
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            5799999999999999999999999999999985      47899999999999999999999 9999999999997

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.69  E-value=1.3e-16  Score=121.09  Aligned_cols=76  Identities=20%  Similarity=0.171  Sum_probs=69.4

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcE-EEEEecCHHHHHHHHHHhCCCeeCC--eeEEEEeecCCCCC
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC-AFVCMNRRQDAAKALYKLKNTKLQG--KTITLAWAPGKGMK  235 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~-aFV~f~~~~~A~~Ai~~l~g~~~~g--~~l~v~~a~~~~~~  235 (282)
                      .|||+||++.+++++|+++|++||.|.+|.+....|| |||+|.+.++|..|++.|||..+.|  ++|+|.+|+++...
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l~  105 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLN  105 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCCC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcce
Confidence            4689999999999999999999999999998765696 9999999999999999999999977  68999999987543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.69  E-value=1e-16  Score=124.41  Aligned_cols=77  Identities=30%  Similarity=0.480  Sum_probs=70.9

Q ss_pred             CCCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEE
Q psy3994         153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL  226 (282)
Q Consensus       153 ~~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v  226 (282)
                      ......++|||+|||..+++++|+++|++||.|.+++++.      ++|||||+|.+.++|++|+..|||..+.|++|+|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3445679999999999999999999999999999999975      5899999999999999999999999999999999


Q ss_pred             Eee
Q psy3994         227 AWA  229 (282)
Q Consensus       227 ~~a  229 (282)
                      +||
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            986

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.68  E-value=6.9e-17  Score=115.04  Aligned_cols=71  Identities=18%  Similarity=0.422  Sum_probs=67.9

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccC----C-------ceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEY----G-------DVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~----G-------~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      ..++|||+|||+++++++|+++|++|    |       .|.++.+..++|||||+|.+.++|++|+ .|||..+.|++|+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   83 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   83 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEE
Confidence            46899999999999999999999999    8       9999999999999999999999999999 9999999999999


Q ss_pred             EEe
Q psy3994         226 LAW  228 (282)
Q Consensus       226 v~~  228 (282)
                      |+.
T Consensus        84 V~r   86 (87)
T 2hzc_A           84 IRR   86 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            974

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.6e-16  Score=115.04  Aligned_cols=78  Identities=19%  Similarity=0.268  Sum_probs=68.8

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCc-EEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG-CAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMK  235 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg-~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~  235 (282)
                      ..++|||+|||+++++++|+++|++||.|.+|.+.+..+ ||||+|.+.++|++|+. |||..+.|+.|+|.++.++...
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~~   85 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEFQ   85 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCCC
Confidence            457999999999999999999999999999983333222 99999999999999999 9999999999999999876544

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=4.6e-17  Score=122.14  Aligned_cols=76  Identities=22%  Similarity=0.361  Sum_probs=70.9

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||+|||.++++++|+++|+.||.|..+.++.      ++|||||+|.+.++|++|+ .|||..+.|+.|+|.|++
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            358999999999999999999999999999999974      6799999999999999999 999999999999999998


Q ss_pred             CCC
Q psy3994         231 GKG  233 (282)
Q Consensus       231 ~~~  233 (282)
                      ++.
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            653

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.3e-16  Score=113.45  Aligned_cols=72  Identities=21%  Similarity=0.313  Sum_probs=65.4

Q ss_pred             cEEEecCCCccCcHHH----HHhhhccC-CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         159 TTLWIGHLSKLVQEEE----LSDTFGEY-GDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~----l~~~f~~~-G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      +.|||+|||..+++++    |+++|++| |+|.+|.    .|+|||.|.+.++|++|++.|||..+.||+|+|.+|+.+.
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt----gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~s   85 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT----GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNR   85 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC----TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSC
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe----cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCc
Confidence            4499999999999987    56899999 5999982    3999999999999999999999999999999999999875


Q ss_pred             C
Q psy3994         234 M  234 (282)
Q Consensus       234 ~  234 (282)
                      .
T Consensus        86 d   86 (96)
T 2diu_A           86 E   86 (96)
T ss_dssp             C
T ss_pred             c
Confidence            3

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.68  E-value=1.2e-16  Score=126.39  Aligned_cols=77  Identities=16%  Similarity=0.189  Sum_probs=70.7

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhCCCeeCC--eeEEEEeecCCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--PRGCAFVCMNRRQDAAKALYKLKNTKLQG--KTITLAWAPGKG  233 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~--~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g--~~l~v~~a~~~~  233 (282)
                      ..+|||+||++.+|+++|+++|++||.|.+|.+..  ++|||||+|.+.++|+.|++.|||..+.|  ++|+|.||+++.
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            46799999999999999999999999999999863  57899999999999999999999999955  999999999875


Q ss_pred             C
Q psy3994         234 M  234 (282)
Q Consensus       234 ~  234 (282)
                      .
T Consensus       126 l  126 (164)
T 1sjr_A          126 L  126 (164)
T ss_dssp             C
T ss_pred             c
Confidence            3

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.68  E-value=9.8e-17  Score=125.27  Aligned_cols=80  Identities=33%  Similarity=0.456  Sum_probs=70.9

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEE--------EEEe---CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeE
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVS--------INLI---PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTI  224 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~--------~~~~---~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l  224 (282)
                      .++++|||+|||+.+|+++|+.+|++||.|..        +.+.   .++|||||+|.+.++|.+|+..|||..+.|++|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            35689999999999999999999999998865        3333   478999999999999999999999999999999


Q ss_pred             EEEeecCCCCC
Q psy3994         225 TLAWAPGKGMK  235 (282)
Q Consensus       225 ~v~~a~~~~~~  235 (282)
                      +|.||++...+
T Consensus       123 ~V~~a~~~~~~  133 (143)
T 3egn_A          123 VVQFARSARPK  133 (143)
T ss_dssp             EEEECCCSCC-
T ss_pred             EEEECCCCCCc
Confidence            99999876544

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.67  E-value=1.2e-16  Score=121.65  Aligned_cols=75  Identities=19%  Similarity=0.413  Sum_probs=70.5

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||+|||.++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+ .|||..+.|+.|+|.|+++
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            58999999999999999999999999999999874      4899999999999999999 7999999999999999986


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.67  E-value=1.5e-16  Score=116.73  Aligned_cols=79  Identities=24%  Similarity=0.250  Sum_probs=69.7

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEE-----EEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVS-----INLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~-----~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ...++|||+|||.++++++|+++|++||.|..     .....++|||||+|.+.++|++|++ |||..+.|+.|+|.+|+
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            35689999999999999999999999997765     1222478999999999999999998 99999999999999999


Q ss_pred             CCCCC
Q psy3994         231 GKGMK  235 (282)
Q Consensus       231 ~~~~~  235 (282)
                      ++..+
T Consensus        94 ~~~~~   98 (101)
T 1fj7_A           94 GRDGT   98 (101)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87644

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.67  E-value=5.2e-17  Score=135.28  Aligned_cols=76  Identities=21%  Similarity=0.458  Sum_probs=71.8

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .++|||+|||+.+|+++|+++|++||.|.+++++.    ++|||||+|.+.++|++|++.|||..++|++|+|.||+++.
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            47899999999999999999999999999999875    68999999999999999999999999999999999998764

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.66  E-value=4e-16  Score=123.89  Aligned_cols=113  Identities=19%  Similarity=0.232  Sum_probs=87.8

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ++|||+|||+++|+++|+++|++||.|.++++..     ++|||||+|.+.++|.+|+..|||..+.|++|+|.|+.+..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            5899999999999999999999999999999974     56999999999999999999999999999999999998765


Q ss_pred             CCCCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccCCC
Q psy3994         234 MKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDTV  277 (282)
Q Consensus       234 ~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~  277 (282)
                      .....      ....+.+-+++.-.++++|..+++ .|.+....+
T Consensus        81 ~~~~~------~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i  119 (166)
T 3md3_A           81 QSSSD------DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHV  119 (166)
T ss_dssp             CCCCT------TCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEE
T ss_pred             CCCCC------CCceEEECCCCCCCCHHHHHHHHhccCCeeEEEE
Confidence            43211      011122223333346788887655 455554433

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.66  E-value=5.9e-16  Score=122.91  Aligned_cols=115  Identities=22%  Similarity=0.373  Sum_probs=89.2

Q ss_pred             HhhcCChhhHHHHHHHHHhhc-cCcccCCccccccccCCCCCCCChhhhHHhhhcCCCCCCCCcEEEecCCCccCcHHHH
Q psy3994          97 HLYQCPPEDKSKIIRVLNLWQ-KNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEEL  175 (282)
Q Consensus        97 ~v~~~~~~~~~k~~~~l~~w~-~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~te~~l  175 (282)
                      ++.....+++.+++..++... .+..+....       +.+.             ........++|||+|||..+++++|
T Consensus        45 fV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~-------~~~~-------------~~~~~~~~~~l~v~nl~~~~t~~~l  104 (166)
T 3md3_A           45 FVEYHQSHDANIALQTLNGKQIENNIVKINW-------AFQS-------------QQSSSDDTFNLFVGDLNVNVDDETL  104 (166)
T ss_dssp             EEEESSHHHHHHHHHHHTTCEETTEECEEEE-------CCCC-------------CCCCCTTCEEEEEESCCTTCCHHHH
T ss_pred             EEEeCCHHHHHHHHHHcCCCccCCCeeEEEE-------cCCC-------------CCCCCCCCceEEECCCCCCCCHHHH
Confidence            333356888889998887332 222222221       2111             0122335689999999999999999


Q ss_pred             HhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         176 SDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       176 ~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +++|++||.|.++.+..      ++|||||+|.+.++|.+|+..|||..++|++|+|.||++
T Consensus       105 ~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          105 RNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             HHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            99999999999999974      478999999999999999999999999999999999863

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3.2e-16  Score=115.67  Aligned_cols=77  Identities=21%  Similarity=0.181  Sum_probs=70.2

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEE-EEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVS-INLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~-~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||+++|+++|+++|++||.|.. +.++.     ++|||||+|.+.++|++|+.. ||..++|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEEC
Confidence            35689999999999999999999999999987 77763     689999999999999999997 999999999999999


Q ss_pred             cCCC
Q psy3994         230 PGKG  233 (282)
Q Consensus       230 ~~~~  233 (282)
                      ..+.
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7664

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.66  E-value=1.7e-16  Score=119.29  Aligned_cols=76  Identities=24%  Similarity=0.305  Sum_probs=68.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCee-----EEEEeecC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKT-----ITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~-----l~v~~a~~  231 (282)
                      ..++|||+|||.++++++|+++|++||.|..+.++.. |||||+|.+.++|++|++.|||..+.|+.     ++|..+.+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~   93 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP   93 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC-
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCC
Confidence            4689999999999999999999999999999999877 99999999999999999999999999998     88888776


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      +.
T Consensus        94 ~~   95 (115)
T 3beg_B           94 RS   95 (115)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.1e-16  Score=118.64  Aligned_cols=77  Identities=13%  Similarity=0.110  Sum_probs=70.8

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCce-EEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDV-VSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i-~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||+++|+++|+++|+.||.| ..++++.     ++|||||+|.+.++|++|+.. ||..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVV   91 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEEC
Confidence            356899999999999999999999999999 7888874     789999999999999999987 999999999999999


Q ss_pred             cCCC
Q psy3994         230 PGKG  233 (282)
Q Consensus       230 ~~~~  233 (282)
                      .++.
T Consensus        92 ~~~~   95 (114)
T 2cpy_A           92 TLED   95 (114)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            8653

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=3e-16  Score=113.87  Aligned_cols=77  Identities=25%  Similarity=0.273  Sum_probs=70.6

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEE-EeC--CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSIN-LIP--PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~-~~~--~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .+++|||+|||+++++++|+++|++||.|.+++ ++.  ..+.|||+|.+.++|++|+..|||..+.|++|+|.+|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            468999999999999999999999999999995 665  34569999999999999999999999999999999999873

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4e-16  Score=114.74  Aligned_cols=77  Identities=16%  Similarity=0.196  Sum_probs=69.2

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ...++|||+|||+++|+++|+++|++||. .+++++.     ++|||||+|.+.++|++|+. +|+..+.|+.|+|.++.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            35689999999999999999999999995 4888874     57999999999999999995 79999999999999998


Q ss_pred             CCCC
Q psy3994         231 GKGM  234 (282)
Q Consensus       231 ~~~~  234 (282)
                      ....
T Consensus        91 ~~~~   94 (102)
T 1wez_A           91 TAGT   94 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=2.2e-16  Score=112.86  Aligned_cols=75  Identities=25%  Similarity=0.369  Sum_probs=66.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCC--eeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNT--KLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~--~~~g~~l~v~~a~~~~  233 (282)
                      .+++|||+|||.++++++|+++|++||.|.+++++. ++|||||+|.+.++|++|    ++.  .+.|++|+|.++.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~----~~~~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSL----CGEDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHT----TTCEEEETTEEEEEECCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHH----hcCCceeCCEEEEEEecCCCC
Confidence            469999999999999999999999999999999986 699999999999999754    444  4599999999998875


Q ss_pred             CC
Q psy3994         234 MK  235 (282)
Q Consensus       234 ~~  235 (282)
                      ..
T Consensus        80 ~~   81 (88)
T 1wf0_A           80 NS   81 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.65  E-value=4.2e-16  Score=124.79  Aligned_cols=111  Identities=15%  Similarity=0.220  Sum_probs=88.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccC----C-------ceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEY----G-------DVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~----G-------~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      ++++|||+|||+++|+++|+++|++|    |       .|.++.+.+++|||||+|.+.++|++|+ .+||..+.|++|+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~   81 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceee
Confidence            35899999999999999999999999    7       8899999999999999999999999999 8999999999999


Q ss_pred             EEeecCCCCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccCC
Q psy3994         226 LAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDT  276 (282)
Q Consensus       226 v~~a~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~  276 (282)
                      |.++...........-      -+..+|.+  .++++|..+++ .|.+....
T Consensus        82 v~~~~~~~~~~~~~~l------~v~nlp~~--~t~~~l~~~f~~~G~v~~v~  125 (172)
T 2g4b_A           82 IRRPHDYQPLPGAHKL------FIGGLPNY--LNDDQVKELLTSFGPLKAFN  125 (172)
T ss_dssp             EECCSSCCCCTTTTCE------EEECCCTT--CCHHHHHHHHHTTSCEEEEE
T ss_pred             ecCCcccCCCCCCCEE------EEEcCCCc--CCHHHHHHHHHhcCCceEEE
Confidence            9998766433221111      14445553  35788887555 45554443

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.65  E-value=2.5e-16  Score=118.94  Aligned_cols=75  Identities=16%  Similarity=0.148  Sum_probs=69.6

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCc---eEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGD---VVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~---i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ..++|||+|||+++|+++|+++|+.||.   |..++++.     ++|||||+|.+.++|++|+. +||..+.|+.|+|.+
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~   94 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFK   94 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEE
Confidence            4689999999999999999999999999   88898874     58999999999999999999 999999999999999


Q ss_pred             ecCC
Q psy3994         229 APGK  232 (282)
Q Consensus       229 a~~~  232 (282)
                      +..+
T Consensus        95 a~~~   98 (118)
T 2db1_A           95 SHRT   98 (118)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            9754

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.65  E-value=2.9e-16  Score=128.42  Aligned_cols=119  Identities=18%  Similarity=0.216  Sum_probs=86.0

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||+++|+++|+++|+.||.|.++.++.      ++|||||+|.+.++|++|+.. +|..+.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            3568999999999999999999999999999999884      478999999999999999986 999999999999999


Q ss_pred             cCCCCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccCCC
Q psy3994         230 PGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDTV  277 (282)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~  277 (282)
                      .++...............-+..+|.+  .++++|..+++ .|.+..+.+
T Consensus        90 ~~~~~~~~~~~~~~~~~l~V~nLp~~--~t~~~l~~~F~~~G~i~~v~i  136 (196)
T 1l3k_A           90 VSREDSQRPGAHLTVKKIFVGGIKED--TEEHHLRDYFEQYGKIEVIEI  136 (196)
T ss_dssp             CC-----------CCSEEEEECCTTT--CCHHHHHHHHTTTSCEEEEEE
T ss_pred             cCcccccccccCCCcceEEEeCCCCC--CCHHHHHHHHhcCCCeEEEEE
Confidence            87643321111100011113444544  36888887665 455554433

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.45  E-value=1.4e-17  Score=125.35  Aligned_cols=79  Identities=23%  Similarity=0.332  Sum_probs=72.5

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEE--------EEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCe
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVS--------INLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGK  222 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~--------~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~  222 (282)
                      +.++|||+|||.++++++|+++|++||.|..        ++++.      ++|||||+|.+.++|++|+..|||..+.|+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   85 (116)
Confidence            4689999999999999999999999999998        77764      579999999999999999999999999999


Q ss_pred             eEEEEeecCCCCC
Q psy3994         223 TITLAWAPGKGMK  235 (282)
Q Consensus       223 ~l~v~~a~~~~~~  235 (282)
                      +|+|.||+++...
T Consensus        86 ~l~V~~a~~~~~~   98 (116)
T 2lcw_A           86 PIKVSFATRRADF   98 (116)
Confidence            9999999887543

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.64  E-value=8.8e-16  Score=131.79  Aligned_cols=108  Identities=19%  Similarity=0.257  Sum_probs=88.6

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMK  235 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~  235 (282)
                      ..+++|||||||+++|+++|+++|+.||.|.++.+.+++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+.+..  
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~~~--   97 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGA--   97 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCSS--
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecccCC--
Confidence            356899999999999999999999999999999999999999999999999999999999999999999999987531  


Q ss_pred             CCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccCCC
Q psy3994         236 DKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDTV  277 (282)
Q Consensus       236 ~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~  277 (282)
                          .-+      +..+|..  .++++|+.++. .|.+..+.+
T Consensus        98 ----~l~------v~nl~~~--~t~~~l~~~F~~~G~i~~v~i  128 (261)
T 3sde_A           98 ----ALT------VKNLSPV--VSNELLEQAFSQFGPVEKAVV  128 (261)
T ss_dssp             ----EEE------EESCCTT--CCHHHHHHHHGGGSCEEEEEE
T ss_pred             ----ccc------ccCCCCC--CCHHHHHHHHHhcCCeEEEEe
Confidence                111      3344433  35788887555 455544433

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.2e-16  Score=121.72  Aligned_cols=77  Identities=17%  Similarity=0.157  Sum_probs=68.6

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe------CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||+++|+++|+++|+.||.|..+.++      .++|||||+|.+.++|++|+. |||..+.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456899999999999999999999999998763333      258999999999999999999 999999999999999


Q ss_pred             ecCC
Q psy3994         229 APGK  232 (282)
Q Consensus       229 a~~~  232 (282)
                      |.++
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            9764

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.64  E-value=1e-16  Score=110.87  Aligned_cols=69  Identities=28%  Similarity=0.445  Sum_probs=64.6

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      +|||+|||+++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+.. +|..+.|++|+|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            589999999999999999999999999999874      589999999999999999984 899999999999986

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.63  E-value=2.6e-16  Score=121.60  Aligned_cols=75  Identities=15%  Similarity=0.137  Sum_probs=69.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCc---eEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGD---VVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~---i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ..++|||+|||+++|+++|+++|++||.   |.+++++.     ++|||||+|.+.++|++|++ +||..++|+.|+|.+
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~  121 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFK  121 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            4689999999999999999999999999   78888874     58999999999999999999 999999999999999


Q ss_pred             ecCC
Q psy3994         229 APGK  232 (282)
Q Consensus       229 a~~~  232 (282)
                      +.++
T Consensus       122 a~~~  125 (136)
T 2hgl_A          122 SHRT  125 (136)
T ss_dssp             CCHH
T ss_pred             CChH
Confidence            8644

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.62  E-value=8.6e-16  Score=124.22  Aligned_cols=80  Identities=23%  Similarity=0.334  Sum_probs=74.2

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....+++|||+|||..+++++|+++|++||.|..|.+..     ++|||||+|.+.++|++|+..|||..+.|+.|+|.|
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            445679999999999999999999999999999999975     579999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy3994         229 APGKG  233 (282)
Q Consensus       229 a~~~~  233 (282)
                      |....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            98654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.62  E-value=2.1e-16  Score=116.12  Aligned_cols=75  Identities=25%  Similarity=0.464  Sum_probs=70.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .+++|||+|||.++++++|+++|++||.|.+++++.     ++|||||+|.+.++|++|+.  +|..++|+.|.|.++.+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCc
Confidence            468999999999999999999999999999999985     57999999999999999998  99999999999999986


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      +.
T Consensus        86 ~~   87 (102)
T 2xs2_A           86 KQ   87 (102)
T ss_dssp             CC
T ss_pred             Cc
Confidence            64

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.62  E-value=1.8e-15  Score=127.27  Aligned_cols=78  Identities=27%  Similarity=0.397  Sum_probs=73.1

Q ss_pred             CCCCcEEEecCCCc-cCcHHHHHhhhccCCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSK-LVQEEELSDTFGEYGDVVSINLIPP-RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~-~~te~~l~~~f~~~G~i~~~~~~~~-kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ..++++|||+|||+ ++++++|+++|++||.|.++++... +|||||+|.+.++|++|++.|||..+.|+.|+|.|++.+
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  110 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ  110 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCc
Confidence            34579999999999 9999999999999999999999874 699999999999999999999999999999999999865

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.62  E-value=3.4e-16  Score=116.11  Aligned_cols=76  Identities=17%  Similarity=0.117  Sum_probs=70.1

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCc---eEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGD---VVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~---i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ...++|||+|||+++|+++|+++|+.||.   |..++++.     ++|||||+|.+.++|++|+. +||..++|+.|+|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVY   87 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEE
Confidence            35689999999999999999999999988   88998874     68999999999999999999 99999999999999


Q ss_pred             eecCC
Q psy3994         228 WAPGK  232 (282)
Q Consensus       228 ~a~~~  232 (282)
                      ++.++
T Consensus        88 ~a~~~   92 (107)
T 2lmi_A           88 EINNE   92 (107)
T ss_dssp             ECCHH
T ss_pred             ECCHH
Confidence            98754

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=9.6e-16  Score=113.93  Aligned_cols=73  Identities=18%  Similarity=0.205  Sum_probs=67.5

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .++|||+|||+++|+++|+++|+.| .|.++.++.     ++|||||+|.+.++|++|+ .+||..++||.|.|..+.++
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            4799999999999999999999999 899999874     6899999999999999999 69999999999999888643

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.61  E-value=5e-16  Score=130.73  Aligned_cols=75  Identities=21%  Similarity=0.394  Sum_probs=69.5

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCC--ceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYG--DVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G--~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ..++|||+|||+++|+++|+++|++||  .|.+|+|+.      +||||||+|.+.++|++||..|||..+.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            468999999999999999999999999  999999874      579999999999999999999999999999999999


Q ss_pred             ecC
Q psy3994         229 APG  231 (282)
Q Consensus       229 a~~  231 (282)
                      |++
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.61  E-value=2.2e-15  Score=123.64  Aligned_cols=76  Identities=28%  Similarity=0.408  Sum_probs=71.7

Q ss_pred             CCcEEEecCCCc-cCcHHHHHhhhccCCceEEEEEeCC-CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         157 CSTTLWIGHLSK-LVQEEELSDTFGEYGDVVSINLIPP-RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~-~~te~~l~~~f~~~G~i~~~~~~~~-kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .+++|||+|||+ .+++++|+++|++||.|.++++... +|||||+|.+.++|++|+..|||..+.|++|+|.|+..+
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~   79 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   79 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCC
Confidence            368999999999 9999999999999999999999874 699999999999999999999999999999999999865

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.61  E-value=2e-15  Score=120.98  Aligned_cols=114  Identities=23%  Similarity=0.362  Sum_probs=87.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe--------CCCcEEEEEecCHHHHHHHHHHhCCCeeC---CeeEE
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI--------PPRGCAFVCMNRRQDAAKALYKLKNTKLQ---GKTIT  225 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~--------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~---g~~l~  225 (282)
                      .+++|||+|||+++|+++|+++|++||.|.+++++        .++|||||+|.+.++|++|+..|||..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            36899999999999999999999999999999987        35789999999999999999999998875   67889


Q ss_pred             EEeecCCCCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccCCC
Q psy3994         226 LAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDTV  277 (282)
Q Consensus       226 v~~a~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~  277 (282)
                      +.++.+.........     ..-+..+|.+  .++++|+.+++ .|.+....+
T Consensus        82 ~~~~~~~~~~~~~~~-----~l~v~nl~~~--~t~~~l~~~F~~~G~i~~v~~  127 (175)
T 3nmr_A           82 MKPADSEKNNAVEDR-----KLFIGMISKK--CTENDIRVMFSSFGQIEECRI  127 (175)
T ss_dssp             EEECGGGCCSCGGGS-----EEEEESCCTT--CCHHHHHHHHGGGSCEEEEEE
T ss_pred             EccccccccccCCCC-----eEEEcCCCCc--CCHHHHHHHHHhCCCEEEEEE
Confidence            998876654321111     1113444544  36788887655 455554433

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.60  E-value=8.7e-16  Score=122.31  Aligned_cols=111  Identities=23%  Similarity=0.343  Sum_probs=85.8

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ++++|||+|||+++|+++|+++|++||.|.+++++.      ++|||||+|.+.++|++|+..  +..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            368999999999999999999999999999999875      579999999999999999984  678999999999987


Q ss_pred             CCCCCCCccccccccCCCeeeecCCCCCcchhhhhhhc-CcccccCCC
Q psy3994         231 GKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDTV  277 (282)
Q Consensus       231 ~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~  277 (282)
                      ++......      ...-+..+|.+-  ++++|..+++ .|.+....+
T Consensus        80 ~~~~~~~~------~~l~V~nlp~~~--t~~~l~~~F~~~G~i~~~~i  119 (167)
T 2cjk_A           80 PRDEQDKT------GKIFVGGIGPDV--RPKEFEEFFSQWGTIIDAQL  119 (167)
T ss_dssp             CHHHHHHC------EEEEEEEECTTC--CHHHHHHHHHTTSCCSEEEC
T ss_pred             chhhccCC------CeEEECCCCCCC--CHHHHHHHHHhCccEEEEEE
Confidence            65321111      112245566543  5788887555 455554444

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.59  E-value=3.8e-15  Score=121.86  Aligned_cols=79  Identities=19%  Similarity=0.339  Sum_probs=74.1

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~------kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||..+++++|+++|++||.|.++.+...      +|||||+|.+.++|.+|+..|||..+.|++|+|.||
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            56799999999999999999999999999999998853      799999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy3994         230 PGKGM  234 (282)
Q Consensus       230 ~~~~~  234 (282)
                      .++..
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98754

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.59  E-value=4.7e-15  Score=124.76  Aligned_cols=78  Identities=24%  Similarity=0.349  Sum_probs=73.1

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCC-ceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeC-CeeEEEEeecC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYG-DVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQ-GKTITLAWAPG  231 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G-~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~-g~~l~v~~a~~  231 (282)
                      ..++++|||+|||..+++++|+++|++|| .|..+++.+ ++|||||+|.+.++|.+|+..|||..+. |++|+|.|+++
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            34579999999999999999999999999 999999954 8999999999999999999999999999 99999999986


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      +
T Consensus       228 ~  228 (229)
T 2adc_A          228 T  228 (229)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.59  E-value=6.7e-15  Score=117.88  Aligned_cols=74  Identities=24%  Similarity=0.495  Sum_probs=68.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeC---CeeEEEEe
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQ---GKTITLAW  228 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~---g~~l~v~~  228 (282)
                      ..++|||+|||..+|+++|+++|++||.|.++.++.     ++|||||+|.+.++|.+|+..|||..+.   |++|+|.|
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~  173 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF  173 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEe
Confidence            468999999999999999999999999999999986     3899999999999999999999998775   49999999


Q ss_pred             ec
Q psy3994         229 AP  230 (282)
Q Consensus       229 a~  230 (282)
                      |.
T Consensus       174 ad  175 (175)
T 3nmr_A          174 AD  175 (175)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.59  E-value=4.8e-15  Score=121.27  Aligned_cols=75  Identities=17%  Similarity=0.383  Sum_probs=70.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccC----C-------ceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEY----G-------DVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~----G-------~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      .+++|||+|||+++|+++|+++|++|    |       .|.++.+..++|||||+|.+.++|++|+ .|||..+.|++|+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~   81 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLK   81 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEE
Confidence            46899999999999999999999999    6       7888999899999999999999999999 8999999999999


Q ss_pred             EEeecCC
Q psy3994         226 LAWAPGK  232 (282)
Q Consensus       226 v~~a~~~  232 (282)
                      |.++...
T Consensus        82 v~~~~~~   88 (198)
T 2yh0_A           82 IRRPHDY   88 (198)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9999865

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.59  E-value=4.1e-15  Score=119.43  Aligned_cols=75  Identities=23%  Similarity=0.391  Sum_probs=69.5

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe--CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI--PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~--~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ..++|||+|||..+++++|+++|++||.|..+ ..  .++|||||+|.+.++|.+|+..|||..+.|++|+|.||.++
T Consensus        98 ~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B           98 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            46899999999999999999999999999887 22  37899999999999999999999999999999999999876

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.59  E-value=8.2e-15  Score=116.66  Aligned_cols=110  Identities=30%  Similarity=0.545  Sum_probs=86.1

Q ss_pred             hhcCChhhHHHHHHHHHhhc-cCcccCCccccccccCCCCCCCChhhhHHhhhcCCCCCCCCcEEEecCCCccCcHHHHH
Q psy3994          98 LYQCPPEDKSKIIRVLNLWQ-KNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELS  176 (282)
Q Consensus        98 v~~~~~~~~~k~~~~l~~w~-~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~te~~l~  176 (282)
                      +...+++++.+++..++... .+..+..       .++.+.               ......++|||+|||..+++++|+
T Consensus        50 V~f~~~~~A~~a~~~l~~~~~~g~~l~v-------~~~~~~---------------~~~~~~~~l~v~nl~~~~t~~~l~  107 (168)
T 1b7f_A           50 VDFTSEMDSQRAIKVLNGITVRNKRLKV-------SYARPG---------------GESIKDTNLYVTNLPRTITDDQLD  107 (168)
T ss_dssp             EEESSHHHHHHHHHHHTTCEETTEECEE-------EECCCC---------------SSTTTTCEEEEESCCTTCCHHHHH
T ss_pred             EEECCHHHHHHHHHhcCCCEeCCcEEEE-------EecCCC---------------cccCCCCCEEEeCCCCCCCHHHHH
Confidence            33356888888988877332 2222222       122222               122346899999999999999999


Q ss_pred             hhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCC--eeEEEEee
Q psy3994         177 DTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQG--KTITLAWA  229 (282)
Q Consensus       177 ~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g--~~l~v~~a  229 (282)
                      ++|++||.|..+.+..      ++|||||+|.+.++|.+|+..|||..+.|  ++|+|.||
T Consensus       108 ~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          108 TIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999999999875      35999999999999999999999999987  99999986

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.59  E-value=4.2e-15  Score=121.94  Aligned_cols=77  Identities=25%  Similarity=0.367  Sum_probs=72.7

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCC-ceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeC-CeeEEEEeecCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYG-DVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQ-GKTITLAWAPGK  232 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G-~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~-g~~l~v~~a~~~  232 (282)
                      .++++|||+|||..+++++|+++|++|| .|.++++.+ ++|||||+|.+.++|.+|+..|||..++ |++|+|.|++++
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            4589999999999999999999999999 999999954 8999999999999999999999999999 999999999864

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.59  E-value=6.5e-16  Score=119.78  Aligned_cols=78  Identities=17%  Similarity=0.202  Sum_probs=70.0

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ...++|||+|||+++|+++|+++|++|| +.+|.++.     ++|||||+|.+.++|++|+ .+|+..+.|+.|+|.++.
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECC
Confidence            3468999999999999999999999999 67998874     6899999999999999999 789999999999999998


Q ss_pred             CCCCC
Q psy3994         231 GKGMK  235 (282)
Q Consensus       231 ~~~~~  235 (282)
                      ++...
T Consensus       122 ~~~~~  126 (139)
T 2hgn_A          122 TTGAS  126 (139)
T ss_dssp             CSCC-
T ss_pred             CCCCC
Confidence            77543

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.59  E-value=5.7e-15  Score=127.97  Aligned_cols=151  Identities=11%  Similarity=0.101  Sum_probs=107.4

Q ss_pred             HHHhhcCChhhHHHHHHHHHhhc-cCcccCCccccccccCCCCCCCChhhhHHhhhcCCCCCCCCcEEEecCCCccCcHH
Q psy3994          95 FQHLYQCPPEDKSKIIRVLNLWQ-KNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEE  173 (282)
Q Consensus        95 f~~v~~~~~~~~~k~~~~l~~w~-~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~te~  173 (282)
                      +.++...+++++.+++..++... .+..+...       +..                     ..++|||+|||+.++++
T Consensus        59 ~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~-------~~~---------------------~~~~l~v~nlp~~~t~~  110 (284)
T 3smz_A           59 TAFVTLLNGEQAEAAINAFHQSRLRERELSVQ-------LQP---------------------TDALLCVANLPPSLTQQ  110 (284)
T ss_dssp             EEEEEESSHHHHHHHHHHHTTCEETTEECEEE-------ECC---------------------CSCEEEEESCCTTCCHH
T ss_pred             EEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEE-------ecC---------------------CCCEEEEcCCCCcCCHH
Confidence            33444467888888988887322 22221111       111                     24899999999999999


Q ss_pred             HHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCCCCCccccccccCC
Q psy3994         174 ELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQD  247 (282)
Q Consensus       174 ~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~  247 (282)
                      +|+++|++||.|.++.++.      ++|||||+|.+.++|.+|+..|||..+.|++|+|.|+.++........   ....
T Consensus       111 ~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~---~~~l  187 (284)
T 3smz_A          111 QFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLH---SRCL  187 (284)
T ss_dssp             HHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCCTTTTS---CSEE
T ss_pred             HHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCcccCC---ccEE
Confidence            9999999999999998874      478999999999999999999999999999999999987654322111   0111


Q ss_pred             CeeeecCCCCCcchhhhhhhc-CcccccCCC
Q psy3994         248 GVSYIPYDRLSKEIDYDYLED-GGVFDEDTV  277 (282)
Q Consensus       248 g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~  277 (282)
                      -+..+|.+-. ++++|+.+++ .|.+..+.+
T Consensus       188 ~v~nlp~~~~-~~~~l~~~f~~~G~i~~v~i  217 (284)
T 3smz_A          188 CVDRLPPGFN-DVDALCRALSAVHSPTFCQL  217 (284)
T ss_dssp             EEECCCTTCC-CHHHHHHHTCSSSCCSEEEE
T ss_pred             EEecCCcccC-CHHHHHHHhhCCCCeEEEEE
Confidence            2445555533 5788888665 455544433

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.58  E-value=2e-15  Score=123.35  Aligned_cols=79  Identities=23%  Similarity=0.433  Sum_probs=68.9

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||..+|+++|+++|++||.|..+.+..      ++|||||+|.+.++|.+|+.. +|..+.|+.|.|.||
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            3568999999999999999999999999999999884      479999999999999999986 899999999999999


Q ss_pred             cCCCCC
Q psy3994         230 PGKGMK  235 (282)
Q Consensus       230 ~~~~~~  235 (282)
                      .++...
T Consensus       181 ~~k~~~  186 (196)
T 1l3k_A          181 LSKQEM  186 (196)
T ss_dssp             C-----
T ss_pred             CChhHh
Confidence            987543

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.58  E-value=5.3e-15  Score=135.68  Aligned_cols=77  Identities=23%  Similarity=0.449  Sum_probs=72.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      +.++|||+|||..+|+++|..+|++||.|..|.|+.      ++|||||+|.+.++|.+||..|||..|.|+.|.|.||.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            468999999999999999999999999999999974      58999999999999999999999999999999999998


Q ss_pred             CCC
Q psy3994         231 GKG  233 (282)
Q Consensus       231 ~~~  233 (282)
                      ++.
T Consensus       181 ~~~  183 (437)
T 3pgw_S          181 GRT  183 (437)
T ss_pred             CCC
Confidence            754

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.58  E-value=5.2e-15  Score=118.34  Aligned_cols=74  Identities=20%  Similarity=0.389  Sum_probs=69.7

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~------kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||+|||..+++++|+++|++||.|.++.+...      +|||||+|.+.++|.+|+..|||..++|++|+|.||.
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            3689999999999999999999999999999999753      7999999999999999999999999999999999983

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.58  E-value=6.3e-15  Score=122.24  Aligned_cols=79  Identities=15%  Similarity=0.343  Sum_probs=73.5

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCC------CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~------kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||+|||..+++++|+++|++||.|..+++...      +|||||+|.+.++|.+|+..|||..++|+.|+|.||.
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~  203 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV  203 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEec
Confidence            4589999999999999999999999999999999853      7999999999999999999999999999999999999


Q ss_pred             CCCCC
Q psy3994         231 GKGMK  235 (282)
Q Consensus       231 ~~~~~  235 (282)
                      ++...
T Consensus       204 ~~~~~  208 (216)
T 2qfj_A          204 TPPMP  208 (216)
T ss_dssp             SCSST
T ss_pred             CCCCC
Confidence            87543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.57  E-value=4.6e-15  Score=123.03  Aligned_cols=118  Identities=19%  Similarity=0.271  Sum_probs=87.6

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +++|||+|||.++|+++|+++|+.||.|.+++++.      ++|||||+|.+.++|++|+..|||..+.|+.|+|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            58999999999999999999999999999999974      589999999999999999999999999999999999876


Q ss_pred             CCCCCCccc---cccccCCC--eeeecCCCCCcchhhhhhhc-CcccccCCC
Q psy3994         232 KGMKDKDWK---DFWEVQDG--VSYIPYDRLSKEIDYDYLED-GGVFDEDTV  277 (282)
Q Consensus       232 ~~~~~~~~~---~~~~~~~g--~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~  277 (282)
                      .........   ........  +..+|.+  .++++|..+++ .|.+..+.+
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~l~v~nlp~~--~t~~~l~~~f~~~G~v~~v~i  157 (216)
T 2qfj_A          108 IGQAQPIIDQLAEEARAFNRIYVASVHQD--LSDDDIKSVFEAFGKIKSATL  157 (216)
T ss_dssp             CGGGHHHHHHHHHHHTTSCEEEEECCCTT--CCHHHHHHHHTTSSCEEEEEE
T ss_pred             ccccchhhhhhhcccCCCcEEEEeCCCCc--CCHHHHHHHHhccCCeeEEEE
Confidence            642210000   00001111  3444544  46888887665 455554433

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.57  E-value=1.3e-14  Score=115.26  Aligned_cols=110  Identities=26%  Similarity=0.491  Sum_probs=85.1

Q ss_pred             hhcCChhhHHHHHHHHHhhcc-CcccCCccccccccCCCCCCCChhhhHHhhhcCCCCCCCCcEEEecCCCccCcHHHHH
Q psy3994          98 LYQCPPEDKSKIIRVLNLWQK-NEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELS  176 (282)
Q Consensus        98 v~~~~~~~~~k~~~~l~~w~~-~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~te~~l~  176 (282)
                      +....++++.++++.++...- +..+..       .++.+..               .....++|||+|||..+++++|+
T Consensus        49 V~f~~~~~A~~a~~~l~~~~~~g~~l~v-------~~~~~~~---------------~~~~~~~l~v~nl~~~~t~~~l~  106 (167)
T 1fxl_A           49 VNYIDPKDAEKAINTLNGLRLQTKTIKV-------SYARPSS---------------ASIRDANLYVSGLPKTMTQKELE  106 (167)
T ss_dssp             EEESSHHHHHHHHHHHTTCEETTEECEE-------EECCCCC---------------GGGTTCEEEEESCCTTCCHHHHH
T ss_pred             EEECCHHHHHHHHHHcCCCccCCceEEE-------EecCCCc---------------ccCCCCcEEECCCCCcCCHHHHH
Confidence            333568888999988874322 222111       2223221               11245899999999999999999


Q ss_pred             hhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCee--EEEEee
Q psy3994         177 DTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKT--ITLAWA  229 (282)
Q Consensus       177 ~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~--l~v~~a  229 (282)
                      ++|++||.|..+++..      ++|||||+|.+.++|.+|+..|||..+.|+.  |+|.||
T Consensus       107 ~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          107 QLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            9999999999999874      3799999999999999999999999999975  899886

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.57  E-value=3.3e-15  Score=118.90  Aligned_cols=74  Identities=18%  Similarity=0.406  Sum_probs=69.8

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||+|||..+++++|+++|++||.|.++.+..      ++|||||+|.+.++|.+|++ ++|..++|++|+|.||.+
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCC
Confidence            57999999999999999999999999999999875      57899999999999999998 899999999999999987


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      +
T Consensus       166 k  166 (167)
T 2cjk_A          166 R  166 (167)
T ss_dssp             C
T ss_pred             C
Confidence            6

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.56  E-value=1.2e-14  Score=125.83  Aligned_cols=77  Identities=25%  Similarity=0.368  Sum_probs=72.3

Q ss_pred             CCCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCC-cEEEEEecCHHHHHHHHHHhCCCeeC-CeeEEEEeec
Q psy3994         154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR-GCAFVCMNRRQDAAKALYKLKNTKLQ-GKTITLAWAP  230 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~k-g~aFV~f~~~~~A~~Ai~~l~g~~~~-g~~l~v~~a~  230 (282)
                      ...++++|||+|||..+++++|+++|++||.|.++++...+ |||||+|.+.++|.+|+..|||..+. |+.|+|.||+
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            34467899999999999999999999999999999999855 99999999999999999999999998 9999999986

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.56  E-value=1.9e-14  Score=106.17  Aligned_cols=77  Identities=16%  Similarity=0.188  Sum_probs=68.2

Q ss_pred             CCCcEEEecCCCc-----cCcHHHHHhhhccCCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhCCCeeCCee
Q psy3994         156 MCSTTLWIGHLSK-----LVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKT  223 (282)
Q Consensus       156 ~~~~~l~V~nl~~-----~~te~~l~~~f~~~G~i~~~~~~~-------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~  223 (282)
                      .++++|++.|+..     +-++++|++.|++||.|.++.++.       ++|||||+|.+.++|.+|+..|||..+.||+
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            3578999999973     236899999999999999999873       4899999999999999999999999999999


Q ss_pred             EEEEeecCC
Q psy3994         224 ITLAWAPGK  232 (282)
Q Consensus       224 l~v~~a~~~  232 (282)
                      |+|.++...
T Consensus        86 i~v~~a~~~   94 (105)
T 2pe8_A           86 VKACFYNLD   94 (105)
T ss_dssp             CEEEECCHH
T ss_pred             EEEEEcCHH
Confidence            999999753

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.56  E-value=1e-14  Score=126.85  Aligned_cols=120  Identities=17%  Similarity=0.215  Sum_probs=89.2

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCC-ceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYG-DVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G-~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||+|||+.+++++|+++|+.|| .|.++.++.     ++|||||+|.+.++|.+|+..|||..+.|++|.|.|+.+
T Consensus       117 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~  196 (292)
T 2ghp_A          117 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP  196 (292)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCC
Confidence            58999999999999999999999999 999999875     689999999999999999999999999999999999987


Q ss_pred             CCCCCCc-cccccccCCCeeeecCCCCCcchhhhhhhc-CcccccCCCC
Q psy3994         232 KGMKDKD-WKDFWEVQDGVSYIPYDRLSKEIDYDYLED-GGVFDEDTVP  278 (282)
Q Consensus       232 ~~~~~~~-~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~p  278 (282)
                      .....+. .........-+..+|.+.+ ++++|..+++ .|.+....++
T Consensus       197 ~~~~~~~~~~~~~~~~l~v~nlp~~~~-t~~~l~~~F~~~G~v~~v~i~  244 (292)
T 2ghp_A          197 LEKSKRTDSATLEGREIMIRNLSTELL-DENLLRESFEGFGSIEKINIP  244 (292)
T ss_dssp             C---------CCTTTEEEEEEECTTTC-CHHHHHHHHGGGSCEEEEECC
T ss_pred             CcccccccccCCCCceEEEECCCcccC-CHHHHHHHHhccCCeeEEEEE
Confidence            7543322 0111011112456666634 6788887665 4555555443

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=2.9e-14  Score=106.51  Aligned_cols=79  Identities=19%  Similarity=0.260  Sum_probs=69.1

Q ss_pred             CCCCcEEEecCCCccC-----------cHHHHHhhhccCCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3994         155 NMCSTTLWIGHLSKLV-----------QEEELSDTFGEYGDVVSINLIP--PRGCAFVCMNRRQDAAKALYKLKNTKLQG  221 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~-----------te~~l~~~f~~~G~i~~~~~~~--~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g  221 (282)
                      ..++++|+|.||....           ++++|+++|++||.|.++.+..  ++|||||+|.+.++|++|+..|||..+.|
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   91 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   91 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3457999999995432           2579999999999999997753  68999999999999999999999999999


Q ss_pred             eeEEEEeecCCC
Q psy3994         222 KTITLAWAPGKG  233 (282)
Q Consensus       222 ~~l~v~~a~~~~  233 (282)
                      ++|+|.|+.++.
T Consensus        92 r~l~v~~a~~~~  103 (112)
T 2dit_A           92 RQITAQAWDGTT  103 (112)
T ss_dssp             EECEEEECCSCC
T ss_pred             cEEEEEEeCCCC
Confidence            999999998764

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.56  E-value=6.2e-15  Score=112.20  Aligned_cols=75  Identities=21%  Similarity=0.204  Sum_probs=67.1

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceE--EEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVV--SINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~--~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ...++|||+|||+++|+++|+++|++| .|.  +|+++.     ++|||||+|.+.++|++|+. +++..++||.|+|..
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            346899999999999999999999999 576  888874     68999999999999999998 478999999999999


Q ss_pred             ecCC
Q psy3994         229 APGK  232 (282)
Q Consensus       229 a~~~  232 (282)
                      +..+
T Consensus       118 a~~~  121 (126)
T 2hgm_A          118 SSQE  121 (126)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8643

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.55  E-value=1.7e-14  Score=124.84  Aligned_cols=78  Identities=23%  Similarity=0.436  Sum_probs=72.5

Q ss_pred             CCCcEEEecCCCccCcHHHHH----hhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         156 MCSTTLWIGHLSKLVQEEELS----DTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~----~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      .++++|||+|||.++++++|+    ++|++||.|.+|++.+   ++|||||+|.+.++|++|+..|||..+.|+.|+|.|
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   86 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   86 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEE
Confidence            357999999999999999977    8999999999999875   789999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy3994         229 APGKG  233 (282)
Q Consensus       229 a~~~~  233 (282)
                      ++.+.
T Consensus        87 a~~~~   91 (282)
T 3pgw_A           87 AKTDS   91 (282)
T ss_pred             eccCc
Confidence            98654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=3e-15  Score=113.65  Aligned_cols=75  Identities=24%  Similarity=0.270  Sum_probs=67.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCce----EEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDV----VSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i----~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ..++|||+|||+++|+++|+++|++||.|    ..|.++.     ++|||||+|.+.++|++|+.. |+..+.||.|.|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~  100 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEE
Confidence            45899999999999999999999999875    5777763     689999999999999999986 9999999999999


Q ss_pred             eecCC
Q psy3994         228 WAPGK  232 (282)
Q Consensus       228 ~a~~~  232 (282)
                      .+.++
T Consensus       101 ~a~~~  105 (123)
T 2dha_A          101 RSTAA  105 (123)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            88644

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=8.7e-15  Score=109.70  Aligned_cols=74  Identities=20%  Similarity=0.388  Sum_probs=63.8

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEE
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL  226 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v  226 (282)
                      ..+++|||||||+++++++|+++|++||.|. +.++.         ++|||||+|.+.++|++|++.|+  .++|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            3468999999999999999999999999999 76653         48999999999999999999984  478888888


Q ss_pred             EeecCC
Q psy3994         227 AWAPGK  232 (282)
Q Consensus       227 ~~a~~~  232 (282)
                      ..+...
T Consensus        83 ~~~~~~   88 (114)
T 2dnl_A           83 VSSPTI   88 (114)
T ss_dssp             ECCSSS
T ss_pred             ccCCCc
Confidence            765543

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.54  E-value=2.2e-14  Score=124.22  Aligned_cols=79  Identities=14%  Similarity=0.138  Sum_probs=73.5

Q ss_pred             CCCcEEEecCCCccC-cHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLV-QEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~-te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||..+ ++++|+++|+.||.|.++++..     ++|||||+|.+.++|.+|+..|||..++|++|+|.|+
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a  261 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC  261 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEe
Confidence            456899999999995 9999999999999999999886     4899999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy3994         230 PGKGM  234 (282)
Q Consensus       230 ~~~~~  234 (282)
                      .++..
T Consensus       262 ~~~~~  266 (284)
T 3smz_A          262 APGPP  266 (284)
T ss_dssp             CSSSC
T ss_pred             cCCCc
Confidence            88764

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.54  E-value=2.9e-14  Score=114.40  Aligned_cols=106  Identities=20%  Similarity=0.192  Sum_probs=81.3

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceE-----EEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVV-----SINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~-----~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ...++|||+|||.++|+++|+++|..||.+.     ......++|||||+|.+.++|++|+ .|||..+.|++|+|.++.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~~~   89 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPK   89 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEecCC
Confidence            3579999999999999999999999998543     3444458999999999999999999 599999999999999998


Q ss_pred             CCCCCCCccccccccCCCeeeecCCCCCcchhhhhhhc
Q psy3994         231 GKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLED  268 (282)
Q Consensus       231 ~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~  268 (282)
                      ++........    ...-+..+|.+  .++++|+.+++
T Consensus        90 ~~~~~~~~~~----~~l~v~nlp~~--~t~~~l~~~F~  121 (175)
T 1fje_B           90 GRDSKKVRAA----RTLLAKNLSFN--ITEDELKEVFE  121 (175)
T ss_dssp             CSSCSTTGGG----GEEEEESCCSS--CCHHHHHHHCT
T ss_pred             CccccccccC----CEEEEeCCCCC--CCHHHHHHHHH
Confidence            7654322110    11123444543  35788887665

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.54  E-value=2.1e-14  Score=124.84  Aligned_cols=78  Identities=24%  Similarity=0.471  Sum_probs=72.0

Q ss_pred             CCCCCcEEEecCCCcc-CcHHHHHhhhccCCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         154 ENMCSTTLWIGHLSKL-VQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       154 ~~~~~~~l~V~nl~~~-~te~~l~~~f~~~G~i~~~~~~~-------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      .....++|||+|||.. +++++|+++|++||.|..++++.       ++|||||+|.+.++|.+|+ .|||..+.|++|+
T Consensus       206 ~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~  284 (292)
T 2ghp_A          206 ATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREIS  284 (292)
T ss_dssp             -CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEE
T ss_pred             cCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEE
Confidence            3446789999999999 99999999999999999999864       4799999999999999999 9999999999999


Q ss_pred             EEeecCC
Q psy3994         226 LAWAPGK  232 (282)
Q Consensus       226 v~~a~~~  232 (282)
                      |.||.++
T Consensus       285 V~~a~~k  291 (292)
T 2ghp_A          285 VSLADKK  291 (292)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9999876

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.53  E-value=8.5e-15  Score=110.03  Aligned_cols=73  Identities=12%  Similarity=0.185  Sum_probs=65.1

Q ss_pred             cEEEecCC----CccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecC----HHH----HHHHHH--HhCCCe
Q psy3994         159 TTLWIGHL----SKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNR----RQD----AAKALY--KLKNTK  218 (282)
Q Consensus       159 ~~l~V~nl----~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~----~~~----A~~Ai~--~l~g~~  218 (282)
                      +.||||||    |+.+++.+|+.+|++||+|.++.++.      ++|||||+|.+    .++    |.+|+.  .+||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            78999999    99999999999999999999999984      78999999996    323    889988  789999


Q ss_pred             eCCeeEEEEeecC
Q psy3994         219 LQGKTITLAWAPG  231 (282)
Q Consensus       219 ~~g~~l~v~~a~~  231 (282)
                      ++|++|+|.+-+.
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998764

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.52  E-value=2.4e-14  Score=117.36  Aligned_cols=74  Identities=14%  Similarity=0.267  Sum_probs=67.8

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .++|||+|||+++|+++|+++|++||.|.++++++     ++|||||+|.+.++|++|+..+ +..+.|++|+|.|+...
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            48999999999999999999999999999999884     6899999999999999999865 46999999999998754

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.47  E-value=9.9e-14  Score=122.66  Aligned_cols=76  Identities=17%  Similarity=0.319  Sum_probs=68.2

Q ss_pred             CCCCcEEEecC--CCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCee---CCe--eEEEE
Q psy3994         155 NMCSTTLWIGH--LSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL---QGK--TITLA  227 (282)
Q Consensus       155 ~~~~~~l~V~n--l~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~---~g~--~l~v~  227 (282)
                      +.++.+|||||  |+..+||++|+++|++||+|.++.+..+||||||+|.+.++|++|++.|||..+   .|+  .|.|.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~   94 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN   94 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEE
Confidence            34578999999  578999999999999999999999999999999999999999999999999988   345  67888


Q ss_pred             eec
Q psy3994         228 WAP  230 (282)
Q Consensus       228 ~a~  230 (282)
                      ++.
T Consensus        95 ~~~   97 (345)
T 3tht_A           95 FVE   97 (345)
T ss_dssp             ECS
T ss_pred             Eee
Confidence            875

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.46  E-value=6.9e-14  Score=115.68  Aligned_cols=75  Identities=19%  Similarity=0.196  Sum_probs=67.4

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCce--EEEEEeCC----CcEEEEEecCHHHHHHHHHHhCCCeeCCe----eE
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDV--VSINLIPP----RGCAFVCMNRRQDAAKALYKLKNTKLQGK----TI  224 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i--~~~~~~~~----kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~----~l  224 (282)
                      ..++++|||+|||+.+|+++|+++|++||.|  .++++...    +|||||+|.+.++|.+|+..|||..+.|+    ++
T Consensus       120 ~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~  199 (205)
T 3tyt_A          120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY  199 (205)
T ss_dssp             CCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCE
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcce
Confidence            3567899999999999999999999999999  89988753    58999999999999999999999999876    67


Q ss_pred             EEEee
Q psy3994         225 TLAWA  229 (282)
Q Consensus       225 ~v~~a  229 (282)
                      .|+||
T Consensus       200 ~vk~~  204 (205)
T 3tyt_A          200 TLKLC  204 (205)
T ss_dssp             ECEEE
T ss_pred             EEEec
Confidence            77775

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.46  E-value=3.1e-13  Score=99.62  Aligned_cols=77  Identities=21%  Similarity=0.270  Sum_probs=67.1

Q ss_pred             CCCcEEEecCCC--ccCc--------HHHHHhhhccCCceEEEEEeC--------CCcEEEEEecCHHHHHHHHHHhCCC
Q psy3994         156 MCSTTLWIGHLS--KLVQ--------EEELSDTFGEYGDVVSINLIP--------PRGCAFVCMNRRQDAAKALYKLKNT  217 (282)
Q Consensus       156 ~~~~~l~V~nl~--~~~t--------e~~l~~~f~~~G~i~~~~~~~--------~kg~aFV~f~~~~~A~~Ai~~l~g~  217 (282)
                      .+++.|.+.|+-  ....        +++|++.|++||.|.++.+++        ++|||||+|.+.++|.+|+..|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            357899999983  3332        368999999999999999984        4799999999999999999999999


Q ss_pred             eeCCeeEEEEeecCC
Q psy3994         218 KLQGKTITLAWAPGK  232 (282)
Q Consensus       218 ~~~g~~l~v~~a~~~  232 (282)
                      .++||+|+|.++...
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999998754

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=8e-13  Score=96.37  Aligned_cols=65  Identities=20%  Similarity=0.305  Sum_probs=58.4

Q ss_pred             ccCcHHHHHhhhccCCceEEEEEe-CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         168 KLVQEEELSDTFGEYGDVVSINLI-PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       168 ~~~te~~l~~~f~~~G~i~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      ..+++++|+++|++||.|.++.++ .++|||||+|.+.++|+.|+..+++  +.|++|+|.|++++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            468999999999999999999998 4899999999999999999998554  6899999999987753

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.43  E-value=8.8e-14  Score=102.45  Aligned_cols=68  Identities=26%  Similarity=0.439  Sum_probs=61.0

Q ss_pred             EecCCCccCcHHHHHhhh------------ccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeE
Q psy3994         162 WIGHLSKLVQEEELSDTF------------GEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTI  224 (282)
Q Consensus       162 ~V~nl~~~~te~~l~~~f------------~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l  224 (282)
                      .++|||..+++++|++.|            ++||.|.++.+++     ++|||||+|.+.++|++|+..|||..+.||+|
T Consensus        19 ~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           19 SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             ccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            367888888888887777            9999999999985     48999999999999999999999999999999


Q ss_pred             EEEee
Q psy3994         225 TLAWA  229 (282)
Q Consensus       225 ~v~~a  229 (282)
                      +|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.41  E-value=3.2e-13  Score=115.72  Aligned_cols=76  Identities=22%  Similarity=0.281  Sum_probs=68.4

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhC-CCeeC---CeeEEEEe
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLK-NTKLQ---GKTITLAW  228 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~-g~~~~---g~~l~v~~  228 (282)
                      +++|||+|||..+|+++|+++|+.||.|.++.++.     ++|||||+|.+.++|.+|+..|| |..+.   |++|.|.+
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~  175 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEP  175 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEE
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEee
Confidence            47999999999999999999999999999999885     48999999999999999999995 44554   99999999


Q ss_pred             ecCCC
Q psy3994         229 APGKG  233 (282)
Q Consensus       229 a~~~~  233 (282)
                      +.+..
T Consensus       176 ~~~~~  180 (261)
T 3sde_A          176 MEQFD  180 (261)
T ss_dssp             CCCEE
T ss_pred             ccccC
Confidence            98653

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.37  E-value=2.8e-12  Score=95.77  Aligned_cols=77  Identities=18%  Similarity=0.269  Sum_probs=66.1

Q ss_pred             CCCcEEEecCCCccC----------cHHHHHhhhccCCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhCCCeeCCee
Q psy3994         156 MCSTTLWIGHLSKLV----------QEEELSDTFGEYGDVVSINLIP--PRGCAFVCMNRRQDAAKALYKLKNTKLQGKT  223 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~----------te~~l~~~f~~~G~i~~~~~~~--~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~  223 (282)
                      .+++.|.+.|+-..-          -+++|++.|++||.|.++.+.+  ++|||||+|.+.++|.+|++.|||..++||.
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~   84 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKM   84 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            356788888875321          1357999999999999999986  4799999999999999999999999999999


Q ss_pred             EEEEeecCC
Q psy3994         224 ITLAWAPGK  232 (282)
Q Consensus       224 l~v~~a~~~  232 (282)
                      |+|.|+...
T Consensus        85 i~v~~~~~~   93 (114)
T 3s6e_A           85 ITAAYVPLP   93 (114)
T ss_dssp             CEEEEECHH
T ss_pred             EEEEEEcHH
Confidence            999998643

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.36  E-value=2.6e-12  Score=96.62  Aligned_cols=75  Identities=17%  Similarity=0.227  Sum_probs=65.7

Q ss_pred             CCcEEEecCCCc--cC---cHHHHHhhhccCCceEEEEEeC----------CCcEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3994         157 CSTTLWIGHLSK--LV---QEEELSDTFGEYGDVVSINLIP----------PRGCAFVCMNRRQDAAKALYKLKNTKLQG  221 (282)
Q Consensus       157 ~~~~l~V~nl~~--~~---te~~l~~~f~~~G~i~~~~~~~----------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g  221 (282)
                      ++++|++.|+-.  .+   -+++|++.|++||.|.++.++.          ++||+||+|.+.++|.+|+..|||..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            468999999852  22   3588999999999999999875          24899999999999999999999999999


Q ss_pred             eeEEEEeecC
Q psy3994         222 KTITLAWAPG  231 (282)
Q Consensus       222 ~~l~v~~a~~  231 (282)
                      |.|+|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999864

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.28  E-value=2.2e-11  Score=85.76  Aligned_cols=76  Identities=24%  Similarity=0.368  Sum_probs=64.5

Q ss_pred             CCCcEEEecCCCc----cCcH----HHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         156 MCSTTLWIGHLSK----LVQE----EELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       156 ~~~~~l~V~nl~~----~~te----~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ++..||+|...+.    ++-.    .+|.+.|.+||+|..+++...+  +||+|.+.++|.+|+. |||..+.||.|+|+
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~   81 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--MWVTFLEGSSALNVLS-LNGKELLNRTITIA   81 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--EEEEESSHHHHHHGGG-GTTCEETTEEEEEE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--EEEEECChHHHHHHHh-cCCeEeCCeEEEEE
Confidence            3458898987662    2323    6799999999999999999855  8999999999999998 99999999999999


Q ss_pred             eecCCCC
Q psy3994         228 WAPGKGM  234 (282)
Q Consensus       228 ~a~~~~~  234 (282)
                      ++++...
T Consensus        82 lkt~dW~   88 (91)
T 2dnr_A           82 LKSPSGP   88 (91)
T ss_dssp             ECCCSSC
T ss_pred             eCCCCcc
Confidence            9987653

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=1.2e-10  Score=87.13  Aligned_cols=77  Identities=16%  Similarity=0.154  Sum_probs=69.2

Q ss_pred             CCCcEEEecCCCcc-CcHHHHHhhhccCCceEEEEEeCCCcEEEEEecC-HHHHHHHHHHhC--CCeeCCeeEEEEeecC
Q psy3994         156 MCSTTLWIGHLSKL-VQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNR-RQDAAKALYKLK--NTKLQGKTITLAWAPG  231 (282)
Q Consensus       156 ~~~~~l~V~nl~~~-~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~-~~~A~~Ai~~l~--g~~~~g~~l~v~~a~~  231 (282)
                      +.++.|||+||++. +++++|+++|++||+|..|.+......|||.|.+ .++|..|+..+|  |..+.|..++++...+
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~G   95 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEG   95 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCH
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECCC
Confidence            45799999999999 9999999999999999999999988899999999 899999999995  6678898888877664


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      .
T Consensus        96 e   96 (121)
T 1owx_A           96 E   96 (121)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.05  E-value=3.6e-10  Score=79.94  Aligned_cols=71  Identities=21%  Similarity=0.353  Sum_probs=61.5

Q ss_pred             CCcEEEecCCCcc-----C-cH---HHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         157 CSTTLWIGHLSKL-----V-QE---EELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       157 ~~~~l~V~nl~~~-----~-te---~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      +..||+|..+++.     + ++   .+|.+.|.+||+|..+++...+  +||+|.+.++|.+|+. |||..+.||.|+|+
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~   90 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--MLVTFADSHSALSVLD-VDGMKVKGRAVKIS   90 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--EEEECSCSHHHHHHHH-GGGSEETTEEEEEE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--EEEEEcChHHHHHHHh-cCCeeeCCeEEEEe
Confidence            4489999988742     2 32   5699999999999999999866  9999999999999998 99999999999999


Q ss_pred             eec
Q psy3994         228 WAP  230 (282)
Q Consensus       228 ~a~  230 (282)
                      +-.
T Consensus        91 ~k~   93 (95)
T 1ufw_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            854

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.81  E-value=7.2e-09  Score=86.27  Aligned_cols=61  Identities=18%  Similarity=0.243  Sum_probs=56.3

Q ss_pred             cHHHHHhhhccCCceEEEEEe----------CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         171 QEEELSDTFGEYGDVVSINLI----------PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       171 te~~l~~~f~~~G~i~~~~~~----------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .+++|++.|++||.|.++.++          +++|++||+|.+.++|.+|+..|||..++||.|+|.+...
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            457899999999999999997          4679999999999999999999999999999999999763

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.66  E-value=1.4e-07  Score=68.12  Aligned_cols=72  Identities=25%  Similarity=0.231  Sum_probs=67.5

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccC-----CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEY-----GDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~-----G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .++|-+-|||+.+++..++.+.+++     |.+..+.+.+..+-|+|+|.+...|-+|.-.|+|.++.|++|+|.-.
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            4789999999999999999999999     99999999998899999999999999999999999999999998643

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.05  E-value=1.9e-05  Score=56.74  Aligned_cols=75  Identities=20%  Similarity=0.216  Sum_probs=65.7

Q ss_pred             CcEEEecCCCccC-cH----HHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         158 STTLWIGHLSKLV-QE----EELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       158 ~~~l~V~nl~~~~-te----~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .++|+|.||+..+ ..    +.++.+|..|+++......++-.-.-|.|.+.++|.+|-..||+..+.|+.++|-+|.+-
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCCC
Confidence            3689999999865 32    467899999999999888887667799999999999999999999999999999999854

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.53  E-value=0.0012  Score=47.10  Aligned_cols=74  Identities=22%  Similarity=0.287  Sum_probs=62.7

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccC-----CceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEY-----GDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~-----G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ...+|.|.|||+.++++.|.-+|+.-     |+|.++....  +-|+|+|.+.+.|++.++. ..+.+.|.+|.|.-..+
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~~   83 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPP   83 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECCC
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCCC
Confidence            46899999999999999999999872     6899998877  7899999999999999863 36788899999977655


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      +.
T Consensus        84 ~~   85 (104)
T 2dhx_A           84 RA   85 (104)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.20  E-value=0.0026  Score=46.85  Aligned_cols=71  Identities=13%  Similarity=0.088  Sum_probs=60.0

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCC-eeEEEEeec
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQG-KTITLAWAP  230 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g-~~l~v~~a~  230 (282)
                      .+.|-|-+.|+.. -..+.+.|++||+|.+........+-.|.|.++.+|++|+. .||..++| -.|-|.+..
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECC
Confidence            5788898999885 46677899999999999886677899999999999999998 59999975 667777754

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.05  E-value=0.0031  Score=44.52  Aligned_cols=55  Identities=22%  Similarity=0.384  Sum_probs=44.3

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK  215 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~  215 (282)
                      .+.+++ +.|+.+...||.++|+.||.|. |+.+ +-.-|||.|.+++.|..|+..+.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~Wi-dDTsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWI-DDTSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEE-ETTEEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEE-cCCeEEEEecCHHHHHHHHHhcc
Confidence            356666 9999999999999999998543 3333 23679999999999999998763

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.98  E-value=0.0061  Score=42.75  Aligned_cols=61  Identities=10%  Similarity=0.156  Sum_probs=52.6

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC--------CCcEEEEEecCHHHHHHHHHHhCCCee
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--------PRGCAFVCMNRRQDAAKALYKLKNTKL  219 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~--------~kg~aFV~f~~~~~A~~Ai~~l~g~~~  219 (282)
                      ++|-|.+||+++||+++.+.++..+.+.......        .-.-|+|.|.+.+++..-.+.++|+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F   70 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEE
Confidence            5788999999999999999999998877666553        225789999999999999999999977

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=96.94  E-value=0.00055  Score=52.75  Aligned_cols=39  Identities=15%  Similarity=0.095  Sum_probs=36.2

Q ss_pred             CCcEEEEEecCHHHHHHHHHHh-CCCeeCCeeEEEEeecCC
Q psy3994         193 PRGCAFVCMNRRQDAAKALYKL-KNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       193 ~kg~aFV~f~~~~~A~~Ai~~l-~g~~~~g~~l~v~~a~~~  232 (282)
                      -+|+++|+|.+.++|++|+..+ ||..+.| .+++.++.++
T Consensus        12 l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A           12 LKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             SCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             ccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            5799999999999999999999 9999999 9999998763

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.56  E-value=0.0037  Score=44.24  Aligned_cols=54  Identities=22%  Similarity=0.397  Sum_probs=43.9

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK  215 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~  215 (282)
                      +.+++ +.|+.+...+|.++|+.||. ..|+.+. -.-|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~Wid-DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWID-DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEE-TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEc-CCeEEEEecCHHHHHHHHHhcc
Confidence            45666 99999999999999999994 3344332 3679999999999999999775

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.46  E-value=0.0021  Score=49.80  Aligned_cols=25  Identities=16%  Similarity=0.081  Sum_probs=22.8

Q ss_pred             CCcEEEEEecCHHHHHHHHHHhCCC
Q psy3994         193 PRGCAFVCMNRRQDAAKALYKLKNT  217 (282)
Q Consensus       193 ~kg~aFV~f~~~~~A~~Ai~~l~g~  217 (282)
                      .+|||||+|.+.++|++|+..+++.
T Consensus        12 ~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A           12 LKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             CEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             ccchhHHHHHHHHhHHHHHHhhccc
Confidence            7899999999999999999888754

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.29  E-value=0.0045  Score=46.23  Aligned_cols=71  Identities=11%  Similarity=0.226  Sum_probs=55.4

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEE-EEEe----------------C---CCcEEEEEecCHHHHHHHHHHhCCCe
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVS-INLI----------------P---PRGCAFVCMNRRQDAAKALYKLKNTK  218 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~-~~~~----------------~---~kg~aFV~f~~~~~A~~Ai~~l~g~~  218 (282)
                      +.|.|-+.|+..+ ..+-+.|++||.|.+ ....                +   ..++--|+|.++.+|.+|+. .||..
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            5677878887765 456778999999876 2111                1   35677999999999999998 59999


Q ss_pred             eCCeeEEEEeecC
Q psy3994         219 LQGKTITLAWAPG  231 (282)
Q Consensus       219 ~~g~~l~v~~a~~  231 (282)
                      ++|..|-|.+..+
T Consensus        86 i~G~mIGV~Py~~   98 (132)
T 3p3d_A           86 FNGVLLGVIPYTK   98 (132)
T ss_dssp             ETTEECEEEECCH
T ss_pred             eCcEEEEEEECCH
Confidence            9999888887754

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.47  E-value=0.061  Score=37.95  Aligned_cols=62  Identities=11%  Similarity=0.097  Sum_probs=49.0

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC--------CCcEEEEEecCHHHHHHHHHHhCCCee
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--------PRGCAFVCMNRRQDAAKALYKLKNTKL  219 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~--------~kg~aFV~f~~~~~A~~Ai~~l~g~~~  219 (282)
                      +-+|.|..||+.+||+++.+.++..-++.......        .-.-|+|.|.+.++...-.+.++|..+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            45799999999999999999888765543333222        124689999999999999999999987

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.46  E-value=0.0072  Score=55.13  Aligned_cols=54  Identities=11%  Similarity=0.132  Sum_probs=42.0

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCC-cEEEEEecCHHHHHHHHH
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR-GCAFVCMNRRQDAAKALY  212 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~k-g~aFV~f~~~~~A~~Ai~  212 (282)
                      .++|+|. .|..+++.+|.++|++||.|.++.+-..+ .||.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHh
Confidence            3789997 79999999999999999999999888755 489999999999887754

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=91.71  E-value=0.029  Score=40.88  Aligned_cols=66  Identities=11%  Similarity=0.039  Sum_probs=19.8

Q ss_pred             HHHhhcCChhhHHHHHHHHHh-hccCcccCCccccccccCCCCCCCChhhhHHhhhcCCCCCCCCcEEEecCCCccCcHH
Q psy3994          95 FQHLYQCPPEDKSKIIRVLNL-WQKNEVFTPDIIHPLFDMADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEE  173 (282)
Q Consensus        95 f~~v~~~~~~~~~k~~~~l~~-w~~~~~f~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~te~  173 (282)
                      |.++.....++++++++.++. ...++.+.+..       +.+..+..       ..........++|||+|||+++|++
T Consensus        47 ~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~-------a~~~~~~~-------~~~~~~~~~~~~lyv~Nl~~~~T~~  112 (115)
T 4f25_A           47 YGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR-------FKSRKERE-------AELGARAKEFTNVYIKNFGPGSTRA  112 (115)
T ss_dssp             EEEEEESCHHHHHHHHHHHTTCEETTEECEEEE-------SSCCCC----------------------------------
T ss_pred             eEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE-------CCCccccc-------cccccccCCCCceEeCCCCCCcccc
Confidence            444444678999999998873 22333333332       22110000       0011223345789999999999876


Q ss_pred             H
Q psy3994         174 E  174 (282)
Q Consensus       174 ~  174 (282)
                      .
T Consensus       113 a  113 (115)
T 4f25_A          113 A  113 (115)
T ss_dssp             -
T ss_pred             c
Confidence            3

>1x5b_A Signal transducing adaptor molecule 2; VHS domain, ubiquitin binding, STAM2, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2l0t_B

Probab=89.12  E-value=0.7  Score=35.87  Aligned_cols=109  Identities=16%  Similarity=0.200  Sum_probs=73.2

Q ss_pred             HHHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCch
Q psy3994           6 TFNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFG   84 (282)
Q Consensus         6 ~f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~   84 (282)
                      .|+..+...+....+ ..-.-|.+++...-..-...+..+..|.+.|+...|...+-.|-|+|..++|--..+..  .++
T Consensus        15 p~~~~IekATs~~~~~~Dw~~~leicD~I~~~~~~~keA~ral~krl~~~n~~vql~AL~LLd~~vkNcG~~Fh~--eva   92 (163)
T 1x5b_A           15 PFEQDVEKATNEYNTTEDWSLIMDICDKVGSTPNGAKDCLKAIMKRVNHKVPHVALQALTLLGACVANCGKIFHL--EVC   92 (163)
T ss_dssp             TTHHHHHHHTCTTCSSCCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHTCHHHHH--HHT
T ss_pred             hHHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhHHHHH--HHh
Confidence            355566555553333 45566777776655544567888888999998888888899999999999996333220  011


Q ss_pred             -hhHHHHHHHHHHHhhcCChhhHHHHHHHHHhhcc
Q psy3994          85 -PRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        85 -~~f~~~l~~~f~~v~~~~~~~~~k~~~~l~~w~~  118 (282)
                       ..|..++.+.+..  ..++..+.+++.++..|..
T Consensus        93 s~~Fl~el~~l~~~--~~~~~Vk~kil~li~~W~~  125 (163)
T 1x5b_A           93 SRDFATEVRAVIKN--KAHPKVCEKLKSLMVEWSE  125 (163)
T ss_dssp             SHHHHHHHHHHHHT--TCCHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHcc--CCCHHHHHHHHHHHHHHHH
Confidence             2355555544431  1567899999999999985

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=88.47  E-value=1.1  Score=41.34  Aligned_cols=56  Identities=21%  Similarity=0.374  Sum_probs=45.1

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN  216 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g  216 (282)
                      ...++|+ +|..+...+|.++|+.||.+ +|+.+ +...|||.|.+.+.|..++..++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~wi-ddt~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWI-DDTSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEEC-SSSEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEE-cCCeEEEEECCHHHHHHHHHHHHh
Confidence            3566666 88888999999999999954 44333 557899999999999999998853

>3zyq_A Hepatocyte growth factor-regulated tyrosine kinas substrate; signaling; 1.48A {Homo sapiens} PDB: 4avx_A*

Probab=88.22  E-value=0.67  Score=37.99  Aligned_cols=111  Identities=21%  Similarity=0.240  Sum_probs=76.8

Q ss_pred             HHHHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCc
Q psy3994           5 KTFNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVF   83 (282)
Q Consensus         5 ~~f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~   83 (282)
                      ..|++.+...++...+ ..-.-|.+++...-..-...+..+.+|.+.|+.-+|.-.|-.|-|+|..++|--..+... +-
T Consensus         7 ~~~~~~i~kAT~~~~~~~dw~~ileicD~I~~~~~~~k~a~ral~krl~~~n~~v~l~aL~LLe~~vkNcG~~f~~e-ia   85 (226)
T 3zyq_A            7 GTFERLLDKATSQLLLETDWESILQICDLIRQGDTQAKYAVNSIKKKVNDKNPHVALYALEVMESVVKNCGQTVHDE-VA   85 (226)
T ss_dssp             CHHHHHHHHHTCTTCSSCCHHHHHHHHHHHHTTSSCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHCHHHHHH-HS
T ss_pred             chHHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcchHHHHh-hc
Confidence            4677777777665544 556678888877654445678888999999998888889999999999999974433200 00


Q ss_pred             hhhHHHHHHHHHHHhhcCChhhHHHHHHHHHhhcc
Q psy3994          84 GPRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        84 ~~~f~~~l~~~f~~v~~~~~~~~~k~~~~l~~w~~  118 (282)
                      -..|...|.+.+..  ..++..+.+++.++..|..
T Consensus        86 s~~fl~~l~~l~~~--~~~~~Vk~kil~li~~W~~  118 (226)
T 3zyq_A           86 NKQTMEELKDLLKR--QVEVNVRNKILYLIQAWAH  118 (226)
T ss_dssp             SHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHHHH
Confidence            11344444444321  2567899999999999974

>1mhq_A ADP-ribosylation factor binding protein GGA2; super helix, protein transport; 2.20A {Homo sapiens} SCOP: a.118.9.2

Probab=87.62  E-value=1.2  Score=34.01  Aligned_cols=111  Identities=16%  Similarity=0.155  Sum_probs=73.0

Q ss_pred             HHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchh
Q psy3994           7 FNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGP   85 (282)
Q Consensus         7 f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~   85 (282)
                      |++.+...++...+ ..=.-|..++...-..-...+..+..|.+.|+..+|...+-.|-|+|..++|--..+... +-..
T Consensus         2 ~~~~iekATs~~l~~~dw~~~leicD~I~~~~~~~k~a~rai~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~e-vas~   80 (148)
T 1mhq_A            2 LELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCMNHCGEKFHSE-VAKF   80 (148)
T ss_dssp             HHHHHHHHHCTTCSSCCHHHHHHHHHHHHHSSHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHH-HTSH
T ss_pred             HHHHHHHHcCCCCCCcCHHHHHHHHHHHHcCCccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHcCHHHHHH-HhhH
Confidence            45555555554433 444567777776655446678888899999999999999999999999999963332100 0011


Q ss_pred             hHHHHHHHHHHHhh--c-CChhhHHHHHHHHHhhcc
Q psy3994          86 RFARNLKATFQHLY--Q-CPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        86 ~f~~~l~~~f~~v~--~-~~~~~~~k~~~~l~~w~~  118 (282)
                      .|..++.+.+..-+  . .+...+.++..++..|..
T Consensus        81 ~Fl~eL~kl~~~k~~~~~~~~~Vk~kil~li~~W~~  116 (148)
T 1mhq_A           81 RFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTV  116 (148)
T ss_dssp             HHHHHHHHTTCCSTTSCCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccccCCCCCCHHHHHHHHHHHHHHHH
Confidence            34445444443222  1 467889999999999974

>1juq_A ADP-ribosylation factor binding protein GGA3; protein-peptide compelx, VHS domain, DXXLL sorting signal, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.9.2 PDB: 1jpl_A 1lf8_A*

Probab=86.28  E-value=0.85  Score=35.68  Aligned_cols=111  Identities=16%  Similarity=0.182  Sum_probs=74.5

Q ss_pred             HHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchh
Q psy3994           7 FNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGP   85 (282)
Q Consensus         7 f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~   85 (282)
                      |++.+...++...+ ..=.-|..++...-..-...+..+..|.+.|+..+|...+-.|-|+|..++|--..+... +--.
T Consensus        14 ~~~~IekATs~~l~~~Dw~~ileicD~I~~~~~~~k~A~ral~krl~~~n~~vql~AL~LLd~~vkNCG~~Fh~e-vas~   92 (171)
T 1juq_A           14 LESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEALQALTVLEACMKNCGRRFHNE-VGKF   92 (171)
T ss_dssp             HHHHHHHHTCTTCSSCCHHHHHHHHHHHHHSTTHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSHHHHHHH-HTSH
T ss_pred             HHHHHHHHcCCCCCCcCHHHHHHHHHHHHcCCccHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHcCHHHHHH-HhhH
Confidence            66666666554433 445567777776655445677788889999988888889999999999999953333210 0111


Q ss_pred             hHHHHHHHHHHHhh--c-CChhhHHHHHHHHHhhcc
Q psy3994          86 RFARNLKATFQHLY--Q-CPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        86 ~f~~~l~~~f~~v~--~-~~~~~~~k~~~~l~~w~~  118 (282)
                      .|..++.+.+...+  . .+...+.|++.++..|..
T Consensus        93 ~Fl~eL~kl~~~k~~~~~~~~~Vk~kil~li~~W~~  128 (171)
T 1juq_A           93 RFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTM  128 (171)
T ss_dssp             HHHHHHHHHHCCCCCCTTSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHH
Confidence            35555555554322  1 457889999999999984

>3g2s_A C-terminal fragment of sortilin-related receptor; ADP-ribosylation factor binding protein GGA1, VHS, acidic- cluster dileucine signal, sorla; 1.70A {Homo sapiens} SCOP: a.118.9.2 PDB: 3g2t_A* 3g2u_A 3g2v_A* 3g2w_A 1ujk_A* 1jwf_A 1ujj_A 1jwg_A* 1py1_A*

Probab=84.31  E-value=1.3  Score=33.85  Aligned_cols=112  Identities=17%  Similarity=0.208  Sum_probs=74.1

Q ss_pred             HHHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCch
Q psy3994           6 TFNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFG   84 (282)
Q Consensus         6 ~f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~   84 (282)
                      .|+..+...++...+ ..=.-|..++...-..-...+..+..|.+.|+..+|.-.+-.|-|+|..++|--..|-. .+--
T Consensus        11 ~~~~~IekATs~~l~~~dw~~ileicD~I~~~~~~pk~a~ral~krl~~~n~~v~l~AL~LLe~cvkNCG~~fh~-eias   89 (149)
T 3g2s_A           11 TLEARINRATNPLNKELDWASINGFCEQLNEDFEGPPLATRLLAHKIQSPQEWEAIQALTVLETCMKSCGKRFHD-EVGK   89 (149)
T ss_dssp             CHHHHHHHHSCTTCSSCCHHHHHHHHHHGGGSSSHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHCCHHHHH-HHTS
T ss_pred             cHHHHHHHHcCCCCCCcCHHHHHHHHHHHHCCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcCHHHHH-HHhh
Confidence            455666666554333 44455666666544333457788889999999888888999999999999997433320 0011


Q ss_pred             hhHHHHHHHHHHHhh---cCChhhHHHHHHHHHhhcc
Q psy3994          85 PRFARNLKATFQHLY---QCPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        85 ~~f~~~l~~~f~~v~---~~~~~~~~k~~~~l~~w~~  118 (282)
                      ..|..++.+.+..-|   ..++..+.+++.++..|..
T Consensus        90 ~~Fl~eL~kl~~~k~~~~~~~~~Vk~kil~li~~W~~  126 (149)
T 3g2s_A           90 FRFLNELIKVVSPKYLGSRTSEKVKNKILELLYSWTV  126 (149)
T ss_dssp             HHHHHHHHHHHCTTTTGGGSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccccCCCCCHHHHHHHHHHHHHHHH
Confidence            245556555554332   2568899999999999974

>1elk_A Target of MYB1; superhelix of helices, endocytosis/exocytosis complex; 1.50A {Homo sapiens} SCOP: a.118.9.2

Probab=84.21  E-value=2  Score=32.96  Aligned_cols=112  Identities=19%  Similarity=0.179  Sum_probs=69.4

Q ss_pred             HHHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHh-cCCCCccceeehhhHHHHHhhhhccCCCCc
Q psy3994           6 TFNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIK-CKPEYKVPALYVIDSLVRQSRHQFQDKDVF   83 (282)
Q Consensus         6 ~f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~-~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~   83 (282)
                      .++..++..++...+ ..-.-|.+++...-..-...+..+..|.+.|+. .+|.-.+-.|-|+|..++|--..+... +-
T Consensus        16 ~~~~~IekATs~~l~~~Dw~~~leicD~I~~~~~~~k~a~ral~krl~~~~n~~v~l~AL~LLd~~vkNcG~~fh~e-va   94 (157)
T 1elk_A           16 PVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDALRAVKKRIVGNKNFHEVMLALTVLETCVKNCGHRFHVL-VA   94 (157)
T ss_dssp             HHHHHHHHHTCTTCSSCCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHSCHHHHHH-HT
T ss_pred             HHHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHhCHHHHHH-Hh
Confidence            456666666554443 455667777775554445778888888999974 556667899999999999963222100 00


Q ss_pred             hhhHHHH-HHHHHHHhhcCChhhHHHHHHHHHhhcc
Q psy3994          84 GPRFARN-LKATFQHLYQCPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        84 ~~~f~~~-l~~~f~~v~~~~~~~~~k~~~~l~~w~~  118 (282)
                      ...|..+ +.+.+..-...+...++|++.++..|..
T Consensus        95 ~~~fl~e~Lvk~~~~k~~~~~~Vk~kil~li~~W~~  130 (157)
T 1elk_A           95 SQDFVESVLVRTILPKNNPPTIVHDKVLNLIQSWAD  130 (157)
T ss_dssp             SHHHHHHHTHHHHSTTTCCCHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHH
Confidence            0123333 2333221122335788999999999975

>3ldz_A STAM-1, signal transducing adapter molecule 1; ubiquitin-binding, cytoplasm, UBL conjugation, endosome, membrane, protein transport, SH3 domain; 2.60A {Homo sapiens} SCOP: a.118.9.0

Probab=84.07  E-value=1  Score=33.92  Aligned_cols=108  Identities=16%  Similarity=0.208  Sum_probs=71.4

Q ss_pred             HHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchh
Q psy3994           7 FNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGP   85 (282)
Q Consensus         7 f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~   85 (282)
                      |+..+...++...+ ..=.-|.+++...-..-...+..+..|.+.++.-.|...+-.|-|+|..++|--..+.. .+--.
T Consensus         6 ~d~~iekAT~~~l~~~dw~~ileicD~I~~~~~~~k~a~rai~Krl~~~n~~~ql~AL~LLe~~vkNcG~~f~~-evas~   84 (140)
T 3ldz_A            6 FDQDVEKATSEMNTAEDWGLILDICDKVGQSRTGPKDCLRSIMRRVNHKDPHVAMQALTLLGACVSNCGKIFHL-EVCSR   84 (140)
T ss_dssp             THHHHHHHTCTTSSSCCHHHHHHHHHHHTTSTTHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHH-HHSSH
T ss_pred             HHHHHHHHcCCCCCCcCHHHHHHHHHHHHCCCcCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhcCHHHHH-HHhhH
Confidence            45555555443333 44556777777655444567888889999998888888888899999999996333220 00012


Q ss_pred             hHHHHHHHHHHHhhcCChhhHHHHHHHHHhhcc
Q psy3994          86 RFARNLKATFQHLYQCPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        86 ~f~~~l~~~f~~v~~~~~~~~~k~~~~l~~w~~  118 (282)
                      .|...+.+.+.   ..++..+.++..++..|..
T Consensus        85 ~Fl~el~~l~~---~~~~~Vk~kil~li~~W~~  114 (140)
T 3ldz_A           85 DFASEVSNVLN---KGHPKVCEKLKALMVEWTD  114 (140)
T ss_dssp             HHHHHHHHHHH---HSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhc---cCCHHHHHHHHHHHHHHHH
Confidence            35555544442   2568899999999999974

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	282
d1szaa_	144	a.118.9.4 (A:) PCF11 protein {Baker's yeast (Sacch	2e-24
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-14
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-10
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-10
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-09
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	7e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	9e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	9e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	8e-08
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	5e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	9e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-06
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-06
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	6e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-05
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	3e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	6e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	6e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	7e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	1e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	5e-04
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	7e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	0.001

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 144

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 94.0 bits (233), Expect = 2e-24
 Identities = 33/134 (24%), Positives = 57/134 (42%), Gaps = 16/134 (11%)

Query: 3   VIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPA 62
           ++K FN  L  L     PI    IT +T+ A   I   ++ V ++E  I KC P+ K+ A
Sbjct: 8   IVKDFNSILEELTFNSRPI----ITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYA 63

Query: 63  LYVIDSLVRQSRHQFQDKDVFGPRFARNLKATFQHLYQCPPED-KSKIIRVLNLWQKN-- 119
            Y +DS+ +     +         F+RNL   ++  Y       ++K+I +  LW     
Sbjct: 64  FYALDSICKNVGSPYTI------YFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPND 117

Query: 120 ---EVFTPDIIHPL 130
               +F    +  +
Sbjct: 118 TGLPLFEGSALEKI 131

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.1 bits (161), Expect = 1e-14
 Identities = 16/72 (22%), Positives = 38/72 (52%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           + T++ G ++  + ++ +  TF  +G ++ I + P +G +FV  +  + AA A+  +  T
Sbjct: 18  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 77

Query: 218 KLQGKTITLAWA 229
            ++G  +   W 
Sbjct: 78  TIEGHVVKCYWG 89

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.6 bits (152), Expect = 3e-13
 Identities = 16/76 (21%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 158 STTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
           ++ ++IG+L+  +V++ ++   F +YG +V  ++   +G AFV     ++A  A+     
Sbjct: 15  NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--HKGFAFVQYVNERNARAAVAGEDG 72

Query: 217 TKLQGKTITLAWAPGK 232
             + G+ + +  A   
Sbjct: 73  RMIAGQVLDINLAAEP 88

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 1e-12
 Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP---RGCAFVCMNRRQDAAKALYKL 214
           +  L+I +L   +  EE+ D FG+YG +  I +      RG A+V      DA  A   L
Sbjct: 7   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 215 KNTKLQGKTITLAWAPGKGMKDK 237
               +  + + + +        K
Sbjct: 67  SGFNVCNRYLVVLYYNANRAFQK 89

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.5 bits (144), Expect = 2e-12
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
           +L++G L   V E  L + F   G ++SI +          G A+V   +  DA +AL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 214 LKNTKLQGKTITLAWA 229
           +    ++GK + + W+
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.6 bits (144), Expect = 3e-12
 Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 6/81 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGC------AFVCMNRRQDAAKAL 211
           S TL++G+LS    EE++ + F + GD+  I +   +         FV    R DA  A+
Sbjct: 7   SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 66

Query: 212 YKLKNTKLQGKTITLAWAPGK 232
             +  T+L  + I   W  G 
Sbjct: 67  RYINGTRLDDRIIRTDWDAGF 87

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.2 bits (143), Expect = 4e-12
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 8/83 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-------PPRGCAFVCMNRRQDAAKA 210
           ++ + + ++     + E+ + F  +G++ ++ L          RG  FV    +QDA KA
Sbjct: 8   TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 67

Query: 211 LYKLKN-TKLQGKTITLAWAPGK 232
              L + T L G+ + L WA  +
Sbjct: 68  FNALCHSTHLYGRRLVLEWADSE 90

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.4 bits (141), Expect = 5e-12
 Identities = 20/75 (26%), Positives = 37/75 (49%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
            + L++G+L   + EEE+   F +YG    + +   +G  F+ +  R  A  A  +L N 
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNM 67

Query: 218 KLQGKTITLAWAPGK 232
            L+GK + + +A   
Sbjct: 68  PLRGKQLRVRFACHS 82

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 57.3 bits (138), Expect = 1e-11
 Identities = 25/84 (29%), Positives = 49/84 (58%), Gaps = 8/84 (9%)

Query: 154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDA 207
           E++  T L++ +L + + +++L   FG+YG +V  N++       PRG AFV  N+R++A
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 208 AKALYKLKNTKLQG--KTITLAWA 229
            +A+  L N   +G  + +++  A
Sbjct: 62  QEAISALNNVIPEGGSQPLSVRLA 85

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 57.3 bits (138), Expect = 1e-11
 Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 7/81 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +T L + +L + + + EL   F   G + +  ++         G AFV      D+ +A+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 212 YKLKNTKLQGKTITLAWA-PG 231
             L    ++ K + +++A PG
Sbjct: 62  KVLNGITVRNKRLKVSYARPG 82

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 54.3 bits (130), Expect = 2e-10
 Identities = 18/77 (23%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-PPRGCAFVCMNRRQDAAKALYKLKN 216
           + TL   +LS  + E+EL + F +  ++  ++     +G A++      DA K L + + 
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 75

Query: 217 TKLQGKTITLAWAPGKG 233
            ++ G++++L +   KG
Sbjct: 76  AEIDGRSVSLYYTGEKG 92

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 3e-10
 Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 154 ENMCST-TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALY 212
           + M S   L++ +L     EE +   F          +   R  AFV  + R+DA +A+ 
Sbjct: 3   DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMK 62

Query: 213 KLKNTKLQGKTITLAWA 229
            L    L G  I +  A
Sbjct: 63  ALNGKVLDGSPIEVTLA 79

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.0 bits (127), Expect = 4e-10
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYKLK 215
           L + +L   V + ++ + F E+G +    +         G A V   R+ DA KA+ +  
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 216 NTKLQGKTITLAWAP 230
              L G+ + +    
Sbjct: 63  GVPLDGRPMNIQLVT 77

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 4e-10
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
             T+++G L + V E  L + F + G VV+ ++         +G  FV     +DA  A+
Sbjct: 9   DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 68

Query: 212 YKLKNTKLQGKTITLAWA 229
             +   KL GK I +  A
Sbjct: 69  KIMDMIKLYGKPIRVNKA 86

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.5 bits (128), Expect = 5e-10
 Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 5/85 (5%)

Query: 154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYK 213
           +   +T LW+G L        L+  F  +G + +I+ +     A++       A  A  K
Sbjct: 13  KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAK 72

Query: 214 LKNTKLQG--KTITLAWA---PGKG 233
           ++   L G  + + + +A   P  G
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSGPSSG 97

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 8e-10
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 4/80 (5%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI---PPRGCAFVCMNRRQDAAKALYKL 214
              +++G+L   ++ +++ D F +YG +  I+L         AFV     +DA  A+Y  
Sbjct: 14  DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGR 73

Query: 215 KNTKLQGKTITLAWA-PGKG 233
                 G  + + +   G+G
Sbjct: 74  DGYDYDGYRLRVEFPRSGRG 93

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.9 bits (126), Expect = 1e-09
 Identities = 17/90 (18%), Positives = 33/90 (36%), Gaps = 2/90 (2%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFV-CMNRRQDAAKALYKLKNT 217
              + G L      E+L   F  +G++  I+ +       +    + ++A        N 
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNG 71

Query: 218 KLQGKTITLAWAPGKGMKDKD-WKDFWEVQ 246
            LQ +   + W   +G  +K+  K   E Q
Sbjct: 72  NLQLRNKEVTWEVLEGEVEKEALKKIIEDQ 101

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 1e-09
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 8/79 (10%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
             L++  L K + ++EL   F +YG +++  ++  +      G  F+  ++R +A +A+ 
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 213 KLKNTKLQGKT--ITLAWA 229
            L   K  G T  IT+ +A
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.5 bits (125), Expect = 1e-09
 Identities = 15/85 (17%), Positives = 26/85 (30%), Gaps = 5/85 (5%)

Query: 158 STTLWIGHLSKLVQEE-----ELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALY 212
           S+ L     +  V  E     +    F  Y    +           +  +    AA A  
Sbjct: 5   SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARL 64

Query: 213 KLKNTKLQGKTITLAWAPGKGMKDK 237
           +L  T+  GK + L +A    +   
Sbjct: 65  RLHKTEFLGKEMKLYFAQTLHIGSS 89

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 1e-09
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
             TL++      +    L   F  +G+++ +++ PPR CAFV   + + A +A+ +L  T
Sbjct: 5   GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGT 62

Query: 218 KLQGKTITLAWA 229
           +++   + +  A
Sbjct: 63  QVESVQLKVNIA 74

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.3 bits (124), Expect = 2e-09
 Identities = 20/93 (21%), Positives = 31/93 (33%)

Query: 149 ARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAA 208
             +G      T +   +L       E+ +TF  +G +  + L      A V      +A 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEAR 60

Query: 209 KALYKLKNTKLQGKTITLAWAPGKGMKDKDWKD 241
           KA   L  +K     + L WAP         K 
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKK 93

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 2e-09
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 4/76 (5%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG----CAFVCMNRRQDAAKALYK 213
             TL++G+LS+ V E  +   F + G   S  +I          FV     +DAA AL  
Sbjct: 8   PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAA 67

Query: 214 LKNTKLQGKTITLAWA 229
           +   K+ GK + + WA
Sbjct: 68  MNGRKILGKEVKVNWA 83

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.2 bits (122), Expect = 2e-09
 Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 9/78 (11%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLI---------PPRGCAFVCMNRRQDAAKAL 211
           L+I +L+    EE L   F + G + S  +             G  FV   + + A KAL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 212 YKLKNTKLQGKTITLAWA 229
            +L+   + G  + +  +
Sbjct: 61  KQLQGHTVDGHKLEVRIS 78

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 3e-09
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL-KNTK 218
            L+IG+LS  V  ++L   FG+    ++  ++   G AFV    +  A +A+  L    +
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 62

Query: 219 LQGKTITLAWAPGKGMK 235
           L GK + + ++  K ++
Sbjct: 63  LHGKIMEVDYSVSKKLR 79

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 3e-09
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYK 213
           ++IG+L   + E+ L DTF  +G ++    I         +G AF+       +  A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 214 LKNTKLQGKTITLAWAPGKGMK 235
           +    L  + IT+++A  K  K
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 3e-09
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSI----NLIPPRGCAFVCMNRRQDAAKALYK 213
              L + ++    ++ +L   FG++G ++ +    N    +G  FV      DA +A  K
Sbjct: 11  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK 70

Query: 214 LKNTKLQGKTITLAWAPGKGMKD 236
           L  T ++G+ I +  A  + M +
Sbjct: 71  LHGTVVEGRKIEVNNATARVMTN 93

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 3e-09
 Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 6/85 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L++G L++ V ++ L   F  +GD+  I +         RG AFV     +DAA A+
Sbjct: 5   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKD 236
             +  ++L G+TI +  A    +K+
Sbjct: 65  DNMNESELFGRTIRVNLAKPMRIKE 89

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 5e-09
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           S+ + + +L +    +E+ D   +Y       +   +  AFV +   + A  A+      
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYDLKY-CYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 218 KLQGKTITLAWAPGKGM 234
             +GK + +   P   +
Sbjct: 64  SFRGKDLIVQLQPTDAL 80

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 7e-09
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 3/81 (3%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSI-NLIPPRGCAFVCMNRRQDAAKALYKLKN 216
           S+ +++G  +  + E+EL + F +YGDV+ +    P R  AFV     Q A       ++
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLC--GED 62

Query: 217 TKLQGKTITLAWAPGKGMKDK 237
             ++G ++ ++ A  K   + 
Sbjct: 63  LIIKGISVHISNAEPKHNSNS 83

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 9e-09
 Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 4/76 (5%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYK 213
              ++I +L K +  + L DTF  +G+++S  ++      +G  FV    ++ A +A+ K
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 214 LKNTKLQGKTITLAWA 229
           +    L  + + +   
Sbjct: 68  MNGMLLNDRKVFVGRF 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 9e-09
 Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +  L +  LS    E +L + F +YG +  ++++        RG AFV      DA +A 
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 212 YKLKNTKLQGKTIT 225
            +    +L G+ I 
Sbjct: 69  ERANGMELDGRRIR 82

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 1e-08
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T L + +L + + +EE    FG  G++ S  L+  +      G  FV     +DA KA+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 213 KLKNTKLQGKTITLAWA 229
            L   +LQ KTI +++A
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 1e-08
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +  L+IG L   + ++++ +    +G + + NL+        +G AF          +A+
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 212 YKLKNTKLQGKTITLAWA 229
             L   +L  K + +  A
Sbjct: 61  AGLNGMQLGDKKLLVQRA 78

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.4 bits (115), Expect = 2e-08
 Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 7/75 (9%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALYKL 214
           ++IG LS    +E L + FG++G+V    ++         G  FV    +    K L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 215 KNTKLQGKTITLAWA 229
              +L  KTI    A
Sbjct: 62  SRHELDSKTIDPKVA 76

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKAL 211
           S  L++ +LS    EE+L   F  YG +  ++           G AFV     + A KA 
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67

Query: 212 YKLKNTKLQGKTITLAWAPGK 232
            ++     QG+ + +  +  K
Sbjct: 68  AEVDGQVFQGRMLHVLPSTIK 88

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 2e-08
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 158 STTLWIGHLSKLVQEEEL----SDTFGEYGDVVSINL---IPPRGCAFVCMNRRQDAAKA 210
           + T++I +L++ ++++EL       F  +G ++ I +   +  RG AFV       A  A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 211 LYKLKNTKLQGKTITLAWA 229
           L  ++      K + + +A
Sbjct: 63  LRSMQGFPFYDKPMRIQYA 81

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 48.2 bits (114), Expect = 3e-08
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 6/82 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNR------RQDAAKAL 211
              L++  + +  QE+E+ + F +YG++ +I+L   R   F            + A  A 
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 212 YKLKNTKLQGKTITLAWAPGKG 233
             L   ++ G+TI + W   KG
Sbjct: 67  EALNGAEIMGQTIQVDWCFVKG 88

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 3e-08
 Identities = 24/90 (26%), Positives = 39/90 (43%), Gaps = 10/90 (11%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--------PRGCAFVCMNRRQDAAKA 210
             L+IG + K+ + EE+ +   +  + V   ++          RG AFV     + AA A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 211 LYKL--KNTKLQGKTITLAWAPGKGMKDKD 238
             KL     +L G  I + WA  +   D+D
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEIDVDED 91

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.6 bits (115), Expect = 3e-08
 Identities = 12/77 (15%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKLK 215
           S  + +  L + V E +L +   ++G +  + ++P +  A V       A + +      
Sbjct: 15  SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADV 74

Query: 216 NTKLQGKTITLAWAPGK 232
              + G+     ++  K
Sbjct: 75  PVYIAGQQAFFNYSTSK 91

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 4e-08
 Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKAL 211
           + T+ + +LS+  +E +L + F  +G +  I L         +G AF+  +RR+DAA+A+
Sbjct: 8   NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 212 YKLKNTKLQGKTITLAWA 229
             +         + + WA
Sbjct: 68  AGVSGFGYDHLILNVEWA 85

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 5e-08
 Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
           S  +  G L   V   +L     + G V ++ + P +  +F      +++ +A   L   
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGK 79

Query: 218 KL---QGKTITLAWA 229
           ++    G+ ITL   
Sbjct: 80  EVVDDLGQKITLYLN 94

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 5e-08
 Identities = 14/85 (16%), Positives = 31/85 (36%), Gaps = 8/85 (9%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKAL 211
           ++ L +  L     E++L + F  +G+V+ + +          G  FV     +   K +
Sbjct: 8   TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 67

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKD 236
            +     + G+         K  +D
Sbjct: 68  SQRH--MIDGRWCDCKLPNSKQSQD 90

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 5e-08
 Identities = 14/76 (18%), Positives = 24/76 (31%), Gaps = 2/76 (2%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI--PPRGCAFVCMNRRQDAAKALYKLKN 216
             + + +L   V  + L   F ++G V+ I       +  A +       A  A   L  
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDG 67

Query: 217 TKLQGKTITLAWAPGK 232
             +     TL     K
Sbjct: 68  QNIYNACCTLRIDFSK 83

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 8e-08
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L+I HL +   +++L   F  +G+VVS  +         +   FV  +    A  A+
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 212 YKLKNTKLQGKTITLAWAPGK 232
             +   ++  K + +     K
Sbjct: 78  QSMNGFQIGMKRLKVQLKRSK 98

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 9e-08
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
              L+IG LS    EE L + + ++G +    ++        RG  FV  +   +   A+
Sbjct: 20  FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 79

Query: 212 YKLKNTKLQGKTITLAWA 229
              +   + G+ +    A
Sbjct: 80  -AARPHSIDGRVVEPKRA 96

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.3 bits (107), Expect = 4e-07
 Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 2/63 (3%)

Query: 172 EEELSDTFGEYGDVVSINLI--PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
            E+L     ++G +  + L    P G A V     ++A   +  L      G+ IT    
Sbjct: 33  REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

Query: 230 PGK 232
            G 
Sbjct: 93  DGT 95

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 4e-07
 Identities = 12/76 (15%), Positives = 28/76 (36%), Gaps = 12/76 (15%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----------PRGCAFVCMNRRQDAA 208
            L++G++   + EE + D F     +  +   P            +  AF+      +  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 209 KALYKLKNTKLQGKTI 224
           +A+        QG+++
Sbjct: 63  QAMA-FDGIIFQGQSL 77

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 4e-07
 Identities = 17/86 (19%), Positives = 25/86 (29%), Gaps = 7/86 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
             T ++G+L   V EE + + F                    +G  +           AL
Sbjct: 15  PYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKDK 237
             L    L  K I +  A     KD 
Sbjct: 75  -SLNEESLGNKRIRVDVADQAQDKDS 99

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.7 bits (105), Expect = 5e-07
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 6/78 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
            T + + ++   V  +E+ D F  Y  +     +       P G A V    R +A  A+
Sbjct: 9   PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 68

Query: 212 YKLKNTKLQGKTITLAWA 229
             L +  +  + + L   
Sbjct: 69  IDLNDRPIGSRKVKLVLG 86

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.0 bits (103), Expect = 7e-07
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALY 212
            TLW+ +      +  + D   +   V     +P       R  A++ +  ++DA   + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 213 KLKNTKLQGKTITLAWA 229
           KL   K++G T+    +
Sbjct: 62  KLNGLKIEGYTLVTKVS 78

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 9e-07
 Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 14/86 (16%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--------------PRGCAFVCMNR 203
           ++ +++  L+  V  ++L+D F + G V                     P+G A V    
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 204 RQDAAKALYKLKNTKLQGKTITLAWA 229
              A  A+        QG  + ++ A
Sbjct: 68  PPTAKAAVEWFDGKDFQGSKLKVSLA 93

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 1e-06
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 6/84 (7%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
           ++++G++     EE+L D F E G VVS  L+       P+G  F     ++ A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 214 LKNTKLQGKTITLAWAPGKGMKDK 237
           L   +  G+ + +  A  +  K++
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEE 93

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 2e-06
 Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 1/72 (1%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT 217
              + +  L      ++L D        V    +   G   V   R++D   AL KL +T
Sbjct: 15  DFRVLVSGLPPSGSWQDLKD-HMREAGDVCYADVQKDGMGMVEYLRKEDMEYALRKLDDT 73

Query: 218 KLQGKTITLAWA 229
           K +      ++ 
Sbjct: 74  KFRSHEGETSYI 85

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 2e-06
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 7/76 (9%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYK 213
            L+IG LS    +E L   F ++G +    ++        RG  FV     ++   A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-N 66

Query: 214 LKNTKLQGKTITLAWA 229
            +  K+ G+ +    A
Sbjct: 67  ARPHKVDGRVVEPKRA 82

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSI------NLIPPRGCAFVCMNRRQDA 207
           E   + T++   L+  ++  +L D F   G V  +      N    +G A+V     Q  
Sbjct: 14  EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 73

Query: 208 AKALYKLKNTKLQGKTITLAWA 229
             A+  L   +L G  I +  +
Sbjct: 74  PLAI-GLTGQRLLGVPIIVQAS 94

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 2e-06
 Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYK 213
           + + +        EE  ++   +YG+V  +N+         G  +V   R +DA KA+  
Sbjct: 28  SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVID 87

Query: 214 LKNTKLQGKTITLAWAP 230
           L N    G+ I    +P
Sbjct: 88  LNNRWFNGQPIHAELSP 104

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 42.6 bits (99), Expect = 3e-06
 Identities = 21/90 (23%), Positives = 32/90 (35%), Gaps = 6/90 (6%)

Query: 148 QARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMN 202
               G E+     L+IG+L+      EL     E      + ++       R   +V   
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 62

Query: 203 RRQDAAKALYKLKNTKLQGKTITLAWAPGK 232
             +D  KAL  L   K+ G  I L    G+
Sbjct: 63  SAEDLEKALE-LTGLKVFGNEIKLEKPKGR 91

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 3e-06
 Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 7/75 (9%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALYKL 214
           +++G LS    EE++ + FG +G+V SI L          G  F+     +   K + + 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 215 KNTKLQGKTITLAWA 229
           K   +      +  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 3e-06
 Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 7/71 (9%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSI------NLIPPRGCAFVCMNRRQDAAKALYKL 214
           ++IG LS    +++L D F ++G+VV             RG  FV     +   K +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 215 KNTKLQGKTIT 225
           K  KL GK I 
Sbjct: 61  KEHKLNGKVID 71

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 6e-06
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPP------RGCAFVCMNRRQDAAKAL 211
              L++G LS    E+ L   F +YG +  + ++        RG  FV      DA  A+
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 212 YKLKNTKLQGKTITLAWAPGK 232
             +    + G+ I +  A   
Sbjct: 65  MAMNGKSVDGRQIRVDQAGKS 85

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 6e-06
 Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPR------GCAFVCMNRRQDAAKALY 212
           T +++G L     +  L   F  +GD+    +I  R      G  FV M  R  A +A  
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC- 69

Query: 213 KLKNTKLQGKTITLAWAPGK 232
           K  N  + G+   +  A   
Sbjct: 70  KDPNPIIDGRKANVNLAYLG 89

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.1 bits (98), Expect = 6e-06
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 158 STTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIPPRG-CAFVCMNRRQDAAKALYKLK 215
           ++ L + +L+ + V  + L   FG YGDV  + ++  +   A V M     A  A+  L 
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 61

Query: 216 NTKLQGKTITLAWA 229
             KL GK I +  +
Sbjct: 62  GHKLHGKPIRITLS 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.1 bits (93), Expect = 1e-05
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 7/75 (9%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINL------IPPRGCAFVCMNRRQDAAKALYKL 214
           +++G LS     E++   F ++G V    L         RG  FV         K   ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 215 KNTKLQGKTITLAWA 229
              ++  K +    A
Sbjct: 61  HFHEINNKMVECKKA 75

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (98), Expect = 2e-05
 Identities = 21/120 (17%), Positives = 42/120 (35%), Gaps = 7/120 (5%)

Query: 160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYK 213
            L+IG LS    +E L   F ++G +    ++        RG  FV     ++   A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-N 66

Query: 214 LKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYIPYDRLSKEIDYDYLEDGGVFD 273
            +  K+ G+ +    A  +    +        +  V  I  D     +   + + G +  
Sbjct: 67  ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 126

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (98), Expect = 2e-05
 Identities = 18/103 (17%), Positives = 39/103 (37%), Gaps = 7/103 (6%)

Query: 133 MADPNHPIHRELAEIQARNGVENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP 192
           +        R ++   ++    ++    +++G + +  +E  L D F +YG +  I ++ 
Sbjct: 72  VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMT 131

Query: 193 ------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA 229
                  RG AFV  +      K +   K   + G    +  A
Sbjct: 132 DRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA 173

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 2e-05
 Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
           +  L++ +LS  V E +L   F  + +     +         RG AF+    ++ A +AL
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 212 YKLKNTKLQGKTITLAWAPGK 232
           + +   KL GK + + +   K
Sbjct: 78  HLVNGYKLYGKILVIEFGKNK 98

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.7 bits (92), Expect = 3e-05
 Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 3/75 (4%)

Query: 158 STTLWIGHL-SKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL--YKL 214
              + I           +L      +G + +  ++     AF+ M   +DA  A+  Y  
Sbjct: 8   RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTT 67

Query: 215 KNTKLQGKTITLAWA 229
               + GK + +  +
Sbjct: 68  TPALVFGKPVRVHLS 82

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (89), Expect = 6e-05
 Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 2/84 (2%)

Query: 154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKAL-- 211
           +   S  L I  L   V E E+      +G V +I ++  +  AF+ +   + A   +  
Sbjct: 4   DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNY 63

Query: 212 YKLKNTKLQGKTITLAWAPGKGMK 235
           Y      L+ + I + ++  K +K
Sbjct: 64  YSAVTPHLRNQPIYIQYSNHKELK 87

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 6e-05
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI--PPRGCAFVCMNRRQDAAKALYKLK 215
           S TL + ++   V EE+L   F   G VV         R  A + M   ++A +AL  L 
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLH 69

Query: 216 NTKL-QGKTITLAWA 229
           N  L +   + ++++
Sbjct: 70  NHDLGENHHLRVSFS 84

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 39.9 bits (92), Expect = 7e-05
 Identities = 19/101 (18%), Positives = 34/101 (33%), Gaps = 9/101 (8%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRR------QDAAKAL 211
              L + ++   V E +L   F  YG + S+ ++  R                  A +A+
Sbjct: 42  LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101

Query: 212 YKLKNTKLQGKTITLAWAPGKGMKDKDWKDFWEVQDGVSYI 252
             L    +  K + +A A     +         V DG  Y+
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQRPGIAGA---VGDGNGYL 139

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 37.9 bits (87), Expect = 1e-04
 Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 2/74 (2%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVV-SINLIPPRGCAFVCMNRRQDAAKALYKLKN 216
           +  L++ +L +   E  LS  F ++        +      AFV       +  A   L+ 
Sbjct: 8   NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQG 67

Query: 217 TKL-QGKTITLAWA 229
            K+     + + +A
Sbjct: 68  FKITPTHAMKITFA 81

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.5 bits (86), Expect = 2e-04
 Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 12/85 (14%)

Query: 152 GVENMCSTTLWIGHLSKLVQEEELSDTF---GEYGDVVSINLI---------PPRGCAFV 199
            V  +    +++  LS+ + + E+       G++G +  + +           P   A+V
Sbjct: 2   SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYV 61

Query: 200 CMNRRQDAAKALYKLKNTKLQGKTI 224
              R +DA +A+  + N  + G+T+
Sbjct: 62  TYIRSEDALRAIQCVNNVVVDGRTL 86

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 2e-04
 Identities = 13/77 (16%), Positives = 26/77 (33%), Gaps = 5/77 (6%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGD-----VVSINLIPPRGCAFVCMNRRQDAAKALY 212
            T L+I +L   + E+EL +    +G      ++  +    RG  F  M   +     + 
Sbjct: 18  PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIG 77

Query: 213 KLKNTKLQGKTITLAWA 229
                 ++      A  
Sbjct: 78  HFNGKFIKTPPGVSAPT 94

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 3e-04
 Identities = 21/99 (21%), Positives = 32/99 (32%), Gaps = 11/99 (11%)

Query: 153 VENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI--------PPRGCAFVCMNRR 204
           + NM      +         E++ D   +YG V SI +         P  G  FV     
Sbjct: 9   LMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSV 68

Query: 205 QDAAKALYKLKNTKLQGKTITLAWAPGKGMKDKDWKDFW 243
            D  KA+  L   K   + +   +           +DFW
Sbjct: 69  FDCQKAMQGLTGRKFANRVVVTKYCD---PDSYHRRDFW 104

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 4e-04
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 6/70 (8%)

Query: 161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRG------CAFVCMNRRQDAAKALYKL 214
           L+I  L     +++L      YG +VS   I  +         FV  +    A KA+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 215 KNTKLQGKTI 224
           K + +Q +  
Sbjct: 61  KASGVQAQMA 70

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.1 bits (83), Expect = 5e-04
 Identities = 9/70 (12%), Positives = 22/70 (31%), Gaps = 2/70 (2%)

Query: 155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL 214
           ++  T + +    +      L   F +YG+++   +        +    +  A KAL   
Sbjct: 1   HLDDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKAL-SK 58

Query: 215 KNTKLQGKTI 224
                    +
Sbjct: 59  DGRIFGESIM 68

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.9 bits (82), Expect = 7e-04
 Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 12/87 (13%)

Query: 158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKAL 211
             T++I +LS   +EE L +   ++GD+  + ++        +GCAF     ++ A K L
Sbjct: 8   GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 67

Query: 212 YKL------KNTKLQGKTITLAWAPGK 232
                       KL G+ + +  A  +
Sbjct: 68  AAASLEAEGGGLKLDGRQLKVDLAVTR 94

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 0.001
 Identities = 10/81 (12%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 154 ENMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAA 208
            ++ + +++I         +++ +   + G V++I +        +G  FV  +  + A 
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 61

Query: 209 KALYKLKNTKLQGKTITLAWA 229
           K + +    K +   + + + 
Sbjct: 62  KFV-ETPGQKYKETDLLILFK 81

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	282
d1szaa_	144	PCF11 protein {Baker's yeast (Saccharomyces cerevi	99.86
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.84
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.83
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.83
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.83
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.83
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.83
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.82
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.82
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.82
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.81
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.81
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.81
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.81
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.8
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.79
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.79
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.79
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.79
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.79
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.79
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.79
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.78
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.78
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.78
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.78
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.77
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.77
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.77
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.77
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.76
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.76
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.76
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.75
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.75
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.75
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.74
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.74
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.74
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.74
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.74
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.74
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.74
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.73
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.73
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.73
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.72
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.71
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.71
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.69
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.68
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.65
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.63
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.62
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.6
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.6
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.55
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.55
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.54
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.51
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.51
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.44
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.34
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.55
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.5
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.92
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.88
d1dvpa1	145	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	88.48
d1mhqa_	143	ADP-ribosylation factor binding protein Gga2 {Huma	87.05
d1ujka_	145	ADP-ribosylation factor binding protein Gga1 {Huma	86.31
d1juqa_	151	ADP-ribosylation factor binding protein Gga3 {Huma	81.26

>d1szaa_ a.118.9.4 (A:) PCF11 protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: RPR domain (SMART 00582 )
domain: PCF11 protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=1.2e-22  Score=156.88  Aligned_cols=120  Identities=27%  Similarity=0.451  Sum_probs=110.2

Q ss_pred             hhHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCC
Q psy3994           3 VIKTFNQELSSLYDTKPPISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDV   82 (282)
Q Consensus         3 ~~~~f~~~L~~l~~~~~p~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~   82 (282)
                      .+++|+..|++|.+    +|+++|++||.||++|.++++++|++|++++++|+|.+||+.|||+|+|+++.      ...
T Consensus         8 ~~~~f~~~L~~L~~----ns~~~I~~Lt~~a~~~~~~a~~Iv~~i~~~i~~~~~~~KL~~LYLiddI~~n~------~~~   77 (144)
T d1szaa_           8 IVKDFNSILEELTF----NSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNV------GSP   77 (144)
T ss_dssp             HHHHHHHHHTTCSS----CCHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHT------CTT
T ss_pred             HHHHHHHHHHHHhh----ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcccchhhhhhHHHHHHHh------HHH
Confidence            48999999999955    68889999999999999999999999999999999999999999999999998      456


Q ss_pred             chhhHHHHHHHHHHHhhc-CChhhHHHHHHHHHhhccCc-----ccCCcccccccc
Q psy3994          83 FGPRFARNLKATFQHLYQ-CPPEDKSKIIRVLNLWQKNE-----VFTPDIIHPLFD  132 (282)
Q Consensus        83 ~~~~f~~~l~~~f~~v~~-~~~~~~~k~~~~l~~w~~~~-----~f~~~~i~~~~~  132 (282)
                      |...|.+.+.+.|.+++. ++++.++++.+++++|..++     +|+.+.++.+..
T Consensus        78 y~~~f~~~l~~~f~~~y~~~~~~~r~kl~rll~iW~~r~~~~~~vFp~~~l~~ie~  133 (144)
T d1szaa_          78 YTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQ  133 (144)
T ss_dssp             HHHHHHTTHHHHHHHHHTTSCHHHHHHHHHHHHHHSSGGGCSSCSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhccCCCCcCCCCHHHHHHHHH
Confidence            888899999999999998 88999999999999999877     688888777655

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3.2e-21  Score=138.70  Aligned_cols=77  Identities=21%  Similarity=0.516  Sum_probs=73.7

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .+++|||||||..+++++|+++|++||.|.+++++++||||||+|.+.++|++|+..|||..++|++|+|.||+++.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999998754

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.84  E-value=5.2e-21  Score=135.48  Aligned_cols=79  Identities=27%  Similarity=0.481  Sum_probs=73.2

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      +..+++|||+|||+.+|+++|+++|++||.|.+++++.      ++|||||+|.+.++|++|+..|||..+.|++|+|+|
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44578999999999999999999999999999999874      578999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy3994         229 APGKG  233 (282)
Q Consensus       229 a~~~~  233 (282)
                      |.++|
T Consensus        84 a~~kG   88 (88)
T d1rk8a_          84 CFVKG   88 (88)
T ss_dssp             SEECC
T ss_pred             ecCCC
Confidence            98875

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.83  E-value=5.5e-21  Score=133.57  Aligned_cols=74  Identities=22%  Similarity=0.370  Sum_probs=70.4

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +++|||+|||+++|+++|+++|++||.|.++++++      ++|||||+|.++++|++|++.|||..+.|++|+|+||+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            57899999999999999999999999999999874      578999999999999999999999999999999999986

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=7.5e-21  Score=134.92  Aligned_cols=78  Identities=29%  Similarity=0.482  Sum_probs=73.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||||||+++|+++|+++|++||+|.+++++.      ++|||||+|.+.++|++|+..|||..++|++|+|.||+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            458999999999999999999999999999999874      68999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy3994         231 GKGM  234 (282)
Q Consensus       231 ~~~~  234 (282)
                      ++..
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.3e-20  Score=133.91  Aligned_cols=77  Identities=26%  Similarity=0.479  Sum_probs=72.6

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||+|||.++++++|+++|++||.|.++.++.      ++|||||+|.+.++|++|++.|||..++|++|+|+||+
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            468999999999999999999999999999999874      57899999999999999999999999999999999999


Q ss_pred             CCC
Q psy3994         231 GKG  233 (282)
Q Consensus       231 ~~~  233 (282)
                      ++.
T Consensus        87 p~~   89 (90)
T d2cq0a1          87 PST   89 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.7e-20  Score=134.17  Aligned_cols=77  Identities=31%  Similarity=0.476  Sum_probs=72.3

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      .+++|||||||+++|+++|+++|++||+|.++.++.      ++|||||+|.+.++|+.|++.|||..++|++|+|.||.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            568999999999999999999999999999999874      57899999999999999999999999999999999998


Q ss_pred             CCC
Q psy3994         231 GKG  233 (282)
Q Consensus       231 ~~~  233 (282)
                      +..
T Consensus        86 ~~~   88 (93)
T d1h2vz_          86 GFK   88 (93)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=1.4e-20  Score=132.53  Aligned_cols=76  Identities=26%  Similarity=0.456  Sum_probs=73.3

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .++|||+|||.++++++|+++|++||.|.++++.+++|||||+|.+.++|++|++.|||..+.|++|+|+||.+..
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            4789999999999999999999999999999999999999999999999999999999999999999999998764

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.2e-20  Score=131.82  Aligned_cols=74  Identities=32%  Similarity=0.481  Sum_probs=70.1

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||+|||+++++++|+++|++||.|.+++++.      ++|||||+|.+.++|+.|++.|||..++|++|+|.||+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            47899999999999999999999999999999873      578999999999999999999999999999999999986

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.4e-20  Score=132.54  Aligned_cols=78  Identities=29%  Similarity=0.450  Sum_probs=73.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      ..++|||||||.++|+++|+++|++||.|.+++++.    .+|||||+|.+.++|++|+..|||..+.|+.|+|.||+++
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~   86 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP   86 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            358999999999999999999999999999999874    6789999999999999999999999999999999999876


Q ss_pred             CC
Q psy3994         233 GM  234 (282)
Q Consensus       233 ~~  234 (282)
                      ..
T Consensus        87 ~~   88 (90)
T d2cqia1          87 SS   88 (90)
T ss_dssp             TC
T ss_pred             CC
Confidence            53

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.8e-20  Score=129.86  Aligned_cols=75  Identities=23%  Similarity=0.473  Sum_probs=71.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .+++|||+|++  +|+++|+++|++||.|.++++.+++|||||+|.+.++|..|+..|||..++|++|+|.||+++.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            46899999996  8999999999999999999999999999999999999999999999999999999999998764

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.8e-20  Score=134.00  Aligned_cols=77  Identities=29%  Similarity=0.363  Sum_probs=72.5

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||||||.++|+++|+++|++||.|.+++++.      ++|||||+|.+.++|++|++.|||..+.|++|+|+||+
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            458999999999999999999999999999999874      67899999999999999999999999999999999998


Q ss_pred             CCC
Q psy3994         231 GKG  233 (282)
Q Consensus       231 ~~~  233 (282)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            775

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=7.2e-20  Score=130.85  Aligned_cols=78  Identities=23%  Similarity=0.468  Sum_probs=73.4

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ...++|||+|||+.+++++|+++|++||.|.++++..    ++|||||+|.++++|.+|+..|||..++|++|+|+||++
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~   88 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   88 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCc
Confidence            3467899999999999999999999999999999885    689999999999999999999999999999999999998


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      +.
T Consensus        89 r~   90 (93)
T d2cq3a1          89 RV   90 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            75

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.6e-20  Score=129.96  Aligned_cols=77  Identities=23%  Similarity=0.298  Sum_probs=73.2

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ..++|||||||+++++++|+++|++||.+..+.+..++|||||+|.+.++|.+|+..|||..+.|+.|+|+||+|+.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            45799999999999999999999999999999988899999999999999999999999999999999999998764

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3e-20  Score=135.15  Aligned_cols=79  Identities=20%  Similarity=0.307  Sum_probs=73.4

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      +++++|||+|||+++++++|+++|++||.|.++.++.      ++|||||+|.+.++|+.|++.|||..++|++|+|+||
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            4568899999999999999999999999999998873      5789999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy3994         230 PGKGM  234 (282)
Q Consensus       230 ~~~~~  234 (282)
                      +++..
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            98753

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=8.3e-21  Score=131.93  Aligned_cols=77  Identities=26%  Similarity=0.430  Sum_probs=71.9

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCC-eeCCeeEEEEeecCCCCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNT-KLQGKTITLAWAPGKGMK  235 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~-~~~g~~l~v~~a~~~~~~  235 (282)
                      .+|||||||+++|+++|+++|++||.+.++.+..++|||||+|.+.++|++|++.|||. .+.|++|+|+||.++..+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            36999999999999999999999999998888889999999999999999999999996 699999999999987643

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3.3e-20  Score=131.58  Aligned_cols=76  Identities=21%  Similarity=0.458  Sum_probs=71.9

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ..+|||+|||+++|+++|+++|++||.|.+++++.    ++|||||+|.+.++|++|++.|||..++|++|+|.+|+++.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            36899999999999999999999999999999985    68999999999999999999999999999999999999775

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.1e-19  Score=130.49  Aligned_cols=77  Identities=21%  Similarity=0.405  Sum_probs=72.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .+++|||+|||+++|+++|+++|++||.|..+.+..   +++||||+|.+.++|+.|++.|||..+.|++|+|+||++..
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~r   92 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGR   92 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCCC
Confidence            458999999999999999999999999999998864   78999999999999999999999999999999999998753

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=8.3e-20  Score=130.74  Aligned_cols=77  Identities=26%  Similarity=0.516  Sum_probs=72.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHh-CCCeeCCeeEEEEe
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYKL-KNTKLQGKTITLAW  228 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-------~kg~aFV~f~~~~~A~~Ai~~l-~g~~~~g~~l~v~~  228 (282)
                      .+++|||+|||.++++++|+++|++||.|.++++++       ++|||||+|.+.++|.+|+..| ||..+.|++|+|+|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            468899999999999999999999999999999864       5899999999999999999998 89999999999999


Q ss_pred             ecCCC
Q psy3994         229 APGKG  233 (282)
Q Consensus       229 a~~~~  233 (282)
                      |.++.
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98765

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.80  E-value=9.1e-20  Score=127.51  Aligned_cols=76  Identities=20%  Similarity=0.305  Sum_probs=70.7

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCee-CCeeEEEEeec
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKL-QGKTITLAWAP  230 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~-~g~~l~v~~a~  230 (282)
                      .+++++|||+|||.++|+++|+++|++||.|.++++.+ .+|||||+|.+.++|..|+..|||..+ +|++|+|.||+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            44579999999999999999999999999999999986 669999999999999999999999988 57899999997

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=3.4e-20  Score=136.99  Aligned_cols=78  Identities=23%  Similarity=0.268  Sum_probs=73.9

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ..+++|||+|||+.+++++|+++|++||.|..|.+.+++|||||+|.+.++|++|++.|||..+.|++|.|+||....
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            356899999999999999999999999999999999999999999999999999999999999999999999997653

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=1.7e-19  Score=130.46  Aligned_cols=79  Identities=27%  Similarity=0.368  Sum_probs=73.4

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ..+++|||+|||+++++++|+++|++||.|.+++++.      ++|||||+|.+.++|++|++.|||..+.|++|+|.+|
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3467899999999999999999999999999999874      6899999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy3994         230 PGKGM  234 (282)
Q Consensus       230 ~~~~~  234 (282)
                      .++..
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            98753

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=8.4e-20  Score=128.31  Aligned_cols=73  Identities=25%  Similarity=0.386  Sum_probs=68.4

Q ss_pred             EEecCCCccCcHHHHHhhhccCCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       161 l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      |||+|||+++|+++|+++|++||.|.++++++         +||||||+|.+.++|++|++.|||..++|++|+|+||++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            79999999999999999999999999999874         478999999999999999999999999999999999975


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=6.6e-20  Score=127.31  Aligned_cols=72  Identities=28%  Similarity=0.521  Sum_probs=68.4

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +|||||||+.+|+++|+++|++||+|.++++++      ++|||||+|.++++|..|++.|||..+.|++|+|.||+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            699999999999999999999999999999984      479999999999999999999999999999999999963

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.80  E-value=7.3e-20  Score=127.43  Aligned_cols=73  Identities=21%  Similarity=0.347  Sum_probs=68.2

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +||||+|||+++|+++|+++|++||.|..+.++.      ++|||||+|.+.++|++|++.|||..+.|++|+|++|+|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            7999999999999999999999999998877653      789999999999999999999999999999999999986

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=5.4e-20  Score=129.28  Aligned_cols=74  Identities=27%  Similarity=0.583  Sum_probs=68.3

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCC--eeEEEE
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQG--KTITLA  227 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g--~~l~v~  227 (282)
                      ..+++|||||||+.+|+++|+++|++||+|.+++++.      ++|||||+|.+.++|++|++.|||..+.|  ++|+|+
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            3468899999999999999999999999999999974      57899999999999999999999999987  569999


Q ss_pred             ee
Q psy3994         228 WA  229 (282)
Q Consensus       228 ~a  229 (282)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            97

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.80  E-value=9.4e-20  Score=128.04  Aligned_cols=74  Identities=32%  Similarity=0.675  Sum_probs=68.8

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCC--eeEEEE
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQG--KTITLA  227 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g--~~l~v~  227 (282)
                      ..+++|||+|||+++++++|+++|++||.|.++++++      ++|||||+|.+.++|.+|++.|||..+.|  ++|+|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            3568899999999999999999999999999999884      57899999999999999999999999976  889999


Q ss_pred             ee
Q psy3994         228 WA  229 (282)
Q Consensus       228 ~a  229 (282)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            97

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.1e-19  Score=127.58  Aligned_cols=75  Identities=20%  Similarity=0.376  Sum_probs=70.9

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .+|||||||+++|+++|+++|++||+|.+++++.      ++|||||+|.+.++|+.|++.|||..+.|++|+|.||.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            4799999999999999999999999999999974      6899999999999999999999999999999999999865


Q ss_pred             C
Q psy3994         233 G  233 (282)
Q Consensus       233 ~  233 (282)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=9.6e-20  Score=129.42  Aligned_cols=77  Identities=25%  Similarity=0.464  Sum_probs=72.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||||||+++++++|+++|++||.|..+.++.      ++|||||+|.++++|+.|+..|||..++|++|+|+||.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999999998774      78999999999999999999999999999999999998


Q ss_pred             CCC
Q psy3994         231 GKG  233 (282)
Q Consensus       231 ~~~  233 (282)
                      ++.
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            775

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.79  E-value=1.5e-19  Score=138.84  Aligned_cols=80  Identities=23%  Similarity=0.373  Sum_probs=73.9

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||||||+++|+++|+++|++||.|.++++++      ++|||||+|.+.++|.+|++.|||..+.|++|+|.||+
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999999999874      57999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q psy3994         231 GKGMKD  236 (282)
Q Consensus       231 ~~~~~~  236 (282)
                      ++..++
T Consensus       121 ~~~~~p  126 (139)
T d1u6fa1         121 SGHQRP  126 (139)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            776554

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.4e-19  Score=132.99  Aligned_cols=76  Identities=25%  Similarity=0.401  Sum_probs=71.9

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  232 (282)
                      .+++|||||||.++++++|+++|++||.|.+|++..   ++|||||+|.+.++|..|++.|||..+.|++|+|.|+...
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            468999999999999999999999999999999985   6899999999999999999999999999999999998754

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=5.9e-19  Score=124.73  Aligned_cols=80  Identities=20%  Similarity=0.242  Sum_probs=73.7

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh--CCCeeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL--KNTKLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l--~g~~~~g~~l~v~~a~~~  232 (282)
                      ..++++|||||||+++++++|+++|++||.|.++++.++++||||+|.+.++|++|++.+  ++..+.|++|+|.|++.+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~   84 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK   84 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCC
Confidence            446799999999999999999999999999999999999999999999999999999876  567899999999999876


Q ss_pred             CC
Q psy3994         233 GM  234 (282)
Q Consensus       233 ~~  234 (282)
                      ..
T Consensus        85 ~l   86 (88)
T d2cq1a1          85 EL   86 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=1.8e-19  Score=124.50  Aligned_cols=72  Identities=22%  Similarity=0.394  Sum_probs=68.6

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +|||+|||+++++++|+++|++||.|.++++..     ++|||||+|.+.++|++|++.|||..+.|++|+|++|.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            599999999999999999999999999999985     688999999999999999999999999999999999864

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=2.8e-19  Score=128.70  Aligned_cols=79  Identities=20%  Similarity=0.371  Sum_probs=73.5

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCC--eeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQG--KTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g--~~l~v~~a~~~  232 (282)
                      ..++++|||+|||+++++++|+++|++||.|..+++.++++||||+|.+.++|+.|++.|||..+.|  ++|+|.||++.
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            3457899999999999999999999999999999999999999999999999999999999999976  58999999875


Q ss_pred             C
Q psy3994         233 G  233 (282)
Q Consensus       233 ~  233 (282)
                      .
T Consensus        94 ~   94 (97)
T d1whya_          94 P   94 (97)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=4.7e-19  Score=128.95  Aligned_cols=76  Identities=24%  Similarity=0.366  Sum_probs=70.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ..++|||||||+.+++++|+++|++||.|.+++++.      ++|||||+|.+.++|++|++.+|+ .+.|++|+|+||.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            357899999999999999999999999999999974      689999999999999999998876 7999999999998


Q ss_pred             CCC
Q psy3994         231 GKG  233 (282)
Q Consensus       231 ~~~  233 (282)
                      .+.
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            764

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.4e-19  Score=126.76  Aligned_cols=77  Identities=26%  Similarity=0.339  Sum_probs=70.3

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhCCCee-CCeeEEEEeecCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--PRGCAFVCMNRRQDAAKALYKLKNTKL-QGKTITLAWAPGK  232 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~--~kg~aFV~f~~~~~A~~Ai~~l~g~~~-~g~~l~v~~a~~~  232 (282)
                      +++++|||+|||+++++++|+++|++||.|..+.+..  ++|||||+|.+.++|.+|+..|||..+ +|++|+|+|+++.
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            3568999999999999999999999999998887664  689999999999999999999999988 5899999999864

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.4e-19  Score=126.54  Aligned_cols=75  Identities=25%  Similarity=0.464  Sum_probs=68.4

Q ss_pred             EEecCCCccCcHHHHHhhhccCCceEEE-EEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         161 LWIGHLSKLVQEEELSDTFGEYGDVVSI-NLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       161 l~V~nl~~~~te~~l~~~f~~~G~i~~~-~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      |||+|||+++|+++|+++|++||.|.++ ++++      ++|||||+|.+.++|++|++.|||..+.|++|+|+||.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998764 5553      67999999999999999999999999999999999999876


Q ss_pred             CC
Q psy3994         234 MK  235 (282)
Q Consensus       234 ~~  235 (282)
                      .+
T Consensus        81 ~k   82 (83)
T d1x5ta1          81 SK   82 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            44

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.78  E-value=1.7e-19  Score=126.98  Aligned_cols=75  Identities=25%  Similarity=0.450  Sum_probs=68.5

Q ss_pred             CCcEEEecCCCccCc-HHHHHhhhccCCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         157 CSTTLWIGHLSKLVQ-EEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       157 ~~~~l~V~nl~~~~t-e~~l~~~f~~~G~i~~~~~~~-------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      .+++|||+|||++++ +++|+++|++||.|.++++..       ++|||||+|.+.++|++|++ |||..++|++|+|+|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            468999999999876 566999999999999999863       68999999999999999995 999999999999999


Q ss_pred             ecCC
Q psy3994         229 APGK  232 (282)
Q Consensus       229 a~~~  232 (282)
                      |.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.1e-19  Score=126.96  Aligned_cols=76  Identities=17%  Similarity=0.281  Sum_probs=69.6

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .+++|||+|||+++++++|+++|++|| +..+.+..++|||||+|.+.++|++|++.|||..+.|++|+|+|++++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~   79 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            357899999999999999999999999 4556667789999999999999999999999999999999999997664

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=5e-19  Score=121.15  Aligned_cols=72  Identities=19%  Similarity=0.344  Sum_probs=68.4

Q ss_pred             EEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       161 l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      |||+|||+++++++|+++|++|| +..+.+.+++|||||+|.+.++|++|+..|||..+.|++|+|+||+...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 7778888999999999999999999999999999999999999997664

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.8e-19  Score=125.02  Aligned_cols=70  Identities=27%  Similarity=0.461  Sum_probs=66.1

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEE
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITL  226 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v  226 (282)
                      ++++|||+|||.++|+++|+++|++||.|.+++++.      ++|||||+|.+.++|+.|+..|||..++|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            468999999999999999999999999999999874      5789999999999999999999999999999987

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.7e-19  Score=128.78  Aligned_cols=76  Identities=21%  Similarity=0.374  Sum_probs=70.9

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||||||+++++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|+. ++|+.+.|+.|.|++|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            37899999999999999999999999999999974      78999999999999999996 799999999999999998


Q ss_pred             CCC
Q psy3994         232 KGM  234 (282)
Q Consensus       232 ~~~  234 (282)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.77  E-value=2.7e-19  Score=128.59  Aligned_cols=80  Identities=23%  Similarity=0.371  Sum_probs=73.2

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe-CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~-~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      ..+++|||+|||.++|+++|+++|++||.|..++.. .++|||||+|.+.++|++|+..|||..++|++|+|.||.+++.
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            346899999999999999999999999998887654 3789999999999999999999999999999999999998875


Q ss_pred             C
Q psy3994         235 K  235 (282)
Q Consensus       235 ~  235 (282)
                      .
T Consensus        94 ~   94 (96)
T d1fjca_          94 T   94 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=4e-19  Score=126.38  Aligned_cols=77  Identities=23%  Similarity=0.446  Sum_probs=70.7

Q ss_pred             CCcEEEecCCCccCcHHHHHh----hhccCCceEEEEEeC---CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         157 CSTTLWIGHLSKLVQEEELSD----TFGEYGDVVSINLIP---PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~----~f~~~G~i~~~~~~~---~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ++++|||||||+.+++++|++    +|++||+|.+|++.+   ++|||||+|.+.++|.+|++.|||..+.|++|+|.||
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            468999999999999998864    689999999999874   6899999999999999999999999999999999999


Q ss_pred             cCCC
Q psy3994         230 PGKG  233 (282)
Q Consensus       230 ~~~~  233 (282)
                      +++.
T Consensus        82 k~~~   85 (91)
T d1nu4a_          82 KTDS   85 (91)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            8764

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=8.2e-19  Score=126.38  Aligned_cols=75  Identities=21%  Similarity=0.438  Sum_probs=68.8

Q ss_pred             CCcEEEecCCC-ccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         157 CSTTLWIGHLS-KLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       157 ~~~~l~V~nl~-~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      .+++|||+||| ..+++++|+++|++||.|.++++.  ||||||+|.+.++|++|++.|||..+.|++|+|.||+++.
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            45789999997 567889999999999999999984  6999999999999999999999999999999999998653

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=8.9e-19  Score=124.14  Aligned_cols=76  Identities=17%  Similarity=0.310  Sum_probs=69.3

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      .+++|||+|||+++|+++|+++|++||.|.+++++.      +||||||+|.+.++|++|++.  ++.++|+.|.|++|.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            458899999999999999999999999999999884      679999999999999999984  558999999999998


Q ss_pred             CCCC
Q psy3994         231 GKGM  234 (282)
Q Consensus       231 ~~~~  234 (282)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            8753

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=5.1e-19  Score=130.14  Aligned_cols=76  Identities=28%  Similarity=0.420  Sum_probs=70.6

Q ss_pred             CcEEEecCCCc-cCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         158 STTLWIGHLSK-LVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       158 ~~~l~V~nl~~-~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      +++|||+|||+ .+|+++|+++|+.||.|.++.+++ .+|||||+|.+.++|.+|++.|||..+.|++|+|.|++.+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            58999999965 599999999999999999999986 57999999999999999999999999999999999997654

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=8.7e-19  Score=126.34  Aligned_cols=77  Identities=26%  Similarity=0.459  Sum_probs=70.6

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhC------CCeeCCeeE
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLK------NTKLQGKTI  224 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~------g~~~~g~~l  224 (282)
                      .+++|||||||+++|+++|+++|++||.|.++.+..      ++|||||+|.+.++|.+|++.||      |..+.|++|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            468999999999999999999999999999998874      68999999999999999999887      667899999


Q ss_pred             EEEeecCCC
Q psy3994         225 TLAWAPGKG  233 (282)
Q Consensus       225 ~v~~a~~~~  233 (282)
                      +|+||.++.
T Consensus        87 ~v~~a~~k~   95 (98)
T d1x4ha1          87 KVDLAVTRD   95 (98)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999998764

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=3.4e-19  Score=125.92  Aligned_cols=77  Identities=25%  Similarity=0.355  Sum_probs=70.7

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGMK  235 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~  235 (282)
                      .+++|||+|||+++|+++|+++|++||.|.++++.. ++|||||+|.+.++|++|+.  +++.+.|++|+|.+|+++...
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCCC
Confidence            468999999999999999999999999999998875 78999999999999999985  888999999999999877543

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=7.2e-19  Score=127.51  Aligned_cols=78  Identities=22%  Similarity=0.310  Sum_probs=69.2

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEE--------EEe------CCCcEEEEEecCHHHHHHHHHHhCCCeeCC
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSI--------NLI------PPRGCAFVCMNRRQDAAKALYKLKNTKLQG  221 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~--------~~~------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g  221 (282)
                      ...++|||+|||.++|+++|+++|++||.|..+        .+.      .++|||||+|.++++|.+|++.|||..++|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            457899999999999999999999999987533        222      156999999999999999999999999999


Q ss_pred             eeEEEEeecCCC
Q psy3994         222 KTITLAWAPGKG  233 (282)
Q Consensus       222 ~~l~v~~a~~~~  233 (282)
                      ++|+|+||+++.
T Consensus        86 r~i~V~~a~~~~   97 (101)
T d2cpea1          86 SKLKVSLARKKP   97 (101)
T ss_dssp             EECEEECSSCCC
T ss_pred             EEEEEEEcCCCC
Confidence            999999998765

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=3.9e-19  Score=129.70  Aligned_cols=76  Identities=26%  Similarity=0.496  Sum_probs=71.2

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||+|||+++++++|+++|++||+|.+++++.      ++|||||+|.+.++|+.|++.|||..+.|++|+|.||.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            47899999999999999999999999999999874      578999999999999999999999999999999999987


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      +.
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.1e-19  Score=130.65  Aligned_cols=80  Identities=24%  Similarity=0.345  Sum_probs=72.8

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe------CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .++++|||+|||.++++++|+++|++||.|..+.+.      .++|||||+|.+.++|++|++.|||..+.|++|+|+||
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            357899999999999999999999999998877665      27899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy3994         230 PGKGMK  235 (282)
Q Consensus       230 ~~~~~~  235 (282)
                      +++..+
T Consensus        96 k~k~~r  101 (102)
T d2cpxa1          96 KNKKQR  101 (102)
T ss_dssp             CCCSCC
T ss_pred             CCcccC
Confidence            987543

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=3.3e-19  Score=122.69  Aligned_cols=70  Identities=30%  Similarity=0.453  Sum_probs=66.3

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ++|||||||+++|+++|+++|++||.|.+++++.      +||||||+|.+.++|++|+. +|++.++|++|+|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            5799999999999999999999999999999875      78999999999999999997 7999999999999987

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.3e-18  Score=121.80  Aligned_cols=73  Identities=23%  Similarity=0.401  Sum_probs=68.0

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||||||.++|+++|+++|++||.|.+++++.      ++|||||+|.+.++|++|++ ++|+.+.|+.|+|+.|.+
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~s   84 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeeeC
Confidence            47899999999999999999999999999999874      68999999999999999997 699999999999998863

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.75  E-value=1.5e-19  Score=128.49  Aligned_cols=75  Identities=25%  Similarity=0.324  Sum_probs=68.8

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe-----CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~-----~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ..++|||+|||+++|+++|+++|+.||.|.+++++     +++|||||+|.+.++|++|++ |||..++|++|+|.+|++
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            46799999999999999999999999988777664     388999999999999999996 999999999999999986


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      +
T Consensus        91 k   91 (91)
T d1fjeb1          91 R   91 (91)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=8.1e-18  Score=122.51  Aligned_cols=81  Identities=15%  Similarity=0.269  Sum_probs=73.6

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhC--CCeeCCeeEEEEeecCC
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK--NTKLQGKTITLAWAPGK  232 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~--g~~~~g~~l~v~~a~~~  232 (282)
                      ..++++|||+|||+.+|+++|+++|++||.|.++++.+.|+||||+|.+.++|++|+..|+  +..+.|++|+|.|++.+
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCC
Confidence            3467899999999999999999999999999999999999999999999999999999884  55678999999999876


Q ss_pred             CCC
Q psy3994         233 GMK  235 (282)
Q Consensus       233 ~~~  235 (282)
                      ...
T Consensus        92 ~~~   94 (104)
T d1wexa_          92 RIT   94 (104)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            543

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=8.5e-19  Score=126.95  Aligned_cols=74  Identities=23%  Similarity=0.376  Sum_probs=69.2

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||||||.++++++|+++|+.||.|.+++++.      +||||||+|.+.++|++|+. |||..+.|++|+|++|.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            47899999999999999999999999999999985      78999999999999999995 999999999999999864


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=4.8e-18  Score=120.08  Aligned_cols=78  Identities=14%  Similarity=0.118  Sum_probs=71.6

Q ss_pred             CCCCcEEEecCCCcc-CcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHh--CCCeeCCeeEEEEeecC
Q psy3994         155 NMCSTTLWIGHLSKL-VQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKL--KNTKLQGKTITLAWAPG  231 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~-~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l--~g~~~~g~~l~v~~a~~  231 (282)
                      ..++++|||+|||.. +|+++|.++|++||.|.++.+.+.+++|||+|.+.++|..|++.|  ++..+.|++|+|.||++
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            345789999999986 789999999999999999999999999999999999999999966  67789999999999985


Q ss_pred             C
Q psy3994         232 K  232 (282)
Q Consensus       232 ~  232 (282)
                      .
T Consensus        85 ~   85 (89)
T d1x4da1          85 Y   85 (89)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=3.4e-18  Score=123.33  Aligned_cols=79  Identities=16%  Similarity=0.232  Sum_probs=71.9

Q ss_pred             CCCCcEEEecCCCcc-CcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHH--HhCCCeeCCeeEEEEeecC
Q psy3994         155 NMCSTTLWIGHLSKL-VQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALY--KLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~-~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~--~l~g~~~~g~~l~v~~a~~  231 (282)
                      ...+++|||+|||.+ +|+++|.++|++||.|.++.+.+++|||||+|.+.++|.+|++  .+++..+.|++|+|.||+.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            345789999999975 8999999999999999999999999999999999999999998  4688889999999999976


Q ss_pred             CC
Q psy3994         232 KG  233 (282)
Q Consensus       232 ~~  233 (282)
                      +.
T Consensus        95 ~~   96 (99)
T d1x4fa1          95 YK   96 (99)
T ss_dssp             CS
T ss_pred             cc
Confidence            53

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.7e-18  Score=124.29  Aligned_cols=78  Identities=28%  Similarity=0.417  Sum_probs=69.3

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCc-eEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhCCC--eeCCeeEEEE
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGD-VVSINLIP-------PRGCAFVCMNRRQDAAKALYKLKNT--KLQGKTITLA  227 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~-i~~~~~~~-------~kg~aFV~f~~~~~A~~Ai~~l~g~--~~~g~~l~v~  227 (282)
                      +++|||||||.++++++|+++|++||+ |..+++++       ++|||||+|.++++|..|++.|++.  .+.|++|+|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            378999999999999999999999996 89998863       6789999999999999999999754  4589999999


Q ss_pred             eecCCCCC
Q psy3994         228 WAPGKGMK  235 (282)
Q Consensus       228 ~a~~~~~~  235 (282)
                      ||+++...
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99887544

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2e-18  Score=118.11  Aligned_cols=69  Identities=33%  Similarity=0.512  Sum_probs=64.5

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .|||||||+++|+++|+++|++||+|.++.++.      ++|||||+|.+.++|++|++ +++..++|+.|+|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            489999999999999999999999999999885      68999999999999999997 7999999999999754

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.1e-18  Score=126.54  Aligned_cols=75  Identities=20%  Similarity=0.326  Sum_probs=69.3

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      ..++|||||||+++++++|+++|++||.|..+.+..     ++|||||+|.+.++|++|++.|||..+.|+++.|.+++|
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            358999999999999999999999999999988774     578999999999999999999999999999999887764

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=3.4e-18  Score=123.10  Aligned_cols=77  Identities=22%  Similarity=0.231  Sum_probs=71.7

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKGM  234 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~  234 (282)
                      ..++|||+|||+++++++|+++|++||+|.++.+. .+|||||+|.+.++|++|++.|||..+.|+.|+|.+++.+..
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~-~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ-KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE-TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccc-ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            46789999999999999999999999999999987 469999999999999999999999999999999999986643

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=3e-18  Score=121.17  Aligned_cols=71  Identities=23%  Similarity=0.460  Sum_probs=65.3

Q ss_pred             CCcEEEecCCCccCcHHHH---HhhhccCCceEEEEEeC---------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeE
Q psy3994         157 CSTTLWIGHLSKLVQEEEL---SDTFGEYGDVVSINLIP---------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTI  224 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l---~~~f~~~G~i~~~~~~~---------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l  224 (282)
                      ..++|||+|||+++++++|   +++|++||.|.++.+++         .+|||||+|.+.++|.+|++.|||..++|++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3467999999999999999   77899999999999985         34899999999999999999999999999999


Q ss_pred             EEE
Q psy3994         225 TLA  227 (282)
Q Consensus       225 ~v~  227 (282)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4.3e-18  Score=117.69  Aligned_cols=71  Identities=24%  Similarity=0.471  Sum_probs=66.2

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .++|||||||+++|+++|+++|++||.|..+.+..      ++|||||+|.+.++|++|+. +||+.++|++|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            37899999999999999999999999999998874      67999999999999999995 8999999999999987

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=2e-18  Score=118.15  Aligned_cols=69  Identities=22%  Similarity=0.332  Sum_probs=65.0

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .|||||||+++|+++|+++|++||.+..+.+..      ++|||||+|.+.++|++|++ +||+.++|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            489999999999999999999999999998874      68999999999999999996 9999999999999987

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=7.2e-19  Score=123.95  Aligned_cols=73  Identities=26%  Similarity=0.285  Sum_probs=68.0

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      +|||||||+++++++|+++|++||.|.++++.. +|||||+|.+.++|++|+..|||..+.|+.|+|.+++.+.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc-cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            599999999999999999999999999999764 5999999999999999999999999999999998886553

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8.7e-18  Score=122.36  Aligned_cols=77  Identities=22%  Similarity=0.283  Sum_probs=68.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      +.++|||+|||+++|+++|+++|+.|| +..+.++.       ++|||||+|.+.++|++|+ .|||..+.|+.|+|.||
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            458999999999999999999999999 67776653       5789999999999998776 59999999999999999


Q ss_pred             cCCCCC
Q psy3994         230 PGKGMK  235 (282)
Q Consensus       230 ~~~~~~  235 (282)
                      .++..+
T Consensus        92 ~~~~~~   97 (104)
T d1wi8a_          92 DQAQDK   97 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            877543

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=8e-18  Score=123.39  Aligned_cols=78  Identities=15%  Similarity=0.169  Sum_probs=70.9

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhCCCee--CCeeEEEEeecCC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--PRGCAFVCMNRRQDAAKALYKLKNTKL--QGKTITLAWAPGK  232 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~--~kg~aFV~f~~~~~A~~Ai~~l~g~~~--~g~~l~v~~a~~~  232 (282)
                      +..+|||+|||..+|+++|+++|++||.|.++.+..  ++|||||+|.+.++|+.|+..|||..+  .|+.|+|.|++++
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~   85 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT   85 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCc
Confidence            357899999999999999999999999999998874  789999999999999999999999998  5789999999876


Q ss_pred             CC
Q psy3994         233 GM  234 (282)
Q Consensus       233 ~~  234 (282)
                      ..
T Consensus        86 ~~   87 (108)
T d2adba1          86 SL   87 (108)
T ss_dssp             SC
T ss_pred             cc
Confidence            43

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.8e-18  Score=117.26  Aligned_cols=69  Identities=26%  Similarity=0.420  Sum_probs=64.3

Q ss_pred             EEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         160 TLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       160 ~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      .|||||||+++|+++|+++|++||.|.+++++.      ++|||||+|.+.++|++|++ .+++.++|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            589999999999999999999999999999885      78999999999999999997 5778999999999876

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=1e-17  Score=114.51  Aligned_cols=70  Identities=16%  Similarity=0.217  Sum_probs=65.4

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ++|||+|||+++++++|+++|+.||.|..+++..    .++||||+|.+.++|++|+. +||+.++|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            5899999999999999999999999999999974    56799999999999999995 8999999999999865

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.1e-17  Score=117.22  Aligned_cols=72  Identities=14%  Similarity=0.285  Sum_probs=67.2

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      .++|||+|||.++|+++|+++|+.||.|..+++..     ++|||||+|.+.++|++|++ ++|..+.|+.|+|.|+.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            57999999999999999999999999999999874     57999999999999999996 79999999999999864

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=7.9e-18  Score=122.35  Aligned_cols=78  Identities=19%  Similarity=0.204  Sum_probs=71.5

Q ss_pred             CCcEEEecCCCccC-cH----HHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         157 CSTTLWIGHLSKLV-QE----EELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       157 ~~~~l~V~nl~~~~-te----~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .+++|||+||+..+ ++    ++|+.+|++||.|.++++.++++||||+|.+.++|.+|+..|||..+.|++|+|.||++
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~   83 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT   83 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeeccc
Confidence            46899999999886 43    56999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q psy3994         232 KGM  234 (282)
Q Consensus       232 ~~~  234 (282)
                      +..
T Consensus        84 ~~~   86 (104)
T d1weya_          84 LHI   86 (104)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            653

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=7.7e-18  Score=114.25  Aligned_cols=65  Identities=28%  Similarity=0.391  Sum_probs=61.6

Q ss_pred             EEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEE
Q psy3994         161 LWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTIT  225 (282)
Q Consensus       161 l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~  225 (282)
                      |||+|||+++|+++|+++|++||.|..+++..      ++|||||+|.+.++|++|++.|||..+.|+.++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999998874      789999999999999999999999999999864

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=1.8e-17  Score=116.38  Aligned_cols=73  Identities=22%  Similarity=0.343  Sum_probs=65.4

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEE-EEEe-----CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVS-INLI-----PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~-~~~~-----~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ..++|||+|||.++++++|+++|+.||.+.. +.+.     .++|||||+|.+.++|++|+..|||..+.|++|+|.+|
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4578999999999999999999999998865 3333     26899999999999999999999999999999999986

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.3e-16  Score=115.49  Aligned_cols=77  Identities=16%  Similarity=0.196  Sum_probs=67.6

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ....+|||+|||+++|+++|+++|..||. ..+.++.     .+|||||+|.+.++|++|++ +|+..++||.|+|.|+.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            34579999999999999999999999985 4555553     57999999999999999986 89999999999999998


Q ss_pred             CCCC
Q psy3994         231 GKGM  234 (282)
Q Consensus       231 ~~~~  234 (282)
                      .++.
T Consensus        91 ~~~~   94 (102)
T d1weza_          91 TAGT   94 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7753

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=2.8e-16  Score=114.03  Aligned_cols=76  Identities=14%  Similarity=0.121  Sum_probs=66.8

Q ss_pred             CCCcEEEecCCCccCcHHHHHhhhccCCceEEE-EEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         156 MCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSI-NLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       156 ~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~-~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      ...++|||+|||+++|+++|+++|..||.+..+ .+..     ++|||||+|.+.++|++|+. +||..++|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            345789999999999999999999999988764 3332     68999999999999999996 8999999999999998


Q ss_pred             cCC
Q psy3994         230 PGK  232 (282)
Q Consensus       230 ~~~  232 (282)
                      ..+
T Consensus        85 ~~~   87 (103)
T d2cpya1          85 TLE   87 (103)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            643

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=9.5e-16  Score=111.34  Aligned_cols=77  Identities=19%  Similarity=0.167  Sum_probs=68.3

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeec
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAP  230 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~  230 (282)
                      ...+|||+|||+++|+++|+++|..+|.+....++.      ++|||||+|.++++|++|++ +|++.++||.|+|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            346799999999999999999999999988754442      67999999999999999996 89999999999999998


Q ss_pred             CCCC
Q psy3994         231 GKGM  234 (282)
Q Consensus       231 ~~~~  234 (282)
                      ++..
T Consensus        93 ~~~~   96 (104)
T d1wg5a_          93 RAEV   96 (104)
T ss_dssp             TTTS
T ss_pred             HHHh
Confidence            7643

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=7e-16  Score=111.29  Aligned_cols=64  Identities=17%  Similarity=0.305  Sum_probs=59.9

Q ss_pred             CCCcEEEe--cCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCee
Q psy3994         156 MCSTTLWI--GHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKL  219 (282)
Q Consensus       156 ~~~~~l~V--~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~  219 (282)
                      .+++++||  ||||.++|+++|+++|++||.|..+++.++++||||+|.+.++|.+|+..|||..+
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            34578888  55999999999999999999999999999999999999999999999999999987

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=5.5e-16  Score=114.28  Aligned_cols=75  Identities=17%  Similarity=0.279  Sum_probs=68.9

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCH-HHHHHHHHHhCCCeeCCeeEEEEeecCCC
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRR-QDAAKALYKLKNTKLQGKTITLAWAPGKG  233 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~-~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  233 (282)
                      ..+||||||+.+|+++|+++|++||+|.+|.+++++|||||.|.++ ++|..|+..+|+..+.++.+.|.|+..++
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~~   87 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEG   87 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCH
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeeccc
Confidence            4569999999999999999999999999999999999999999985 78999999999999988888888887654

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.1e-17  Score=118.47  Aligned_cols=71  Identities=15%  Similarity=0.310  Sum_probs=62.8

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEe-----------CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEE
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI-----------PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLA  227 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~-----------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~  227 (282)
                      ++|||||||.++|+++|+++|++||.+..+.+.           .++|||||+|.+.++|++|+. |||..+.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            689999999999999999999999977655443           378999999999999999985 99999999999997


Q ss_pred             eec
Q psy3994         228 WAP  230 (282)
Q Consensus       228 ~a~  230 (282)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            544

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.3e-15  Score=112.13  Aligned_cols=77  Identities=17%  Similarity=0.157  Sum_probs=66.7

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEe------CCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLI------PPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~------~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      .....+|||+|||+++|+++|+++|+.||.+..+.++      .++|||||+|.+.++|++|+. |||..|+||.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3356799999999999999999999999988653332      267999999999999999996 899999999999998


Q ss_pred             ecCC
Q psy3994         229 APGK  232 (282)
Q Consensus       229 a~~~  232 (282)
                      +..+
T Consensus        94 ~~~~   97 (112)
T d1wela1          94 ITKK   97 (112)
T ss_dssp             ECHH
T ss_pred             cChH
Confidence            8654

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=6.3e-15  Score=101.58  Aligned_cols=73  Identities=15%  Similarity=0.113  Sum_probs=64.6

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCee-EEEEeecCC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKT-ITLAWAPGK  232 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~-l~v~~a~~~  232 (282)
                      .+.|+|+|+|++.+++.| +.|++||+|.++++.+++|||||+|.++++|++|++ +||..++|+. +.|..+..+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            478999999999987655 579999999999999999999999999999999996 8999999984 578876543

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=8.3e-15  Score=116.86  Aligned_cols=77  Identities=23%  Similarity=0.455  Sum_probs=70.6

Q ss_pred             CCCCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         155 NMCSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       155 ~~~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ....++|||+|||+.+|+++|+++|+.||.|..+.+..      ++|||||+|.++++|.+|+. ++++.+.|++|+|.|
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            44568999999999999999999999999999998874      57899999999999999997 799999999999999


Q ss_pred             ecCC
Q psy3994         229 APGK  232 (282)
Q Consensus       229 a~~~  232 (282)
                      |.++
T Consensus       173 A~~k  176 (183)
T d1u1qa_         173 ALSK  176 (183)
T ss_dssp             CCCH
T ss_pred             cCCc
Confidence            9865

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=4.5e-14  Score=101.23  Aligned_cols=80  Identities=19%  Similarity=0.265  Sum_probs=69.6

Q ss_pred             CCCCCcEEEecCC--CccCc---------HHHHHhhhccCCceEEEEEeC--CCcEEEEEecCHHHHHHHHHHhCCCeeC
Q psy3994         154 ENMCSTTLWIGHL--SKLVQ---------EEELSDTFGEYGDVVSINLIP--PRGCAFVCMNRRQDAAKALYKLKNTKLQ  220 (282)
Q Consensus       154 ~~~~~~~l~V~nl--~~~~t---------e~~l~~~f~~~G~i~~~~~~~--~kg~aFV~f~~~~~A~~Ai~~l~g~~~~  220 (282)
                      ....+++|+|.|+  |.++.         +++|++.|++||.|..+.+..  .+|||||+|.+.++|.+|+..|||..++
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            3446799999999  54431         267999999999999999886  5799999999999999999999999999


Q ss_pred             CeeEEEEeecCCC
Q psy3994         221 GKTITLAWAPGKG  233 (282)
Q Consensus       221 g~~l~v~~a~~~~  233 (282)
                      ||+|+|.++.++.
T Consensus        84 gr~i~v~~~~g~~   96 (99)
T d2dita1          84 GRQITAQAWDGTT   96 (99)
T ss_dssp             TEECEEEECCSCC
T ss_pred             CEEEEEEEeCCcC
Confidence            9999999998764

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.3e-15  Score=110.49  Aligned_cols=71  Identities=24%  Similarity=0.343  Sum_probs=66.9

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC-----CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEee
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP-----PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWA  229 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~-----~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  229 (282)
                      +.++|++++..++|++|+++|++||+|.++++++     ++|||||+|.+.++|.+|+..|||..++|++|+|+|.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            5688999999999999999999999999999974     6899999999999999999999999999999999985

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=1.2e-13  Score=109.96  Aligned_cols=113  Identities=19%  Similarity=0.223  Sum_probs=83.5

Q ss_pred             CcEEEecCCCccCcHHHHHhhhccCCceEEEEEeC------CCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         158 STTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP------PRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       158 ~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~------~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      .++|||||||+.+|+++|+++|++||.|.++.++.      ++|||||+|.+.++|++|+. +++..+.++.+.+.+..+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            47999999999999999999999999999999873      67999999999999999997 567788899888888765


Q ss_pred             CCCCCCccccccccCCC--eeeecCCCCCcchhhhhhhc-CcccccC
Q psy3994         232 KGMKDKDWKDFWEVQDG--VSYIPYDRLSKEIDYDYLED-GGVFDED  275 (282)
Q Consensus       232 ~~~~~~~~~~~~~~~~g--~~~~p~~~~~~~~~~~~~~~-~~~~~~~  275 (282)
                      .........  ......  +..+|.  ..++++|..++. .|.+...
T Consensus        85 ~~~~~~~~~--~~~~~~i~V~~lp~--~~te~~L~~~f~~~G~v~~~  127 (183)
T d1u1qa_          85 REDSQRPGA--HLTVKKIFVGGIKE--DTEEHHLRDYFEQYGKIEVI  127 (183)
T ss_dssp             TTGGGSTTT--TCCCSEEEEECCCT--TCCHHHHHHHHGGGSCEEEE
T ss_pred             ccccccccc--ccccceeEEccCCC--cCCHHHHhhhhccCCceeee
Confidence            543221111  111222  344444  346888887655 4555444

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=1.1e-12  Score=94.67  Aligned_cols=76  Identities=21%  Similarity=0.276  Sum_probs=65.6

Q ss_pred             CCCcEEEecCC--CccC--------cHHHHHhhhccCCceEEEEEeC--------CCcEEEEEecCHHHHHHHHHHhCCC
Q psy3994         156 MCSTTLWIGHL--SKLV--------QEEELSDTFGEYGDVVSINLIP--------PRGCAFVCMNRRQDAAKALYKLKNT  217 (282)
Q Consensus       156 ~~~~~l~V~nl--~~~~--------te~~l~~~f~~~G~i~~~~~~~--------~kg~aFV~f~~~~~A~~Ai~~l~g~  217 (282)
                      ++++.|.+.|+  |..+        ..++|++.|++||.|.++.+++        ..|++||+|.+.++|.+|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            35789999999  4333        2357899999999999999874        3589999999999999999999999


Q ss_pred             eeCCeeEEEEeecC
Q psy3994         218 KLQGKTITLAWAPG  231 (282)
Q Consensus       218 ~~~g~~l~v~~a~~  231 (282)
                      .++||+|+|.++..
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999864

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.55  E-value=0.00017  Score=45.86  Aligned_cols=59  Identities=34%  Similarity=0.416  Sum_probs=51.8

Q ss_pred             HHHHhhhccCCceEEEEEeCC---CcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEeecC
Q psy3994         173 EELSDTFGEYGDVVSINLIPP---RGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAWAPG  231 (282)
Q Consensus       173 ~~l~~~f~~~G~i~~~~~~~~---kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  231 (282)
                      +.|...|.++|.|.++.+.+.   .-.|-|...+..+|.-|+..||...+++++|.|.++.+
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            456777999999999998752   34689999999999999999999999999999999874

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.50  E-value=0.00015  Score=48.60  Aligned_cols=69  Identities=23%  Similarity=0.407  Sum_probs=56.3

Q ss_pred             CcEEEecCCCccC------cH---HHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhCCCeeCCeeEEEEe
Q psy3994         158 STTLWIGHLSKLV------QE---EELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLKNTKLQGKTITLAW  228 (282)
Q Consensus       158 ~~~l~V~nl~~~~------te---~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~g~~~~g~~l~v~~  228 (282)
                      ..||.|.=..+..      +|   .+|.+.|..||+|.-++++.  +-..|+|.+-++|-+|+. ++|.++.|+.|+|..
T Consensus        15 DgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~--d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~   91 (95)
T d1ufwa_          15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQ--GQMLVTFADSHSALSVLD-VDGMKVKGRAVKISG   91 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEET--TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEEC
T ss_pred             CcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeC--CeEEEEECCcHHHHHHhc-cCCeEEcceEEEEec
Confidence            3677775443222      22   46888899999999999987  778999999999999997 899999999999976


Q ss_pred             e
Q psy3994         229 A  229 (282)
Q Consensus       229 a  229 (282)
                      .
T Consensus        92 ~   92 (95)
T d1ufwa_          92 P   92 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.92  E-value=0.0035  Score=42.21  Aligned_cols=61  Identities=10%  Similarity=0.156  Sum_probs=53.5

Q ss_pred             cEEEecCCCccCcHHHHHhhhccCCceEEEEEeC--------CCcEEEEEecCHHHHHHHHHHhCCCee
Q psy3994         159 TTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIP--------PRGCAFVCMNRRQDAAKALYKLKNTKL  219 (282)
Q Consensus       159 ~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~--------~kg~aFV~f~~~~~A~~Ai~~l~g~~~  219 (282)
                      ++|.|.+||+++||+++.+.++..|++.......        .-.-|+|.|.+.++...-.+.++|+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F   70 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            5789999999999999999999999988776653        225799999999999999999999987

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.88  E-value=0.12  Score=34.58  Aligned_cols=57  Identities=16%  Similarity=0.194  Sum_probs=47.0

Q ss_pred             CCcEEEecCCCccCcHHHHHhhhccCCceEEEEEeCCCcEEEEEecCHHHHHHHHHHhC
Q psy3994         157 CSTTLWIGHLSKLVQEEELSDTFGEYGDVVSINLIPPRGCAFVCMNRRQDAAKALYKLK  215 (282)
Q Consensus       157 ~~~~l~V~nl~~~~te~~l~~~f~~~G~i~~~~~~~~kg~aFV~f~~~~~A~~Ai~~l~  215 (282)
                      ....||.-..|..+...+|.++|++||.|.---|.-  .-|||...+++.|+.++..+.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIdd--TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDD--TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEET--TEEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEecC--ceEEEEecCHHHHHHHHHHhc
Confidence            457789989999999999999999999865444433  569999999999999887654

>d1dvpa1 a.118.9.2 (A:1-145) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=88.48  E-value=0.28  Score=35.49  Aligned_cols=110  Identities=14%  Similarity=0.187  Sum_probs=77.0

Q ss_pred             HHHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCch
Q psy3994           6 TFNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFG   84 (282)
Q Consensus         6 ~f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~   84 (282)
                      .|++.+..-++...+ ..-.-|..++...-..-...+..+..|.+.++.-.|...+-.|.|+|..++|--..+... +--
T Consensus         5 ~~~~~iekAT~~~~~~~dw~~il~icD~I~~~~~~~k~a~ral~krl~~~n~~v~l~aL~LLd~~vkNcG~~f~~~-i~s   83 (145)
T d1dvpa1           5 SFCKNLENATSHLRLEPDWPSILLICDEINQKDVTPKNAFAAIKKKMNSPNPHSSCYSLLVLESIVKNCGAPVHEE-VFT   83 (145)
T ss_dssp             HHHHHHHHHHCTTCSSCCHHHHHHHHHHHHTTSSCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSHHHHHHH-HSS
T ss_pred             hHHHHHHHHcCcCCCCCCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHccchHHHHH-Hhh
Confidence            577777777665555 666777888887765445678888999999998888999999999999999964443210 111


Q ss_pred             hhHHHHHHHHHHHhhcCChhhHHHHHHHHHhhcc
Q psy3994          85 PRFARNLKATFQHLYQCPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        85 ~~f~~~l~~~f~~v~~~~~~~~~k~~~~l~~w~~  118 (282)
                      ..|...+.+.+..  ..+...+.+++.++..|..
T Consensus        84 ~~fl~~l~~l~~~--~~~~~Vk~kil~li~~W~~  115 (145)
T d1dvpa1          84 KENCEMFSSFLES--TPHENVRQKMLELVQTWAY  115 (145)
T ss_dssp             HHHHHHHHHHHHH--CSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHHH
Confidence            1344444443321  1467889999999999975

>d1mhqa_ a.118.9.2 (A:) ADP-ribosylation factor binding protein Gga2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: ADP-ribosylation factor binding protein Gga2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.05  E-value=0.62  Score=33.46  Aligned_cols=111  Identities=16%  Similarity=0.155  Sum_probs=73.1

Q ss_pred             HHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchh
Q psy3994           7 FNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGP   85 (282)
Q Consensus         7 f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~   85 (282)
                      |++.+...++...+ ..-.-|..++...-..-...+..+..|.+-|+.-+|...+-.|-|+|..++|--..+-.. +=..
T Consensus         2 le~liekAT~~~~~~~dw~~il~icD~I~~~~~~~k~a~ral~krl~~~n~~~~l~aL~LLe~~vkNcG~~fh~e-vask   80 (143)
T d1mhqa_           2 LELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCMNHCGEKFHSE-VAKF   80 (143)
T ss_dssp             HHHHHHHHHCTTCSSCCHHHHHHHHHHHHHSSHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHH-HTSH
T ss_pred             HHHHHHHHcCCCCCCcCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHH-HhhH
Confidence            56666666664444 555667777777765555677888899999988888889999999999999963333110 0001


Q ss_pred             hHHHHHHHHHHHhh--c-CChhhHHHHHHHHHhhcc
Q psy3994          86 RFARNLKATFQHLY--Q-CPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        86 ~f~~~l~~~f~~v~--~-~~~~~~~k~~~~l~~w~~  118 (282)
                      .|...+.+.+...+  . .+...+.+++.++..|..
T Consensus        81 ~Fl~~l~~li~~k~~~~~~~~~Vk~kil~li~~Wa~  116 (143)
T d1mhqa_          81 RFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTV  116 (143)
T ss_dssp             HHHHHHHHTTCCSTTSCCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccccCCCCCCHHHHHHHHHHHHHHHH
Confidence            23333333332211  1 457789999999999964

>d1ujka_ a.118.9.2 (A:) ADP-ribosylation factor binding protein Gga1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: ADP-ribosylation factor binding protein Gga1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.31  E-value=0.34  Score=34.99  Aligned_cols=113  Identities=17%  Similarity=0.202  Sum_probs=74.2

Q ss_pred             HHHHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCc
Q psy3994           5 KTFNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVF   83 (282)
Q Consensus         5 ~~f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~   83 (282)
                      ..|++.+...++.... ..-.-|..++...-..-...+..+.+|.+-|+.-.|...+-.|.|+|..++|--..+-.. +=
T Consensus         7 ~~~e~~iekAT~~~l~~~dw~~ileicD~I~~~~~~~k~a~r~l~krl~~~~~~~~l~aL~LLe~~vkNCG~~f~~e-va   85 (145)
T d1ujka_           7 ETLEARINRATNPLNKELDWASINGFCEQLNEDFEGPPLATRLLAHKIQSPQEWEAIQALTVLETCMKSCGKRFHDE-VG   85 (145)
T ss_dssp             TSHHHHHHHHTCTTCSSCCHHHHHHHHHHHTSSTTHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHTSCCHHHHHH-HT
T ss_pred             chHHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhHHHHHH-Hh
Confidence            3566777766664443 455566677766544444577888888888888888888999999999999853332100 00


Q ss_pred             hhhHHHHHHHHHHHhh--c-CChhhHHHHHHHHHhhcc
Q psy3994          84 GPRFARNLKATFQHLY--Q-CPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        84 ~~~f~~~l~~~f~~v~--~-~~~~~~~k~~~~l~~w~~  118 (282)
                      -..|...+.+.+...+  . .+...+.+++.++..|..
T Consensus        86 s~~Fl~~L~kli~~k~~~~~~~~~Vk~kil~li~~W~~  123 (145)
T d1ujka_          86 KFRFLNELIKVVSPKYLGSRTSEKVKNKILELLYSWTV  123 (145)
T ss_dssp             SHHHHHHHHHHHCTTTTGGGSCHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHHH
Confidence            1135555555553221  2 567888999999999964

>d1juqa_ a.118.9.2 (A:) ADP-ribosylation factor binding protein Gga3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ENTH/VHS domain
family: VHS domain
domain: ADP-ribosylation factor binding protein Gga3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.26  E-value=0.9  Score=32.87  Aligned_cols=111  Identities=16%  Similarity=0.182  Sum_probs=74.0

Q ss_pred             HHHHHHhhhcCCCC-CCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCCCccceeehhhHHHHHhhhhccCCCCchh
Q psy3994           7 FNQELSSLYDTKPP-ISKAKITAITRSAIRAIKFYKHVVQSVEKFIIKCKPEYKVPALYVIDSLVRQSRHQFQDKDVFGP   85 (282)
Q Consensus         7 f~~~L~~l~~~~~p-~s~~~I~~lt~~a~~~~~~~~~~v~~~~~~~~~~~p~~kl~~lYv~Dsi~r~~~~~~~~~~~~~~   85 (282)
                      ||+.+...++...+ ..-.-|.+++...-..-...+..+.+|.+.++...|.-.+-.|-|+|..++|--..+... +=..
T Consensus         3 le~~i~kAT~~~l~~~dw~~ileicD~In~~~~~~k~a~rai~krl~~~~~~~~l~aL~LLe~~vkNCG~~F~~e-vask   81 (151)
T d1juqa_           3 LESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQSPQEWEALQALTVLEACMKNCGRRFHNE-VGKF   81 (151)
T ss_dssp             HHHHHHHHTCTTCSSCCHHHHHHHHHHHHHSTTHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSHHHHHHH-HTSH
T ss_pred             HHHHHHHHcCCCCCCcCHHHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHccHHHHHH-HhhH
Confidence            56666666664444 555667777777665545678888888988988888888889999999999963333210 0011


Q ss_pred             hHHHHHHHHHHHhh--c-CChhhHHHHHHHHHhhcc
Q psy3994          86 RFARNLKATFQHLY--Q-CPPEDKSKIIRVLNLWQK  118 (282)
Q Consensus        86 ~f~~~l~~~f~~v~--~-~~~~~~~k~~~~l~~w~~  118 (282)
                      .|...+.+.+...+  . .+...+.+++.++..|..
T Consensus        82 ~Fl~~l~kli~~k~~~~~~~~~Vk~kil~ll~~Wa~  117 (151)
T d1juqa_          82 RFLNELIKVVSPKYLGDRVSEKVKTKVIELLYSWTM  117 (151)
T ss_dssp             HHHHHHHHHHCCCCCCTTSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccCCCCcccHHHHHHHHHHHHHHHH
Confidence            34445444443222  1 456789999999999975