Citrus Sinensis ID: 025814

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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-------
Protein Sequence
MSMPQSSSSSGQFTYAAAPAAPTTANSSYFPLPFHLQQTDPTAVSQYPPPAAYPAPVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSVLHK
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccHHHHHHHHHHHcccccHHHHHHccccHHHHHHcccccccccccccccccEEEcccccccccHHHHHHHHcccccccEEEEEEEccccccccEEEEEEccHHHHHHHHHHHccEEEccEEEEEEcccccccccHHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccccccHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHccccccHHHHcccccccccccccccccccEEEEccccccccHHHHHHHHHcccccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHcccEcccEEEEEEEccccccccccccccccccccccccccHHHHccc
Coil and Loop (DISEMBL)
msmpqsssssgqftyaaapaapttanssyfplpfhlqqtdptavsqypppaaypapvvpsvyaapvapvyslpqyhQAQQLFQRDAQTITPEALESVKAALASSdiehkaetkkksiprkaagqtwedptlaewpendyrlfcgdlgnevnDDVLSKAfsrfpsfnmakvvrdkrtgktkgygfisfanPSDIAAALKEMngkyvgnrpiklrkskwqerTDFEALersknhnqkkpklskksvlhk
Flexible Loop (DISEMBL)
msmpqsssssgQFTYAAAPAAPTTANSSYFPLPFHLQQTDPTAVSQYPPPAAYPAPVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALassdiehkaetkkksiprkaagqtwedptlaewPENDYRLFCGDLGNEVNDDVLSKAfsrfpsfnmakvvrdkrtgktkgygfisfaNPSDIAAALKEmngkyvgnrpiklrkskwqERTDFealersknhnqkkpklskksvlhk
Low Complexity Region (SEG)
MSMPQsssssGQFTYaaapaapttaNSSYFPLPFHLQQTDPTavsqypppaaypapvvpsvyaapvapvysLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSVLHK
Disordered region (IsUnstruct)
****************************YFPLPFHL**************AAYPAPVVPSVYAAPVAPVYSLPQYHQAQQLFQ********************************************DPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNR***************************************
Disordered Region (DISOPRED)
********************************************************************VY*****************************************************************ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL***********************************
Disordered Region (DISEMBL)
*********************PTTANSSYFPLPFHLQQTDPTAVSQYPPPAAYPAPVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS*********************WEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALER*******************
Disordered Region (DISPRO)
******************PAAPTTANSSYFPLPFHLQQTDPTAVSQYPPPAAYPAPVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSD*******************TWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW******************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSMPQSSSSSGQFTYAAAPAAPTTANSSYFPLPFHLQQTDPTAVSQYPPPAAYPAPVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSVLHK
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	247	2.2.26 [Sep-21-2011]
Q6AXT7	474	RNA-binding protein 42 OS	yes	no	0.412	0.215	0.725	8e-44
Q91V81	474	RNA-binding protein 42 OS	yes	no	0.412	0.215	0.725	8e-44
Q0P5L0	448	RNA-binding protein 42 OS	yes	no	0.412	0.227	0.725	1e-43
Q9BTD8	480	RNA-binding protein 42 OS	yes	no	0.417	0.214	0.718	1e-43
Q6DRG1	402	RNA-binding protein 42 OS	yes	no	0.485	0.298	0.612	8e-43
Q66KL9	392	RNA-binding protein 42 OS	yes	no	0.469	0.295	0.635	2e-42
A2VDB3	392	RNA-binding protein 42 OS	N/A	no	0.469	0.295	0.635	6e-42
Q10355	219	Uncharacterized RNA-bindi	yes	no	0.396	0.447	0.565	8e-29
Q9LEB3	428	Polyadenylate-binding pro	N/A	no	0.303	0.175	0.447	2e-13
Q0WW84	435	Polyadenylate-binding pro	no	no	0.303	0.172	0.460	9e-13

>sp|Q6AXT7|RBM42_RAT RNA-binding protein 42 OS=Rattus norvegicus GN=Rbm42 PE=1 SV=1

 Score =  177 bits (448), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 74/102 (72%), Positives = 90/102 (88%)

Query: 119 RKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGK 178
           R AAG +WEDP+L EW  +D+R+FCGDLGNEVNDD+L++AFSRFPSF  AKV+RDKRTGK
Sbjct: 355 RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTGK 414

Query: 179 TKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQER 220
           TKGYGF+SF +PSD   A++EMNGKYVG+RPIKLRKS W++R
Sbjct: 415 TKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKLRKSMWKDR 456

Binds (via the RRM domain) to the 3' untranslated region (UTR) of p21 mRNA.
Rattus norvegicus (taxid: 10116)

>sp|Q91V81|RBM42_MOUSE RNA-binding protein 42 OS=Mus musculus GN=Rbm42 PE=1 SV=1

 Score =  177 bits (448), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 74/102 (72%), Positives = 90/102 (88%)

Query: 119 RKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGK 178
           R AAG +WEDP+L EW  +D+R+FCGDLGNEVNDD+L++AFSRFPSF  AKV+RDKRTGK
Sbjct: 355 RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTGK 414

Query: 179 TKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQER 220
           TKGYGF+SF +PSD   A++EMNGKYVG+RPIKLRKS W++R
Sbjct: 415 TKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKLRKSMWKDR 456

Binds (via the RRM domain) to the 3'-untranslated region (UTR) of CDKN1A mRNA.

Mus musculus (taxid: 10090)

>sp|Q0P5L0|RBM42_BOVIN RNA-binding protein 42 OS=Bos taurus GN=RBM42 PE=2 SV=1

 Score =  176 bits (447), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 74/102 (72%), Positives = 90/102 (88%)

Query: 119 RKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGK 178
           R AAG +WEDP+L EW  +D+R+FCGDLGNEVNDD+L++AFSRFPSF  AKV+RDKRTGK
Sbjct: 329 RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTGK 388

Query: 179 TKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQER 220
           TKGYGF+SF +PSD   A++EMNGKYVG+RPIKLRKS W++R
Sbjct: 389 TKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKLRKSMWKDR 430

Binds (via the RRM domain) to the 3'-untranslated region (UTR) of CDKN1A mRNA.

Bos taurus (taxid: 9913)

>sp|Q9BTD8|RBM42_HUMAN RNA-binding protein 42 OS=Homo sapiens GN=RBM42 PE=1 SV=1

 Score =  176 bits (446), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 74/103 (71%), Positives = 90/103 (87%)

Query: 119 RKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGK 178
           R AAG +WEDP+L EW  +D+R+FCGDLGNEVNDD+L++AFSRFPSF  AKV+RDKRTGK
Sbjct: 361 RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTGK 420

Query: 179 TKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERT 221
           TKGYGF+SF +PSD   A++EMNGKYVG+RPIKLRKS W++R 
Sbjct: 421 TKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKLRKSMWKDRN 463

Binds (via the RRM domain) to the 3'-untranslated region (UTR) of CDKN1A mRNA.

Homo sapiens (taxid: 9606)

>sp|Q6DRG1|RBM42_DANRE RNA-binding protein 42 OS=Danio rerio GN=rbm42 PE=2 SV=2

 Score =  173 bits (439), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 76/124 (61%), Positives = 99/124 (79%), Gaps = 4/124 (3%)

Query: 119 RKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGK 178
           R AAG +WED +L EW  +D+R+FCGDLGNEVNDD+L++AFSR+PSF  AKVVRDKRTGK
Sbjct: 283 RVAAGVSWEDTSLLEWETDDFRIFCGDLGNEVNDDILARAFSRYPSFLKAKVVRDKRTGK 342

Query: 179 TKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPK 238
           TKGYGF+SF +P+D   A++EMNG+YVG+RPIKLRKS W++R     LE  + + ++K K
Sbjct: 343 TKGYGFVSFKDPNDYVRAMREMNGRYVGSRPIKLRKSAWKDRN----LEVVRKNQKEKKK 398

Query: 239 LSKK 242
           L  +
Sbjct: 399 LGLR 402

May bind RNA.

Danio rerio (taxid: 7955)

>sp|Q66KL9|RBM42_XENTR RNA-binding protein 42 OS=Xenopus tropicalis GN=rbm42 PE=2 SV=1

 Score =  172 bits (436), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 75/118 (63%), Positives = 96/118 (81%), Gaps = 2/118 (1%)

Query: 119 RKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGK 178
           R AAG +WED +L EW  +D+R+FCGDLGNEVNDD+L++AFSR+PSF  AKV+RDKRTGK
Sbjct: 273 RTAAGTSWEDQSLLEWESDDFRIFCGDLGNEVNDDILARAFSRYPSFLRAKVIRDKRTGK 332

Query: 179 TKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKK 236
           TKGYGF+SF +P+D   A++EMNGKYVG+RPIKLRKS+W++R     + R K   +KK
Sbjct: 333 TKGYGFVSFKDPNDYVRAMREMNGKYVGSRPIKLRKSQWKDRN--MDVVRKKQREKKK 388

May bind RNA.

Xenopus tropicalis (taxid: 8364)

>sp|A2VDB3|RBM42_XENLA RNA-binding protein 42 OS=Xenopus laevis GN=rbm42 PE=2 SV=1

 Score =  171 bits (432), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 75/118 (63%), Positives = 95/118 (80%), Gaps = 2/118 (1%)

Query: 119 RKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGK 178
           R AAG +WED +L EW  +D+R+FCGDLGNEVNDD+L++AFSR+PSF  AKV+RDKRTGK
Sbjct: 273 RTAAGTSWEDQSLLEWEPDDFRIFCGDLGNEVNDDILARAFSRYPSFLRAKVIRDKRTGK 332

Query: 179 TKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKK 236
           TKGYGF+SF +P+D   A +EMNGKYVG+RPIKLRKS+W++R     + R K   +KK
Sbjct: 333 TKGYGFVSFKDPNDYVRATREMNGKYVGSRPIKLRKSQWKDRNI--DVVRKKQREKKK 388

May bind RNA.

Xenopus laevis (taxid: 8355)

>sp|Q10355|YDB2_SCHPO Uncharacterized RNA-binding protein C22E12.02 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC22E12.02 PE=4 SV=1

 Score =  127 bits (319), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 56/99 (56%), Positives = 72/99 (72%), Gaps = 1/99 (1%)

Query: 114 KKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRD 173
           K ++ RKA GQ WEDPTL EW  N +RLF G+LGN+VND+ L +AFS +PS    KVVRD
Sbjct: 5   KTTVVRKAGGQVWEDPTLLEWDPNHFRLFVGNLGNDVNDESLYQAFSEYPSLVKTKVVRD 64

Query: 174 KRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
            R GKT+G+GF+SF +      A +E NGKY+G+RP+KL
Sbjct: 65  -REGKTRGFGFVSFKDSDQFLKAWREKNGKYIGSRPVKL 102

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

>sp|Q9LEB3|RBP47_NICPL Polyadenylate-binding protein RBP47 OS=Nicotiana plumbaginifolia GN=RBP47 PE=1 SV=1

 Score = 76.3 bits (186), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/76 (44%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAF-SRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           D+ +F GDL ++V D +L   F SR+PS   AKVV D  TG +KGYGF+ F + S+ + A
Sbjct: 176 DFSIFVGDLASDVTDTMLRDTFASRYPSLKGAKVVVDANTGHSKGYGFVRFGDESERSRA 235

Query: 197 LKEMNGKYVGNRPIKL 212
           + EMNG Y  +R +++
Sbjct: 236 MTEMNGVYCSSRAMRI 251

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|Q0WW84|RB47B_ARATH Polyadenylate-binding protein RBP47B OS=Arabidopsis thaliana GN=RBP47B PE=2 SV=1

 Score = 73.9 bits (180), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFS-RFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           D  +F GDL  +V D +L + FS R+PS   AKVV D  TG++KGYGF+ F + ++ + A
Sbjct: 201 DLSVFVGDLSPDVTDVLLHETFSDRYPSVKSAKVVIDSNTGRSKGYGFVRFGDENERSRA 260

Query: 197 LKEMNGKYVGNRPIKL 212
           L EMNG Y  NR +++
Sbjct: 261 LTEMNGAYCSNRQMRV 276

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	247
225443254	257	PREDICTED: CUGBP Elav-like family member	0.910	0.875	0.754	1e-104
147806450	257	hypothetical protein VITISV_033169 [Viti	0.910	0.875	0.750	1e-104
359488053	257	PREDICTED: uncharacterized protein LOC10	0.910	0.875	0.791	2e-97
224123552	222	predicted protein [Populus trichocarpa]	0.898	1.0	0.795	4e-95
298204769	221	unnamed protein product [Vitis vinifera]	0.821	0.918	0.783	7e-95
356538652	246	PREDICTED: RNA-binding protein 42-like [	0.910	0.914	0.724	8e-94
356576674	247	PREDICTED: RNA-binding protein 42-like [	0.919	0.919	0.720	3e-93
357441373	240	RNA-binding protein [Medicago truncatula	0.906	0.933	0.753	5e-92
356535208	248	PREDICTED: RNA-binding protein 42-like [	0.874	0.870	0.752	6e-92
302143626	222	unnamed protein product [Vitis vinifera]	0.761	0.846	0.897	4e-91

>gi|225443254|ref|XP_002272469.1| PREDICTED: CUGBP Elav-like family member 5 [Vitis vinifera]

 Score =  383 bits (984), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 191/253 (75%), Positives = 209/253 (82%), Gaps = 28/253 (11%)

Query: 12  QFTYAAAPAAPTTANSSYFPLPFHLQQTDPTAVSQYPPP-----------------AAYP 54
           QFTY+         N+SYFPLPFHLQQ+ P AVSQYP P                  +  
Sbjct: 16  QFTYS---------NASYFPLPFHLQQSGPMAVSQYPQPYVAPSPPPVHVPVPPVKISTI 66

Query: 55  APVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKK 114
           APV P+  +AP A VYSLPQY QA QLFQRDAQTITPEALESVKAALASS+IEHKAETKK
Sbjct: 67  APVYPA--SAPGAGVYSLPQYQQAHQLFQRDAQTITPEALESVKAALASSEIEHKAETKK 124

Query: 115 KSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDK 174
           ++IPRK AGQTWEDPTLA+WPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMA+VVRDK
Sbjct: 125 RAIPRKVAGQTWEDPTLADWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMARVVRDK 184

Query: 175 RTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQ 234
           RTGKT+G+GF+SF+NPSD+AAALKEMNGKYVGNRPIKLRKS W+ERTD EALER KNH Q
Sbjct: 185 RTGKTRGFGFVSFSNPSDLAAALKEMNGKYVGNRPIKLRKSNWKERTDSEALERQKNHIQ 244

Query: 235 KKPKLSKKSVLHK 247
           KKPKLSKKS+LHK
Sbjct: 245 KKPKLSKKSILHK 257

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147806450|emb|CAN63219.1| hypothetical protein VITISV_033169 [Vitis vinifera]

 Score =  382 bits (981), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 190/253 (75%), Positives = 209/253 (82%), Gaps = 28/253 (11%)

Query: 12  QFTYAAAPAAPTTANSSYFPLPFHLQQTDPTAVSQYPPP-----------------AAYP 54
           QFTY+         N+SYFPLPFHLQQ+ P AVSQYP P                  +  
Sbjct: 16  QFTYS---------NASYFPLPFHLQQSGPMAVSQYPQPYVAPSPPPVHVPVPPVKISTI 66

Query: 55  APVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKK 114
           APV P+  +AP A VYSLPQY QA QLFQRDAQTITPEALESVKAALASS+IEHKAETKK
Sbjct: 67  APVYPA--SAPGAGVYSLPQYQQAHQLFQRDAQTITPEALESVKAALASSEIEHKAETKK 124

Query: 115 KSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDK 174
           ++IPRK AGQTWEDPTLA+WPENDYRLFCGDLGNEVNDDVLSK+FSRFPSFNMA+VVRDK
Sbjct: 125 RAIPRKVAGQTWEDPTLADWPENDYRLFCGDLGNEVNDDVLSKSFSRFPSFNMARVVRDK 184

Query: 175 RTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQ 234
           RTGKT+G+GF+SF+NPSD+AAALKEMNGKYVGNRPIKLRKS W+ERTD EALER KNH Q
Sbjct: 185 RTGKTRGFGFVSFSNPSDLAAALKEMNGKYVGNRPIKLRKSNWKERTDSEALERQKNHIQ 244

Query: 235 KKPKLSKKSVLHK 247
           KKPKLSKKS+LHK
Sbjct: 245 KKPKLSKKSILHK 257

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488053|ref|XP_002266454.2| PREDICTED: uncharacterized protein LOC100246648 [Vitis vinifera]

 Score =  361 bits (926), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 201/254 (79%), Positives = 212/254 (83%), Gaps = 29/254 (11%)

Query: 12  QFTYAAAPAAPTTANSSYFPLPFHLQQTDPTA-VSQYPPPAAYP---------------- 54
           QFTY+         N+SYFPLPFHLQQ+DP A VSQYP P   P                
Sbjct: 15  QFTYS---------NASYFPLPFHLQQSDPMAAVSQYPKPYVAPPPPPVQVPVPPVKIPA 65

Query: 55  -APVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETK 113
            APV P+   APVA VYSLPQY QAQQLFQRDAQTITPEALESVKAALASS+IEHKAETK
Sbjct: 66  VAPVYPA--PAPVAGVYSLPQYQQAQQLFQRDAQTITPEALESVKAALASSEIEHKAETK 123

Query: 114 KKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRD 173
           KK+IPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRD
Sbjct: 124 KKAIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRD 183

Query: 174 KRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHN 233
           KRTGKT+GYGF+SF+NP D+AAALKEMNGKYVGNRPIKLRKS W+ERTDFEALER KNH 
Sbjct: 184 KRTGKTRGYGFVSFSNPLDLAAALKEMNGKYVGNRPIKLRKSNWRERTDFEALERQKNHI 243

Query: 234 QKKPKLSKKSVLHK 247
           QKKPKLSKKSVLHK
Sbjct: 244 QKKPKLSKKSVLHK 257

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123552|ref|XP_002319108.1| predicted protein [Populus trichocarpa] gi|222857484|gb|EEE95031.1| predicted protein [Populus trichocarpa]

 Score =  353 bits (905), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 179/225 (79%), Positives = 197/225 (87%), Gaps = 3/225 (1%)

Query: 23  TTANSSYFPLPFHLQQTDPTAVSQYPPPAAYPAPVVPSVYAAPVAPVYSLPQYHQAQQLF 82
           T AN +YFP PFHLQQ+DP        P    APV P    AP+ PVYSLPQY QAQQLF
Sbjct: 1   TAANGTYFPTPFHLQQSDPYPKPYVTSPPTVMAPVYPP---APIGPVYSLPQYQQAQQLF 57

Query: 83  QRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLF 142
           QRDAQTITPEALE VKAALASS+IEHKAETKKK++PRKAAG TWEDPTLAEWPENDYR+F
Sbjct: 58  QRDAQTITPEALEGVKAALASSEIEHKAETKKKAVPRKAAGLTWEDPTLAEWPENDYRVF 117

Query: 143 CGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG 202
           CGDLGNEVNDDVLSKAFSRFPSFN+A+VVRDKR+GKTKGYGF+SFANP+D+AAALKEMNG
Sbjct: 118 CGDLGNEVNDDVLSKAFSRFPSFNLARVVRDKRSGKTKGYGFVSFANPTDLAAALKEMNG 177

Query: 203 KYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSVLHK 247
           KYVGNRPIKLRKS W+ERTD+ A++R KNHN KKPKLSKKS+LHK
Sbjct: 178 KYVGNRPIKLRKSNWKERTDYGAVDRHKNHNHKKPKLSKKSILHK 222

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298204769|emb|CBI25267.3| unnamed protein product [Vitis vinifera]

 Score =  352 bits (904), Expect = 7e-95,   Method: Compositional matrix adjust.
 Identities = 174/222 (78%), Positives = 189/222 (85%), Gaps = 19/222 (8%)

Query: 43  AVSQYPPP-----------------AAYPAPVVPSVYAAPVAPVYSLPQYHQAQQLFQRD 85
           AVSQYP P                  +  APV P+  +AP A VYSLPQY QA QLFQRD
Sbjct: 2   AVSQYPQPYVAPSPPPVHVPVPPVKISTIAPVYPA--SAPGAGVYSLPQYQQAHQLFQRD 59

Query: 86  AQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGD 145
           AQTITPEALESVKAALASS+IEHKAETKK++IPRK AGQTWEDPTLA+WPENDYRLFCGD
Sbjct: 60  AQTITPEALESVKAALASSEIEHKAETKKRAIPRKVAGQTWEDPTLADWPENDYRLFCGD 119

Query: 146 LGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV 205
           LGNEVNDDVLSKAFSRFPSFNMA+VVRDKRTGKT+G+GF+SF+NPSD+AAALKEMNGKYV
Sbjct: 120 LGNEVNDDVLSKAFSRFPSFNMARVVRDKRTGKTRGFGFVSFSNPSDLAAALKEMNGKYV 179

Query: 206 GNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSVLHK 247
           GNRPIKLRKS W+ERTD EALER KNH QKKPKLSKKS+LHK
Sbjct: 180 GNRPIKLRKSNWKERTDSEALERQKNHIQKKPKLSKKSILHK 221

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538652|ref|XP_003537815.1| PREDICTED: RNA-binding protein 42-like [Glycine max]

 Score =  348 bits (894), Expect = 8e-94,   Method: Compositional matrix adjust.
 Identities = 176/243 (72%), Positives = 200/243 (82%), Gaps = 18/243 (7%)

Query: 12  QFTYAAAPAAPTTANSSYFPLPFHLQQTDPTAVSQYPPPAAYPA------PVVPSVYAAP 65
           QFTY+          SSYFP+PFHLQQ  P       P  A P+      P+V  V  AP
Sbjct: 15  QFTYSNP--------SSYFPVPFHLQQ--PATTHYAAPYVAAPSVQIPAPPIVGPVVPAP 64

Query: 66  VAPVYS-LPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQ 124
           VA VYS +PQY QAQQLF+RDAQ ITPEALE+VKAA+ASSD+EHKA+ KKK++PRKAAGQ
Sbjct: 65  VAGVYSTVPQY-QAQQLFERDAQIITPEALENVKAAIASSDVEHKADAKKKAVPRKAAGQ 123

Query: 125 TWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGF 184
           +WEDP LAEWPE+DYRLFCGDLGNEVNDDVLSK FSRFPSFN+A+VVRDKRTGKTKGYGF
Sbjct: 124 SWEDPILAEWPEDDYRLFCGDLGNEVNDDVLSKVFSRFPSFNLARVVRDKRTGKTKGYGF 183

Query: 185 ISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSV 244
           +SFANP+D+AAA+KEMNGKYVGNRPIKLRKSKW+ERTD+EALE+ KNH QKKPKL +K V
Sbjct: 184 VSFANPADLAAAVKEMNGKYVGNRPIKLRKSKWKERTDYEALEKQKNHIQKKPKLPRKGV 243

Query: 245 LHK 247
           LHK
Sbjct: 244 LHK 246

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576674|ref|XP_003556455.1| PREDICTED: RNA-binding protein 42-like [Glycine max]

 Score =  347 bits (889), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 175/243 (72%), Positives = 199/243 (81%), Gaps = 16/243 (6%)

Query: 12  QFTYAAAPAAPTTANSSYFPLPFHLQQTDPTAVSQYPPPAAYPA------PVVPSVYAAP 65
           QF Y+        ++SSYFP+PFHLQQ  P       P  A P+      PVV  +  AP
Sbjct: 14  QFAYS------NPSSSSYFPVPFHLQQ--PATTHYAAPYVAAPSVQIPAPPVVGPIAPAP 65

Query: 66  VAPVYS-LPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQ 124
           V  VYS +PQY QAQQLF+RDAQ ITPEALE+VKAA+ASSD+EHK + KKK++PRKAAGQ
Sbjct: 66  VPGVYSAVPQY-QAQQLFERDAQIITPEALENVKAAIASSDVEHKTDAKKKAVPRKAAGQ 124

Query: 125 TWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGF 184
            WEDP LAEWPE+DYRLFCGDLGNEVNDDVLSKAFSRFPSFN+A+VVRDKRTGKTKGYGF
Sbjct: 125 AWEDPILAEWPEDDYRLFCGDLGNEVNDDVLSKAFSRFPSFNLARVVRDKRTGKTKGYGF 184

Query: 185 ISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSV 244
           +SFANPSD+AAALKEMNGKYVGNRPIKLRKSKW+ERTD+EALE+ KNH QKKPK+ +K V
Sbjct: 185 VSFANPSDLAAALKEMNGKYVGNRPIKLRKSKWRERTDYEALEKQKNHIQKKPKMPRKGV 244

Query: 245 LHK 247
           LHK
Sbjct: 245 LHK 247

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441373|ref|XP_003590964.1| RNA-binding protein [Medicago truncatula] gi|355480012|gb|AES61215.1| RNA-binding protein [Medicago truncatula]

 Score =  343 bits (879), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 171/227 (75%), Positives = 195/227 (85%), Gaps = 3/227 (1%)

Query: 23  TTANSSYFPLPFHLQQTDPTAVSQYPPPAAYPAPVVPSVYAAPVA--PVYSLPQYHQAQQ 80
           T +N+ YFP+PFHLQQ   T+    P  AA    + P     PV     YS+PQY QAQQ
Sbjct: 15  TYSNAPYFPVPFHLQQPATTSHYAAPYVAAPAVQLPPPPIVGPVPPPAAYSVPQY-QAQQ 73

Query: 81  LFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYR 140
           LF+RDAQ ITPEALE+VKAA+ASSD+EHKAETKKK++PRKAAGQ WEDP LAEWPE+DYR
Sbjct: 74  LFERDAQIITPEALENVKAAIASSDVEHKAETKKKAVPRKAAGQAWEDPILAEWPEDDYR 133

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LFCGDLGNEVNDDVLSKAF+RFPSFNMA+VVRDKRTGKTKGYGFISFANP+D+AAALKEM
Sbjct: 134 LFCGDLGNEVNDDVLSKAFTRFPSFNMARVVRDKRTGKTKGYGFISFANPADLAAALKEM 193

Query: 201 NGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSVLHK 247
           NGKYVGNRPIKLRKSKW+ERTD++ALE+ KNH QKKPK+S+KS+LHK
Sbjct: 194 NGKYVGNRPIKLRKSKWRERTDYDALEKQKNHIQKKPKMSRKSILHK 240

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356535208|ref|XP_003536140.1| PREDICTED: RNA-binding protein 42-like [Glycine max]

 Score =  342 bits (878), Expect = 6e-92,   Method: Compositional matrix adjust.
 Identities = 170/226 (75%), Positives = 190/226 (84%), Gaps = 10/226 (4%)

Query: 29  YFPLPFHLQQTDPTAVSQYPPPAAYPA------PVVPSVYAAPVAPVYS-LPQYHQAQQL 81
           YFP+PFHLQQ  P       P  A P+      PVV  V  APV  VYS +PQY QAQQL
Sbjct: 26  YFPVPFHLQQ--PATTHYAAPYVAAPSVQIPAPPVVGPVAPAPVPGVYSAVPQY-QAQQL 82

Query: 82  FQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRL 141
           F+RDAQ ITPEALE+VKAA+ASSD+EHK + KKK++PRKAAG  WEDP LAEWPE+DYRL
Sbjct: 83  FERDAQIITPEALENVKAAIASSDVEHKTDAKKKAVPRKAAGHAWEDPILAEWPEDDYRL 142

Query: 142 FCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN 201
           FCGDLGNEVNDDVLSKAFSRFPSFNMA+VVRDKRTGKTKGYGF+SFANPSD+A ALKEMN
Sbjct: 143 FCGDLGNEVNDDVLSKAFSRFPSFNMARVVRDKRTGKTKGYGFVSFANPSDLAGALKEMN 202

Query: 202 GKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSVLHK 247
           GKYVGNRPIKLRKSKW+ERTD+EALE+ KNH QKKPK+++K VLHK
Sbjct: 203 GKYVGNRPIKLRKSKWRERTDYEALEKQKNHIQKKPKMARKGVLHK 248

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143626|emb|CBI22379.3| unnamed protein product [Vitis vinifera]

 Score =  340 bits (871), Expect = 4e-91,   Method: Compositional matrix adjust.
 Identities = 175/195 (89%), Positives = 182/195 (93%), Gaps = 7/195 (3%)

Query: 53  YPAPVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAET 112
           YPAP       APVA VYSLPQY QAQQLFQRDAQTITPEALESVKAALASS+IEHKAET
Sbjct: 35  YPAP-------APVAGVYSLPQYQQAQQLFQRDAQTITPEALESVKAALASSEIEHKAET 87

Query: 113 KKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVR 172
           KKK+IPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVR
Sbjct: 88  KKKAIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVR 147

Query: 173 DKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNH 232
           DKRTGKT+GYGF+SF+NP D+AAALKEMNGKYVGNRPIKLRKS W+ERTDFEALER KNH
Sbjct: 148 DKRTGKTRGYGFVSFSNPLDLAAALKEMNGKYVGNRPIKLRKSNWRERTDFEALERQKNH 207

Query: 233 NQKKPKLSKKSVLHK 247
            QKKPKLSKKSVLHK
Sbjct: 208 IQKKPKLSKKSVLHK 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

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	247
TAIR|locus:2100840	245	AT3G04500 [Arabidopsis thalian	0.708	0.714	0.84	2.6e-79
UNIPROTKB|F1N7X9	448	RBM42 "RNA-binding protein 42"	0.566	0.312	0.604	5.2e-42
UNIPROTKB|Q0P5L0	448	RBM42 "RNA-binding protein 42"	0.566	0.312	0.604	5.2e-42
UNIPROTKB|F1PT81	483	RBM42 "Uncharacterized protein	0.566	0.289	0.604	6.6e-42
UNIPROTKB|K7EP90	458	RBM42 "RNA-binding protein 42"	0.566	0.305	0.604	6.6e-42
UNIPROTKB|K7EQ03	426	RBM42 "RNA-binding protein 42"	0.566	0.328	0.604	6.6e-42
UNIPROTKB|Q9BTD8	480	RBM42 "RNA-binding protein 42"	0.566	0.291	0.604	6.6e-42
UNIPROTKB|F1RM56	477	RBM42 "Uncharacterized protein	0.566	0.293	0.604	6.6e-42
MGI|MGI:1915285	474	Rbm42 "RNA binding motif prote	0.566	0.295	0.604	6.6e-42
RGD|1306184	474	Rbm42 "RNA binding motif prote	0.566	0.295	0.604	6.6e-42

TAIR|locus:2100840 AT3G04500 [Arabidopsis thaliana (taxid:3702)]

 Score = 797 (285.6 bits), Expect = 2.6e-79, P = 2.6e-79
 Identities = 147/175 (84%), Positives = 163/175 (93%)

Query:    73 PQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLA 132
             PQY QA QLFQRDAQTITPEALE+VKAALASS+ EHKAETKK++IPRKAAGQ+WEDPTL+
Sbjct:    71 PQYQQAHQLFQRDAQTITPEALENVKAALASSETEHKAETKKRAIPRKAAGQSWEDPTLS 130

Query:   133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSD 192
             EWPENDYRLFCGDLGNEVNDDVLSKAF+RFP+FNMAKV+RDKRTGKTKGYGF+SF NP+D
Sbjct:   131 EWPENDYRLFCGDLGNEVNDDVLSKAFARFPTFNMAKVIRDKRTGKTKGYGFVSFLNPAD 190

Query:   193 IAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSVLHK 247
             +AAALKEMNGKYVGNRPIKLRKS W+ERTD EA ER K+H+ KK K  KKS+LHK
Sbjct:   191 LAAALKEMNGKYVGNRPIKLRKSSWKERTDQEAAERQKHHSNKKQKTVKKSILHK 245

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|F1N7X9 RBM42 "RNA-binding protein 42" [Bos taurus (taxid:9913)]

 Score = 445 (161.7 bits), Expect = 5.2e-42, P = 5.2e-42
 Identities = 87/144 (60%), Positives = 110/144 (76%)

Query:    93 ALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVND 152
             ALE V   L+    + K E  K+ I R AAG +WEDP+L EW  +D+R+FCGDLGNEVND
Sbjct:   305 ALE-VPEPLSEDKKKGKPEKLKRCI-RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVND 362

Query:   153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
             D+L++AFSRFPSF  AKV+RDKRTGKTKGYGF+SF +PSD   A++EMNGKYVG+RPIKL
Sbjct:   363 DILARAFSRFPSFLKAKVIRDKRTGKTKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKL 422

Query:   213 RKSKWQERTDFEALERSKNHNQKK 236
             RKS W++R + + + R K   +KK
Sbjct:   423 RKSMWKDR-NLDVV-RKKQKEKKK 444

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q0P5L0 RBM42 "RNA-binding protein 42" [Bos taurus (taxid:9913)]

 Score = 445 (161.7 bits), Expect = 5.2e-42, P = 5.2e-42
 Identities = 87/144 (60%), Positives = 110/144 (76%)

Query:    93 ALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVND 152
             ALE V   L+    + K E  K+ I R AAG +WEDP+L EW  +D+R+FCGDLGNEVND
Sbjct:   305 ALE-VPEPLSEDKKKGKPEKLKRCI-RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVND 362

Query:   153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
             D+L++AFSRFPSF  AKV+RDKRTGKTKGYGF+SF +PSD   A++EMNGKYVG+RPIKL
Sbjct:   363 DILARAFSRFPSFLKAKVIRDKRTGKTKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKL 422

Query:   213 RKSKWQERTDFEALERSKNHNQKK 236
             RKS W++R + + + R K   +KK
Sbjct:   423 RKSMWKDR-NLDVV-RKKQKEKKK 444

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1PT81 RBM42 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 87/144 (60%), Positives = 109/144 (75%)

Query:    93 ALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVND 152
             ALE V   L     + K E  K+ I R AAG +WEDP+L EW  +D+R+FCGDLGNEVND
Sbjct:   341 ALE-VPEPLGEDKKKGKPEKLKRCI-RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVND 398

Query:   153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
             D+L++AFSRFPSF  AKV+RDKRTGKTKGYGF+SF +PSD   A++EMNGKYVG+RPIKL
Sbjct:   399 DILARAFSRFPSFLKAKVIRDKRTGKTKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKL 458

Query:   213 RKSKWQERTDFEALERSKNHNQKK 236
             RKS W++R + + + R K   +KK
Sbjct:   459 RKSMWKDR-NLDVV-RKKQKEKKK 480

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|K7EP90 RBM42 "RNA-binding protein 42" [Homo sapiens (taxid:9606)]

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 87/144 (60%), Positives = 109/144 (75%)

Query:    93 ALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVND 152
             ALE V   L     + K E  K+ I R AAG +WEDP+L EW  +D+R+FCGDLGNEVND
Sbjct:   315 ALE-VPEPLGEDKKKGKPEKLKRCI-RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVND 372

Query:   153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
             D+L++AFSRFPSF  AKV+RDKRTGKTKGYGF+SF +PSD   A++EMNGKYVG+RPIKL
Sbjct:   373 DILARAFSRFPSFLKAKVIRDKRTGKTKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKL 432

Query:   213 RKSKWQERTDFEALERSKNHNQKK 236
             RKS W++R + + + R K   +KK
Sbjct:   433 RKSMWKDR-NLDVV-RKKQKEKKK 454

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|K7EQ03 RBM42 "RNA-binding protein 42" [Homo sapiens (taxid:9606)]

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 87/144 (60%), Positives = 109/144 (75%)

Query:    93 ALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVND 152
             ALE V   L     + K E  K+ I R AAG +WEDP+L EW  +D+R+FCGDLGNEVND
Sbjct:   283 ALE-VPEPLGEDKKKGKPEKLKRCI-RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVND 340

Query:   153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
             D+L++AFSRFPSF  AKV+RDKRTGKTKGYGF+SF +PSD   A++EMNGKYVG+RPIKL
Sbjct:   341 DILARAFSRFPSFLKAKVIRDKRTGKTKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKL 400

Query:   213 RKSKWQERTDFEALERSKNHNQKK 236
             RKS W++R + + + R K   +KK
Sbjct:   401 RKSMWKDR-NLDVV-RKKQKEKKK 422

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q9BTD8 RBM42 "RNA-binding protein 42" [Homo sapiens (taxid:9606)]

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 87/144 (60%), Positives = 109/144 (75%)

Query:    93 ALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVND 152
             ALE V   L     + K E  K+ I R AAG +WEDP+L EW  +D+R+FCGDLGNEVND
Sbjct:   337 ALE-VPEPLGEDKKKGKPEKLKRCI-RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVND 394

Query:   153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
             D+L++AFSRFPSF  AKV+RDKRTGKTKGYGF+SF +PSD   A++EMNGKYVG+RPIKL
Sbjct:   395 DILARAFSRFPSFLKAKVIRDKRTGKTKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKL 454

Query:   213 RKSKWQERTDFEALERSKNHNQKK 236
             RKS W++R + + + R K   +KK
Sbjct:   455 RKSMWKDR-NLDVV-RKKQKEKKK 476

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|F1RM56 RBM42 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 87/144 (60%), Positives = 109/144 (75%)

Query:    93 ALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVND 152
             ALE V   L     + K E  K+ I R AAG +WEDP+L EW  +D+R+FCGDLGNEVND
Sbjct:   334 ALE-VPEPLGEDKKKGKPEKLKRCI-RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVND 391

Query:   153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
             D+L++AFSRFPSF  AKV+RDKRTGKTKGYGF+SF +PSD   A++EMNGKYVG+RPIKL
Sbjct:   392 DILARAFSRFPSFLKAKVIRDKRTGKTKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKL 451

Query:   213 RKSKWQERTDFEALERSKNHNQKK 236
             RKS W++R + + + R K   +KK
Sbjct:   452 RKSMWKDR-NLDVV-RKKQKEKKK 473

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1915285 Rbm42 "RNA binding motif protein 42" [Mus musculus (taxid:10090)]

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 87/144 (60%), Positives = 109/144 (75%)

Query:    93 ALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVND 152
             ALE V   L     + K E  K+ I R AAG +WEDP+L EW  +D+R+FCGDLGNEVND
Sbjct:   331 ALE-VPEPLGEDKKKGKPEKLKRCI-RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVND 388

Query:   153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
             D+L++AFSRFPSF  AKV+RDKRTGKTKGYGF+SF +PSD   A++EMNGKYVG+RPIKL
Sbjct:   389 DILARAFSRFPSFLKAKVIRDKRTGKTKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKL 448

Query:   213 RKSKWQERTDFEALERSKNHNQKK 236
             RKS W++R + + + R K   +KK
Sbjct:   449 RKSMWKDR-NLDVV-RKKQKEKKK 470

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:0005737 "cytoplasm" evidence=IEA

RGD|1306184 Rbm42 "RNA binding motif protein 42" [Rattus norvegicus (taxid:10116)]

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 87/144 (60%), Positives = 109/144 (75%)

Query:    93 ALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVND 152
             ALE V   L     + K E  K+ I R AAG +WEDP+L EW  +D+R+FCGDLGNEVND
Sbjct:   331 ALE-VPEPLGEDKKKGKPEKLKRCI-RTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVND 388

Query:   153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
             D+L++AFSRFPSF  AKV+RDKRTGKTKGYGF+SF +PSD   A++EMNGKYVG+RPIKL
Sbjct:   389 DILARAFSRFPSFLKAKVIRDKRTGKTKGYGFVSFKDPSDYVRAMREMNGKYVGSRPIKL 448

Query:   213 RKSKWQERTDFEALERSKNHNQKK 236
             RKS W++R + + + R K   +KK
Sbjct:   449 RKSMWKDR-NLDVV-RKKQKEKKK 470

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:0005737 "cytoplasm" 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)
Q91V81	RBM42_MOUSE	No assigned EC number	0.7254	0.4129	0.2151	yes	no
Q9BTD8	RBM42_HUMAN	No assigned EC number	0.7184	0.4170	0.2145	yes	no
Q6AXT7	RBM42_RAT	No assigned EC number	0.7254	0.4129	0.2151	yes	no
Q0P5L0	RBM42_BOVIN	No assigned EC number	0.7254	0.4129	0.2276	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00025247001	SubName- Full=Chromosome chr9 scaffold_33, whole genome shotgun sequence; (257 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00000274001	SubName- Full=Chromosome chr12 scaffold_103, whole genome shotgun sequence; (284 aa)			•						0.476
	GSVIVG00015240001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (257 aa)			•						0.455
	GSVIVG00024233001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (296 aa)			•						0.453
	GSVIVG00002571001	SubName- Full=Chromosome chr2 scaffold_132, whole genome shotgun sequence; (211 aa)			•						0.447
	GSVIVG00018411001	SubName- Full=Chromosome chr13 scaffold_17, whole genome shotgun sequence; (301 aa)			•						0.442
	GSVIVG00018272001	SubName- Full=Chromosome chr13 scaffold_17, whole genome shotgun sequence; (287 aa)			•						0.441
	GSVIVG00008544001	SubName- Full=Chromosome undetermined scaffold_1542, whole genome shotgun sequence; (133 aa)			•						0.436
	GSVIVG00034829001	SubName- Full=Chromosome chr4 scaffold_73, whole genome shotgun sequence; (202 aa)			•						0.429
	GSVIVG00000872001	SubName- Full=Chromosome undetermined scaffold_109, whole genome shotgun sequence; (170 aa)			•						0.427

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	247
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	1e-57
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	4e-24
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-22
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-21
smart00360	73	smart00360, RRM, RNA recognition motif	4e-21
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-19
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-17
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	4e-17
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-16
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-16
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-15
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-15
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-15
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-15
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-15
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-14
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-14
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-14
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	6e-14
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-13
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-12
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-12
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-12
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	9e-12
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-11
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-11
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-11
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-11
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-10
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	5e-10
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	5e-10
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-09
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-09
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	1e-09
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-09
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	2e-09
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-09
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	8e-09
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-08
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-08
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	1e-08
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-08
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-08
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	4e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	6e-08
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	6e-08
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-07
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-07
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-07
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-07
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-07
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-07
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-07
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	4e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	4e-07
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	5e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	6e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	6e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	9e-07
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-06
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-06
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-06
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	1e-06
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-06
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	1e-06
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	1e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	1e-06
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	3e-06
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	3e-06
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	3e-06
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	4e-06
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	4e-06
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	5e-06
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	5e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	6e-06
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	7e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	9e-06
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	9e-06
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	1e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-05
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	1e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	3e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	3e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-05
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	3e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	4e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	4e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	6e-05
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	6e-05
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	6e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	6e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-05
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	8e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	8e-05
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	1e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-04
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-04
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	2e-04
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-04
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	3e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	4e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	5e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-04
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	7e-04
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	8e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	9e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.001
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.001
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.001
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	0.001
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	0.001
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.001
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.001
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	0.001
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.002
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.002
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	0.002
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.002
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	0.003
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	0.003
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.003
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	0.003
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	0.004
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	0.004
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.004
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.004

>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score =  177 bits (452), Expect = 1e-57
 Identities = 63/83 (75%), Positives = 76/83 (91%)

Query: 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSD 192
           EWPEND+R+F GDLGNEV D+VL++AFS++PSF  AKVVRDKRTGK+KGYGF+SF++P+D
Sbjct: 1   EWPENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPND 60

Query: 193 IAAALKEMNGKYVGNRPIKLRKS 215
              A+KEMNGKYVGNRPIKLRKS
Sbjct: 61  YLKAMKEMNGKYVGNRPIKLRKS 83

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 91.4 bits (227), Expect = 4e-24
 Identities = 35/71 (49%), Positives = 51/71 (71%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F GDL  EV D  L  AFS FPS + A+V+ D ++G+++GYGF+SF +  D   A+ EM
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 201 NGKYVGNRPIK 211
           NGK++G+RPI+
Sbjct: 62  NGKWLGSRPIR 72

This subgroup corresponds to the RRM2 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. It 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 = 75

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 86.9 bits (216), Expect = 2e-22
 Identities = 34/76 (44%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAF-SRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           D+ +F GDL  +V D +L + F +R+PS   AKVV D  TG++KGYGF+ F +  +   A
Sbjct: 1   DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 197 LKEMNGKYVGNRPIKL 212
           L EMNG Y  +RP+++
Sbjct: 61  LTEMNGVYCSSRPMRV 76

This subfamily corresponds to the RRM2 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 = 80

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

 Score = 84.7 bits (210), Expect = 2e-21
 Identities = 31/71 (43%), Positives = 48/71 (67%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F GDL  E++ + L  AF+ F   + A+VV+D +TGK+KGYGF+SF    D   A++ M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 201 NGKYVGNRPIK 211
           NG+++G R I+
Sbjct: 62  NGQWLGGRAIR 72

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|214636 smart00360, RRM, RNA recognition motif

 Score = 83.4 bits (207), Expect = 4e-21
 Identities = 28/73 (38%), Positives = 45/73 (61%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            LF G+L  +  ++ L + FS+F      ++VRDK TGK+KG+ F+ F +  D   AL+ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 200 MNGKYVGNRPIKL 212
           +NGK +  RP+K+
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 78.8 bits (195), Expect = 3e-19
 Identities = 25/71 (35%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF G+L  +  ++ L   FS+F      ++VRD+ TG++KG+ F+ F +  D   AL+ +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 201 NGKYVGNRPIK 211
           NGK +G R ++
Sbjct: 60  NGKELGGRELR 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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 73.3 bits (180), Expect = 4e-17
 Identities = 35/76 (46%), Positives = 51/76 (67%), Gaps = 1/76 (1%)

Query: 138 DYRLFCGDLGNEVND-DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           +Y +F GDL  EVN+ D++S   SRFPS   AK++ D  TG ++GYGF+ F++ +D   A
Sbjct: 1   EYSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRA 60

Query: 197 LKEMNGKYVGNRPIKL 212
           L EM G Y G RP+++
Sbjct: 61  LIEMQGVYCGGRPMRI 76

This subgroup corresponds to the RRM2 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 = 80

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 73.1 bits (180), Expect = 4e-17
 Identities = 33/77 (42%), Positives = 50/77 (64%), Gaps = 3/77 (3%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFS-RFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           ++ LF GDL  +V+D  L + FS R+PS   AKVV D+  G ++GYGF+ F++ S+   A
Sbjct: 1   EFSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRA 59

Query: 197 LKEMNGKY-VGNRPIKL 212
           L EM G   +G +PI++
Sbjct: 60  LTEMQGASGLGGKPIRV 76

This subgroup corresponds to the RRM2 of SECp43, 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. . Length = 82

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

 Score = 71.7 bits (176), Expect = 1e-16
 Identities = 27/76 (35%), Positives = 47/76 (61%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            LF G+L   V+D+ L   F +F +   A+V+ D+ TG+++G+G++ F +P D   A++ 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 200 MNGKYVGNRPIKLRKS 215
           M+GK +  RPI +  S
Sbjct: 61  MDGKELDGRPINVDFS 76

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

 Score = 70.4 bits (173), Expect = 3e-16
 Identities = 26/73 (35%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF G+L  +  ++ L + FS+F      ++VRD + GK+KG+ F+ F +P D   AL+ +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 201 NGKYVGNRPIKLR 213
           NGK +  R +K+ 
Sbjct: 60  NGKELDGRKLKVS 72

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|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 = 70.3 bits (173), Expect = 5e-16
 Identities = 25/76 (32%), Positives = 44/76 (57%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF   L     +  L   FS+F       +++D  TG+++G+GF++F +  D  AA++++
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 201 NGKYVGNRPIKLRKSK 216
           NGK +  R IK+ K+K
Sbjct: 64  NGKELEGRVIKVEKAK 79

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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 69.7 bits (170), Expect = 1e-15
 Identities = 33/82 (40%), Positives = 51/82 (62%), Gaps = 3/82 (3%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + +F GDL  E+  D +  AF+ F   + A+VV+D  TGK+KGYGF+SF N  D   A++
Sbjct: 2   FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

Query: 199 EMNGKYVGNRPIKLRKSKWQER 220
           +M G+++G R I   ++ W  R
Sbjct: 62  QMGGQWLGGRQI---RTNWATR 80

This subgroup corresponds to the RRM2 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 = 80

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 69.5 bits (170), Expect = 1e-15
 Identities = 27/73 (36%), Positives = 45/73 (61%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +LF G L  + N+  L + FS++   +   VV+D+ T +++G+GF++F NP D   A+  
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 200 MNGKYVGNRPIKL 212
           MNGK V  R I++
Sbjct: 62  MNGKSVDGRQIRV 74

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 69.0 bits (168), Expect = 2e-15
 Identities = 32/82 (39%), Positives = 49/82 (59%), Gaps = 3/82 (3%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + +F GDL  E+  + +  AF+ F   + A+VV+D  TGK+KGYGF+SF N  D   A+ 
Sbjct: 2   FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61

Query: 199 EMNGKYVGNRPIKLRKSKWQER 220
            M G+++G R I   ++ W  R
Sbjct: 62  HMGGQWLGGRQI---RTNWATR 80

This subgroup corresponds to the RRM2 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 = 80

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

 Score = 68.8 bits (169), Expect = 2e-15
 Identities = 25/70 (35%), Positives = 48/70 (68%), Gaps = 1/70 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+  +L + ++D+ L + FS F +   AKV+ D++ G++KG+GF+ F++P +   A+ EM
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEM 62

Query: 201 NGKYVGNRPI 210
           NG+ +G +P+
Sbjct: 63  NGRIIGGKPL 72

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

 Score = 67.9 bits (167), Expect = 4e-15
 Identities = 23/72 (31%), Positives = 40/72 (55%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ GDL  +V + +L + FS        +V RD  T ++ GY +++F NP+D   AL  +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 201 NGKYVGNRPIKL 212
           N   +  +PI++
Sbjct: 62  NFDVIKGKPIRI 73

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

 Score = 66.9 bits (164), Expect = 1e-14
 Identities = 32/73 (43%), Positives = 46/73 (63%), Gaps = 5/73 (6%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSF-NMAKVVRDKRTGKTKGYGFISFAN--PSDIAAAL 197
           LF G+L  EV++ +L   FS F       K++RD  TG +KG+ FIS+ +   SD  AA+
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASD--AAI 61

Query: 198 KEMNGKYVGNRPI 210
           + MNG+Y+ NRPI
Sbjct: 62  EAMNGQYLCNRPI 74

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

 Score = 66.5 bits (163), Expect = 1e-14
 Identities = 21/77 (27%), Positives = 44/77 (57%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L+ G+L   V ++ L   F +F     A+V+ D+ TG+++G+GF+      +  AA+++
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 200 MNGKYVGNRPIKLRKSK 216
           +NG   G R + + +++
Sbjct: 61  LNGTDFGGRTLTVNEAR 77

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

 Score = 71.5 bits (174), Expect = 1e-14
 Identities = 28/105 (26%), Positives = 57/105 (54%), Gaps = 2/105 (1%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            E +  LF G+L  +V ++ L + F +F      ++VRD+ TGK++G+ F+ F +     
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171

Query: 195 AALKEMNGKYVGNRPIKLRKSK--WQERTDFEALERSKNHNQKKP 237
            A++E+NGK +  RP++++K++   Q R++      +    +   
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSR 216

Length = 306

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 64.6 bits (158), Expect = 5e-14
 Identities = 28/72 (38%), Positives = 42/72 (58%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G+L   + +D L   F  F      ++ RD  TG++KGYGFI FA+  D   AL+++
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 201 NGKYVGNRPIKL 212
           NG  +  RPIK+
Sbjct: 61  NGFELAGRPIKV 72

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 64.6 bits (158), Expect = 6e-14
 Identities = 31/71 (43%), Positives = 42/71 (59%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF   L NE  D  L + F+ F +   AKV  DK TG++K +GF+S+ NP    AA+K M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 201 NGKYVGNRPIK 211
           NG  VG + +K
Sbjct: 61  NGFQVGGKRLK 71

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed 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. . Length = 73

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

 Score = 63.7 bits (156), Expect = 1e-13
 Identities = 23/65 (35%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 146 LGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV 205
           LG +++D+ L + F ++     AKV++D   GK+KG+GF++F N      A++E+NGK V
Sbjct: 9   LGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEELNGKEV 67

Query: 206 GNRPI 210
             + +
Sbjct: 68  NGKKL 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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 63.1 bits (153), Expect = 1e-12
 Identities = 27/73 (36%), Positives = 44/73 (60%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +LF G L    +D  L  AF+ F     AKV+ D+ TG+++G+GF++F +     AA+ E
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 200 MNGKYVGNRPIKL 212
           M+GK +  R I++
Sbjct: 96  MDGKELNGRHIRV 108

Length = 144

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

 Score = 61.2 bits (149), Expect = 1e-12
 Identities = 20/72 (27%), Positives = 41/72 (56%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF G+L  + ++D + +AF  +   +  ++  D  +G+ KG+G++ F++     AAL  +
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 201 NGKYVGNRPIKL 212
            G  +  RP++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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 60.4 bits (147), Expect = 3e-12
 Identities = 19/66 (28%), Positives = 35/66 (53%)

Query: 146 LGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV 205
           L  ++  + L   F         K+VRD+ TG++ GYGF+ + + +D   A+  +NG  +
Sbjct: 8   LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEI 67

Query: 206 GNRPIK 211
            N+ +K
Sbjct: 68  RNKRLK 73

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

 Score = 59.2 bits (144), Expect = 9e-12
 Identities = 24/70 (34%), Positives = 37/70 (52%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF   L  +  +  L + F  +      ++VRDK+TGK +GY FI F +  D+ AA K  
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 201 NGKYVGNRPI 210
           +GK +  R +
Sbjct: 64  DGKKIDGRRV 73

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

 Score = 58.8 bits (143), Expect = 1e-11
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ GDL   +++  +  AF+        K++R+K+TGK+ GYGF+ FA       AL+ +
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 201 NGKYVGNRPIKLR 213
           NGK + N   + R
Sbjct: 62  NGKPIPNTQQRFR 74

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 58.1 bits (141), Expect = 2e-11
 Identities = 30/76 (39%), Positives = 43/76 (56%), Gaps = 5/76 (6%)

Query: 140 RLF--CGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           RLF  CG     V +D L +AF+ F       VV+DK+T ++KG  ++ FA  S  A A+
Sbjct: 5   RLFIVCG---KSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61

Query: 198 KEMNGKYVGNRPIKLR 213
           +EMNGK +G     L+
Sbjct: 62  EEMNGKCLGGDTKPLK 77

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 57.7 bits (140), Expect = 2e-11
 Identities = 23/72 (31%), Positives = 41/72 (56%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + +F  +L  + ++ +L + FS F +    KV+RD  T K KGYGF++  N  +  +A+ 
Sbjct: 2   WCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIA 61

Query: 199 EMNGKYVGNRPI 210
            +NG  +G R +
Sbjct: 62  SLNGYRLGGRVL 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 61.9 bits (150), Expect = 3e-11
 Identities = 39/164 (23%), Positives = 64/164 (39%), Gaps = 8/164 (4%)

Query: 48  PPPAAYPAPVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIE 107
               A   P    V  + +     +   H A   F+  A   T      +        + 
Sbjct: 181 SQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFT----AVLAHQQQQHAVA 236

Query: 108 HKAETKKKSIPRKAAGQT---WEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPS 164
            +   ++ S P    GQT        +A      Y +F  +L  + ++ VL + F  F +
Sbjct: 237 QQHAAQRAS-PPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGA 295

Query: 165 FNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNR 208
               K++RD  T + KGYGF+S  N  + A A+  +NG  +GNR
Sbjct: 296 VQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNR 339

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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 55.7 bits (135), Expect = 1e-10
 Identities = 24/62 (38%), Positives = 36/62 (58%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L     DD L K FS+F     A V+ D++TGK++GYGF++F +      A K+
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 200 MN 201
            N
Sbjct: 62  PN 63

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 60.6 bits (147), Expect = 1e-10
 Identities = 24/70 (34%), Positives = 43/70 (61%), Gaps = 1/70 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+  +L + V D+ L + FS       AKV+ D+  G ++G+GF+ F+NP +   A+ EM
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEM 346

Query: 201 NGKYVGNRPI 210
           +G+ +G +P+
Sbjct: 347 HGRMLGGKPL 356

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

 Score = 54.5 bits (132), Expect = 4e-10
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 142 FCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN 201
           F G+L  ++ ++ L K F         ++VRD++TG  KG+G++ F     +A ALK +N
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK-LN 61

Query: 202 GKYVGNRPIKL 212
           G  +  R I++
Sbjct: 62  GIKLKGRKIRV 72

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

 Score = 59.1 bits (143), Expect = 5e-10
 Identities = 33/93 (35%), Positives = 50/93 (53%), Gaps = 5/93 (5%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ GDL  +V +  L   F  F      +V RD  T ++ GYG+++F NP+D   AL+ M
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 201 NGKYVGNRPIKLRKSKWQERTDFEALERSKNHN 233
           N K +G +PI++    W +R    +L RS   N
Sbjct: 63  NFKRLGGKPIRI---MWSQRD--PSLRRSGVGN 90

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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 54.1 bits (131), Expect = 5e-10
 Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 4/69 (5%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE- 199
           LF G L  +  ++ L + FS++       +++D  TG+++G+GF++FA+PS +   L   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 200 ---MNGKYV 205
              ++G+ +
Sbjct: 61  PHVLDGREI 69

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 54.6 bits (132), Expect = 5e-10
 Identities = 27/77 (35%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PEN   LF   L     D+ L   FSRF      +V+RDK+TG +  Y FI F    D  
Sbjct: 2   PEN--VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCE 59

Query: 195 AALKEMNGKYVGNRPIK 211
            A  +M+   + +R I 
Sbjct: 60  EAYFKMDNVLIDDRRIH 76

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

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

 Score = 54.3 bits (131), Expect = 5e-10
 Identities = 20/60 (33%), Positives = 32/60 (53%)

Query: 152 DDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK 211
           D+     F         K+VRDKRTG + G+GF+ + +  D   A++ +NG  + N+ IK
Sbjct: 14  DEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIK 73

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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 53.8 bits (130), Expect = 6e-10
 Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R+F G +  +  ++ L   FSRF S    K++ D R G +KGYGF++F    D    L  
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62

Query: 200 MN 201
            N
Sbjct: 63  GN 64

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

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

 Score = 58.3 bits (141), Expect = 7e-10
 Identities = 33/103 (32%), Positives = 57/103 (55%), Gaps = 3/103 (2%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+  +L   VN+D L + F++F     A V++D  +G+++G+ F++F    D A A++EM
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 201 NGKYVG--NRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSK 241
           NGK +G      KL   + Q+R + EA  R K    ++ +  K
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMK 282

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

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 150 VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRP 209
             +  L K FS F       + R K  GK KG+ F+ F + +D   A+K +NGK +  RP
Sbjct: 11  CTEADLKKLFSPFGFVWEVTIPR-KPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRP 69

Query: 210 I 210
           +
Sbjct: 70  V 70

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|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 53.1 bits (127), Expect = 1e-09
 Identities = 27/73 (36%), Positives = 42/73 (57%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF   L  E  D  L++ F  F +   AKV  DK+T  +K +GF+S+ NP    AA++ M
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 201 NGKYVGNRPIKLR 213
           NG  +G + +K++
Sbjct: 67  NGFQIGTKRLKVQ 79

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. 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 = 79

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

 Score = 52.6 bits (127), Expect = 1e-09
 Identities = 22/71 (30%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+  +L   V ++ L + FS +      ++VR+K   + +G+ F+ FA+P D  AALK++
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 201 NGKYVGNRPIK 211
           NG  +  R ++
Sbjct: 59  NGLVLDGRTLR 69

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

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 53.1 bits (127), Expect = 1e-09
 Identities = 22/72 (30%), Positives = 43/72 (59%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F  +LG + ++ +L + F  F +    KV+RD  T K KG+GF++  N  + A A+  +
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 201 NGKYVGNRPIKL 212
           NG  +G++ +++
Sbjct: 64  NGYRLGDKILQV 75

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), 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. 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 = 84

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 52.9 bits (127), Expect = 2e-09
 Identities = 23/59 (38%), Positives = 33/59 (55%)

Query: 155 LSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR 213
           L K FS+F +    +V R K+TG +K YGFI F NP   A A K MN   +  + +++ 
Sbjct: 16  LKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQVH 74

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>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 = 52.6 bits (127), Expect = 2e-09
 Identities = 21/70 (30%), Positives = 37/70 (52%)

Query: 142 FCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN 201
           F G++  +  ++ L + FS        ++V D+ TGK KGYGF  F +    A+A++ +N
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 202 GKYVGNRPIK 211
           G     R ++
Sbjct: 62  GYEFNGRALR 71

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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 52.8 bits (126), Expect = 2e-09
 Identities = 24/72 (33%), Positives = 43/72 (59%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F  +L  + ++ VL + F  F + N  KV+RD  T K KG+GF++  N  + A A+  +
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 201 NGKYVGNRPIKL 212
           NG  +G+R +++
Sbjct: 66  NGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 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. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound 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 = 86

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 52.2 bits (126), Expect = 2e-09
 Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 10/79 (12%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVV-----RDKRTGKTKGYGFISFANPSDIAA 195
           ++ G+L  +V +++L + F +        VV     +D+ T   +GYGF+ F +  D   
Sbjct: 1   VYVGNLDEKVTEELLWELFIQ-----AGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADY 55

Query: 196 ALKEMNGKYVGNRPIKLRK 214
           A+K MN   +  +PI++ K
Sbjct: 56  AIKIMNMIKLYGKPIRVNK 74

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

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

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 23/72 (31%), Positives = 36/72 (50%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF  +L  +  D+ L + FS         VV+DK + K +G+G+++FA   D   AL+E 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 201 NGKYVGNRPIKL 212
                G R I +
Sbjct: 62  KKTKFGGRKIHV 73

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|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 52.2 bits (125), Expect = 3e-09
 Identities = 27/73 (36%), Positives = 42/73 (57%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF   L  E  D  L + F  F +   AKV  D+ T ++K +GF+SF NP+   AA++ M
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 201 NGKYVGNRPIKLR 213
           NG  +G + +K++
Sbjct: 67  NGFQIGMKRLKVQ 79

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains 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 effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

>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 = 51.5 bits (124), Expect = 4e-09
 Identities = 19/64 (29%), Positives = 31/64 (48%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RLF  +L     ++ L + F  F   +   +  DK T ++KG+ F+SF  P     A  E
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 200 MNGK 203
           ++G 
Sbjct: 61  LDGS 64

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

 Score = 51.4 bits (123), Expect = 5e-09
 Identities = 25/72 (34%), Positives = 38/72 (52%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF  +L   V  + L+  FS       A VV D  TG+++GYGF++FA   D   AL ++
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 201 NGKYVGNRPIKL 212
             K +  R ++L
Sbjct: 62  KNKKLHGRILRL 73

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

 Score = 51.4 bits (124), Expect = 5e-09
 Identities = 16/57 (28%), Positives = 33/57 (57%)

Query: 146 LGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG 202
           L  + ++D L + F  F   +   + +DK TG+++G+ F++F    D   A++++NG
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 55.7 bits (134), Expect = 6e-09
 Identities = 26/76 (34%), Positives = 42/76 (55%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           N  +L+ G+L   + +  L + F  F      ++ RD  TG++KG+GFI F +  +   A
Sbjct: 185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA 244

Query: 197 LKEMNGKYVGNRPIKL 212
           L+ MNG  +  RPIK+
Sbjct: 245 LEVMNGFELAGRPIKV 260

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 50.9 bits (122), Expect = 8e-09
 Identities = 27/71 (38%), Positives = 40/71 (56%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RLF  +L     +D L K FS+F   +   V  DK++GK+KG+ ++ F +P D   A KE
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 200 MNGKYVGNRPI 210
           ++GK    R I
Sbjct: 64  LDGKVFQGRLI 74

This subgroup corresponds to the RRM2 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). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 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 = 79

>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 = 51.1 bits (123), Expect = 1e-08
 Identities = 20/70 (28%), Positives = 35/70 (50%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF G L  +  ++ L + FSR+      ++VRD  TG +KGY F+ + +  D   A ++ 
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 201 NGKYVGNRPI 210
           +   +    I
Sbjct: 66  HKLVIDGSEI 75

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

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

 Score = 50.3 bits (121), Expect = 1e-08
 Identities = 23/62 (37%), Positives = 32/62 (51%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G L  EV++ VL  AF  F      ++  D  T K +G+ F+ F  P D AAA+  M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 201 NG 202
           N 
Sbjct: 61  NE 62

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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 50.9 bits (121), Expect = 1e-08
 Identities = 22/72 (30%), Positives = 42/72 (58%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F  +L  + ++ +L + F  F +    KV+RD  T K KG+GF++  N  + A A+  +
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 201 NGKYVGNRPIKL 212
           NG  +G+R +++
Sbjct: 66  NGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 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. It 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 = 86

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 50.5 bits (120), Expect = 1e-08
 Identities = 24/72 (33%), Positives = 42/72 (58%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F  +L  E ++ VL + F  F +    KV+RD  T K KG+GF++  N  + A A+  +
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 201 NGKYVGNRPIKL 212
           NG  +G+R +++
Sbjct: 64  NGYRLGDRVLQV 75

This subgroup corresponds to the RRM3 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 = 85

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 50.3 bits (121), Expect = 1e-08
 Identities = 23/80 (28%), Positives = 47/80 (58%), Gaps = 6/80 (7%)

Query: 139 YRLFCGDLGNEVNDDV---LSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
            ++F G L N +++D    L ++F +  +FN   +V+D  TG +KGY F  + +PS    
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFN---LVKDSATGLSKGYAFCEYLDPSVTDQ 57

Query: 196 ALKEMNGKYVGNRPIKLRKS 215
           A+  +NG  +G++ + ++++
Sbjct: 58  AIAGLNGMQLGDKKLTVQRA 77

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

>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 = 49.9 bits (120), Expect = 2e-08
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 6/71 (8%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           ++ G+L + + ++ L + FS F        + + R  K KGY F+ F      A A+  +
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPF------GAIEEVRVFKDKGYAFVRFDTHEAAATAIVAV 56

Query: 201 NGKYVGNRPIK 211
           NG  +  + +K
Sbjct: 57  NGTSINGQTVK 67

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

 Score = 49.7 bits (119), Expect = 2e-08
 Identities = 21/59 (35%), Positives = 34/59 (57%)

Query: 153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK 211
           D +   FS        K++RDK TG++ GYGF+++ +P D   A+  +NG  + N+ IK
Sbjct: 16  DEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIK 74

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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 49.5 bits (118), Expect = 2e-08
 Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 3/68 (4%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE- 199
           +F G L  E  DD L + F +F       V+RD  TG+++G+GF++F  P  +   +K+ 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 200 --MNGKYV 205
             ++GK +
Sbjct: 61  HILDGKII 68

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 48.8 bits (116), Expect = 4e-08
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           D  LF G+L   V +++L + F +        + +DK  GK K +GF+ F +   +  A+
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAI 59

Query: 198 KEMNGKYVGNRPIKLR 213
             +NG  +  RPIK+ 
Sbjct: 60  ALLNGIRLYGRPIKVH 75

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 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. RBM11 contains 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 of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 48.5 bits (116), Expect = 6e-08
 Identities = 25/68 (36%), Positives = 36/68 (52%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +LF G+L   V    L + FS+F       V  DK TG +KGYGF+SF++   +  AL++
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 200 MNGKYVGN 207
                 GN
Sbjct: 61  QKHILEGN 68

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 48.8 bits (117), Expect = 6e-08
 Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 137 NDYR----LFCGDLGNEVND-DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPS 191
           + Y+    ++ G L  E+ + D+L   FS++       +VRDK+TGK+KG+ F+++ +  
Sbjct: 4   DQYKDSAYIYIGGLPYELTEGDILC-VFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQR 62

Query: 192 DIAAALKEMNGKYVGNRPIK 211
               A+  +NG  +  R I+
Sbjct: 63  STILAVDNLNGIKLLGRTIR 82

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 47.6 bits (113), Expect = 1e-07
 Identities = 25/61 (40%), Positives = 39/61 (63%), Gaps = 2/61 (3%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFAN--PSDIAAAL 197
           +LF G L  +V +  L++ FS+F     A+V+ DK+TGK +G+GF+ F N   +D AA +
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 198 K 198
           K
Sbjct: 61  K 61

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 20/57 (35%), Positives = 31/57 (54%)

Query: 155 LSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK 211
           L K FS+F +    ++ R K+TGK+KGY F+ F +P       + MN   +  R +K
Sbjct: 16  LRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLK 72

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 21/68 (30%), Positives = 37/68 (54%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L  G+L  E  D+   +  S F +     +V  + TG++KGYGF+ +A+ +    A  ++
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 201 NGKYVGNR 208
           +GK +G R
Sbjct: 62  DGKQIGGR 69

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 47.5 bits (113), Expect = 2e-07
 Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R+F G +  + N++ L K FS++ +    K+V D R G +KGYGF++F    D    L+E
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQE 62

Query: 200 MN 201
            N
Sbjct: 63  AN 64

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 8/70 (11%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+  +L     ++ L + FS +      +V R K   K K Y F+ F    D   A++EM
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEY-----GEVERVK---KIKDYAFVHFEERDDAVKAMEEM 55

Query: 201 NGKYVGNRPI 210
           NGK +   PI
Sbjct: 56  NGKELEGSPI 65

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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 32/94 (34%), Positives = 49/94 (52%), Gaps = 12/94 (12%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF   L  E  D  L + F  F +   AKV  DK+T  +K +GF+S+ NP    AA++ M
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 201 NGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQ 234
           NG  +G + +K++            L+RSKN ++
Sbjct: 70  NGFQIGMKRLKVQ------------LKRSKNDSK 91

This subgroup corresponds to the RRM3 of 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), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. 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 specifically binds 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 contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are 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. . Length = 92

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSR--FPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
            ++ G+L  ++ +D + + F      S  +A    DK TG+ KG+G + FA+   + AAL
Sbjct: 1   TVYIGNLAWDITEDDVREFFKGCEITSVRLAT---DKETGEFKGFGHVDFADEESLDAAL 57

Query: 198 KEMNGKYVGNRPIKL 212
           K ++G  +  RPI++
Sbjct: 58  K-LDGTVLCGRPIRI 71

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 9/78 (11%)

Query: 146 LGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV 205
           L     +  L + FSR+      +VV D++TG+++G+GF+ F +  D   A + +NG  +
Sbjct: 7   LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66

Query: 206 GNRPIKLRKSKWQERTDF 223
             R I         R D+
Sbjct: 67  DGRRI---------RVDY 75

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 46.7 bits (111), Expect = 3e-07
 Identities = 24/73 (32%), Positives = 39/73 (53%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R++ G +  E+ +D + +AFS F       +  D  T K KG+ F+ +  P     AL++
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 200 MNGKYVGNRPIKL 212
           MNG  +G R IK+
Sbjct: 62  MNGVMLGGRNIKV 74

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 46.3 bits (110), Expect = 3e-07
 Identities = 17/58 (29%), Positives = 33/58 (56%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           +LF G L  E   + L + FS++       +++DK T +++G+GF+ F +P+ +   L
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVL 58

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 46.3 bits (110), Expect = 3e-07
 Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +LF G L  + +D  L + F+R+       V+ D  T +++G+GFI+F++  +   A++ 
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 200 MNGKYVGNRPIKLRKSK 216
                 GN+ I+L+++K
Sbjct: 64  QPHSIDGNQ-IELKRAK 79

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 46.3 bits (110), Expect = 4e-07
 Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + LF G+L    + D L  A S F S     V  D R G +K +G++ F +  D+  AL 
Sbjct: 1   FSLFVGNLNPNKDFDELKTAISEFFSKKNLAVQ-DVRIGSSKKFGYVDFESAEDLEKAL- 58

Query: 199 EMNGKYVGNRPIKLRKS 215
           E+ GK +    IKL K+
Sbjct: 59  ELTGKKLLGNEIKLEKA 75

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

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

 Score = 46.2 bits (109), Expect = 4e-07
 Identities = 22/71 (30%), Positives = 37/71 (52%)

Query: 146 LGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV 205
           L   +  D L   FS       AK++RDK  G + GYGF+++ N  D   A+  +NG  +
Sbjct: 9   LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRL 68

Query: 206 GNRPIKLRKSK 216
            ++ IK+  ++
Sbjct: 69  QSKTIKVSYAR 79

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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 45.9 bits (109), Expect = 5e-07
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 7/74 (9%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVR-D-KRTGKTKGYGFISFANPSDIAAALK 198
           LF G+L        L +AF RF      +++  D K+ G    Y FI +A+ + +  A++
Sbjct: 5   LFIGNLEKTTTYSDLREAFERF-----GEIIDIDIKKQGGNPAYAFIQYADIASVVKAMR 59

Query: 199 EMNGKYVGNRPIKL 212
           +M+G+Y+GN  +KL
Sbjct: 60  KMDGEYLGNNRVKL 73

This subfamily corresponds to the RRM3 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 = 74

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 46.0 bits (110), Expect = 6e-07
 Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 146 LGNEVNDDVLSKAFSRFPSFNMA--KVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK 203
           L     ++ + +A S   S  +   +++RDK TG ++G+ F+ F +  D    +  +N  
Sbjct: 10  LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNL 69

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 45.8 bits (109), Expect = 6e-07
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 8/73 (10%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +LF G L  E  DD L   FS++       V++D  T +++G+GF++FA+ S++ AA+  
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM-- 58

Query: 200 MNGKYVGNRPIKL 212
                   RP K+
Sbjct: 59  ------NARPHKV 65

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 45.5 bits (108), Expect = 6e-07
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF G+L  E  +D L   F R       +++  + +GK KG+ F+ F    +I  A   +
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF---EEIEFATNAL 57

Query: 201 NGKYVGNRPIKLRK 214
            GK++  R +++  
Sbjct: 58  KGKHLNGRALRVEY 71

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . 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 = 44.9 bits (107), Expect = 9e-07
 Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 4/66 (6%)

Query: 149 EVNDDVLSKAFSRF---PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV 205
           ++++D L   FS+F    S  + K   +K+     G+ F++F + S    AL ++NG  +
Sbjct: 11  KLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL-QLNGTEL 69

Query: 206 GNRPIK 211
           G R I 
Sbjct: 70  GGRKIS 75

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVV---RDKRTGKTKGYGFISFANPSDIAAAL 197
           L+ G+L  +V ++VL + F RF      K++    ++   + +  GF++F N +D   AL
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 198 KEMNGKYVGNRPIKL 212
            E++GK V    +KL
Sbjct: 64  DELDGKDVMGYELKL 78

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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 17/75 (22%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L  +V ++   + FS+F     A++++D  TG+++G+GF++F + S +      
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVF-S 59

Query: 200 MNGKYVGNRPIKLRK 214
                +G + +++++
Sbjct: 60  AGMLELGGKQVEVKR 74

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 44.8 bits (107), Expect = 1e-06
 Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F  +L   +++  L   FS F +    KV  D+  G +KGYGF+ F        A++++
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 201 NGKYVGNR 208
           NG  + ++
Sbjct: 64  NGMLLNDK 71

This subfamily corresponds to the RRM2 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 mammalian, such as ovary and testis. It may play an important role in germ cell development. 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 = 77

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMA-KVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           L+ GDL   ++++ + +AF+      ++ K++R+K TG   GY F+ FA+ +     L +
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 200 MNGKYV-GNRPIK 211
           +NGK + G+ P K
Sbjct: 62  LNGKPIPGSNPPK 74

This subgroup corresponds to the RRM1 of SECp43, 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. . Length = 84

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 6/70 (8%)

Query: 150 VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKY-VGNR 208
             +  L   FS F    M +V +D +TG++KG+GF+ FA+  D    +K ++ ++ +  R
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYED---QVKVLSQRHMIDGR 67

Query: 209 --PIKLRKSK 216
              +K+  SK
Sbjct: 68  WCDVKIPNSK 77

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

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

 Score = 44.6 bits (105), Expect = 1e-06
 Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 8/63 (12%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF  +L N V +++L KAF +F           +R  K K Y FI F        A++EM
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKL--------ERVKKLKDYAFIHFDERDGAVKAMEEM 55

Query: 201 NGK 203
           NGK
Sbjct: 56  NGK 58

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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 44.9 bits (106), Expect = 1e-06
 Identities = 29/81 (35%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 136 ENDYR----LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPS 191
           E+D R    LF G+L   V +  L +AF RF       + R  R G+T  YGF+ F N  
Sbjct: 1   EDDQRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGR-GQTSTYGFLKFENLD 59

Query: 192 DIAAALKEMNGKYVGNRPIKL 212
               A   M+GK +   PIK+
Sbjct: 60  MAHRAKLAMSGKVLRRNPIKI 80

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 19/63 (30%), Positives = 30/63 (47%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R++   +  ++++D +   F  F       +  D  TGK KGYGFI + NP     A+  
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 200 MNG 202
           MN 
Sbjct: 62  MNL 64

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

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

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G+L   V +D+L++ FS+       K++R+        Y F+ + +    AAAL+ M
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDHRSAAAALQTM 57

Query: 201 NGKYVGNRPIK 211
           NG+ +  + IK
Sbjct: 58  NGRLILGQEIK 68

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|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 20/72 (27%), Positives = 38/72 (52%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F G++  E  ++ L   FS        ++V D+ TGK KGYGF  + +     +A++ +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 201 NGKYVGNRPIKL 212
           NG  +  R +++
Sbjct: 61  NGYELNGRQLRV 72

This subgroup 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. . Length = 75

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

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 20/71 (28%), Positives = 37/71 (52%)

Query: 146 LGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV 205
           L   +  +     F         K+VRDK TG++ GYGF+++ +P+D   A+  +NG  +
Sbjct: 11  LPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKL 70

Query: 206 GNRPIKLRKSK 216
             + IK+  ++
Sbjct: 71  QTKTIKVSYAR 81

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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 17/52 (32%), Positives = 32/52 (61%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPS 191
           +LF G L  +V ++ L + FS++ +    ++V DK TGK +G+ F++F +  
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYD 52

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

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

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%)

Query: 146 LGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV 205
           L   +  + L   F         K+VRDK TG++ GYGF+++ +P D   A+  +NG  +
Sbjct: 12  LPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL 71

Query: 206 GNRPIKLRKSK 216
             + IK+  ++
Sbjct: 72  QTKTIKVSYAR 82

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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 47.6 bits (113), Expect = 2e-06
 Identities = 22/84 (26%), Positives = 46/84 (54%), Gaps = 6/84 (7%)

Query: 135 PENDYRLFCGDLGNEVNDDV---LSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPS 191
            ++  R++ G+L   + +D    L ++F    +FN+   ++D  TG +KGY F  + +PS
Sbjct: 292 LDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNL---IKDIATGLSKGYAFCEYKDPS 348

Query: 192 DIAAALKEMNGKYVGNRPIKLRKS 215
               A+  +NGK  G+  + ++++
Sbjct: 349 VTDVAIAALNGKDTGDNKLHVQRA 372

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 43.8 bits (103), Expect = 3e-06
 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RLF G+L  ++ ++   K F ++   +   + RD+      G+GFI   + +    A  E
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAE 56

Query: 200 MNGKYVGNRPIKLR 213
           ++G  + NRP+++R
Sbjct: 57  LDGTILKNRPLRIR 70

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK-E 199
           LF G+L   + ++ L +AF R+       + R  R G+   Y F+ F N  D+A   K  
Sbjct: 5   LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPR-GQGNAYAFVKFLN-LDMAHRAKVA 62

Query: 200 MNGKYVGNRPIKL 212
           M+G+Y+G   IK+
Sbjct: 63  MSGQYIGRNQIKI 75

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 43.8 bits (103), Expect = 3e-06
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 155 LSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK 214
           L + FSR+       VV D+RTG+++G+ F+ F    D   A++  NG  +  R I++  
Sbjct: 16  LREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRVDY 75

Query: 215 S 215
           S
Sbjct: 76  S 76

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 16/53 (30%), Positives = 30/53 (56%)

Query: 150 VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG 202
           V  + L + F   P      + RD  TGK+KG+ +++++NP+    A +++NG
Sbjct: 11  VTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNG 63

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 43.6 bits (102), Expect = 4e-06
 Identities = 18/58 (31%), Positives = 36/58 (62%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           +LF G L  E  DD L + F ++ +     V+RD +T +++G+GF++++   ++ AA+
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 43.1 bits (101), Expect = 5e-06
 Identities = 19/60 (31%), Positives = 35/60 (58%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L  + + D L   FS+F       V+RD  T +++G+GF++FA+P+ +   L +
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 43.0 bits (101), Expect = 5e-06
 Identities = 22/69 (31%), Positives = 40/69 (57%), Gaps = 4/69 (5%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF   L  +  ++ L ++F    +   A++V D+ TG +KG+GF+ F++  D  AA + M
Sbjct: 3   LFVKGLSEDTTEETLKESFDGSIA---ARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 201 -NGKYVGNR 208
            +G+  GN+
Sbjct: 60  EDGEIDGNK 68

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 43.8 bits (103), Expect = 6e-06
 Identities = 23/61 (37%), Positives = 33/61 (54%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           D+ LF  +L  +  ++ L+  FS+F S   A  V DK TG+ KG GF+ F +     A L
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

Query: 198 K 198
           K
Sbjct: 61  K 61

This subgroup corresponds to the RRM3 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 = 107

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 17/63 (26%), Positives = 30/63 (47%)

Query: 149 EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNR 208
           E  ++ +   F+ F       +  D+RTG  KGY  I +    +  AA++ +NGK +  +
Sbjct: 17  EAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQ 76

Query: 209 PIK 211
            I 
Sbjct: 77  TIS 79

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

 Score = 42.8 bits (100), Expect = 9e-06
 Identities = 19/58 (32%), Positives = 33/58 (56%)

Query: 159 FSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
           F         K+VRDK TG++ GYGF+++ +P D   A+  +NG  +  + IK+  ++
Sbjct: 23  FGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 80

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|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 42.3 bits (99), Expect = 9e-06
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF  +L   V +++L K+FS F           +R  K K Y F+ F        A+ EM
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKL--------ERVKKLKDYAFVHFEERDAAVRAMDEM 55

Query: 201 NGKYVGNRPIKLRKSK 216
           NGK +    I++  +K
Sbjct: 56  NGKEIEGEEIEIVLAK 71

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R 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 R binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 10/67 (14%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYG---FISFANPSDIAAAL 197
           LF  +LG    ++ L + FSR P F   K+         KG G   F+ F + S    AL
Sbjct: 5   LFVANLGPNTTEEELRQLFSRQPGFRRLKMHN-------KGGGPVCFVEFEDVSFATQAL 57

Query: 198 KEMNGKY 204
             + G  
Sbjct: 58  NSLQGAV 64

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 19/53 (35%), Positives = 28/53 (52%)

Query: 151 NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK 203
            D+ L K    F      K + DK+T K KGYGF+ F +P     A++ +NG+
Sbjct: 13  TDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
              ++F G L   V +  L K FS+F +     V+ D    + +G+GFI+F +   +   
Sbjct: 1   RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

Query: 197 LKE----MNGKYV 205
           + E    +NGK V
Sbjct: 61  VNEHFHDINGKKV 73

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

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

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +++ G+LG       L   F ++       V R        G+ F+ F +P D   A++ 
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55

Query: 200 MNGKYVGNRPIKLRKSK 216
           ++G+ +    +++  S+
Sbjct: 56  LDGRRICGNRVRVELSR 72

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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R+   +L   V +D L + F         KV+R  R GK++ +GF+ F +  D   A+K 
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMR-TRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 200 MNGKYVG 206
            N  ++ 
Sbjct: 61  FNKTFID 67

This subgroup corresponds to the RRM1 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 149 EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSD----IAAALKEMNGKY 204
           +  ++ L + FS+F     A++V+DK TG +KG  F+ F         + AA    +   
Sbjct: 11  DATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGL 70

Query: 205 -VGNRPIKLRKS 215
            +  R + +  +
Sbjct: 71  SLDGRRLIVTLA 82

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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 24/55 (43%), Positives = 31/55 (56%), Gaps = 9/55 (16%)

Query: 154 VLSKAFSRFPSFNMAKVV-----RDKRTGKTKGYGFISFANPSDIAAALKEMNGK 203
           VL K FS+F      K+V      D+ TGKTKGY F+ FA P +   A+K +NG 
Sbjct: 23  VLRKIFSKFGV---GKIVGIYMPVDE-TGKTKGYAFVEFATPEEAKEAVKALNGY 73

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), 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-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

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

 Score = 41.0 bits (97), Expect = 2e-05
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 155 LSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK 214
           L K FS F       V + K   K  G+ F+ F+       A++ +NG   G RP+++  
Sbjct: 1   LYKLFSPF-----GNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 215 S 215
           S
Sbjct: 56  S 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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 16/53 (30%), Positives = 27/53 (50%)

Query: 150 VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG 202
           VN D L + FS + +     +  D+     +GY ++ F +P D   A+K M+G
Sbjct: 10  VNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDG 62

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 151 NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKY 204
            ++ L + F  F       +V+DK TG++KG+G++ F  PS  A AL+  +  +
Sbjct: 13  TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCDKSF 66

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+  +L  ++ +D L K F  + +     ++RDK TG  +G  F+ +    +  AA+  +
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 201 NGKYV--GNRPIKLR 213
           NG        P+ +R
Sbjct: 63  NGTIPPGSTMPLSVR 77

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|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 = 41.0 bits (97), Expect = 2e-05
 Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +LF G L     ++ +   F  + +     ++RDK TG++KG  F+ F++  +   A++ 
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 200 MNGKYV---GNRPI 210
           ++GK      +RP+
Sbjct: 61  LHGKVTMPGASRPL 74

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

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRF---PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           RL+ G+L + + +  L K FS++     F+          G+ +GY F++F    +   A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 197 LKEMNGKYVGNRPIKLR 213
           LK +NGK    + + +R
Sbjct: 61  LKSLNGKTALGKKLVVR 77

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 44.2 bits (104), Expect = 3e-05
 Identities = 20/54 (37%), Positives = 32/54 (59%)

Query: 159 FSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
           F+        K+VRDK TG++ GYGF+++  P D   A+  +NG  + N+ IK+
Sbjct: 24  FTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKV 77

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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 7/73 (9%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF  +L  E   ++L   F++FP F      ++ R    +G  F+ F        AL+ +
Sbjct: 5   LFLQNLPEETTKEMLEMLFNQFPGF------KEVRLVPRRGIAFVEFETEEQATVALQAL 58

Query: 201 NGKYV-GNRPIKL 212
            G  +     +K+
Sbjct: 59  QGFKITPGHAMKI 71

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 29/82 (35%)

Query: 140 RLFCGDLGNEVNDDVLSKA-----FSRFPSFNMAKVVRDKRTGKT------KGYGFISFA 188
           R+F G+L    N D +SK      FS++              GK       KGYGF+ F 
Sbjct: 2   RVFVGNL----NTDKVSKEDLEEIFSKY--------------GKILGISLHKGYGFVQFD 43

Query: 189 NPSDIAAALKEMNGKYVGNRPI 210
           N  D  AA+   NG+ +  + +
Sbjct: 44  NEEDARAAVAGENGREIAGQKL 65

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 41.0 bits (96), Expect = 3e-05
 Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 1/53 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDI 193
           +F G +   +++  +   F+++ S    K++ D RTG +KGYGF+SF +  D+
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDV 59

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 43.9 bits (103), Expect = 3e-05
 Identities = 21/67 (31%), Positives = 36/67 (53%)

Query: 146 LGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV 205
           L  ++ D  L   F      N  +++RD +TG + GY F+ F + +D   A+K +NG  V
Sbjct: 115 LPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITV 174

Query: 206 GNRPIKL 212
            N+ +K+
Sbjct: 175 RNKRLKV 181

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 40.9 bits (96), Expect = 3e-05
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 4/67 (5%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK-- 198
           +F G L  +   + L + FS+F       V+RD  T +++G+GF++F++P+ +   L   
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 199 --EMNGK 203
             E++GK
Sbjct: 61  PHELDGK 67

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 5/69 (7%)

Query: 152 DDVLSKAFSRFPSFNMAKVVRDK-----RTGKTKGYGFISFANPSDIAAALKEMNGKYVG 206
           ++ L K F +        + + K         + GYGF+ F +      ALK + G  + 
Sbjct: 14  EETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVLD 73

Query: 207 NRPIKLRKS 215
              ++L+ S
Sbjct: 74  GHALELKLS 82

This subfamily corresponds to the RRM5 of RBM19 and RRM4 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). . Length = 82

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 40.6 bits (95), Expect = 4e-05
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G+L   V +D+L + F         K++ DK   K   YGF+ +    D   AL+ +
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIALQTL 59

Query: 201 NGKYVGNRPIKL 212
           NG+ + N  I++
Sbjct: 60  NGRQIENNEIRV 71

This subgroup corresponds to the RRM1 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. It 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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 40.8 bits (95), Expect = 4e-05
 Identities = 17/58 (29%), Positives = 35/58 (60%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           +LF G L  E  D+ L   F ++ +     V+RD  T +++G+GF+++++  ++ AA+
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

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

 Score = 40.4 bits (95), Expect = 5e-05
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           Y +F G L  +V  + L++ FSR        ++  KR   T  + FI F      A A++
Sbjct: 4   YSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVE 61

Query: 199 EMNGKYVGNRPIKLRK 214
             N   + N+ + ++ 
Sbjct: 62  SENHSMLKNKTMHVQY 77

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

 Score = 43.3 bits (102), Expect = 6e-05
 Identities = 23/85 (27%), Positives = 46/85 (54%), Gaps = 3/85 (3%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F  +L   V++  L   FS+F +    KV  D+  GK++GYGF+ F       AA++++
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 201 NGKYVGNRPIKLRKSKWQERTDFEA 225
           NG  + ++ +     ++ ++ + EA
Sbjct: 150 NGMLLNDKEVY--VGRFIKKHEREA 172

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

 Score = 39.9 bits (94), Expect = 6e-05
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RL   +L  +V ++ L + F R       K+  D R+G+++G   + F    D   A+K+
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIKQ 60

Query: 200 MNGKYVGNRPIKLRK 214
            NG  +  +P+++  
Sbjct: 61  FNGVLLDGQPMQVEL 75

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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 40.0 bits (94), Expect = 6e-05
 Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 169 KVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
           ++VRDK T K KG+ ++ F +   +  AL E +G    +R +++
Sbjct: 31  RLVRDKETDKFKGFCYVEFEDVESLKEAL-EYDGALFDDRSLRV 73

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 40.2 bits (94), Expect = 6e-05
 Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +LF G L  + N++ +   F+ F S     V+RD+  G+++G  F++FA+      A+K 
Sbjct: 3   KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNAIKA 61

Query: 200 MN 201
           M+
Sbjct: 62  MH 63

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. 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 = 81

>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 = 40.0 bits (94), Expect = 6e-05
 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 151 NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPI 210
           N+D L K FS++       +V+DK T K+KG  FI F +  D    +K +N K +  R +
Sbjct: 15  NND-LHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTL 73

Query: 211 K 211
           K
Sbjct: 74  K 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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 39.6 bits (93), Expect = 7e-05
 Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 170 VVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK 211
           ++ DK TG+ KG+ +I F + S +  AL  +N      R IK
Sbjct: 31  ILCDKFTGQPKGFAYIEFLDKSSVENALL-LNESEFRGRQIK 71

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are 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. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 40.0 bits (93), Expect = 8e-05
 Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 5/86 (5%)

Query: 135 PENDYR----LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANP 190
           PE+D R    LF G+L + V++  L +AF ++       + R  R G+   Y F+ F N 
Sbjct: 1   PEDDQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPAR-GQGGAYAFLKFQNL 59

Query: 191 SDIAAALKEMNGKYVGNRPIKLRKSK 216
                A   M+G+ +G  PIK+   K
Sbjct: 60  DMAHRAKVAMSGRVIGRNPIKIGYGK 85

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 85

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 43.1 bits (101), Expect = 8e-05
 Identities = 24/73 (32%), Positives = 40/73 (54%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R++ G +  E+ +D + +AF  F       +  D  TGK KG+ F+ +  P     AL++
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 200 MNGKYVGNRPIKL 212
           MNG+ +G R IK+
Sbjct: 169 MNGQMLGGRNIKV 181

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           D +++ G+LGN  N   L +AF  +       V R+       G+ F+ F +P D A A+
Sbjct: 4   DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 58

Query: 198 KEMNGKYVGNRPIKLRKSKWQER 220
           +E++G+ +    +++  S  ++R
Sbjct: 59  RELDGRTLCGCRVRVELSNGEKR 81

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that 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. SRSF3 can shuttle between the nucleus and cytoplasm. It contains 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 = 81

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            LF G+L      D L + F         ++ +D   G++KG+G + FA       AL E
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKAL-E 58

Query: 200 MNGKYVGNRPIKL 212
            +G+ +  R I++
Sbjct: 59  KSGEELLGREIRV 71

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

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

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+   L   +    L + FS++     ++++RD+ TG ++G GFI F    +   A+K +
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 201 NGKYV--GNRPIKLR 213
           NG+     + PI ++
Sbjct: 63  NGQKPEGASEPITVK 77

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|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 2/45 (4%)

Query: 169 KVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR 213
            +V D   G+  G  ++ FA+P D   AL+  +   +G R I++ 
Sbjct: 31  HIVYDDD-GRPTGEAYVEFASPEDARRALR-KHNNKMGGRYIEVF 73

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 10/45 (22%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 169 KVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR 213
           +++RD+ + ++KG  ++ F +   +  AL  + G+ +  +PI ++
Sbjct: 30  RIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLTGQRLLGQPIMVQ 73

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RLF G+L N++ ++   + FS++        V +    K KG+GFI     ++   A  E
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGE------VSEVFLNKEKGFGFIRLDTRTNAEKAKAE 56

Query: 200 MNGKYVGNRPIKLR 213
           ++G     R +++R
Sbjct: 57  LDGIMRKGRQLRVR 70

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

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 21/79 (26%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISF-ANPSDIAAALK 198
           RLF G L   V +  L + FSRF + +  ++++ K  G  +G+ +I    + + +     
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60

Query: 199 EMNG-KYVGNRPIKLRKSK 216
            +NG K+ G+  +K+ ++K
Sbjct: 61  TLNGTKWKGSV-LKIEEAK 78

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|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 = 38.8 bits (91), Expect = 1e-04
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 6/72 (8%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F G L   V +D L   F  F      K+         KG GF+ F + +   AA++++
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKI------PPGKGCGFVQFVHRAAAEAAIQQL 57

Query: 201 NGKYVGNRPIKL 212
            G  +G   I+L
Sbjct: 58  QGTIIGGSRIRL 69

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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 3/76 (3%)

Query: 140 RLFCGDLG-NEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           ++F G L  N   +DV  + F +F   + A ++ DK T + +G+GF++F +  DI   + 
Sbjct: 1   KIFVGGLSVNTTVEDV-KQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVC 58

Query: 199 EMNGKYVGNRPIKLRK 214
           E++   + N+ ++ +K
Sbjct: 59  EIHFHEINNKMVECKK 74

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . 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 = 38.9 bits (91), Expect = 2e-04
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +LF   L   V  + L K F +       ++V + R+GK KG  ++ + N S  + A+ +
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQAVLK 62

Query: 200 MNGKYVGNRPIK 211
           M+G  +  + I 
Sbjct: 63  MDGTEIKEKTIS 74

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|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 177 GKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
            +   Y F+ FA  + +  ALK +NG   G RP+K+  S 
Sbjct: 41  TQPTRYAFVEFAEQTSVINALK-LNGAMFGGRPLKVNHSN 79

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 17/59 (28%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 155 LSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR 213
           L + F +F      +++ ++R   +KG+GF++FAN +D   A ++++G  V  R I++ 
Sbjct: 17  LRQMFGQFGPILDVEIIFNER--GSKGFGFVTFANSADADRAREKLHGTVVEGRKIEVN 73

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 7/80 (8%)

Query: 141 LFCGDLGNEVNDDVLSKA----FSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           +F   L    +DD L  A    FS++ +    KV+RD R    + Y F+ F N  D   A
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQ---RPYAFVQFTNDDDAKNA 61

Query: 197 LKEMNGKYVGNRPIKLRKSK 216
           L +  G  +  R I+  ++K
Sbjct: 62  LAKGQGTILDGRHIRCERAK 81

This subfamily corresponds to the RRM1 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 = 86

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           D  LF G+L  +V ++++ + F +       K+ +DK  GK K + F++F +   +  A+
Sbjct: 1   DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAM 59

Query: 198 KEMNGKYVGNRPIKLR 213
             +NG  +  RP+ ++
Sbjct: 60  NLLNGIKLYGRPLNIQ 75

This subfamily corresponds to the RRM of RBM7, a 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. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It 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. RBM7 contains 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. . Length = 75

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +L   +L   V+DD + + F+ F +   A V  D R+G++ G   + F   +D   A+K+
Sbjct: 2   KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYD-RSGRSLGTADVVFERRADALKAMKQ 60

Query: 200 MNGKYVGNRPIKLR 213
            NG  +  RP+K++
Sbjct: 61  YNGVPLDGRPMKIQ 74

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, 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. THOC4 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. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 37.3 bits (87), Expect = 6e-04
 Identities = 15/59 (25%), Positives = 31/59 (52%)

Query: 153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK 211
           D L + F ++       + RD+ T +++G+ F+ F +  D   A+  M+GK +  R ++
Sbjct: 13  DDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELR 71

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|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 37.2 bits (86), Expect = 7e-04
 Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFN--------MAKVVRDKRTGKTKGYGFISFANPSD 192
           +F   LG +V  + ++  F +             M  +  D+ TGK KG   +SF +P  
Sbjct: 5   IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64

Query: 193 IAAALKEMNGKYVGNRPIKL 212
             AA+   +GK     PIK+
Sbjct: 65  AKAAIDWFDGKEFSGNPIKV 84

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 145 DLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN 201
           +L   V++++L +AFS+F     A V+ D R G++ G G + F+      AA+K  +
Sbjct: 6   NLSPFVSNELLEQAFSQFGEVERAVVIVDDR-GRSTGEGIVEFSRKPGAQAAIKRCS 61

This subfamily corresponds to the RRM2 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. The family 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 contains 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 = 80

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 40.0 bits (93), Expect = 9e-04
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+  +L     ++++ K+FS F      KV R K   K + Y F+ F +  D   A+ E+
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEF---KPGKVERVK---KIRDYAFVHFEDREDAVKAMDEL 289

Query: 201 NGKYVGNRPIKLRKSK 216
           NGK +    I++  +K
Sbjct: 290 NGKELEGSEIEVTLAK 305

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. Length = 578

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 39.5 bits (92), Expect = 0.001
 Identities = 21/105 (20%), Positives = 44/105 (41%), Gaps = 2/105 (1%)

Query: 113 KKKSIPRKAAGQTWEDPTLAEWPENDYR-LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVV 171
             +S  R                E D R +F   L  +  +  L + FS+       + +
Sbjct: 63  GDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCI 122

Query: 172 RDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
           +D+ + ++KG  ++ F +   +  AL  + G+ +  RPI ++ S+
Sbjct: 123 KDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQSSQ 166

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 15/60 (25%), Positives = 32/60 (53%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L  +   + L + F +F       V+RD  T +++G+GF++F + + +   L +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 18/73 (24%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF G+L   V +++L + F +       K+ +D   GK K + F++F +   +  A++ +
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 201 NGKYVGNRPIKLR 213
           NG  +  R ++++
Sbjct: 63  NGIRLFGRELRIK 75

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 12/68 (17%)

Query: 147 GNEVNDDVLSKAFSRFP---SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK 203
           G  + +++L KAFS F    + +M K          K  GF++F        A+ E+NG 
Sbjct: 11  GYGLTEEILKKAFSPFGNIINISMEK---------EKNCGFVTFEKMESADRAIAELNGT 61

Query: 204 YVGNRPIK 211
            V    +K
Sbjct: 62  TVQGVQLK 69

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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 22/73 (30%), Positives = 37/73 (50%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            +F G++   V+DD + K   +       K V+D  TGK K +GF  F +P     AL+ 
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 200 MNGKYVGNRPIKL 212
           +NG  +G + + +
Sbjct: 62  LNGLELGGKKLLV 74

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 2/73 (2%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRF-PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           RL   +L   + +  L + FS+        K++R +  GK++   FI +    +   A  
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKAKD 60

Query: 199 EMNGKYVGNRPIK 211
             N  Y+    I 
Sbjct: 61  YFNNTYINTSKIS 73

This subfamily corresponds to the RRM1 of RBM19 and 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 = 77

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 15/58 (25%), Positives = 34/58 (58%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           +LF G L  E  ++ L   + ++       V+RD  + +++G+GF++F+  +++ AA+
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 16/60 (26%), Positives = 31/60 (51%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L  + +   L   F++F       +  D  TG+++G+GFI F + S +   L++
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 5/80 (6%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRD---KRTGKT--KGYGFISFANPSDIAA 195
           LF  +L     +  L+ AF     F  A+V      KR G+T   G+GF+ F       A
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 196 ALKEMNGKYVGNRPIKLRKS 215
           ALK M+G  +    + ++ S
Sbjct: 63  ALKAMDGFVLDGHTLVVKFS 82

This subfamily corresponds to the RRM4 of MRD1which 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 = 84

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 10/48 (20%), Positives = 27/48 (56%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISF 187
           ++F G +  +  +  L   F ++    + +++ D+ +GK +G+ F++F
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 3/77 (3%)

Query: 140 RLFCGDL-GNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           ++F G L  N V +DV  + F +F     A ++ DK T + +G+GF++F    D+   + 
Sbjct: 5   KIFVGGLSANTVVEDV-KQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF-ENEDVVEKVC 62

Query: 199 EMNGKYVGNRPIKLRKS 215
           E++   + N+ ++ +K+
Sbjct: 63  EIHFHEINNKMVECKKA 79

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 6/73 (8%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRF---PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
           + LF G+L  +   + L   F      PS  +     DK+TGK+KG  F+ F     +  
Sbjct: 1   FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLT---DKKTGKSKGCAFVEFDTAEAMTK 57

Query: 196 ALKEMNGKYVGNR 208
           ALK  +    G +
Sbjct: 58  ALKLHHTLLKGRK 70

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 11/56 (19%)

Query: 157 KAFSRF-----PSFNMAKVVRDKR------TGKTKGYGFISFANPSDIAAALKEMN 201
           KA S       P     K++RD +       GK+KGYGF+ F N      AL+ +N
Sbjct: 23  KAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHALKALRALN 78

This subfamily corresponds to the RRM4 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 = 98

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F  +L  +V    L + FS   +   A +  DK  GK++G G ++F  P +   A+   
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDK-DGKSRGMGTVTFEQPIEAVQAISMF 61

Query: 201 NGKYVGNRPIKLR 213
           NG+++ +RP+ ++
Sbjct: 62  NGQFLFDRPMHVK 74

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL-- 197
           ++F G L     +D + K FS+F     A ++ DK+T + +G+GF++F +  D+   +  
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFES-EDVVDKVCE 59

Query: 198 ---KEMNGKYV 205
               E+N K V
Sbjct: 60  IHFHEINNKMV 70

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F  +L  +V    L + FS       A ++ DK  GK++G G ++F  P +   A+   
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDK-DGKSRGIGTVTFEQPIEAVQAISMF 61

Query: 201 NGKYVGNRPIKLR 213
           NG+ + +RP+ ++
Sbjct: 62  NGQLLFDRPMHVK 74

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 5/46 (10%)

Query: 168 AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR 213
           A V RD+     +G G + F +  D+  AL++++G     R +++ 
Sbjct: 30  ADVDRDQ-----EGEGVVEFTSQEDMERALRKLDGTEFRGRRVRVE 70

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising 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. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 34.8 bits (80), Expect = 0.004
 Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 8/72 (11%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           +++F G++      D L   F  F      +VV      K K Y F+      +  AA++
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEF-----GRVVE---CDKVKDYAFVHMEREEEALAAIE 52

Query: 199 EMNGKYVGNRPI 210
            +NGK V  R I
Sbjct: 53  ALNGKEVKGRRI 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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F G+LG E  ++ L + F +       ++VRD +T   KG+ ++ F + + +  AL  +
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALL-L 60

Query: 201 NGK-YVGNRPIKLRKSK 216
           N K +    P +LR S+
Sbjct: 61  NEKKFPPMLPRELRVSR 77

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 19/63 (30%), Positives = 32/63 (50%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RLF  +L     ++ L K FS++   +   +  DK T K KG+ F+++  P     A  E
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 200 MNG 202
           ++G
Sbjct: 64  LDG 66

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	247
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.86
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.86
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.86
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.86
KOG0226	290	consensus RNA-binding proteins [General function p	99.84
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.83
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.81
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.81
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.79
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.79
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.78
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.77
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.77
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.74
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.74
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.74
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.74
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.73
KOG0122	270	consensus Translation initiation factor 3, subunit	99.73
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.72
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.71
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.7
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.7
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.67
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.67
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.66
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.66
PLN03213	759	repressor of silencing 3; Provisional	99.66
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.66
PLN03120	260	nucleic acid binding protein; Provisional	99.65
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.65
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.63
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.63
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.63
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.62
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.62
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.61
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.61
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.61
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.6
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.6
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.6
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.6
smart00362	72	RRM_2 RNA recognition motif.	99.59
PLN03121	243	nucleic acid binding protein; Provisional	99.59
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.59
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.56
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.56
smart00360	71	RRM RNA recognition motif.	99.56
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.56
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.55
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.54
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.54
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.51
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.51
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.51
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.5
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.47
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.47
smart00361	70	RRM_1 RNA recognition motif.	99.46
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.43
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.42
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.39
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.37
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.36
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.28
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.27
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.26
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.25
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.22
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.19
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.18
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.09
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.07
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.07
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	99.05
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.02
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.97
KOG0151	877	consensus Predicted splicing regulator, contains R	98.95
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.93
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.89
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.86
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.83
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.77
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.76
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.76
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.68
KOG4210	285	consensus Nuclear localization sequence binding pr	98.67
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.61
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.57
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.54
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.52
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.37
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.32
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.32
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.31
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.3
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.29
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.27
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.16
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.09
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.0
KOG3152	278	consensus TBP-binding protein, activator of basal	97.97
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.95
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.82
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.81
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.79
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.79
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.75
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.71
KOG2314	698	consensus Translation initiation factor 3, subunit	97.69
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.64
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	97.57
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.55
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.46
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.43
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.29
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.26
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.18
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.13
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.1
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.04
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.92
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.84
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	96.74
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.65
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.61
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.59
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.57
COG0724	306	RNA-binding proteins (RRM domain) [General functio	96.53
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.51
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.43
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.23
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.93
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	95.88
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	95.55
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.46
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.42
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.42
KOG2135	526	consensus Proteins containing the RNA recognition	95.33
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.0
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	94.6
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.13
KOG4210	285	consensus Nuclear localization sequence binding pr	93.85
KOG4660	549	consensus Protein Mei2, essential for commitment t	93.24
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	93.11
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.07
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	91.98
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	91.75
KOG2318	650	consensus Uncharacterized conserved protein [Funct	91.74
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.32
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	89.81
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	88.72
KOG4207	256	consensus Predicted splicing factor, SR protein su	87.83
KOG0226	290	consensus RNA-binding proteins [General function p	87.76
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	87.34
KOG0122	270	consensus Translation initiation factor 3, subunit	85.63
KOG4483	528	consensus Uncharacterized conserved protein [Funct	85.48

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.86  E-value=1.9e-21  Score=170.64  Aligned_cols=140  Identities=16%  Similarity=0.294  Sum_probs=115.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      +.|..+.+..+..+..+++++||+|++.++|.+|+..   ..+.++.+.+..+.+...             ....++|||
T Consensus       132 G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~-------------~~~~~~lfV  198 (346)
T TIGR01659       132 GPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGE-------------SIKDTNLYV  198 (346)
T ss_pred             CCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeeccccccc-------------ccccceeEE
Confidence            5566666666666777899999999999999999853   466777776655432211             123458999


Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EeEEEEEccccc
Q 025814          144 GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN--RPIKLRKSKWQE  219 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~a~~k~  219 (247)
                      +||++++++++|+++|++||.|+.++|++|+.+|+++|||||+|.+.++|++||+.||+..+.|  +.|+|++++.+.
T Consensus       199 ~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       199 TNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             eCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccc
Confidence            9999999999999999999999999999999999999999999999999999999999998866  789999887543

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).

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

Probab=99.86  E-value=2.1e-21  Score=179.37  Aligned_cols=151  Identities=16%  Similarity=0.204  Sum_probs=121.9

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEE
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLF  142 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lf  142 (247)
                      +|.+..+....+..+..++|++||+|++.+.+..|+.   +..+.++.+.+............  ...........++||
T Consensus       131 fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~--~~~~~~~~~~~~rLf  208 (612)
T TIGR01645       131 FGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPI--IDMVQEEAKKFNRIY  208 (612)
T ss_pred             cCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccccccccccc--cccccccccccceEE
Confidence            4777777666777778899999999999999999985   45678888877643322111100  000111123456899


Q ss_pred             EcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          143 CGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       143 V~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      |+||++++++++|+++|+.||.|.+++|.+|+.+|.++|||||+|.+.++|.+||..|||..|+|+.|+|.++...
T Consensus       209 VgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       209 VASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             eecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999988753

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.

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.86  E-value=2.3e-22  Score=164.30  Aligned_cols=87  Identities=31%  Similarity=0.481  Sum_probs=84.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .+++|+|||..||.++.+.||.++|-.||.|++.+|..|+.|+.+||||||.|+++.+++.||..|||+.|+.++|+|.+
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQL  361 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQL  361 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhh
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccc
Q 025814          215 SKWQERT  221 (247)
Q Consensus       215 a~~k~~~  221 (247)
                      .++|+.+
T Consensus       362 KRPkdan  368 (371)
T KOG0146|consen  362 KRPKDAN  368 (371)
T ss_pred             cCccccC
Confidence            9988754

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.86  E-value=7.4e-21  Score=168.14  Aligned_cols=82  Identities=30%  Similarity=0.542  Sum_probs=78.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      +.+|||+||++++++++|+++|++||.|.+++|++|+.||.++|||||+|.+.++|.+||..|||..|+||.|+|.+...
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            44799999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             cc
Q 025814          218 QE  219 (247)
Q Consensus       218 k~  219 (247)
                      +.
T Consensus       349 ~~  350 (352)
T TIGR01661       349 KA  350 (352)
T ss_pred             CC
Confidence            64

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

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=99.84  E-value=4.5e-21  Score=155.62  Aligned_cols=151  Identities=60%  Similarity=0.986  Sum_probs=123.1

Q ss_pred             ccccccchhhhcCCCceeeCccCHHHHHHHHhcCccchhhhhhcccc--cccccCCCCCCCCCCCCCCCCcEEEEcCCCC
Q 025814           71 SLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSI--PRKAAGQTWEDPTLAEWPENDYRLFCGDLGN  148 (247)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~~~~~~~~~~~~~~--~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~  148 (247)
                      ...+.......+..+-+-+..+..++.+..+............+...  -|...+..|.++.+.+|.+++++||+|.|..
T Consensus       121 ~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl~ew~~~DfRIfcgdlgN  200 (290)
T KOG0226|consen  121 SEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSLAEWDEDDFRIFCGDLGN  200 (290)
T ss_pred             ccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCcccccCccccceeecccccc
Confidence            33334444555566666666666666665555443333333333333  4888999999999999999999999999999


Q ss_pred             CCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccccc
Q 025814          149 EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERT  221 (247)
Q Consensus       149 ~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~~  221 (247)
                      +++++.|-+.|.+|-.....++++|+.||+++|||||.|.+..++.+|+++|||..++.+.|+++.+.|++|+
T Consensus       201 evnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wkeRn  273 (290)
T KOG0226|consen  201 EVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKERN  273 (290)
T ss_pred             cccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHhhh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999998754

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

Probab=99.83  E-value=8.9e-20  Score=141.26  Aligned_cols=85  Identities=32%  Similarity=0.559  Sum_probs=80.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||++++++++|+++|++||.|.++.|+.|+.|++++|||||+|.+.++|++||+.||+..|+|+.|+|++
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            34566899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +..+.
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            87654

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.81  E-value=1.6e-19  Score=147.80  Aligned_cols=149  Identities=15%  Similarity=0.260  Sum_probs=120.5

Q ss_pred             CCCCCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC---ccchhhhhhcccccccc---cCCCCCCCCCCCCCCC
Q 025814           64 APVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS---DIEHKAETKKKSIPRKA---AGQTWEDPTLAEWPEN  137 (247)
Q Consensus        64 ~P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~---~~~~~~~~~~~~~~r~~---~~~~~~~~~~~~~~~~  137 (247)
                      +|||.|....+.+|.++.-++|++||.|-.-++|+.|+..+   =+.+|.++..=+..+..   .+...-+.-......+
T Consensus        84 ~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~  163 (321)
T KOG0148|consen   84 APFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPD  163 (321)
T ss_pred             ccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCccHHHHhccCCCC
Confidence            67899999999999999999999999998777777776544   46666666544433321   1111111122344677


Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||||++..++|++|++.|+.||.|.+|+|..+      +||+||.|++.|+|..||..|||.+|+|..+++.|.+.
T Consensus       164 NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe  237 (321)
T KOG0148|consen  164 NTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKE  237 (321)
T ss_pred             CceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEecccc
Confidence            889999999999999999999999999999999988      57999999999999999999999999999999998764


Q ss_pred             c
Q 025814          218 Q  218 (247)
Q Consensus       218 k  218 (247)
                      .
T Consensus       238 ~  238 (321)
T KOG0148|consen  238 G  238 (321)
T ss_pred             C
Confidence            3

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.81  E-value=2.3e-19  Score=163.99  Aligned_cols=149  Identities=23%  Similarity=0.320  Sum_probs=115.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCG  144 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~  144 (247)
                      |.+..+....+.....++|++||+|.+.++|.+||...  .+.++.+.+................. .......++|||+
T Consensus       114 G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~-~~~~p~~~~l~v~  192 (457)
T TIGR01622       114 GKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQ-PGDIPNFLKLYVG  192 (457)
T ss_pred             CCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecchhhhhhhhccccc-CCCCCCCCEEEEc
Confidence            45555555555566778999999999999999998643  55666665544322211111000000 0012235799999


Q ss_pred             CCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          145 DLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       145 nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ||+..+++++|+++|+.||.|..|.|+++..+|.++|||||+|.+.++|.+|+..|||..|.|+.|+|.++.
T Consensus       193 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       193 NLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999976

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.

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.79  E-value=2.1e-19  Score=155.32  Aligned_cols=148  Identities=19%  Similarity=0.309  Sum_probs=118.9

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc-Ccc---c--hhhhhhcccccccccCCCCCCCCCCCCCCCCc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS-SDI---E--HKAETKKKSIPRKAAGQTWEDPTLAEWPENDY  139 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~-~~~---~--~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~  139 (247)
                      ++.|+.+-...|..+..++|||||+|..-++++++++. +++   .  ...+.++.+......            ..+++
T Consensus        58 yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er------------~~~e~  125 (510)
T KOG0144|consen   58 YGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERER------------IVEER  125 (510)
T ss_pred             hCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhc------------cccch
Confidence            48899999999999999999999999988888888764 322   2  222333222111110            23456


Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCc-eeCC--EeEEEEEcc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK-YVGN--RPIKLRKSK  216 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~-~i~g--~~l~V~~a~  216 (247)
                      +||||-|+..++|.+++++|++||.|++|.|++|. .|.+|||+||.|.+.+.|..||+.|||. .+.|  ..|.|++++
T Consensus       126 KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFAD  204 (510)
T KOG0144|consen  126 KLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFAD  204 (510)
T ss_pred             hhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecc
Confidence            89999999999999999999999999999999994 7999999999999999999999999998 4555  679999999


Q ss_pred             ccccccHHHH
Q 025814          217 WQERTDFEAL  226 (247)
Q Consensus       217 ~k~~~~~~~~  226 (247)
                      .+..++.++.
T Consensus       205 tqkdk~~~~l  214 (510)
T KOG0144|consen  205 TQKDKDGKRL  214 (510)
T ss_pred             cCCCchHHHH
Confidence            8876665554

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.79  E-value=1.1e-18  Score=144.59  Aligned_cols=86  Identities=28%  Similarity=0.505  Sum_probs=80.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .++-+||||+.|+++++|+.|+..|+.||.|+.|.||+|+.||+++|||||+|++..++..|.+..+|..|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            46678999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      .+.+..
T Consensus       178 ERgRTv  183 (335)
T KOG0113|consen  178 ERGRTV  183 (335)
T ss_pred             cccccc
Confidence            765543

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.78  E-value=3.4e-18  Score=158.27  Aligned_cols=137  Identities=18%  Similarity=0.272  Sum_probs=106.7

Q ss_pred             cCCCceeeCccCHHHHHHHHhc--CccchhhhhhcccccccccC-------CCCCC---------CCCCCCCCCCcEEEE
Q 025814           82 FQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRKAAG-------QTWED---------PTLAEWPENDYRLFC  143 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~~~~-------~~~~~---------~~~~~~~~~~~~lfV  143 (247)
                      ..++++||+|++.+.|..||..  ..+.+..+.+..........       .....         ...........+|||
T Consensus       221 ~~kg~afVeF~~~e~A~~Al~l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v  300 (509)
T TIGR01642       221 KEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYI  300 (509)
T ss_pred             CCCCEEEEEeCCHHHHhhhhcCCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEE
Confidence            4588999999999999999864  34556665554322111000       00000         000112344579999


Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          144 GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      +|||+.+++++|+++|+.||.|..+.|+.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++...
T Consensus       301 ~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       301 GNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             eCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999998643

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.77  E-value=2.7e-18  Score=151.79  Aligned_cols=141  Identities=18%  Similarity=0.259  Sum_probs=119.3

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEE
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLF  142 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lf  142 (247)
                      +|.+..+....+..+..++|++||.|.+.++|.+|++   +..+.++.+.+....+...             ....++||
T Consensus        27 ~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~-------------~~~~~~l~   93 (352)
T TIGR01661        27 IGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSD-------------SIKGANLY   93 (352)
T ss_pred             cCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeeccccc-------------ccccceEE
Confidence            4778787777777778899999999999999999986   4467787777765543321             22345899


Q ss_pred             EcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EeEEEEEccccc
Q 025814          143 CGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN--RPIKLRKSKWQE  219 (247)
Q Consensus       143 V~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~a~~k~  219 (247)
                      |+||+.++++++|+.+|+.||.|..+.++.+..+|.++|||||+|.+.++|++||+.|||..+.|  +.|.|.++....
T Consensus        94 v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661        94 VSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             ECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            99999999999999999999999999999998889999999999999999999999999998877  678888886543

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

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

Probab=99.77  E-value=1.9e-18  Score=161.87  Aligned_cols=152  Identities=22%  Similarity=0.340  Sum_probs=112.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccc----hhhhhhcccccccccCCC-----CCCCCCCCC
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIE----HKAETKKKSIPRKAAGQT-----WEDPTLAEW  134 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~----~~~~~~~~~~~r~~~~~~-----~~~~~~~~~  134 (247)
                      |.+..+....+ ....+++++||.|++.+++.+|+..   ..+.    ++.+.+.....+......     .........
T Consensus       203 G~i~~~~i~~~-~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~  281 (562)
T TIGR01628       203 GEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKM  281 (562)
T ss_pred             CCEEEEEEEEC-CCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhc
Confidence            55544444333 3456789999999999999988753   3454    444444333322211000     000000011


Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .....+|||+||++++++++|+++|+.||.|.+|+|+.| .+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~  360 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL  360 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEe
Confidence            334568999999999999999999999999999999999 6899999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      +..+..
T Consensus       361 a~~k~~  366 (562)
T TIGR01628       361 AQRKEQ  366 (562)
T ss_pred             ccCcHH
Confidence            987653

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>PF00076 RRM_1: RNA recognition motif

Probab=99.74  E-value=2e-17  Score=111.89  Aligned_cols=70  Identities=39%  Similarity=0.737  Sum_probs=67.6

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       141 lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      |||+|||.++++++|+++|+.||.|..+.+..+ .++..+|||||+|.+.++|+.|++.|||..++|+.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 6899999999999999999999999999999999986

(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 ....

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

Probab=99.74  E-value=1.1e-17  Score=156.86  Aligned_cols=141  Identities=21%  Similarity=0.309  Sum_probs=117.1

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEE
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLF  142 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lf  142 (247)
                      +|.+..+.+..+..+..++|++||+|.+.++|.+|++.   ..+.++.+++........         .  ......+||
T Consensus        24 ~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~---------~--~~~~~~~vf   92 (562)
T TIGR01628        24 FGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPS---------L--RRSGVGNIF   92 (562)
T ss_pred             cCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccccc---------c--cccCCCceE
Confidence            37777888888888888999999999999999999864   357777777654321110         0  012234799


Q ss_pred             EcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          143 CGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       143 V~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      |+||+.++++++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++.|||..++|+.|.|.....+
T Consensus        93 V~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~  167 (562)
T TIGR01628        93 VKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK  167 (562)
T ss_pred             EcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccc
Confidence            99999999999999999999999999999984 7999999999999999999999999999999999999765443

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.74  E-value=1e-17  Score=147.17  Aligned_cols=84  Identities=26%  Similarity=0.449  Sum_probs=79.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|++|+|++|+.+++++|||||+|.+.++|++||..|||..|.+++|+|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            44577999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      +++.
T Consensus       184 a~p~  187 (346)
T TIGR01659       184 ARPG  187 (346)
T ss_pred             cccc
Confidence            8753

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).

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.74  E-value=2.4e-17  Score=152.28  Aligned_cols=127  Identities=19%  Similarity=0.296  Sum_probs=101.4

Q ss_pred             hcCCCceeeCccCHHHHHHHHhcC-----ccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHH
Q 025814           81 LFQRDAQTITPEALESVKAALASS-----DIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVL  155 (247)
Q Consensus        81 ~~~~~~~~v~~~~~~~a~~al~~~-----~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L  155 (247)
                      ...++++||+|++.++|..|+...     .+.++.+.+....+......        +......+|||+||++++++++|
T Consensus       179 gKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~--------~~~~~~k~LfVgNL~~~~tee~L  250 (578)
T TIGR01648       179 KKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDE--------DVMAKVKILYVRNLMTTTTEEII  250 (578)
T ss_pred             CccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccccc--------cccccccEEEEeCCCCCCCHHHH
Confidence            456899999999999999887532     34566666655443322111        11223458999999999999999


Q ss_pred             HHHhccC--CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccccccH
Q 025814          156 SKAFSRF--PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDF  223 (247)
Q Consensus       156 ~~~F~~~--G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~~~~  223 (247)
                      +++|+.|  |.|++|+++++        ||||+|.+.++|++|++.|||.+|+|+.|+|.+++++.+...
T Consensus       251 ~~~F~~f~~G~I~rV~~~rg--------fAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~~~  312 (578)
T TIGR01648       251 EKSFSEFKPGKVERVKKIRD--------YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSY  312 (578)
T ss_pred             HHHHHhcCCCceEEEEeecC--------eEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCcccc
Confidence            9999999  99999988654        999999999999999999999999999999999988765533

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.

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.73  E-value=1.1e-17  Score=140.45  Aligned_cols=84  Identities=23%  Similarity=0.411  Sum_probs=76.9

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       133 ~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      +.....++|+|+|||+.+.|-||+.+|++||.|.+|+|+.+  -..+||||||+|++.+||++|-.+|||..|.||+|.|
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEV  168 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEV  168 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEE
Confidence            33555679999999999999999999999999999999987  3568999999999999999999999999999999999


Q ss_pred             EEcccc
Q 025814          213 RKSKWQ  218 (247)
Q Consensus       213 ~~a~~k  218 (247)
                      +.+..+
T Consensus       169 n~ATar  174 (376)
T KOG0125|consen  169 NNATAR  174 (376)
T ss_pred             eccchh
Confidence            998754

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.73  E-value=1.8e-17  Score=134.08  Aligned_cols=83  Identities=27%  Similarity=0.459  Sum_probs=80.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .+.++|-|.||+.+++|++|+++|..||.|.++.|.+|+.||.+||||||.|.+.++|.+||..|||.-+++..|+|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 025814          216 KWQ  218 (247)
Q Consensus       216 ~~k  218 (247)
                      +++
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            876

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.72  E-value=1.2e-17  Score=134.54  Aligned_cols=79  Identities=28%  Similarity=0.504  Sum_probs=72.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      -++||||||+|++..++|+++|++||+|++..|+.|+.||++||||||+|.+.++|.+|++. -.-.|+||+..++++.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            35799999999999999999999999999999999999999999999999999999999954 45689999999988753

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.71  E-value=7e-17  Score=143.44  Aligned_cols=154  Identities=23%  Similarity=0.277  Sum_probs=121.9

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---CccchhhhhhcccccccccCCCC-----------CC--CC
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKAAGQTW-----------ED--PT  130 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~~~~~~-----------~~--~~  130 (247)
                      |++...-+.........||++||+|.-.+++.+|+..   ..++++.+++..+..|.......           ..  +.
T Consensus        30 GPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~  109 (678)
T KOG0127|consen   30 GPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPT  109 (678)
T ss_pred             cCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccccccchhcccccchhhhcccccCCcc
Confidence            4444444445555677899999999999999998875   46899999998887776544111           00  11


Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeE
Q 025814          131 LAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPI  210 (247)
Q Consensus       131 ~~~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l  210 (247)
                      -.......-+|.|.||||.|.+.+|+.+|+.||.|..|.|.+.+. |+..|||||.|....+|..||+.|||..|+||.|
T Consensus       110 k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~V  188 (678)
T KOG0127|consen  110 KAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPV  188 (678)
T ss_pred             hhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCcee
Confidence            111233356899999999999999999999999999999998765 4445999999999999999999999999999999


Q ss_pred             EEEEccccccc
Q 025814          211 KLRKSKWQERT  221 (247)
Q Consensus       211 ~V~~a~~k~~~  221 (247)
                      -|.||..++..
T Consensus       189 AVDWAV~Kd~y  199 (678)
T KOG0127|consen  189 AVDWAVDKDTY  199 (678)
T ss_pred             EEeeecccccc
Confidence            99999988754

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

Probab=99.70  E-value=1.9e-17  Score=153.21  Aligned_cols=81  Identities=30%  Similarity=0.592  Sum_probs=76.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++||||||++++++++|+++|+.||.|.+|+|++|+.+|+++|||||+|.+.++|++|++.|||..|+|+.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             c
Q 025814          216 K  216 (247)
Q Consensus       216 ~  216 (247)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            4

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.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.70  E-value=3e-17  Score=127.39  Aligned_cols=143  Identities=26%  Similarity=0.376  Sum_probs=119.0

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      ++|..+....+.-+..++|++|+.|...++++-|+.   .-.+-++.+++.++...+..            ...+.+|||
T Consensus        34 gpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~~~n------------l~vganlfv  101 (203)
T KOG0131|consen   34 GPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAHQKN------------LDVGANLFV  101 (203)
T ss_pred             CceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEeccccccc------------ccccccccc
Confidence            667777777777788899999999987777776654   45778888888776521111            233468999


Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEE-EEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccccc
Q 025814          144 GDLGNEVNDDVLSKAFSRFPSFNMA-KVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERT  221 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~i~~v-~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~~  221 (247)
                      +||.++++|..|.+.|+.||.+.+. +|+++..||.++|||||.|.+.+.+.+|+..|||..++++.|.|.++..++..
T Consensus       102 gNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  102 GNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             cccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence            9999999999999999999998764 89999999999999999999999999999999999999999999999766543

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.67  E-value=6.5e-16  Score=104.85  Aligned_cols=70  Identities=26%  Similarity=0.611  Sum_probs=65.4

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       141 lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      |||+|||+++++++|+++|+.||.|..+.+..++. |..+|+|||+|.+.++|.+|++.++|..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999976 99999999999999999999999999999999985

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 RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.67  E-value=9.5e-17  Score=131.05  Aligned_cols=139  Identities=18%  Similarity=0.260  Sum_probs=118.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      |.+.+....++..+..+-|++||.+-+.+++++|++   +..+..+.+.+..+.+....             -.+.+|||
T Consensus        66 GeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~~-------------Ik~aNLYv  132 (360)
T KOG0145|consen   66 GEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSDS-------------IKDANLYV  132 (360)
T ss_pred             cceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChhh-------------hcccceEE
Confidence            777888888899999999999999998888888876   44566677777666554332             23448999


Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EeEEEEEcccc
Q 025814          144 GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN--RPIKLRKSKWQ  218 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~a~~k  218 (247)
                      ++||..++..||+++|++||.|...+|+.|..||.+||.|||.|+..++|+.||+.|||..--|  ..|.|.++...
T Consensus       133 SGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  133 SGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             ecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            9999999999999999999999999999999999999999999999999999999999997655  67999998744

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.66  E-value=1.4e-17  Score=129.21  Aligned_cols=80  Identities=24%  Similarity=0.496  Sum_probs=75.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .+..-|||||||++.||.+|.-+|++||.|.+|.++||+.||+++||||+.|++..+.--|+..|||..|.||.|+|..-
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            44557999999999999999999999999999999999999999999999999999999999999999999999999654

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=2.6e-16  Score=136.90  Aligned_cols=97  Identities=21%  Similarity=0.392  Sum_probs=85.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEeEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG-NRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~-g~~l~V~  213 (247)
                      +..++.||||.||.++.|++|.-+|+..|.|-+++|++|+.+|.+||||||.|.+.++|+.||+.||+.+|. |+.|.|+
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            467889999999999999999999999999999999999999999999999999999999999999999885 8999999


Q ss_pred             EccccccccHHHHHhhhc
Q 025814          214 KSKWQERTDFEALERSKN  231 (247)
Q Consensus       214 ~a~~k~~~~~~~~~~~~~  231 (247)
                      .+..+.|--...+.+.++
T Consensus       160 ~Svan~RLFiG~IPK~k~  177 (506)
T KOG0117|consen  160 VSVANCRLFIGNIPKTKK  177 (506)
T ss_pred             EeeecceeEeccCCcccc
Confidence            887776644434433333

>PLN03213 repressor of silencing 3; Provisional

Probab=99.66  E-value=6.6e-16  Score=135.96  Aligned_cols=80  Identities=26%  Similarity=0.445  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCH--HHHHHHHHHhCCceeCCEeEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANP--SDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~--~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ....+||||||.+.+++++|+.+|..||.|.+|.|+++  +|  ||||||+|.+.  .++.+||..|||..++|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            34458999999999999999999999999999999954  77  99999999987  78999999999999999999999


Q ss_pred             Eccccc
Q 025814          214 KSKWQE  219 (247)
Q Consensus       214 ~a~~k~  219 (247)
                      .|++..
T Consensus        84 KAKP~Y   89 (759)
T PLN03213         84 KAKEHY   89 (759)
T ss_pred             eccHHH
Confidence            998754

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.66  E-value=2.9e-16  Score=121.25  Aligned_cols=78  Identities=26%  Similarity=0.562  Sum_probs=73.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++||||||+..+++.||+.+|..||.|.+|+|-+++     .|||||+|++..+|+.|+..|||..|.|..|+|+++..
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            5689999999999999999999999999999998764     68999999999999999999999999999999999987


Q ss_pred             ccc
Q 025814          218 QER  220 (247)
Q Consensus       218 k~~  220 (247)
                      ..+
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            655

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.65  E-value=6.9e-16  Score=128.18  Aligned_cols=76  Identities=9%  Similarity=0.222  Sum_probs=70.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+||++.+++++|+++|+.||.|.+|.|++|+.   .+|||||+|.+.++++.|| .|||..|+|+.|+|..+..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence            34899999999999999999999999999999999853   5789999999999999999 5999999999999999863

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

Probab=99.65  E-value=1.7e-15  Score=139.36  Aligned_cols=142  Identities=16%  Similarity=0.104  Sum_probs=106.2

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc-----CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcE
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS-----SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYR  140 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~-----~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~  140 (247)
                      +|.|..+...      .+++++||+|++.++|..|++.     ..+.++.+.+.....+........+ ..........+
T Consensus        26 fG~V~~v~i~------~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~~~~~~~-~~~~~~~~~~~   98 (481)
T TIGR01649        26 FGPVSYVMML------PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIKRDGNSD-FDSAGPNKVLR   98 (481)
T ss_pred             cCCeeEEEEE------CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccccCCCCc-ccCCCCCceEE
Confidence            4666554332      2578999999999999999963     3578888887766543211111000 00011223347


Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EeEEEEEcccc
Q 025814          141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN--RPIKLRKSKWQ  218 (247)
Q Consensus       141 lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~a~~k  218 (247)
                      |||+||++++++++|+++|+.||.|.+|.|+++..    +|+|||+|.+.++|.+|++.|||..|.|  +.|+|.+++..
T Consensus        99 v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649        99 VIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             EEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCC
Confidence            99999999999999999999999999999987642    4799999999999999999999999964  58999998753

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).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.63  E-value=5.6e-16  Score=127.17  Aligned_cols=83  Identities=40%  Similarity=0.766  Sum_probs=79.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ...-+||+.|..+++.++|++.|.+||+|.+++|++|..|+++||||||.|-+.++|++||..|||.-|++|.|+-.|+.
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             ccc
Q 025814          217 WQE  219 (247)
Q Consensus       217 ~k~  219 (247)
                      .|.
T Consensus       141 RKp  143 (321)
T KOG0148|consen  141 RKP  143 (321)
T ss_pred             cCc
Confidence            665

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.63  E-value=4e-16  Score=123.48  Aligned_cols=82  Identities=21%  Similarity=0.452  Sum_probs=78.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      ..|-|-||.+.++.++|+.+|++||.|-+|.|.+|+.|+.++|||||.|....+|+.|+..|+|..|+|+.|.|.++++-
T Consensus        14 ~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~aryg   93 (256)
T KOG4207|consen   14 TSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARYG   93 (256)
T ss_pred             eeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhcC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             cc
Q 025814          219 ER  220 (247)
Q Consensus       219 ~~  220 (247)
                      ..
T Consensus        94 r~   95 (256)
T KOG4207|consen   94 RP   95 (256)
T ss_pred             CC
Confidence            43

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.63  E-value=1.2e-15  Score=132.81  Aligned_cols=129  Identities=23%  Similarity=0.287  Sum_probs=99.1

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhcC-----ccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHH
Q 025814           80 QLFQRDAQTITPEALESVKAALASS-----DIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDV  154 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~~-----~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~  154 (247)
                      ...-||++||.+++-..|..+-...     .+.+..+.+.=+.++......        .-..-..|||.||+.++|++.
T Consensus       204 k~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded--------~ms~VKvLYVRNL~~~tTeE~  275 (506)
T KOG0117|consen  204 KTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDED--------TMSKVKVLYVRNLMESTTEET  275 (506)
T ss_pred             cccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChh--------hhhheeeeeeeccchhhhHHH
Confidence            5667999999999877666654321     344444444333332221111        011223699999999999999


Q ss_pred             HHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccccccHH
Q 025814          155 LSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFE  224 (247)
Q Consensus       155 L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~~~~~  224 (247)
                      |+++|..||.|.+|+.++|        ||||.|.+.++|.+|++.+||.+|+|..|.|.+|++..+...+
T Consensus       276 lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k~~  337 (506)
T KOG0117|consen  276 LKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKKKE  337 (506)
T ss_pred             HHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhccc
Confidence            9999999999999999988        9999999999999999999999999999999999987655433

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.62  E-value=2.9e-16  Score=125.37  Aligned_cols=84  Identities=30%  Similarity=0.509  Sum_probs=79.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++||||+|..+++|..|...|-.||.|.+|.+..|-.++++||||||+|...|+|.+||..||+.++.||.|+|+++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            44569999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          216 KWQE  219 (247)
Q Consensus       216 ~~k~  219 (247)
                      ++..
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            8743

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.62  E-value=3.4e-15  Score=138.04  Aligned_cols=81  Identities=21%  Similarity=0.424  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEeEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG-NRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~-g~~l~V~  213 (247)
                      ...+++|||+|||++++|++|+++|++||.|.+++|++| .+|.++|||||+|.+.++|++||+.||+..|. |+.|.|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            445689999999999999999999999999999999999 79999999999999999999999999999885 7888776


Q ss_pred             Ecc
Q 025814          214 KSK  216 (247)
Q Consensus       214 ~a~  216 (247)
                      .+.
T Consensus       134 ~S~  136 (578)
T TIGR01648       134 ISV  136 (578)
T ss_pred             ccc
Confidence            654

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.

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.61  E-value=3.3e-15  Score=132.13  Aligned_cols=131  Identities=22%  Similarity=0.347  Sum_probs=113.4

Q ss_pred             CCCCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC---ccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEE
Q 025814           65 PVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS---DIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRL  141 (247)
Q Consensus        65 P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~---~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~l  141 (247)
                      |.+++.++.++.+. +  +-++++|.|.+.+++.+||...   .+.++.+++....                  .+...|
T Consensus        21 ~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~------------------rd~~~~   79 (369)
T KOG0123|consen   21 PAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQ------------------RDPSLV   79 (369)
T ss_pred             ccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhc------------------cCCcee
Confidence            44888899999999 6  9999999999999999998754   6778887774432                  122239


Q ss_pred             EEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          142 FCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       142 fV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      ||.||+.+++..+|.++|+.||.|.+|++..+. .| ++|| ||+|++.++|.+|+..|||..+.|+.|.|.....+.
T Consensus        80 ~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~  154 (369)
T KOG0123|consen   80 FIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKE  154 (369)
T ss_pred             eecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchh
Confidence            999999999999999999999999999999995 56 9999 999999999999999999999999999998876544

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.61  E-value=6e-16  Score=137.82  Aligned_cols=149  Identities=23%  Similarity=0.294  Sum_probs=113.4

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhccccc---ccccCCCCCCCCCCCCCCCCcEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETKKKSIP---RKAAGQTWEDPTLAEWPENDYRL  141 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~~---r~~~~~~~~~~~~~~~~~~~~~l  141 (247)
                      +.|-.+-...+.....++|++||.|.+.+++-.++...  -+-+..+.++....   +.+....+.....  ...+-..|
T Consensus       204 gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEaeknr~a~~s~a~~~k~--~~~p~~rl  281 (549)
T KOG0147|consen  204 GKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAEKNRAANASPALQGKG--FTGPMRRL  281 (549)
T ss_pred             cCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHHHHHHHHhccccccccc--cccchhhh
Confidence            66666666777778889999999999999999988654  23333333322221   1111111111111  11222239


Q ss_pred             EEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          142 FCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       142 fV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      |||||.+++++++|+.+|+.||.|..|.+.+|..||.++|||||+|.+.++|.+|+..|||.+|.|+.|+|..-..
T Consensus       282 ~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  282 YVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             hhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence            9999999999999999999999999999999988999999999999999999999999999999999999976543

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

Probab=99.61  E-value=7.8e-15  Score=134.99  Aligned_cols=133  Identities=14%  Similarity=0.142  Sum_probs=100.9

Q ss_pred             CCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCC-------------C--------CCCCC---CCCCC
Q 025814           84 RDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQT-------------W--------EDPTL---AEWPE  136 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~-------------~--------~~~~~---~~~~~  136 (247)
                      ++++||.|++.++|..|+.   +..+.++.+.+............             .        ..+..   .....
T Consensus       313 ~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~  392 (481)
T TIGR01649       313 KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQP  392 (481)
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCC
Confidence            7999999999999998885   55788888887654332110000             0        00000   00123


Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCC--eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEe-----
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPS--FNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRP-----  209 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~--i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~-----  209 (247)
                      ...+|||+|||.++++++|+++|+.||.  |..+++.... ++ .+|||||+|.+.++|.+||..|||..|.|+.     
T Consensus       393 ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~-~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~  470 (481)
T TIGR01649       393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-NE-RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPY  470 (481)
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC-CC-cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccc
Confidence            4568999999999999999999999998  8888886553 33 5899999999999999999999999999985     


Q ss_pred             -EEEEEcccc
Q 025814          210 -IKLRKSKWQ  218 (247)
Q Consensus       210 -l~V~~a~~k  218 (247)
                       |+|.+++++
T Consensus       471 ~lkv~fs~~~  480 (481)
T TIGR01649       471 HLKVSFSTSR  480 (481)
T ss_pred             eEEEEeccCC
Confidence             999998754

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).

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.60  E-value=1.9e-15  Score=111.02  Aligned_cols=81  Identities=17%  Similarity=0.363  Sum_probs=75.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++||||||.+.++|+.|.++|+.||.|..|.+=.|+.+-..=|||||+|.+.++|+.|++.+||..++.+.|++.+.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            34569999999999999999999999999999988888888888899999999999999999999999999999999875


Q ss_pred             c
Q 025814          216 K  216 (247)
Q Consensus       216 ~  216 (247)
                      -
T Consensus       114 ~  114 (153)
T KOG0121|consen  114 A  114 (153)
T ss_pred             c
Confidence            3

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.60  E-value=3e-15  Score=122.38  Aligned_cols=85  Identities=29%  Similarity=0.516  Sum_probs=80.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .+...+|.|.=||..+|++||+.+|...|+|++|+++||+-+|.+.|||||.|.+++||++|+..|||..+..+.|+|.+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            45566899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +++..
T Consensus       118 ARPSs  122 (360)
T KOG0145|consen  118 ARPSS  122 (360)
T ss_pred             ccCCh
Confidence            99865

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.60  E-value=1.1e-15  Score=118.73  Aligned_cols=81  Identities=28%  Similarity=0.492  Sum_probs=77.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ..+.+||||||+..++++.|.++|-+.|+|.++++.+|+.+...+|||||+|.+.++|+-|++.||...+.||+|+|+.+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             c
Q 025814          216 K  216 (247)
Q Consensus       216 ~  216 (247)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.60  E-value=8.6e-16  Score=130.76  Aligned_cols=151  Identities=17%  Similarity=0.235  Sum_probs=122.4

Q ss_pred             CCCCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcE
Q 025814           64 APVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYR  140 (247)
Q Consensus        64 ~P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~  140 (247)
                      .|||++.++-..-+..++.+++++||.+|-.+.+.-+++   +.-+.++.+.+.+...-.+.....+.  ..+....-++
T Consensus       135 ~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~--vqeeAk~fnR  212 (544)
T KOG0124|consen  135 DPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDM--VQEEAKKFNR  212 (544)
T ss_pred             cCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCCcccchHHHH--HHHHHHhhhe
Confidence            678999998888888899999999999998887777765   44678888887654332222111100  0011233458


Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       141 lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      |||..+.++.+|+||+.+|+.||.|..|.+-+++.++.+|||||++|.+..+...||..||-+.++|..|+|..+.
T Consensus       213 iYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  213 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             EEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            9999999999999999999999999999999999888999999999999999999999999999999999997664

>smart00362 RRM_2 RNA recognition motif

Probab=99.59  E-value=9.7e-15  Score=98.04  Aligned_cols=72  Identities=33%  Similarity=0.737  Sum_probs=67.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      +|||+|||.++++++|+++|..||.|..+.+..+.  +.++|+|||+|.+.++|++|+..++|..+.|+.|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999999885  7889999999999999999999999999999999873

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.59  E-value=8.3e-15  Score=119.97  Aligned_cols=76  Identities=12%  Similarity=0.286  Sum_probs=69.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      .+.+|||+||++.+++++|+++|+.||.|.+|+|++|   +..+|||||+|.+.++++.|+ .|||..|.++.|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            4569999999999999999999999999999999998   445689999999999999999 899999999999997654

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.59  E-value=3.4e-15  Score=133.38  Aligned_cols=83  Identities=24%  Similarity=0.462  Sum_probs=79.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      +.|||||+|+++++++|..+|+..|.|.+++++.|+.||+.+|||||+|.+.+++..|++.|||.++.||+|+|.++...
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            68999999999999999999999999999999999999999999999999999999999999999999999999998755


Q ss_pred             ccc
Q 025814          219 ERT  221 (247)
Q Consensus       219 ~~~  221 (247)
                      ...
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            443

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.56  E-value=3.9e-15  Score=123.40  Aligned_cols=114  Identities=14%  Similarity=0.287  Sum_probs=99.4

Q ss_pred             CCceeeCccCHHHHHHHH---hcCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhc
Q 025814           84 RDAQTITPEALESVKAAL---ASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFS  160 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al---~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L~~~F~  160 (247)
                      ++++||..|+...+.+++   ....+++..+.++..+.+..               ...+|+||||.+.++.+||+..|+
T Consensus        36 KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk---------------~stkl~vgNis~tctn~ElRa~fe  100 (346)
T KOG0109|consen   36 KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSK---------------ASTKLHVGNISPTCTNQELRAKFE  100 (346)
T ss_pred             cccceEEeecccccHHHHhhcccceecceEEEEEeccccCC---------------CccccccCCCCccccCHHHhhhhc
Confidence            888999888766655555   45689999999988776622               233799999999999999999999


Q ss_pred             cCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccccc
Q 025814          161 RFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQER  220 (247)
Q Consensus       161 ~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~  220 (247)
                      +||.|+++.|++|        |+||.|+-.++|..|++.|||.++.|++++|.++..+-+
T Consensus       101 ~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlr  152 (346)
T KOG0109|consen  101 KYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR  152 (346)
T ss_pred             ccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeeeccccc
Confidence            9999999999988        999999999999999999999999999999999877654

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.56  E-value=4.7e-15  Score=127.23  Aligned_cols=147  Identities=15%  Similarity=0.264  Sum_probs=129.0

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCG  144 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~  144 (247)
                      +.+...-...+..+..++++.||+|++.+.+.++|..  +.++++.++.+++.+|..........       ....||||
T Consensus        31 Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r~~~~~~~~~~-------~tkkiFvG  103 (311)
T KOG4205|consen   31 GEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSREDQTKVGRHL-------RTKKIFVG  103 (311)
T ss_pred             CceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccCccccccccccc-------ceeEEEec
Confidence            6666666677777899999999999999999999975  58999999999999988766543222       34489999


Q ss_pred             CCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccccc
Q 025814          145 DLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERT  221 (247)
Q Consensus       145 nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~~  221 (247)
                      +|+.++++++|+++|.+||.|..+.++.|..+.+.+||+||.|.+.+++.+++ ...-+.|+|+.+.|..|.+++..
T Consensus       104 G~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~-~~~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  104 GLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVT-LQKFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             CcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceec-ccceeeecCceeeEeeccchhhc
Confidence            99999999999999999999999999999999999999999999999999998 56788999999999999988754

>smart00360 RRM RNA recognition motif

Probab=99.56  E-value=2.1e-14  Score=96.03  Aligned_cols=71  Identities=38%  Similarity=0.748  Sum_probs=67.4

Q ss_pred             EcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          143 CGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       143 V~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      |+||+.++++++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|+..|++..++|+.|+|+
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            67999999999999999999999999999988789999999999999999999999999999999999873

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.56  E-value=2.1e-14  Score=131.29  Aligned_cols=82  Identities=21%  Similarity=0.407  Sum_probs=76.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||..+++++|+++|+.||.|.+|+|+.|+.+|.++|||||+|.+.++|.+|| .|+|..+.|+.|.|..
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 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHH-HhCCCEECCeeeEEee
Confidence            344679999999999999999999999999999999999999999999999999999999999 6999999999999987


Q ss_pred             ccc
Q 025814          215 SKW  217 (247)
Q Consensus       215 a~~  217 (247)
                      +..
T Consensus       165 ~~~  167 (457)
T TIGR01622       165 SQA  167 (457)
T ss_pred             cch
Confidence            654

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.

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.55  E-value=2.2e-14  Score=120.67  Aligned_cols=79  Identities=32%  Similarity=0.707  Sum_probs=76.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      .++|||+||++.+++++|.++|..||.|..+.+..|+.+|.++|||||+|.+.+++..|+..++|..|.|+.|.|.++.
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            5799999999999999999999999999999999998899999999999999999999999999999999999999965

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.54  E-value=1.1e-14  Score=107.94  Aligned_cols=82  Identities=17%  Similarity=0.360  Sum_probs=77.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      -.+..|||.++....+|++|...|..||.|+++.+..|+.||..+||++|+|++.+.|++|+..|||..|.|..|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q 025814          216 KW  217 (247)
Q Consensus       216 ~~  217 (247)
                      --
T Consensus       150 Fv  151 (170)
T KOG0130|consen  150 FV  151 (170)
T ss_pred             Ee
Confidence            53

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.54  E-value=7e-14  Score=129.53  Aligned_cols=150  Identities=11%  Similarity=0.069  Sum_probs=105.0

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCC----------CCC--
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWED----------PTL--  131 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~----------~~~--  131 (247)
                      |.+..+....+.....++|++||+|++.+.+..|+.   +..+.++.+.+..+............          ...  
T Consensus       320 G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  399 (509)
T TIGR01642       320 GDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQ  399 (509)
T ss_pred             CCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchh
Confidence            333333334444456679999999999888888875   45677777776665432211110000          000  


Q ss_pred             ---CCCCCCCcEEEEcCCCCC----------CcHHHHHHHhccCCCeeEEEEEecC---CCCCcceEEEEEecCHHHHHH
Q 025814          132 ---AEWPENDYRLFCGDLGNE----------VNDDVLSKAFSRFPSFNMAKVVRDK---RTGKTKGYGFISFANPSDIAA  195 (247)
Q Consensus       132 ---~~~~~~~~~lfV~nLp~~----------~~e~~L~~~F~~~G~i~~v~i~~~~---~tg~~kg~~FV~f~~~~~a~~  195 (247)
                         ........+|+|.||...          ...++|+++|+.||.|.+|.|.++.   .++...|++||+|.+.++|++
T Consensus       400 ~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~  479 (509)
T TIGR01642       400 SILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEK  479 (509)
T ss_pred             hhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHH
Confidence               001224567999999542          1235789999999999999998753   346678999999999999999


Q ss_pred             HHHHhCCceeCCEeEEEEEcc
Q 025814          196 ALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       196 Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      |+..|||..|+|+.|.|.+..
T Consensus       480 A~~~lnGr~~~gr~v~~~~~~  500 (509)
T TIGR01642       480 AMEGMNGRKFNDRVVVAAFYG  500 (509)
T ss_pred             HHHHcCCCEECCeEEEEEEeC
Confidence            999999999999999999864

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.51  E-value=1.1e-13  Score=123.28  Aligned_cols=86  Identities=22%  Similarity=0.409  Sum_probs=78.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHh-----CC-ceeCCE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM-----NG-KYVGNR  208 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l-----~g-~~i~g~  208 (247)
                      ...+.+|||.||++++++++|.++|++||.|..+.|+.++.||.++|.|||.|.+..++.+||...     .| ..|+||
T Consensus       289 ~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR  368 (678)
T KOG0127|consen  289 ITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGR  368 (678)
T ss_pred             ccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEecc
Confidence            344689999999999999999999999999999999999999999999999999999999999865     23 688999


Q ss_pred             eEEEEEcccccc
Q 025814          209 PIKLRKSKWQER  220 (247)
Q Consensus       209 ~l~V~~a~~k~~  220 (247)
                      .|+|..+..+..
T Consensus       369 ~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  369 LLKVTLAVTRKE  380 (678)
T ss_pred             EEeeeeccchHH
Confidence            999999987653

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.51  E-value=1.2e-14  Score=123.76  Aligned_cols=77  Identities=31%  Similarity=0.647  Sum_probs=74.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      |+||||.+.+++.|+.|+..|..||+|++|.+.+|+.|+++|||+||+|+-+|.|+-|++.|||..++||.|+|..-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999754

>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=99.51  E-value=2.1e-13  Score=91.96  Aligned_cols=74  Identities=38%  Similarity=0.742  Sum_probs=68.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      +|||+|||.++++++|+++|+.||.|..+.+..+..+ ..+|+|||+|.+.++|..|++.+++..++|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999988644 7789999999999999999999999999999999863

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).

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.50  E-value=1.2e-13  Score=97.90  Aligned_cols=81  Identities=19%  Similarity=0.329  Sum_probs=72.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ++-.+-|||.|||+.++.++..++|+.||.|..|+|-..+.   .+|-|||.|++..+|.+|+..|+|..+.++.|.|-+
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vly   91 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLY   91 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEe
Confidence            33455799999999999999999999999999999966544   489999999999999999999999999999999988


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      -.+.
T Consensus        92 yq~~   95 (124)
T KOG0114|consen   92 YQPE   95 (124)
T ss_pred             cCHH
Confidence            7643

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.47  E-value=6.4e-14  Score=118.98  Aligned_cols=88  Identities=28%  Similarity=0.405  Sum_probs=81.5

Q ss_pred             CCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeE
Q 025814          131 LAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPI  210 (247)
Q Consensus       131 ~~~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l  210 (247)
                      .++..++.+.|||.-|.+-+++++|.-+|+.||.|.+|.|++|..||.+..|+||+|++.+++++|.-.|++..|+.++|
T Consensus       232 dAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRI  311 (479)
T KOG0415|consen  232 DADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRI  311 (479)
T ss_pred             ccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceE
Confidence            34446667799999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcccc
Q 025814          211 KLRKSKWQ  218 (247)
Q Consensus       211 ~V~~a~~k  218 (247)
                      +|.++..-
T Consensus       312 HVDFSQSV  319 (479)
T KOG0415|consen  312 HVDFSQSV  319 (479)
T ss_pred             Eeehhhhh
Confidence            99887543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.47  E-value=9.5e-14  Score=127.06  Aligned_cols=136  Identities=16%  Similarity=0.248  Sum_probs=110.4

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhc---CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHH
Q 025814           80 QLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLS  156 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L~  156 (247)
                      ...+.|++||.|.+.+++..|+..   ..++|..+.++....+......   .... ....+..|+|.|||+..+-.+++
T Consensus       556 k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~g---K~~~-~kk~~tKIlVRNipFeAt~rEVr  631 (725)
T KOG0110|consen  556 KYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVG---KKKS-KKKKGTKILVRNIPFEATKREVR  631 (725)
T ss_pred             cccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccc---cccc-cccccceeeeeccchHHHHHHHH
Confidence            445679999999999988888764   5788888888776632222211   1111 12225689999999999999999


Q ss_pred             HHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          157 KAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       157 ~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      ++|..||.|.+|+|..-...+.++|||||+|-++.+|.+|+..|....+.||+|.++|+..-+
T Consensus       632 ~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  632 KLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             HHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            999999999999998875667789999999999999999999999999999999999997544

>smart00361 RRM_1 RNA recognition motif

Probab=99.46  E-value=3.2e-13  Score=91.72  Aligned_cols=62  Identities=26%  Similarity=0.507  Sum_probs=56.6

Q ss_pred             HHHHHHHhc----cCCCeeEEE-EEecCCC--CCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          152 DDVLSKAFS----RFPSFNMAK-VVRDKRT--GKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       152 e~~L~~~F~----~~G~i~~v~-i~~~~~t--g~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      +++|+++|+    .||.|.++. |+.++.+  |.++|||||+|.+.++|.+|++.|||..++|+.|+++
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            578889998    999999995 7887767  9999999999999999999999999999999999873

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.43  E-value=1.8e-13  Score=118.90  Aligned_cols=85  Identities=29%  Similarity=0.420  Sum_probs=81.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ++++.+|||++||.++-+.+|..+|..||.|.+.++..|+.||.++|||||.|++..+|.+||..|||..|++++|+|..
T Consensus       421 GpeGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQl  500 (510)
T KOG0144|consen  421 GPEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQL  500 (510)
T ss_pred             CCCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEe
Confidence            66778999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      .+.+.
T Consensus       501 k~~~~  505 (510)
T KOG0144|consen  501 KRDRN  505 (510)
T ss_pred             eeccC
Confidence            87654

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.42  E-value=3e-13  Score=105.58  Aligned_cols=81  Identities=14%  Similarity=0.333  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||||||.++.+.+|+.+|.+||.|..|.+-.-   -...+||||+|++..+|+.||..-||..++|.+|+|++
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEf   79 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEF   79 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEe
Confidence            345679999999999999999999999999999987433   22356999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      ++.-
T Consensus        80 prgg   83 (241)
T KOG0105|consen   80 PRGG   83 (241)
T ss_pred             ccCC
Confidence            8754

>PF13893 RRM_5: RNA recognition motif

Probab=99.39  E-value=2.5e-12  Score=83.35  Aligned_cols=56  Identities=32%  Similarity=0.669  Sum_probs=50.9

Q ss_pred             HHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          155 LSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       155 L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      |.++|++||.|.++.+..+.     +|+|||+|.+.++|..|++.|||..++|+.|+|.+|
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999997763     589999999999999999999999999999999985

(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 ....

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.37  E-value=8.6e-13  Score=109.58  Aligned_cols=72  Identities=22%  Similarity=0.479  Sum_probs=69.1

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      +|||||||..+++.+|+.+|++||.|.+|.|+++        ||||..++...++.||+.|||..|+|..|+|+-++.|.
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            6999999999999999999999999999999988        99999999999999999999999999999999887763

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.36  E-value=2.1e-12  Score=102.60  Aligned_cols=81  Identities=19%  Similarity=0.321  Sum_probs=74.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccC-CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRF-PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~-G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..-+||+.++..+.+.+|..+|.+| |.|..+++.|++.||.++|||||+|++.+.|.-|-+.||+..++|+.|.+.+=-
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmp  128 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMP  128 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeC
Confidence            4469999999999999999999998 677888888999999999999999999999999999999999999999998754


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      +.
T Consensus       129 pe  130 (214)
T KOG4208|consen  129 PE  130 (214)
T ss_pred             ch
Confidence            43

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.28  E-value=8.8e-12  Score=110.40  Aligned_cols=142  Identities=22%  Similarity=0.357  Sum_probs=111.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      |.+.+..+..+...  ++++ ||.|++.+++.+++..   ..+.++.+-+.....+.........     ....-.++||
T Consensus       101 g~ilS~kv~~~~~g--~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~-----~~~~~t~v~v  172 (369)
T KOG0123|consen  101 GNILSCKVATDENG--SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGE-----YKKRFTNVYV  172 (369)
T ss_pred             cCeeEEEEEEcCCC--ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccc-----hhhhhhhhhe
Confidence            66666666555544  8999 9999999999999863   3455555555444444333322111     1223347999


Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          144 GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .|+..+.+++.|..+|..+|.|.++.++.+ ..|+++||+||.|.+.++|..|++.|||..+++..+.|..+..
T Consensus       173 k~~~~~~~~~~l~~~f~~~g~i~s~~v~~~-~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  173 KNLEEDSTDEELKDLFSAYGSITSVAVMRD-SIGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQK  245 (369)
T ss_pred             eccccccchHHHHHhhcccCcceEEEEeec-CCCCCCCccceeecChhHHHHHHHhccCCcCCccceeeccccc
Confidence            999999999999999999999999999999 4788999999999999999999999999999999999988765

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.27  E-value=1.8e-11  Score=106.87  Aligned_cols=85  Identities=18%  Similarity=0.367  Sum_probs=76.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhc-cCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFS-RFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~-~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ...+.+||.|||+++.+.+|+++|. +.|.|..|.++.| ..|+.+||+.|+|+++|.+++|++.||.+++.||.|+|..
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            3455699999999999999999995 6899999999999 5899999999999999999999999999999999999977


Q ss_pred             ccccccc
Q 025814          215 SKWQERT  221 (247)
Q Consensus       215 a~~k~~~  221 (247)
                      ....++.
T Consensus       121 d~d~q~~  127 (608)
T KOG4212|consen  121 DHDEQRD  127 (608)
T ss_pred             cCchhhh
Confidence            6554433

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.26  E-value=2.2e-11  Score=98.23  Aligned_cols=79  Identities=23%  Similarity=0.432  Sum_probs=73.1

Q ss_pred             EEEEcCCCCCCcHHHHHH----HhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          140 RLFCGDLGNEVNDDVLSK----AFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~----~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ||||.||+..+..++|++    +|++||.|.+|....   |.+.+|-|||.|.+.+.|-.|++.|+|..+.|+.++|.+|
T Consensus        11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA   87 (221)
T KOG4206|consen   11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYA   87 (221)
T ss_pred             eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecc
Confidence            999999999999999988    999999999987764   6889999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          216 KWQERT  221 (247)
Q Consensus       216 ~~k~~~  221 (247)
                      +.+..+
T Consensus        88 ~s~sdi   93 (221)
T KOG4206|consen   88 KSDSDI   93 (221)
T ss_pred             cCccch
Confidence            876543

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.25  E-value=1.8e-11  Score=100.78  Aligned_cols=84  Identities=21%  Similarity=0.459  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-C--CEeEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV-G--NRPIK  211 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i-~--g~~l~  211 (247)
                      +.++++||||-|...-.|||++++|..||.|.+|.+.+.. .|.+|||+||.|.+..+|+.||..|+|... -  ...|.
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLV   94 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLV   94 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceE
Confidence            4467799999999999999999999999999999999985 699999999999999999999999999843 3  37799


Q ss_pred             EEEccccc
Q 025814          212 LRKSKWQE  219 (247)
Q Consensus       212 V~~a~~k~  219 (247)
                      |++++..+
T Consensus        95 VK~ADTdk  102 (371)
T KOG0146|consen   95 VKFADTDK  102 (371)
T ss_pred             EEeccchH
Confidence            99998644

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.22  E-value=9.7e-12  Score=106.93  Aligned_cols=84  Identities=29%  Similarity=0.563  Sum_probs=76.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      +.++||||+|.|+++++.|+..|.+||.|.++.+++|+.+++++||+||+|++.+...++| ...-+.|+|+.|.+..+.
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 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVL-NARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheee-cccccccCCccccceecc
Confidence            5668999999999999999999999999999999999999999999999999999998888 445668999999999988


Q ss_pred             ccccc
Q 025814          217 WQERT  221 (247)
Q Consensus       217 ~k~~~  221 (247)
                      ++...
T Consensus        84 ~r~~~   88 (311)
T KOG4205|consen   84 SREDQ   88 (311)
T ss_pred             Ccccc
Confidence            77643

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.19  E-value=1.1e-10  Score=99.35  Aligned_cols=84  Identities=17%  Similarity=0.357  Sum_probs=75.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCee--------EEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEe
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFN--------MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRP  209 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~--------~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~  209 (247)
                      ...|||.|||.++|.+++.++|++||.|.        .|+|.++. .|..+|=|.|.|...++++-|++.|++..+.|+.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            44699999999999999999999999884        48899995 5999999999999999999999999999999999


Q ss_pred             EEEEEcccccccc
Q 025814          210 IKLRKSKWQERTD  222 (247)
Q Consensus       210 l~V~~a~~k~~~~  222 (247)
                      |+|+.|+...+..
T Consensus       213 ~rVerAkfq~Kge  225 (382)
T KOG1548|consen  213 LRVERAKFQMKGE  225 (382)
T ss_pred             EEEehhhhhhccC
Confidence            9999997655443

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.18  E-value=4.8e-11  Score=107.19  Aligned_cols=81  Identities=21%  Similarity=0.385  Sum_probs=76.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ..+++|||.+|...+...+|+.+|++||.|+-.+|+.+-.+--.+|||||++.+.++|.+||..|+..+|.|+.|.|+.+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34678999999999999999999999999999999998878888999999999999999999999999999999999887


Q ss_pred             c
Q 025814          216 K  216 (247)
Q Consensus       216 ~  216 (247)
                      +
T Consensus       483 K  483 (940)
T KOG4661|consen  483 K  483 (940)
T ss_pred             c
Confidence            5

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.09  E-value=3.2e-10  Score=96.48  Aligned_cols=75  Identities=17%  Similarity=0.338  Sum_probs=66.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHH-HhCCceeCCEeEEEEEc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK-EMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~-~l~g~~i~g~~l~V~~a  215 (247)
                      ...+|||+||...++|.+|+++|.+||.|.++.++..      +|+|||+|.+.++|+.|.. .+|...|+|++|+|.|.
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            3468999999999999999999999999999999776      3599999999999998876 55666899999999999


Q ss_pred             cc
Q 025814          216 KW  217 (247)
Q Consensus       216 ~~  217 (247)
                      ++
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            88

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.07  E-value=2.9e-10  Score=105.36  Aligned_cols=77  Identities=19%  Similarity=0.363  Sum_probs=71.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .+|||||+|+..+++.||..+|+.||.|.+|.++..      +|||||...+..+|.+|+..|+...+.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            468999999999999999999999999999988765      67999999999999999999999999999999999987


Q ss_pred             ccc
Q 025814          218 QER  220 (247)
Q Consensus       218 k~~  220 (247)
                      +.-
T Consensus       495 ~G~  497 (894)
T KOG0132|consen  495 KGP  497 (894)
T ss_pred             CCc
Confidence            653

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.07  E-value=4.4e-10  Score=103.39  Aligned_cols=78  Identities=26%  Similarity=0.453  Sum_probs=70.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCC---CCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRT---GKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~t---g~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ++|||.||+++.+.++|..+|...|.|.++.|...+..   -.+.|||||+|.+.++|++|++.|+|..|+|+.|.|+++
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            34999999999999999999999999999988765421   235699999999999999999999999999999999999


Q ss_pred             c
Q 025814          216 K  216 (247)
Q Consensus       216 ~  216 (247)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            8

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=99.05  E-value=2.9e-10  Score=94.41  Aligned_cols=81  Identities=19%  Similarity=0.335  Sum_probs=75.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      +...+||+|+.+.++.+++..+|+.||.|..+.+..|+.+|.++||+||+|.+.+.++.+|. |||..|.|+.|+|.+.+
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeee
Confidence            34479999999999999999999999999999999999999999999999999999999996 99999999999998876


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      .+
T Consensus       179 ~~  180 (231)
T KOG4209|consen  179 TN  180 (231)
T ss_pred             ee
Confidence            54

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.02  E-value=5.1e-10  Score=97.84  Aligned_cols=76  Identities=24%  Similarity=0.366  Sum_probs=69.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....|+|||.|||+++|+..|++-|..||.|..+.|+   ..|+++|  .|.|.++++|++|+..|||..++||.|+|.+
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            3556789999999999999999999999999999884   3588887  8999999999999999999999999999987


Q ss_pred             c
Q 025814          215 S  215 (247)
Q Consensus       215 a  215 (247)
                      .
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            3

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.97  E-value=2.4e-09  Score=88.87  Aligned_cols=81  Identities=25%  Similarity=0.361  Sum_probs=74.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      ..+|+|.||++.+.+++|+++|..||.++.+.|..|+ .|.+.|.|-|.|...++|.+|++.+||..++|+.|++.....
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            3589999999999999999999999999999999995 799999999999999999999999999999999999987654


Q ss_pred             cc
Q 025814          218 QE  219 (247)
Q Consensus       218 k~  219 (247)
                      ..
T Consensus       162 ~~  163 (243)
T KOG0533|consen  162 PS  163 (243)
T ss_pred             cc
Confidence            43

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.95  E-value=1.9e-09  Score=99.12  Aligned_cols=86  Identities=27%  Similarity=0.466  Sum_probs=75.4

Q ss_pred             CCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCC---CCCcceEEEEEecCHHHHHHHHHHhCCceeCCE
Q 025814          132 AEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKR---TGKTKGYGFISFANPSDIAAALKEMNGKYVGNR  208 (247)
Q Consensus       132 ~~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~---tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~  208 (247)
                      .+..+..++|||+||++.++++.|...|+.||+|.+|+|++.+.   ....+-||||.|.+..++++|++.|+|..+.+.
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            33456678999999999999999999999999999999998652   234456999999999999999999999999999


Q ss_pred             eEEEEEccc
Q 025814          209 PIKLRKSKW  217 (247)
Q Consensus       209 ~l~V~~a~~  217 (247)
                      .+++-|++.
T Consensus       248 e~K~gWgk~  256 (877)
T KOG0151|consen  248 EMKLGWGKA  256 (877)
T ss_pred             eeeeccccc
Confidence            999999854

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.93  E-value=2.7e-09  Score=95.20  Aligned_cols=83  Identities=18%  Similarity=0.368  Sum_probs=69.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      ..+|||.|||.+++.++|+++|..||.|+...|..-.-.++..|||||+|.+.++++.||++ +-..|++++|.|+..+.
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            34599999999999999999999999999988765432355559999999999999999965 57789999999998876


Q ss_pred             cccc
Q 025814          218 QERT  221 (247)
Q Consensus       218 k~~~  221 (247)
                      ..+.
T Consensus       367 ~~~g  370 (419)
T KOG0116|consen  367 GFRG  370 (419)
T ss_pred             cccc
Confidence            5543

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.89  E-value=2.2e-09  Score=96.48  Aligned_cols=70  Identities=26%  Similarity=0.397  Sum_probs=63.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      ..++|+|-|||..+++++|+++|+.||+|..|+.     |-..+|.+||+|.|..+|++|+++||+.+|.|+.|+
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3458999999999999999999999999998654     444578999999999999999999999999999988

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.86  E-value=1.9e-08  Score=81.09  Aligned_cols=86  Identities=21%  Similarity=0.304  Sum_probs=70.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEe-cCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---CEeE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVR-DKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG---NRPI  210 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~-~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~---g~~l  210 (247)
                      .+.-+||||.+||.++.-.+|..+|..|-..+.+.+-. ++.....+-+|||+|.+..+|.+|++.|||..++   +..|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            34467999999999999999999999998777665543 2222234579999999999999999999999886   7899


Q ss_pred             EEEEcccccc
Q 025814          211 KLRKSKWQER  220 (247)
Q Consensus       211 ~V~~a~~k~~  220 (247)
                      ++++++...+
T Consensus       111 hiElAKSNtK  120 (284)
T KOG1457|consen  111 HIELAKSNTK  120 (284)
T ss_pred             EeeehhcCcc
Confidence            9999876543

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.83  E-value=2.1e-08  Score=89.15  Aligned_cols=132  Identities=17%  Similarity=0.164  Sum_probs=99.7

Q ss_pred             hcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhcccccccccCCCCCCCCCC-CCCCCCcEEEEcCCCCCCcHHHHHH
Q 025814           81 LFQRDAQTITPEALESVKAALASS--DIEHKAETKKKSIPRKAAGQTWEDPTLA-EWPENDYRLFCGDLGNEVNDDVLSK  157 (247)
Q Consensus        81 ~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~~r~~~~~~~~~~~~~-~~~~~~~~lfV~nLp~~~~e~~L~~  157 (247)
                      ....+-++|.++..+++..||...  .+..+-+++-........   |...... .....+..|-+.+||+.|+++||.+
T Consensus        46 Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~e~d---~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~  122 (510)
T KOG4211|consen   46 GRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGAEAD---WVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVE  122 (510)
T ss_pred             CCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCcccc---ccccCCCCCCCCCCceEEecCCCccCcHHHHHH
Confidence            556889999999999999999864  667777777665444332   1111111 1124556899999999999999999


Q ss_pred             HhccCCCeeE-EEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          158 AFSRFPSFNM-AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       158 ~F~~~G~i~~-v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      ||+..-.|.. +.++.+. .++..|-|||.|++.+.|+.||. -|...|+.|-|.|..+.-
T Consensus       123 FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~Ss~  181 (510)
T KOG4211|consen  123 FFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRSSR  181 (510)
T ss_pred             HhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehhHH
Confidence            9998765555 5566664 67888999999999999999995 477788999999977653

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.77  E-value=6.3e-09  Score=84.69  Aligned_cols=71  Identities=20%  Similarity=0.486  Sum_probs=65.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      .||||+|++.+.+.+|+.+|..||.|.++.+..        ||+||+|.+.-+|..|+..+||.+|.|.++.|++++..
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            699999999999999999999999999887753        49999999999999999999999999999999999854

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.76  E-value=1.1e-08  Score=92.69  Aligned_cols=138  Identities=18%  Similarity=0.360  Sum_probs=108.2

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhcccccccc----------cCCCCCCCCCCCCCCCCcEEEEcCCC
Q 025814           80 QLFQRDAQTITPEALESVKAALASS--DIEHKAETKKKSIPRKA----------AGQTWEDPTLAEWPENDYRLFCGDLG  147 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~~r~~----------~~~~~~~~~~~~~~~~~~~lfV~nLp  147 (247)
                      -...+.+.++.+...+.+..++...  ..++.............          .+..........+....+.+||++|+
T Consensus       219 ~n~~~nfa~ie~~s~~~at~~~~~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp  298 (500)
T KOG0120|consen  219 LNLEKNFAFIEFRSISEATEAMALDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLP  298 (500)
T ss_pred             ecccccceeEEecCCCchhhhhcccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCc
Confidence            3455889999999999988888654  33444444333221111          11122233344456667789999999


Q ss_pred             CCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          148 NEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       148 ~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      ..++++.+.++...||.+....++.|..+|.++||+|.+|-+......|+..|||..++++.|.|..+-.
T Consensus       299 ~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~  368 (500)
T KOG0120|consen  299 LYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIV  368 (500)
T ss_pred             CccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhc
Confidence            9999999999999999999999999999999999999999999999999999999999999999988754

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.76  E-value=2.8e-09  Score=85.58  Aligned_cols=82  Identities=16%  Similarity=0.207  Sum_probs=74.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .+.+++|||+||...++|+-|.++|-+-|+|..|.|..++ .++.+ |+||.|.++.+..-|++.|||..+.++.|.|.+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            4567799999999999999999999999999999998885 56777 999999999999999999999999999999877


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      -.+.
T Consensus        84 r~G~   87 (267)
T KOG4454|consen   84 RCGN   87 (267)
T ss_pred             ccCC
Confidence            6544

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.68  E-value=1.7e-07  Score=67.17  Aligned_cols=81  Identities=16%  Similarity=0.290  Sum_probs=70.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhcc--CCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC----CEeEEE
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSR--FPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG----NRPIKL  212 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~--~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~----g~~l~V  212 (247)
                      +||.|.|||...+.++|.+++..  .|....+.+..|-.++-+.|||||.|.+.+.+.+-.+.++|..+.    .+...|
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            48999999999999999988854  467788899999889999999999999999999999999999775    466788


Q ss_pred             EEccccc
Q 025814          213 RKSKWQE  219 (247)
Q Consensus       213 ~~a~~k~  219 (247)
                      .+|+-..
T Consensus        82 ~yAriQG   88 (97)
T PF04059_consen   82 SYARIQG   88 (97)
T ss_pred             ehhHhhC
Confidence            8876543

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.67  E-value=4.5e-08  Score=83.91  Aligned_cols=143  Identities=17%  Similarity=0.285  Sum_probs=105.7

Q ss_pred             ccchhhhcCCCceeeCccCHHHHHHHHhcCc---cchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEE-EcCCCCCC
Q 025814           75 YHQAQQLFQRDAQTITPEALESVKAALASSD---IEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLF-CGDLGNEV  150 (247)
Q Consensus        75 ~~~~~~~~~~~~~~v~~~~~~~a~~al~~~~---~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lf-V~nLp~~~  150 (247)
                      .........++...+.|+..+....+|....   +....+.......+..   ........-......++| |+||++.+
T Consensus       121 S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~~~~~---~~~n~~~~~~~~~s~~~~~~~~~~f~~  197 (285)
T KOG4210|consen  121 SSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNTRRGL---RPKNKLSRLSSGPSDTIFFVGELDFSL  197 (285)
T ss_pred             hhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccccccc---cccchhcccccCccccceeeccccccc
Confidence            3334566679999999999999999987653   2333333333332221   111111111122333555 99999999


Q ss_pred             cHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccccc
Q 025814          151 NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERT  221 (247)
Q Consensus       151 ~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~~  221 (247)
                      ++++|..+|..+|.|..+++..+..+|..+||+||.|.+......++.. +...+.++.+.+.+...+...
T Consensus       198 ~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  198 TRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             chHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCccc
Confidence            9999999999999999999999999999999999999999999999866 788999999999988776443

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.61  E-value=1.7e-07  Score=83.52  Aligned_cols=81  Identities=17%  Similarity=0.299  Sum_probs=68.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .....-|-+.+|||++|++||.++|+.|+ |.++.+.+.  +|+..|-|||+|.+.+++++|+ +.|...++.|-|.|-.
T Consensus         7 ~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Al-kkdR~~mg~RYIEVf~   82 (510)
T KOG4211|consen    7 GSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKAL-KKDRESMGHRYIEVFT   82 (510)
T ss_pred             CCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHH-HhhHHHhCCceEEEEc
Confidence            44455788899999999999999999996 666666554  8999999999999999999999 5688889999999988


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +...+
T Consensus        83 ~~~~e   87 (510)
T KOG4211|consen   83 AGGAE   87 (510)
T ss_pred             cCCcc
Confidence            75544

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.57  E-value=6.1e-08  Score=78.96  Aligned_cols=125  Identities=15%  Similarity=0.258  Sum_probs=86.8

Q ss_pred             CCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccc-cccCCCC-----C-CCCCCCCCCCCcEEEEcCCCCCCcH
Q 025814           83 QRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPR-KAAGQTW-----E-DPTLAEWPENDYRLFCGDLGNEVND  152 (247)
Q Consensus        83 ~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r-~~~~~~~-----~-~~~~~~~~~~~~~lfV~nLp~~~~e  152 (247)
                      ..+++||.|++..++.+++..   ..+.+..+.+..+... ...+...     . ...........+.|+|.|+..++.+
T Consensus        34 k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~  113 (216)
T KOG0106|consen   34 KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSW  113 (216)
T ss_pred             ecccceeccCchhhhhcccchhcCceecceeeeeecccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhH
Confidence            367779999998888888753   3444433222222211 1111100     0 1111112345678999999999999


Q ss_pred             HHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       153 ~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .+|.++|+.+|.+....+        ..+++||+|...+++.+||..|+|..+.|+.|.+...
T Consensus       114 qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  114 QDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             HHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            999999999999844433        2459999999999999999999999999999999443

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.54  E-value=1.1e-07  Score=81.20  Aligned_cols=96  Identities=16%  Similarity=0.275  Sum_probs=77.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCC--CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFP--SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G--~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      .....+|||||-|++|++||.+.+...|  .+.++++..++.+|.+|||++|...+..+.++.++.|--.+|+|..-.|-
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            3445799999999999999999988776  56778889999999999999999999999999999999999999877765


Q ss_pred             EccccccccHHHHHhhhc
Q 025814          214 KSKWQERTDFEALERSKN  231 (247)
Q Consensus       214 ~a~~k~~~~~~~~~~~~~  231 (247)
                      --...+....+..+++..
T Consensus       158 ~~NK~~~ak~E~~~~K~~  175 (498)
T KOG4849|consen  158 SYNKTNQAKLEDAQAKNQ  175 (498)
T ss_pred             ccchhhHHHHHHHHhhhc
Confidence            555455555555444443

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.52  E-value=1.3e-06  Score=70.83  Aligned_cols=132  Identities=18%  Similarity=0.266  Sum_probs=95.6

Q ss_pred             hhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCC-------------------------------
Q 025814           80 QLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQT-------------------------------  125 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~-------------------------------  125 (247)
                      +.-.||-++|.|.+.+.+-.|+.   +--.-++.+++.++.........                               
T Consensus        48 t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~  127 (221)
T KOG4206|consen   48 TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFY  127 (221)
T ss_pred             CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCccchhhccCceeccccCccccccccccCCccccccccc
Confidence            44569999999998777777664   44455666555554432211110                               


Q ss_pred             -----CCCCCC-CCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHH
Q 025814          126 -----WEDPTL-AEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE  199 (247)
Q Consensus       126 -----~~~~~~-~~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~  199 (247)
                           ...+.. .........||+.|||.+++.+.|..+|.+|...+.|+++..+     +|.+||+|.+...+..|...
T Consensus       128 ~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~  202 (221)
T KOG4206|consen  128 NMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQA  202 (221)
T ss_pred             ccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhh
Confidence                 000000 1224556789999999999999999999999999999998764     46999999999999999999


Q ss_pred             hCCceeC-CEeEEEEEcc
Q 025814          200 MNGKYVG-NRPIKLRKSK  216 (247)
Q Consensus       200 l~g~~i~-g~~l~V~~a~  216 (247)
                      +.|..|- ...+.|.+++
T Consensus       203 lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  203 LQGFKITKKNTMQITFAK  220 (221)
T ss_pred             hccceeccCceEEecccC
Confidence            9999876 7788887764

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.37  E-value=2.9e-07  Score=79.20  Aligned_cols=84  Identities=21%  Similarity=0.300  Sum_probs=76.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCee--------EEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFN--------MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNR  208 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~--------~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~  208 (247)
                      ...+|||-+|+..+++++|..+|.+||.|.        .|+|.+|+.|+..||-|.|.|++...|+.|+..+++..+.|.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            344899999999999999999999999884        467889999999999999999999999999999999999999


Q ss_pred             eEEEEEcccccc
Q 025814          209 PIKLRKSKWQER  220 (247)
Q Consensus       209 ~l~V~~a~~k~~  220 (247)
                      .|+|..+..+..
T Consensus       145 ~ikvs~a~~r~~  156 (351)
T KOG1995|consen  145 TIKVSLAERRTG  156 (351)
T ss_pred             CchhhhhhhccC
Confidence            999988876554

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.32  E-value=2.1e-07  Score=83.90  Aligned_cols=80  Identities=18%  Similarity=0.409  Sum_probs=74.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .+.+++|+.-|....+..+|.++|+.+|.|.+|.++.|+.++.++|.|||+|.+.+++..|| .|.|..+.|..|.|...
T Consensus       177 Rd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  177 RDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLS  255 (549)
T ss_pred             HhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEeccc
Confidence            44678999999999999999999999999999999999999999999999999999999999 89999999999999765


Q ss_pred             c
Q 025814          216 K  216 (247)
Q Consensus       216 ~  216 (247)
                      .
T Consensus       256 E  256 (549)
T KOG0147|consen  256 E  256 (549)
T ss_pred             H
Confidence            3

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.32  E-value=1.1e-06  Score=75.03  Aligned_cols=85  Identities=15%  Similarity=0.285  Sum_probs=65.5

Q ss_pred             cEEEEcCCCCCCcHHHH------HHHhccCCCeeEEEEEecCCC-CCcce-E-EEEEecCHHHHHHHHHHhCCceeCCEe
Q 025814          139 YRLFCGDLGNEVNDDVL------SKAFSRFPSFNMAKVVRDKRT-GKTKG-Y-GFISFANPSDIAAALKEMNGKYVGNRP  209 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L------~~~F~~~G~i~~v~i~~~~~t-g~~kg-~-~FV~f~~~~~a~~Al~~l~g~~i~g~~  209 (247)
                      .-+||-+|++.+.+++.      .++|++||.|+.|.|-+.... ....+ + .||+|.+.++|.+||.+.+|..++||.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            35999999999877762      589999999998866543211 11122 2 399999999999999999999999999


Q ss_pred             EEEEEccccccccH
Q 025814          210 IKLRKSKWQERTDF  223 (247)
Q Consensus       210 l~V~~a~~k~~~~~  223 (247)
                      |+..+...|-...+
T Consensus       195 lkatYGTTKYCtsY  208 (480)
T COG5175         195 LKATYGTTKYCTSY  208 (480)
T ss_pred             EeeecCchHHHHHH
Confidence            99988776654433

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.31  E-value=2.7e-06  Score=74.30  Aligned_cols=76  Identities=20%  Similarity=0.370  Sum_probs=68.2

Q ss_pred             CcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          138 DYRLFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       138 ~~~lfV~nLp~~-~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ...|-|.||... +|.+.|..+|+-||.|.+|+|+.++.     --|.|.|.+...|+-|+..|+|..|.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            467888888665 89999999999999999999998863     379999999999999999999999999999999987


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      -.
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            43

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.30  E-value=4.2e-06  Score=65.91  Aligned_cols=123  Identities=13%  Similarity=0.138  Sum_probs=88.8

Q ss_pred             CCceeeCccCHHHHHHHHhc---CccchhhhhhcccccccccCCCC---------C----CCCCCCCCCCCcEEEEcCCC
Q 025814           84 RDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKAAGQTW---------E----DPTLAEWPENDYRLFCGDLG  147 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~~~~~~---------~----~~~~~~~~~~~~~lfV~nLp  147 (247)
                      -.++||.||++.+|++|+.+   .+.++-.+++....--.......         .    .......-....+|.|.+||
T Consensus        45 ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp  124 (241)
T KOG0105|consen   45 PPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLP  124 (241)
T ss_pred             CCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCC
Confidence            56899999999999999864   46666666665543221111000         0    00001112345689999999


Q ss_pred             CCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--CCEeEEEE
Q 025814          148 NEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV--GNRPIKLR  213 (247)
Q Consensus       148 ~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i--~g~~l~V~  213 (247)
                      .+.++.+|+.+...-|.|....+.+|       |+|.|+|...++++.|++.|+...+  .|....++
T Consensus       125 ~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yir  185 (241)
T KOG0105|consen  125 PSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIR  185 (241)
T ss_pred             CCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccccCcCcEeeEE
Confidence            99999999999999999999999888       4899999999999999999998754  35444443

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.29  E-value=7.7e-06  Score=70.15  Aligned_cols=134  Identities=14%  Similarity=0.185  Sum_probs=93.3

Q ss_pred             CCceeeCccCHHHHHHHHhcCccchhhhhhcccccccccC------------------------CCCCCCC-CCCCCCCC
Q 025814           84 RDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAG------------------------QTWEDPT-LAEWPEND  138 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al~~~~~~~~~~~~~~~~~r~~~~------------------------~~~~~~~-~~~~~~~~  138 (247)
                      .-|+|+.-++.+-|...|++..+++..+++.++.-.....                        -.|.... ........
T Consensus       186 aLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~  265 (382)
T KOG1548|consen  186 ALCCYIKRESVELAIKILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARAD  265 (382)
T ss_pred             eEEEeecccHHHHHHHHhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCC
Confidence            3355666777888888888888888877776654321111                        1111111 12234556


Q ss_pred             cEEEEcCCCC----CCc-------HHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q 025814          139 YRLFCGDLGN----EVN-------DDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN  207 (247)
Q Consensus       139 ~~lfV~nLp~----~~~-------e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g  207 (247)
                      ++|.|.||=.    ..+       .++|.+-..+||.|.+|.|.-    ..+.|.+-|.|.+.++|..||+.|+|..++|
T Consensus       266 ~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdg  341 (382)
T KOG1548|consen  266 RTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGRWFDG  341 (382)
T ss_pred             cEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCeeecc
Confidence            7899998721    222       245666778999999997753    2346899999999999999999999999999


Q ss_pred             EeEEEEEccccccc
Q 025814          208 RPIKLRKSKWQERT  221 (247)
Q Consensus       208 ~~l~V~~a~~k~~~  221 (247)
                      |.|......++.+-
T Consensus       342 Rql~A~i~DG~t~~  355 (382)
T KOG1548|consen  342 RQLTASIWDGKTKF  355 (382)
T ss_pred             eEEEEEEeCCccee
Confidence            99999988776543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.27  E-value=8e-07  Score=71.88  Aligned_cols=65  Identities=25%  Similarity=0.496  Sum_probs=54.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV  205 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i  205 (247)
                      -+.+|||.||..+|+|++|+++|+.|-....++|...  .|  .+.+|++|++.+.|..|+..|.|..|
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHHHhhccee
Confidence            3568999999999999999999999987766666322  22  35899999999999999999999866

>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=98.16  E-value=5.2e-06  Score=57.17  Aligned_cols=67  Identities=19%  Similarity=0.187  Sum_probs=47.1

Q ss_pred             EEEEcCCCCCCcHHH----HHHHhccCCC-eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          140 RLFCGDLGNEVNDDV----LSKAFSRFPS-FNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~----L~~~F~~~G~-i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .|||.|||.+.+-..    |++++..||. |.+|  .        .|-|+|.|.+.+.|.+|.+.|+|..+.|++|.|++
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~--------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            699999999988754    5677778874 4433  1        25799999999999999999999999999999998


Q ss_pred             cc
Q 025814          215 SK  216 (247)
Q Consensus       215 a~  216 (247)
                      ..
T Consensus        74 ~~   75 (90)
T PF11608_consen   74 SP   75 (90)
T ss_dssp             S-
T ss_pred             cC
Confidence            74

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>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=98.09  E-value=4.2e-06  Score=61.15  Aligned_cols=76  Identities=20%  Similarity=0.352  Sum_probs=46.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCC-----ceeCCEeEEEE
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG-----KYVGNRPIKLR  213 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g-----~~i~g~~l~V~  213 (247)
                      +.|+|.++...++-++|+.+|+.||.|..|.+.+.-.      .|||.|.+.+.|+.|+..+..     ..|.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            4689999999999999999999999999988876522      799999999999999885543     36778777777


Q ss_pred             Ecccccc
Q 025814          214 KSKWQER  220 (247)
Q Consensus       214 ~a~~k~~  220 (247)
                      .=...+.
T Consensus        76 vLeGeeE   82 (105)
T PF08777_consen   76 VLEGEEE   82 (105)
T ss_dssp             ---HHHH
T ss_pred             ECCCHHH
Confidence            6554443

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.00  E-value=4.4e-05  Score=66.22  Aligned_cols=126  Identities=14%  Similarity=0.099  Sum_probs=84.3

Q ss_pred             CCCceeeCccCHHHHHHHHhcCc-----cchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEE--EcCCCCCCcHHHH
Q 025814           83 QRDAQTITPEALESVKAALASSD-----IEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLF--CGDLGNEVNDDVL  155 (247)
Q Consensus        83 ~~~~~~v~~~~~~~a~~al~~~~-----~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lf--V~nLp~~~~e~~L  155 (247)
                      ++.-+.|.||+++.++.+.+-..     +.+...-..+...+.-.     .+.. +.......|.  |-|--+-+|-+.|
T Consensus        66 ~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyStsq~i~-----R~g~-es~~pN~VLl~TIlNp~YpItvDVl  139 (494)
T KOG1456|consen   66 HKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYSTSQCIE-----RPGD-ESATPNKVLLFTILNPQYPITVDVL  139 (494)
T ss_pred             ccceeeeeeccccchhhheehhccCcccccCchhhcccchhhhhc-----cCCC-CCCCCCeEEEEEeecCccccchhhh
Confidence            35567789999999999876432     22222222221111100     0000 0011222333  3455667999999


Q ss_pred             HHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--CEeEEEEEccccc
Q 025814          156 SKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG--NRPIKLRKSKWQE  219 (247)
Q Consensus       156 ~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~--g~~l~V~~a~~k~  219 (247)
                      ..+...+|.|.+|-|++.  +|.   -|.|+|++.+.|++|...|||..|.  =..|+|+++++..
T Consensus       140 y~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  140 YTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             hhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcce
Confidence            999999999999988775  444   5899999999999999999999775  3789999998754

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.97  E-value=3.9e-06  Score=69.17  Aligned_cols=71  Identities=10%  Similarity=0.189  Sum_probs=61.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCC--------CCcce----EEEEEecCHHHHHHHHHHhCCceeC
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRT--------GKTKG----YGFISFANPSDIAAALKEMNGKYVG  206 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~t--------g~~kg----~~FV~f~~~~~a~~Al~~l~g~~i~  206 (247)
                      ..||++|||+.++-.-|+++|+.||.|-+|.+-....+        |.+++    -|+|+|.+...|.++...|||..|+
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Ig  154 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIG  154 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccC
Confidence            47999999999999999999999999999988765444        33332    2789999999999999999999999


Q ss_pred             CEe
Q 025814          207 NRP  209 (247)
Q Consensus       207 g~~  209 (247)
                      |++
T Consensus       155 gkk  157 (278)
T KOG3152|consen  155 GKK  157 (278)
T ss_pred             CCC
Confidence            876

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=97.95  E-value=2.9e-05  Score=70.73  Aligned_cols=142  Identities=14%  Similarity=0.130  Sum_probs=87.8

Q ss_pred             cccchhhhcCCCceeeCccC---HHHHHHHHhcCccchhhhhhcccccccccCCCCCC--C-C------C--CCCCCCCc
Q 025814           74 QYHQAQQLFQRDAQTITPEA---LESVKAALASSDIEHKAETKKKSIPRKAAGQTWED--P-T------L--AEWPENDY  139 (247)
Q Consensus        74 ~~~~~~~~~~~~~~~v~~~~---~~~a~~al~~~~~~~~~~~~~~~~~r~~~~~~~~~--~-~------~--~~~~~~~~  139 (247)
                      ...+....++++++|-.+-+   .+.+++.|+++.+.++.+.+..+.........+..  . .      .  ........
T Consensus       321 lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~  400 (500)
T KOG0120|consen  321 LVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTE  400 (500)
T ss_pred             eecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCcch
Confidence            33344456778888766654   55666777777777777766665544433333222  0 0      0  00111122


Q ss_pred             EEEEcCC--CCC-CcH-------HHHHHHhccCCCeeEEEEEecCCC---CCcceEEEEEecCHHHHHHHHHHhCCceeC
Q 025814          140 RLFCGDL--GNE-VND-------DVLSKAFSRFPSFNMAKVVRDKRT---GKTKGYGFISFANPSDIAAALKEMNGKYVG  206 (247)
Q Consensus       140 ~lfV~nL--p~~-~~e-------~~L~~~F~~~G~i~~v~i~~~~~t---g~~kg~~FV~f~~~~~a~~Al~~l~g~~i~  206 (247)
                      .|-+.|+  +.+ .++       ++++.-++.||.|.+|.|.++-..   .-.-|--||+|.+.+++++|..+|+|..+.
T Consensus       401 Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~  480 (500)
T KOG0120|consen  401 VLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFA  480 (500)
T ss_pred             hhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeC
Confidence            2333332  111 122       233455679999999999887222   233466799999999999999999999999


Q ss_pred             CEeEEEEEc
Q 025814          207 NRPIKLRKS  215 (247)
Q Consensus       207 g~~l~V~~a  215 (247)
                      ||.|...|-
T Consensus       481 nRtVvtsYy  489 (500)
T KOG0120|consen  481 NRTVVASYY  489 (500)
T ss_pred             CcEEEEEec
Confidence            999998874

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.82  E-value=0.00016  Score=65.24  Aligned_cols=118  Identities=18%  Similarity=0.180  Sum_probs=83.6

Q ss_pred             hcCCC---ceeeCccCHHHHHHHHhcCccchhhhhhcccccccc----cCCCCC--CCC----CCCCCCCCcEEEEcCCC
Q 025814           81 LFQRD---AQTITPEALESVKAALASSDIEHKAETKKKSIPRKA----AGQTWE--DPT----LAEWPENDYRLFCGDLG  147 (247)
Q Consensus        81 ~~~~~---~~~v~~~~~~~a~~al~~~~~~~~~~~~~~~~~r~~----~~~~~~--~~~----~~~~~~~~~~lfV~nLp  147 (247)
                      ...+|   +.|+-|++..++.+.+..-..+....-.+...++..    .-..|.  +..    .....+..+|||||+||
T Consensus       300 ~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvp  379 (520)
T KOG0129|consen  300 APPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLP  379 (520)
T ss_pred             CCCCCcccEEEEEecchHHHHHHHHHHhhcccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCC
Confidence            34466   999999999999999875432222111111111100    000110  000    11224567799999999


Q ss_pred             CCCcHHHHHHHhc-cCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHH
Q 025814          148 NEVNDDVLSKAFS-RFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK  198 (247)
Q Consensus       148 ~~~~e~~L~~~F~-~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~  198 (247)
                      .-++.++|..+|. -||.|.-+.|-.|++-+..+|-|-|.|.+..+-.+||.
T Consensus       380 rpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  380 RPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             CcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            9999999999998 79999999999998889999999999999999999995

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.81  E-value=0.00011  Score=63.92  Aligned_cols=78  Identities=15%  Similarity=0.207  Sum_probs=69.4

Q ss_pred             CCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          136 ENDYRLFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp~~-~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .+++.+.|.+|... ++-+.|-.+|..||.|.+|++++.+     .|-|.|+..+..+.++|+..||+..+.|.+|.|..
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            45678999999876 7778999999999999999999875     36899999999999999999999999999999988


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      ++..
T Consensus       360 SkQ~  363 (494)
T KOG1456|consen  360 SKQN  363 (494)
T ss_pred             cccc
Confidence            7643

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.79  E-value=1.2e-05  Score=76.05  Aligned_cols=110  Identities=14%  Similarity=0.050  Sum_probs=88.1

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhcCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHh
Q 025814           80 QLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAF  159 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L~~~F  159 (247)
                      ...-||.+++.|...+.+.+++......-..                           ...|||.|+|+..|.++|+.++
T Consensus       705 ~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g---------------------------K~~v~i~g~pf~gt~e~~k~l~  757 (881)
T KOG0128|consen  705 EKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG---------------------------KISVAISGPPFQGTKEELKSLA  757 (881)
T ss_pred             ccccccceeeEeecCCchhhhhhhhhhhhhh---------------------------hhhhheeCCCCCCchHHHHhhc
Confidence            3344777788777777777766543221110                           1269999999999999999999


Q ss_pred             ccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          160 SRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       160 ~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      ..+|.+.+++++..+ .|+.+|.+||.|.+..++.+++..+++..+.-+.+.|..+.+
T Consensus       758 ~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  758 SKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             cccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            999999999988885 699999999999999999999988888888878888877655

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.79  E-value=5.8e-05  Score=65.71  Aligned_cols=135  Identities=16%  Similarity=0.160  Sum_probs=96.4

Q ss_pred             cCCCceeeCccCHHHHHHHHhcC--ccchhhhhhccccc--------ccccCCCCC---CCC-------CCCCCCCCcEE
Q 025814           82 FQRDAQTITPEALESVKAALASS--DIEHKAETKKKSIP--------RKAAGQTWE---DPT-------LAEWPENDYRL  141 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~~--------r~~~~~~~~---~~~-------~~~~~~~~~~l  141 (247)
                      .--|-+|+-|+..+.+..+|..+  .+..+.++..+...        |........   .+.       ..........|
T Consensus       204 rpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcv  283 (508)
T KOG1365|consen  204 RPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCV  283 (508)
T ss_pred             CcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCee
Confidence            44678899999999999999765  45555555544332        222111111   110       11112224579


Q ss_pred             EEcCCCCCCcHHHHHHHhccCCC-eeE--EEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          142 FCGDLGNEVNDDVLSKAFSRFPS-FNM--AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       142 fV~nLp~~~~e~~L~~~F~~~G~-i~~--v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      -+++||++.+.++|..+|..|.. |..  |.++.+ ..|+..|-|||+|.+.++|..|....+.....+|.|.|--+..
T Consensus       284 RLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~  361 (508)
T KOG1365|consen  284 RLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSV  361 (508)
T ss_pred             EecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccH
Confidence            99999999999999999998864 333  677777 4799999999999999999999998888888899999977654

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.75  E-value=0.0002  Score=54.85  Aligned_cols=74  Identities=22%  Similarity=0.334  Sum_probs=54.0

Q ss_pred             CCCCcEEEEcCCC------CCCcH---HHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 025814          135 PENDYRLFCGDLG------NEVND---DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV  205 (247)
Q Consensus       135 ~~~~~~lfV~nLp------~~~~e---~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i  205 (247)
                      ++.+.||.|.=+.      ..+.+   .+|.+.|..||.+.=++++.+        .-+|+|.+-++|.+|+ .|+|..|
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaal-s~dg~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAAL-SLDGIQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHH-HGCCSEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHH-ccCCcEE
Confidence            5666688887555      12333   266788899999988888766        4689999999999999 8999999


Q ss_pred             CCEeEEEEEccc
Q 025814          206 GNRPIKLRKSKW  217 (247)
Q Consensus       206 ~g~~l~V~~a~~  217 (247)
                      +|+.|+|+...+
T Consensus        95 ~g~~l~i~LKtp  106 (146)
T PF08952_consen   95 NGRTLKIRLKTP  106 (146)
T ss_dssp             TTEEEEEEE---
T ss_pred             CCEEEEEEeCCc
Confidence            999999988654

; PDB: 1UFW_A 2DNR_A.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.71  E-value=0.00012  Score=68.11  Aligned_cols=74  Identities=19%  Similarity=0.369  Sum_probs=65.6

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCee-EEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFN-MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~-~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .|-+.|+|++++-+||.++|.-|-.+- +|.+.++ +.|...|-|.|.|++.++|.+|...|++..|.+|+|+|.+
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            688899999999999999999997764 4444444 6799999999999999999999999999999999999864

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.69  E-value=0.00011  Score=66.80  Aligned_cols=77  Identities=29%  Similarity=0.331  Sum_probs=62.7

Q ss_pred             CcEEEEcCCCCCCc------HHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEeE
Q 025814          138 DYRLFCGDLGNEVN------DDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG-NRPI  210 (247)
Q Consensus       138 ~~~lfV~nLp~~~~------e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~-g~~l  210 (247)
                      +..|+|.|+|---.      ...|..+|+++|.|....+..+.. |..+||.|++|.+..+|+.|++.|||..|+ ++++
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            34789999876322      234568899999999999988865 449999999999999999999999999876 6788


Q ss_pred             EEEEc
Q 025814          211 KLRKS  215 (247)
Q Consensus       211 ~V~~a  215 (247)
                      .|+.-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            87654

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.64  E-value=7.6e-05  Score=61.73  Aligned_cols=101  Identities=23%  Similarity=0.328  Sum_probs=80.3

Q ss_pred             cCHHHHHHHHhcCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEE
Q 025814           92 EALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVV  171 (247)
Q Consensus        92 ~~~~~a~~al~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~  171 (247)
                      .-++.++..|+..-..++.+++..+..                    ..|||.||...+..+.|.+.|+.||.|....++
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~--------------------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~   64 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH--------------------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAK   64 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc--------------------ceEEEEecchhhhhHHHHHhhhhcCccchheee
Confidence            446778888888888888887766543                    379999999999999999999999999987777


Q ss_pred             ecCCCCCcceEEEEEecCHHHHHHHHHHhC--Cc--eeCCEeEEEE
Q 025814          172 RDKRTGKTKGYGFISFANPSDIAAALKEMN--GK--YVGNRPIKLR  213 (247)
Q Consensus       172 ~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~--g~--~i~g~~l~V~  213 (247)
                      .| ..++..|-++|.|.+.-.+.+|+..++  |.  .+.++..-|.
T Consensus        65 vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~Ve  109 (275)
T KOG0115|consen   65 VD-DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVE  109 (275)
T ss_pred             ec-ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCC
Confidence            77 468888899999999999999988773  22  3445555553

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=97.57  E-value=9.2e-05  Score=68.56  Aligned_cols=66  Identities=12%  Similarity=0.178  Sum_probs=59.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ++||+|+...+.++.+..+...||.|.++..+.         |||+.|.......+|+..++-..++|..+.+..
T Consensus        42 ~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   42 TVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             eeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            899999999999999999999999998876543         999999999999999999999999998887755

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.55  E-value=0.00054  Score=60.30  Aligned_cols=130  Identities=13%  Similarity=0.076  Sum_probs=89.8

Q ss_pred             CCceeeCccCHHHH---HHHHhcCccchhhhhhcccccccccCCCCCCCC-------------------C---CCCCCCC
Q 025814           84 RDAQTITPEALESV---KAALASSDIEHKAETKKKSIPRKAAGQTWEDPT-------------------L---AEWPEND  138 (247)
Q Consensus        84 ~~~~~v~~~~~~~a---~~al~~~~~~~~~~~~~~~~~r~~~~~~~~~~~-------------------~---~~~~~~~  138 (247)
                      ++-+.|.+.+...+   ...|+++.+-++.+++...+...-......++.                   .   ....++.
T Consensus       335 kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~Pps  414 (492)
T KOG1190|consen  335 KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPS  414 (492)
T ss_pred             CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCccccccccCCCCchhhccCcccccccccCCch
Confidence            56677777765554   455667888888888766554322111111110                   0   0123556


Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC-EeEEEEEccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN-RPIKLRKSKW  217 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g-~~l~V~~a~~  217 (247)
                      .+|.+.|+|.+++|++|+.+|..-|.........    ++.+-++++.+.+.|.|-.|+..++...+++ ..|+|++++.
T Consensus       415 atlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  415 ATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             hheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            6899999999999999999999888765543322    2233499999999999999999999998875 4899998763

>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=97.46  E-value=0.00079  Score=48.59  Aligned_cols=78  Identities=15%  Similarity=0.192  Sum_probs=50.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEE-EEecCC------CCCcceEEEEEecCHHHHHHHHHHhCCceeCCE-e
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAK-VVRDKR------TGKTKGYGFISFANPSDIAAALKEMNGKYVGNR-P  209 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~-i~~~~~------tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~-~  209 (247)
                      .+.|.|-+.|.. ....+.+.|++||.|.+.. +.++..      .......-.|.|+++.+|.+|| ..||..++|. .
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL-~~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL-QKNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHH-TTTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH-HhCCeEEcCcEE
Confidence            346888899998 5566888999999997664 111100      0112237789999999999999 6699999874 5


Q ss_pred             EEEEEccc
Q 025814          210 IKLRKSKW  217 (247)
Q Consensus       210 l~V~~a~~  217 (247)
                      +-|.+.+.
T Consensus        84 vGV~~~~~   91 (100)
T PF05172_consen   84 VGVKPCDP   91 (100)
T ss_dssp             EEEEE-HH
T ss_pred             EEEEEcHH
Confidence            66777643

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.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.43  E-value=0.00036  Score=44.34  Aligned_cols=51  Identities=12%  Similarity=0.268  Sum_probs=40.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHH
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL  197 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al  197 (247)
                      .|-|.+.+.+..+. +..+|..||.|.++.+-..      .-+.||.|.+..+|++||
T Consensus         3 wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    3 WISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             EEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            67888998887755 4558889999999887522      238999999999999985

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.29  E-value=0.00024  Score=62.81  Aligned_cols=70  Identities=14%  Similarity=0.169  Sum_probs=56.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEec---CCC--CCc--------ceEEEEEecCHHHHHHHHHHhCCc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRD---KRT--GKT--------KGYGFISFANPSDIAAALKEMNGK  203 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~---~~t--g~~--------kg~~FV~f~~~~~a~~Al~~l~g~  203 (247)
                      ..++|.+.|||.+-.-+.|.++|+.||.|+.|+|...   ...  |..        +-+|||+|+..+.|.+|.+.||..
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence            5679999999999888999999999999999999765   222  222        456899999999999999887665


Q ss_pred             eeC
Q 025814          204 YVG  206 (247)
Q Consensus       204 ~i~  206 (247)
                      ..+
T Consensus       310 ~~w  312 (484)
T KOG1855|consen  310 QNW  312 (484)
T ss_pred             hhh
Confidence            433

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.26  E-value=0.00099  Score=60.27  Aligned_cols=62  Identities=21%  Similarity=0.454  Sum_probs=45.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEe-cCCCC--Ccce---EEEEEecCHHHHHHHHHHh
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVR-DKRTG--KTKG---YGFISFANPSDIAAALKEM  200 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~-~~~tg--~~kg---~~FV~f~~~~~a~~Al~~l  200 (247)
                      .+.||||+||++++|+.|...|..||.+. |.+.. ....+  ..+|   |.|+.|+++.++..-|.++
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            46799999999999999999999999874 33331 11111  2456   9999999988877665543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.18  E-value=0.00082  Score=58.72  Aligned_cols=134  Identities=19%  Similarity=0.157  Sum_probs=87.2

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhccccccc----ccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHH
Q 025814           80 QLFQRDAQTITPEALESVKAALASS--DIEHKAETKKKSIPRK----AAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDD  153 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~~r~----~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~  153 (247)
                      +..-.+++.|.|-+.+.-+-++..+  .+..+.+++-++....    +.+...+..... ..++.-.|-+++||+++++.
T Consensus        98 qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~ge~f~~iagg~s~e~~~fl-sk~~qvivRmRGLPfdat~~  176 (508)
T KOG1365|consen   98 QGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATGEEFLKIAGGTSNEAAPFL-SKENQVIVRMRGLPFDATAL  176 (508)
T ss_pred             hhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCchhheEecCCccccCCCCC-CcccceEEEecCCCCCcchH
Confidence            3444677888888888888887654  5666666665544322    122221111111 01223346677999999999


Q ss_pred             HHHHHhccC----CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          154 VLSKAFSRF----PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       154 ~L~~~F~~~----G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ++.++|..-    |..+.|.++... .|+..|-|||.|..+++|+.||.. |...|+-|.|.+-.+.
T Consensus       177 dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRST  241 (508)
T KOG1365|consen  177 DVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRST  241 (508)
T ss_pred             HHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHHh
Confidence            999999632    344566555543 689999999999999999999964 5555666666664443

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.13  E-value=0.0037  Score=43.15  Aligned_cols=57  Identities=14%  Similarity=0.244  Sum_probs=43.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG  202 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g  202 (247)
                      .+...||+ +|..+...||.++|+.||.|. |.++.|.       -|||...+.+.+..++..++-
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            34456666 999999999999999999974 6666663       799999999999999988763

; 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.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.10  E-value=0.00054  Score=60.53  Aligned_cols=75  Identities=17%  Similarity=0.321  Sum_probs=59.6

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCc-eeCCEeEEEEEcccc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK-YVGNRPIKLRKSKWQ  218 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~-~i~g~~l~V~~a~~k  218 (247)
                      .||||||.+.++.++|+.+|...---.+-.++.      ..||+||.+.+...+.+|++.++|. ++.|+++.|..+.++
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            699999999999999999997541111111111      2479999999999999999999998 789999999998776


Q ss_pred             cc
Q 025814          219 ER  220 (247)
Q Consensus       219 ~~  220 (247)
                      ..
T Consensus        77 kq   78 (584)
T KOG2193|consen   77 KQ   78 (584)
T ss_pred             HH
Confidence            53

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.04  E-value=5.3e-05  Score=71.85  Aligned_cols=77  Identities=18%  Similarity=0.407  Sum_probs=63.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      +-+++||+||+..+.+.+|...|..+|.+..+.+.....+++.+|+||++|.+.+++.+|+...++..++...+-|+
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i~  742 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAIS  742 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhhee
Confidence            34579999999999999999999999999988887666789999999999999999999996555555443334443

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.92  E-value=0.003  Score=53.47  Aligned_cols=63  Identities=14%  Similarity=0.249  Sum_probs=51.0

Q ss_pred             HHHHHHhccCCCeeEEEEEecCCCCCcce-EEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKG-YGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       153 ~~L~~~F~~~G~i~~v~i~~~~~tg~~kg-~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +++.+..++||.|..|.|..++..-...- --||+|...++|.+|+-.|||..++||.+...+-
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            45677788999999998877753332222 3699999999999999999999999999988764

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.84  E-value=0.0015  Score=62.73  Aligned_cols=79  Identities=25%  Similarity=0.430  Sum_probs=68.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EeEEEEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN--RPIKLRK  214 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~  214 (247)
                      ....+||++|..|+....|.+.|..||.|..|.+-.    |.  -|++|.|++...++.|+..|.|.-|+|  ++|.|.+
T Consensus       454 ~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----gq--~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdl  527 (975)
T KOG0112|consen  454 PTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----GQ--PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDL  527 (975)
T ss_pred             cceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----CC--cceeeecccCccchhhHHHHhcCcCCCCCccccccc
Confidence            345799999999999999999999999998876633    22  399999999999999999999999986  7899999


Q ss_pred             ccccccc
Q 025814          215 SKWQERT  221 (247)
Q Consensus       215 a~~k~~~  221 (247)
                      +..-...
T Consensus       528 a~~~~~~  534 (975)
T KOG0112|consen  528 ASPPGAT  534 (975)
T ss_pred             ccCCCCC
Confidence            8866554

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=96.74  E-value=0.0064  Score=57.83  Aligned_cols=10  Identities=30%  Similarity=0.178  Sum_probs=3.9

Q ss_pred             CCCCCCcccc
Q 025814           28 SYFPLPFHLQ   37 (247)
Q Consensus        28 ~~~p~p~~~~   37 (247)
                      +..|+||.+|
T Consensus       555 g~PPPPpplP  564 (1102)
T KOG1924|consen  555 GPPPPPPPLP  564 (1102)
T ss_pred             CCCccCCCCC
Confidence            3333333333

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.65  E-value=0.0036  Score=54.96  Aligned_cols=76  Identities=8%  Similarity=0.181  Sum_probs=61.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecC---CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDK---RTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~---~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ..|.|.||.+.++.+.++.+|...|.|..+.|+-+.   ......-.|||-|.+...+..|- .|.++.+-++.|.|...
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            379999999999999999999999999999886532   12233458999999999888886 77888777777777544

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.61  E-value=0.00089  Score=62.56  Aligned_cols=79  Identities=16%  Similarity=0.118  Sum_probs=65.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE-EEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNM-AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~-v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      +-+..|||-.||..+++.++..+|...-.|++ |.|.+.+ +++.++.|||.|.+++++..|+..-+-..++.|.|+|+-
T Consensus       432 ~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             CccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            33568999999999999999999998777776 7776664 788899999999998888888766556677889999965


Q ss_pred             c
Q 025814          215 S  215 (247)
Q Consensus       215 a  215 (247)
                      .
T Consensus       511 i  511 (944)
T KOG4307|consen  511 I  511 (944)
T ss_pred             h
Confidence            4

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.59  E-value=0.00094  Score=55.43  Aligned_cols=54  Identities=22%  Similarity=0.428  Sum_probs=46.4

Q ss_pred             cCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          161 RFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       161 ~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +||.|+.+.|-.+ ..-...|-.+|.|...++|++|+..|||..+.|+.|...+.
T Consensus        92 kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   92 KYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             Hhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            8999999876554 23345788999999999999999999999999999998775

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.57  E-value=0.0022  Score=58.95  Aligned_cols=75  Identities=12%  Similarity=0.057  Sum_probs=61.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhc-cCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee---CCEeEEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFS-RFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV---GNRPIKL  212 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~-~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i---~g~~l~V  212 (247)
                      ..+.|||.||-.-+|.-.|+.++. .+|.|...  ++|+    -|..|||.|.+.++|.+.+.+|||..+   +++.|.+
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            356799999999999999999998 67777666  3342    245899999999999999999999976   5788888


Q ss_pred             EEccc
Q 025814          213 RKSKW  217 (247)
Q Consensus       213 ~~a~~  217 (247)
                      .|...
T Consensus       517 df~~~  521 (718)
T KOG2416|consen  517 DFVRA  521 (718)
T ss_pred             eecch
Confidence            88753

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=96.53  E-value=0.0075  Score=50.08  Aligned_cols=131  Identities=18%  Similarity=0.167  Sum_probs=85.1

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccc----cccccCCC-------CCCCCCC
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSI----PRKAAGQT-------WEDPTLA  132 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~----~r~~~~~~-------~~~~~~~  132 (247)
                      +.+..+....+......+|++||.|...+.+..|+..   ..+.++.+.+....    .+......       .......
T Consensus       140 g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  219 (306)
T COG0724         140 GPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKA  219 (306)
T ss_pred             CceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccccccccccccccccchhhhcccccccc
Confidence            4454444455556778899999999999999999864   46788888877743    22221100       0011112


Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHH
Q 025814          133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL  197 (247)
Q Consensus       133 ~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al  197 (247)
                      ........+++++++..++...+...|..+|.+..+.+..........++.++.+.....+...+
T Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (306)
T COG0724         220 LLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESN  284 (306)
T ss_pred             ccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccchhHHHhhhhhh
Confidence            22455668999999999999999999999999977766655433334444554444444444444

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.51  E-value=0.0011  Score=57.19  Aligned_cols=86  Identities=12%  Similarity=0.190  Sum_probs=65.6

Q ss_pred             cEEEEcCCCCCCcHHHHH---HHhccCCCeeEEEEEecCC--CCCc-ceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          139 YRLFCGDLGNEVNDDVLS---KAFSRFPSFNMAKVVRDKR--TGKT-KGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~---~~F~~~G~i~~v~i~~~~~--tg~~-kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      .-+||-+|+..+.++++.   +.|.+||.|..|.+.++..  .+.. -+-++|+|...++|..||...+|..++|+.|+.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            358888898887665553   6799999999998887752  1111 123799999999999999999999999999888


Q ss_pred             EEccccccccHH
Q 025814          213 RKSKWQERTDFE  224 (247)
Q Consensus       213 ~~a~~k~~~~~~  224 (247)
                      .+...+....+.
T Consensus       158 ~~gttkycs~~l  169 (327)
T KOG2068|consen  158 SLGTTKYCSFYL  169 (327)
T ss_pred             hhCCCcchhHHh
Confidence            877766554333

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.43  E-value=0.00066  Score=65.02  Aligned_cols=80  Identities=19%  Similarity=0.303  Sum_probs=65.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .....+||+|||+..+++.+|+..|..+|.|.+|.|-+-+ -+...-|+||.|.+...+-.|+.++.+..|....+++.+
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            4446689999999999999999999999999999886653 233334899999999999999999999988766666655


Q ss_pred             c
Q 025814          215 S  215 (247)
Q Consensus       215 a  215 (247)
                      .
T Consensus       448 G  448 (975)
T KOG0112|consen  448 G  448 (975)
T ss_pred             c
Confidence            4

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.23  E-value=0.025  Score=37.00  Aligned_cols=53  Identities=15%  Similarity=0.192  Sum_probs=43.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccC---CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHh
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRF---PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM  200 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~---G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l  200 (247)
                      .|+|.|+.. ++.++|+.+|..|   ....+|.++-|.       -|-|.|.+.+.|.+||..|
T Consensus         7 avhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    7 AVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            799999955 7778899999988   235688898884       5789999999999999764

>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=95.93  E-value=0.041  Score=37.35  Aligned_cols=67  Identities=13%  Similarity=0.332  Sum_probs=40.4

Q ss_pred             EEEEc-CCCCCCcHHHHHHHhccCCCe-----eEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          140 RLFCG-DLGNEVNDDVLSKAFSRFPSF-----NMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       140 ~lfV~-nLp~~~~e~~L~~~F~~~G~i-----~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ++||. +--..++..+|..++...+.|     -.|.|..+        |.||+... +.+..++..|++..+.|++|+|+
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            46663 334568888999998876544     45666544        89998865 58889999999999999999998


Q ss_pred             Ec
Q 025814          214 KS  215 (247)
Q Consensus       214 ~a  215 (247)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            65

; PDB: 2G0C_A 3MOJ_B.

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.88  E-value=0.0077  Score=49.07  Aligned_cols=58  Identities=16%  Similarity=0.134  Sum_probs=48.8

Q ss_pred             CCCCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccccc
Q 025814           64 APVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        64 ~P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~  121 (247)
                      -|||.+..+....+...+.+|+++||+|+..+++.+|++.   +++-++.+++..+.+-+.
T Consensus        32 IPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~ki   92 (298)
T KOG0111|consen   32 IPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKI   92 (298)
T ss_pred             ccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCccc
Confidence            3678898988888888999999999999999888888764   578899999888776543

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=95.55  E-value=0.0037  Score=50.83  Aligned_cols=93  Identities=23%  Similarity=0.416  Sum_probs=74.3

Q ss_pred             ceeeCccCHHHHHHHHhc---CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcC----CCCCCcHHHHHHH
Q 025814           86 AQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGD----LGNEVNDDVLSKA  158 (247)
Q Consensus        86 ~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~n----Lp~~~~e~~L~~~  158 (247)
                      +++|.|+..-++.=|++.   ..+.+.++.+                          +++.|+    |...++++.+.+.
T Consensus        51 Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~--------------------------~~r~G~shapld~r~~~ei~~~v  104 (267)
T KOG4454|consen   51 FAYVFFPNENSVQLAGQLENGDDLEEDEEQR--------------------------TLRCGNSHAPLDERVTEEILYEV  104 (267)
T ss_pred             eeeeecccccchhhhhhhcccchhccchhhc--------------------------ccccCCCcchhhhhcchhhheee
Confidence            899999988777766654   4555555544                          677887    8888999999999


Q ss_pred             hccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 025814          159 FSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV  205 (247)
Q Consensus       159 F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i  205 (247)
                      |+.-|.+..+++.++. .|.++.++|+.+......-.++....+...
T Consensus       105 ~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~  150 (267)
T KOG4454|consen  105 FSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLEL  150 (267)
T ss_pred             ecccCCCCCccccccc-cCCccCccchhhhhhhcCcHHhhhhcccCc
Confidence            9999999999999886 488899999999887777777777666543

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.46  E-value=0.09  Score=44.89  Aligned_cols=69  Identities=14%  Similarity=0.155  Sum_probs=50.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEe-EEEEE
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRP-IKLRK  214 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~-l~V~~  214 (247)
                      +.-|-|.++++.-. ..|..+|++||.|.+....      ..-.+-+|.|.+.-+|++|| ..||..|+|.. |-|..
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KAL-skng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKAL-SKNGTIIDGDVMIGVKP  266 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhh-hhcCeeeccceEEeeee
Confidence            34566668888644 5577899999998765332      22238899999999999999 56999998754 44544

>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=95.42  E-value=0.038  Score=44.17  Aligned_cols=81  Identities=15%  Similarity=0.217  Sum_probs=49.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhcc-CCCeeEEEEEe---cCC-CCC-cceEEEEEecCHHHHHHHHHHhCCceeC---C
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSR-FPSFNMAKVVR---DKR-TGK-TKGYGFISFANPSDIAAALKEMNGKYVG---N  207 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~-~G~i~~v~i~~---~~~-tg~-~kg~~FV~f~~~~~a~~Al~~l~g~~i~---g  207 (247)
                      ....|.|++||+.++++++.+.+.. ++....+..+.   +.. ... .-.-|||.|.+.+++..-...++|..+.   |
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            3458999999999999999987776 66653222222   211 111 2245899999999999999999998653   2


Q ss_pred             --EeEEEEEccc
Q 025814          208 --RPIKLRKSKW  217 (247)
Q Consensus       208 --~~l~V~~a~~  217 (247)
                        ..-.|++|-.
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence              3455666643

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.

>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=95.42  E-value=0.23  Score=36.50  Aligned_cols=66  Identities=17%  Similarity=0.142  Sum_probs=48.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFP-SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN  207 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G-~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g  207 (247)
                      .+.+...++.++.++|..+.+.+- .|..++|++|.  ..++-.+.+.|.+.++|..-...+||..++.
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            344455566666677776666554 56788999983  2355578999999999999999999997653

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.33  E-value=0.012  Score=52.87  Aligned_cols=74  Identities=19%  Similarity=0.145  Sum_probs=58.6

Q ss_pred             CCcEEEEcCCCCCCc-HHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          137 NDYRLFCGDLGNEVN-DDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~-e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +.+.|-+.-.++..+ -.+|..+|.+||.|..|.|-...      -.|.|+|.+..+|-.|. ...+..|+||-|+|.|-
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWH  443 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchh-ccccceecCceeEEEEe
Confidence            344555555666654 47899999999999998775442      26899999999997787 67899999999999998


Q ss_pred             cc
Q 025814          216 KW  217 (247)
Q Consensus       216 ~~  217 (247)
                      +.
T Consensus       444 np  445 (526)
T KOG2135|consen  444 NP  445 (526)
T ss_pred             cC
Confidence            76

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.00  E-value=0.068  Score=49.19  Aligned_cols=70  Identities=16%  Similarity=0.262  Sum_probs=55.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhc--cCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCc--eeCCEeEEEE
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFS--RFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK--YVGNRPIKLR  213 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~--~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~--~i~g~~l~V~  213 (247)
                      .|.|.|+-|+...-.++++.+|.  .|-.+++|.+-.+-       -=||+|++..||+.|.+.|...  +|.|+.|..+
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            45677889999999999999996  48888888876552       3589999999999998877653  5667776654


Q ss_pred             E
Q 025814          214 K  214 (247)
Q Consensus       214 ~  214 (247)
                      +
T Consensus       248 I  248 (684)
T KOG2591|consen  248 I  248 (684)
T ss_pred             h
Confidence            4

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=94.60  E-value=0.0026  Score=56.36  Aligned_cols=117  Identities=14%  Similarity=0.256  Sum_probs=91.0

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhc----CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHH
Q 025814           80 QLFQRDAQTITPEALESVKAALAS----SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVL  155 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~----~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L  155 (247)
                      -++..+++|+...+..-+.+++..    .++.|+..++....+++.+..               .+-|.|++....++.|
T Consensus        33 fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqrsr---------------k~Qirnippql~wevl   97 (584)
T KOG2193|consen   33 FLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQRSR---------------KIQIRNIPPQLQWEVL   97 (584)
T ss_pred             eeeecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHHhh---------------hhhHhcCCHHHHHHHH
Confidence            345688899998887777777653    266777777776666654433               5889999999999999


Q ss_pred             HHHhccCCCeeEEEEE-ecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          156 SKAFSRFPSFNMAKVV-RDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       156 ~~~F~~~G~i~~v~i~-~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ..++.+||.+..|..+ .|..|    -..-|+|...+.+..||..+||..+....++|.|-
T Consensus        98 d~Ll~qyg~ve~~eqvnt~~et----avvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen   98 DSLLAQYGTVENCEQVNTDSET----AVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             HHHHhccCCHhHhhhhccchHH----HHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence            9999999999988653 33332    12236788999999999999999999999999775

>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=94.13  E-value=0.16  Score=40.94  Aligned_cols=62  Identities=13%  Similarity=0.120  Sum_probs=45.0

Q ss_pred             cHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCEeEEEEEcccc
Q 025814          151 NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN--GKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       151 ~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~--g~~i~g~~l~V~~a~~k  218 (247)
                      ..+.|+.+|..|+.+..+.+++.-      +=..|.|.+.++|.+|...|+  +..+.|..|+|.++...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            447899999999999888776541      236799999999999999999  99999999999988543

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.

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=93.85  E-value=0.028  Score=48.41  Aligned_cols=79  Identities=19%  Similarity=0.132  Sum_probs=64.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|++++.+.+.+.++..++..+|.+....+........++|++.+.|...+.+..||.......+.++.+...+.
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            4568999999999999999999999998888877776678899999999999999999999543334666666555444

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=93.24  E-value=0.17  Score=46.53  Aligned_cols=82  Identities=20%  Similarity=0.274  Sum_probs=58.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHh-ccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee---C-CEeEEE
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAF-SRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV---G-NRPIKL  212 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F-~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i---~-g~~l~V  212 (247)
                      .+++.|.|++...|-..|...- ...|.-..+.+..|=.+....|||||.|.+.+++..+.+++||+.+   + .+...+
T Consensus       388 rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~i  467 (549)
T KOG4660|consen  388 RTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASI  467 (549)
T ss_pred             hhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeee
Confidence            3456666666665555444432 2356667788888866666789999999999999999999999954   3 355666


Q ss_pred             EEccccc
Q 025814          213 RKSKWQE  219 (247)
Q Consensus       213 ~~a~~k~  219 (247)
                      .||+-..
T Consensus       468 tYArIQG  474 (549)
T KOG4660|consen  468 TYARIQG  474 (549)
T ss_pred             ehhhhhc
Confidence            7776443

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

Probab=93.11  E-value=0.068  Score=41.26  Aligned_cols=57  Identities=9%  Similarity=0.014  Sum_probs=45.7

Q ss_pred             CCCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccccc
Q 025814           65 PVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        65 P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~  121 (247)
                      +++.+..+....+..+..+++++||+|++.++|.+|++.   ..++++.+.++....+..
T Consensus        57 ~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         57 HFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS  116 (144)
T ss_pred             cCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence            347777777777777888999999999999999999863   578888888877665543

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.07  E-value=0.53  Score=36.03  Aligned_cols=68  Identities=9%  Similarity=0.125  Sum_probs=48.4

Q ss_pred             cEEEEcCCCCCC----cHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          139 YRLFCGDLGNEV----NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       139 ~~lfV~nLp~~~----~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .+|.|.=|..++    +-..+...++.||+|.+|.+.     |+  .-|.|.|.+..+|-+|+.++.. ..-|..+...+
T Consensus        87 sTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----Gr--qsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   87 STIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----GR--QSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             eeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----CC--ceEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            478887554443    334455667899999999763     33  2689999999999999988776 44566666655

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=91.98  E-value=0.12  Score=44.79  Aligned_cols=44  Identities=14%  Similarity=0.074  Sum_probs=35.4

Q ss_pred             cCCCceeeCccCHHHHHHH---HhcCccchhhhhhcccccccccCCC
Q 025814           82 FQRDAQTITPEALESVKAA---LASSDIEHKAETKKKSIPRKAAGQT  125 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~a---l~~~~~~~~~~~~~~~~~r~~~~~~  125 (247)
                      -+||++|||++..+++++|   |.+..++||.+++..+..|-...+.
T Consensus       134 GSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATarV~n~K~  180 (376)
T KOG0125|consen  134 GSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATARVHNKKK  180 (376)
T ss_pred             CCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchhhccCCc
Confidence            4599999999987777766   5677999999999999888655443

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=91.75  E-value=0.49  Score=42.68  Aligned_cols=67  Identities=19%  Similarity=0.233  Sum_probs=56.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEEecCCCCCcce-EEEEEecCHHHHHHHHHHhCCceeCC
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFP-SFNMAKVVRDKRTGKTKG-YGFISFANPSDIAAALKEMNGKYVGN  207 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G-~i~~v~i~~~~~tg~~kg-~~FV~f~~~~~a~~Al~~l~g~~i~g  207 (247)
                      +..|+|-.+|..++-.||..|...|- .|.+++|+||.   .... ...|.|.+.++|..-.+.+||..++.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~---~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG---MPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC---CCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            56899999999999999999987654 57899999973   2222 47899999999999999999997754

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.74  E-value=0.55  Score=43.64  Aligned_cols=80  Identities=21%  Similarity=0.228  Sum_probs=59.5

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhccC----CCeeEEEEEecC----------CCCC---------------------
Q 025814          135 PENDYRLFCGDLGNE-VNDDVLSKAFSRF----PSFNMAKVVRDK----------RTGK---------------------  178 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~-~~e~~L~~~F~~~----G~i~~v~i~~~~----------~tg~---------------------  178 (247)
                      ....++|-|.||.|. +...+|..+|..|    |.|.+|.|....          ..|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            445678999999997 7889999998765    588888875421          1121                     


Q ss_pred             ---------------cce-EEEEEecCHHHHHHHHHHhCCceeCC--EeEEEEE
Q 025814          179 ---------------TKG-YGFISFANPSDIAAALKEMNGKYVGN--RPIKLRK  214 (247)
Q Consensus       179 ---------------~kg-~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~  214 (247)
                                     .+. ||.|+|.+.+.|.+.+..++|.++..  ..|-+++
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                           122 58999999999999999999998874  4444443

>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=91.32  E-value=1.6  Score=28.96  Aligned_cols=55  Identities=15%  Similarity=0.309  Sum_probs=43.3

Q ss_pred             CCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          149 EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       149 ~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      .++-++|+..+..|+-.   +|..|+ |    | =||.|.+..+|++|....||..+.+.+|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~---~I~~d~-t----G-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD---RIRDDR-T----G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc---eEEecC-C----E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            46778999999999642   344453 3    2 379999999999999999999988887765

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=89.81  E-value=0.26  Score=47.69  Aligned_cols=75  Identities=20%  Similarity=0.225  Sum_probs=64.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--CCEeEEEEEc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV--GNRPIKLRKS  215 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i--~g~~l~V~~a  215 (247)
                      .-+.++.|..-..+...|..+|..||.|.+++.++|-.      .+.|+|...+.|-.|+.+++|.++  -|-..+|.++
T Consensus       298 qp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~a  371 (1007)
T KOG4574|consen  298 QPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFA  371 (1007)
T ss_pred             cchhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEec
Confidence            33577778888889999999999999999999988732      799999999999999999999964  5788899888


Q ss_pred             ccc
Q 025814          216 KWQ  218 (247)
Q Consensus       216 ~~k  218 (247)
                      +.-
T Consensus       372 k~~  374 (1007)
T KOG4574|consen  372 KTL  374 (1007)
T ss_pred             ccc
Confidence            754

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=88.72  E-value=0.26  Score=40.78  Aligned_cols=50  Identities=8%  Similarity=-0.033  Sum_probs=41.2

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhcc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETKKK  115 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~  115 (247)
                      ||.|...-+.-|..+..++|++||||.+.+++.+|....  -|+||......
T Consensus        36 fGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnl   87 (247)
T KOG0149|consen   36 FGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNL   87 (247)
T ss_pred             hCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccch
Confidence            478888888889999999999999999999999998764  56776655433

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=87.83  E-value=0.31  Score=39.57  Aligned_cols=51  Identities=8%  Similarity=-0.049  Sum_probs=40.3

Q ss_pred             CCccccccccchhhhcCCCceeeCcc---CHHHHHHHHhcCccchhhhhhcccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPE---ALESVKAALASSDIEHKAETKKKSI  117 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~---~~~~a~~al~~~~~~~~~~~~~~~~  117 (247)
                      |.|-++-...+..+..++|++||.|-   ++++|.++|++..++++++++..+.
T Consensus        38 G~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   38 GRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             CcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            67777777778889999999999997   5666666677778999998776544

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=87.76  E-value=1.3  Score=37.22  Aligned_cols=96  Identities=32%  Similarity=0.524  Sum_probs=76.3

Q ss_pred             cccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHH-H--HHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHH
Q 025814          116 SIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDV-L--SKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSD  192 (247)
Q Consensus       116 ~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~-L--~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~  192 (247)
                      ...+......|.++....+.+.-..+|++|+-..+..+- |  ...|+.+-.+...++++++ -+.-++++|+.|.....
T Consensus        74 av~~~s~~a~~~~Pt~l~~~P~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a  152 (290)
T KOG0226|consen   74 AVGRKSAPAVWADPTLLAPAPAVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDA  152 (290)
T ss_pred             hccccccccccCCCccCCCCcccccccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhh
Confidence            334556677788888888888888999999988877765 4  7888888888888888885 57788999999998888


Q ss_pred             HHHHHHHhCCceeCCEeEEE
Q 025814          193 IAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       193 a~~Al~~l~g~~i~g~~l~V  212 (247)
                      ...+-..-+++.++-+.|++
T Consensus       153 ~~k~~~~~~~Kki~~~~VR~  172 (290)
T KOG0226|consen  153 LLKAETEKEKKKIGKPPVRL  172 (290)
T ss_pred             hhhhccccccccccCcceee
Confidence            88887777777777766555

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=87.34  E-value=0.076  Score=46.87  Aligned_cols=69  Identities=13%  Similarity=0.021  Sum_probs=53.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      ++|+|++|...+...++.+.|..+|.|....+-    .|...-+|-|+|....+...|+ .++|.++.-....+
T Consensus       152 Rt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a----sk~~s~~c~~sf~~qts~~hal-r~~gre~k~qhsr~  220 (479)
T KOG4676|consen  152 RTREVQSLISAAILPESGESFERKGEVSYAHTA----SKSRSSSCSHSFRKQTSSKHAL-RSHGRERKRQHSRR  220 (479)
T ss_pred             hhhhhhcchhhhcchhhhhhhhhcchhhhhhhh----ccCCCcchhhhHhhhhhHHHHH-Hhcchhhhhhhhhh
Confidence            579999999999999999999999998766553    3444558889999988988898 56777655333333

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=85.63  E-value=0.51  Score=39.27  Aligned_cols=50  Identities=12%  Similarity=0.124  Sum_probs=37.7

Q ss_pred             CCCCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhh
Q 025814           64 APVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETK  113 (247)
Q Consensus        64 ~P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~  113 (247)
                      -|++++.-+-+..+..++.+||++||+|++-++|.+|++.   ...+...+++
T Consensus       211 ~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrv  263 (270)
T KOG0122|consen  211 RPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRV  263 (270)
T ss_pred             hccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEE
Confidence            4567777777788889999999999999998888888764   3444444333

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=85.48  E-value=3.2  Score=37.15  Aligned_cols=54  Identities=26%  Similarity=0.216  Sum_probs=46.0

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCe-eEEEEEecCCCCCcceEEEEEecCHHHHHHHHH
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSF-NMAKVVRDKRTGKTKGYGFISFANPSDIAAALK  198 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i-~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~  198 (247)
                      ...|=|.++|.....+||...|+.||.- .+|+++-|.       .+|..|.+...|..||-
T Consensus       391 pHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt  445 (528)
T KOG4483|consen  391 PHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALT  445 (528)
T ss_pred             cceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhh
Confidence            4578899999999999999999999753 567777774       79999999999999983

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	247
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		1e-12
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		3e-12
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		7e-12
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		8e-12
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-09
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		4e-09
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		4e-09
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		5e-09
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-09
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		7e-09
2khc_A	118	Bruno Rrm3+ Length = 118		1e-07
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		1e-07
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		3e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		8e-07
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-06
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		6e-06
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		6e-06
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		9e-06
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		1e-05
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		1e-05
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		1e-05
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		1e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		1e-05
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-05
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		2e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-05
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-05
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		2e-05
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		2e-05
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-05
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		3e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		3e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		5e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		5e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-04
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		1e-04
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		2e-04
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		2e-04
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		2e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-04
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-04
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		3e-04
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		3e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		4e-04
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		4e-04
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		4e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-04
2div_A	99	Solution Structure Of The Rrm Domain Of Trna Seleno		5e-04

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 70.1 bits (170), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/84 (39%), Positives = 52/84 (61%), Gaps = 3/84 (3%)
Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           N + +F GDL  E+  + +  AF+ F   + A+VV+D  TGK+KGYGF+SF N  D   A
Sbjct: 14  NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 73
Query: 197 LKEMNGKYVGNRPIKLRKSKWQER 220
           +++M G+++G R I   ++ W  R
Sbjct: 74  IQQMGGQWLGGRQI---RTNWATR 94

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 68.6 bits (166), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 50/85 (58%), Gaps = 3/85 (3%)
Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
            N + +F GDL  E+  + +  AF+ F   + A+VV+D  TGK+KGYGF+SF N  D   
Sbjct: 13  SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 196 ALKEMNGKYVGNRPIKLRKSKWQER 220
           A+  M G+++G R I   ++ W  R
Sbjct: 73  AIVHMGGQWLGGRQI---RTNWATR 94

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 67.4 bits (163), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 32/98 (32%), Positives = 51/98 (52%)
Query: 115 KSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDK 174
           K I        W   +     ++ + LF GDL   V+D+ L  AF  FPS+    V+ D 
Sbjct: 64  KQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM 123
Query: 175 RTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
           +TG ++GYGF+SF +  D   A+  M G+ +  RP+++
Sbjct: 124 QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 67.0 bits (162), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 45/74 (60%)
Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + LF GDL   V+D+ L  AF  FPS+    V+ D +TG ++GYGF+SF +  D   A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 199 EMNGKYVGNRPIKL 212
            M G+ +  RP+++
Sbjct: 62  SMQGQDLNGRPLRI 75

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 46/79 (58%)
Query: 134 WPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDI 193
              ++ +LF G L  + N+  L + FS++   +   VV+D+ T +++G+GF++F N  D 
Sbjct: 8   MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 194 AAALKEMNGKYVGNRPIKL 212
             A+  MNGK V  R I++
Sbjct: 68  KDAMMAMNGKSVDGRQIRV 86

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/82 (39%), Positives = 51/82 (62%), Gaps = 3/82 (3%)
Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + +F GDL  E+    ++ AF+ F   + A+VV+D  TGK+KGYGF+SF N  D   A++
Sbjct: 7   FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
Query: 199 EMNGKYVGNRPIKLRKSKWQER 220
           +M G+++G R I   ++ W  R
Sbjct: 67  QMGGQWLGGRQI---RTNWATR 85

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +LF G L  E N+ +L   F +    +   +++D RT K++G+ FI+F NP+D   A K+
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67
Query: 200 MNGKYVGNRPIKLRKSK 216
           MNGK +  + IK+ ++K
Sbjct: 68  MNGKSLHGKAIKVEQAK 84

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 57.8 bits (138), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPS-FNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +F G+L  E+++ +L   FS F       K++RD  TG +KGY FI+FA+     AA++ 
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 200 MNGKYVGNRPIKL 212
           MNG+Y+ NRPI +
Sbjct: 68  MNGQYLCNRPITV 80

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 57.8 bits (138), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RL+ G L   + +D+L   F  F      +++ D  TG++KGYGFI+F++      AL++
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 200 MNGKYVGNRPIKLRKSKWQERTD 222
           +NG  +  RP+K+      ERTD
Sbjct: 88  LNGFELAGRPMKV--GHVTERTD 108

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 57.4 bits (137), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 51/79 (64%), Gaps = 2/79 (2%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+  +L + ++D+ L KAFS F +   AKV+ +   G++KG+GF+ F++P +   A+ EM
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 201 NGKYVGNRPIKLRKSKWQE 219
           NG+ V  +P+ +  ++ +E
Sbjct: 76  NGRIVATKPLYVALAQRKE 94

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/84 (39%), Positives = 44/84 (52%), Gaps = 1/84 (1%)
Query: 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSD 192
           E PE    LF   L  E  D  L+  F  F +   AKV  DK+T  +K +GF+SF NP  
Sbjct: 36  EGPEG-CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94
Query: 193 IAAALKEMNGKYVGNRPIKLRKSK 216
              A+K MNG  VG + +K++  K
Sbjct: 95  AQVAIKAMNGFQVGTKRLKVQLKK 118

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 48/77 (62%), Gaps = 3/77 (3%)
Query: 138 DYRLFCGDLGNEVNDDVLSKAFSR-FPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           +Y LF GDL  +V+D +L + F + +PS    KVV D+ TG +KGYGF+ F +  +   A
Sbjct: 9   EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRA 67
Query: 197 LKEMNGKY-VGNRPIKL 212
           L E  G   +G++P++L
Sbjct: 68  LTECQGAVGLGSKPVRL 84

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 36/105 (34%), Positives = 53/105 (50%), Gaps = 13/105 (12%)
Query: 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSD 192
           E PE    LF   L  E  D  L + F  F +   AKV  DK+T  +K +GF+S+ NP  
Sbjct: 21  EGPEG-ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS 79
Query: 193 IAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKP 237
             AA++ MNG  +G + +K++            L+RSKN ++  P
Sbjct: 80  AQAAIQSMNGFQIGMKRLKVQ------------LKRSKNDSKSGP 112

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 50.4 bits (119), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G L   + +D+L   F  F   +   +++D  TG++KGYGFI+F++      AL+++
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 201 NGKYVGNRPIKLRKSKWQERTD 222
           NG  +  RP  +R     ER D
Sbjct: 68  NGFELAGRP--MRVGHVTERLD 87

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/81 (27%), Positives = 46/81 (56%)
Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           P++ ++LF G L N +NDD + +  + F       +V+D  TG +KGY F  + + +   
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 195 AALKEMNGKYVGNRPIKLRKS 215
            A+  +NG  +G++ + ++++
Sbjct: 171 QAIAGLNGMQLGDKKLLVQRA 191

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 38/76 (50%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G L  EV+D VL  AF  F      ++  D  T K +G+ F+ F    D AAA+  M
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 201 NGKYVGNRPIKLRKSK 216
           N   +  R I++  +K
Sbjct: 68  NESELFGRTIRVNLAK 83

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 38/76 (50%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G L  EV+D VL  AF  F      ++  D  T K +G+ F+ F    D AAA+  M
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 201 NGKYVGNRPIKLRKSK 216
           N   +  R I++  +K
Sbjct: 70  NESELFGRTIRVNLAK 85

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 47.0 bits (110), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 36/72 (50%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G L  EV+D VL  AF  F      ++  D  T K +G+ F+ F    D AAA+  M
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 201 NGKYVGNRPIKL 212
           N   +  R I++
Sbjct: 126 NESELFGRTIRV 137

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 38/76 (50%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G L  EV+D VL  AF  F      ++  D  T K +G+ F+ F    D AAA+  M
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 201 NGKYVGNRPIKLRKSK 216
           N   +  R I++  +K
Sbjct: 75  NESELFGRTIRVNLAK 90

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
           E D  +F G+L   V +++L + F +        + +D R GK K +GF+ F +P  ++ 
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESVSY 72
Query: 196 ALKEMNGKYVGNRPIKL 212
           A+  +NG  +  RPI +
Sbjct: 73  AIALLNGIRLYGRPINV 89

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 43/77 (55%)
Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           ++LF G L N +NDD + +  + F       +V+D  TG +KGY F  + + +    A+ 
Sbjct: 95  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
Query: 199 EMNGKYVGNRPIKLRKS 215
            +NG  +G++ + ++++
Sbjct: 155 GLNGMQLGDKKLLVQRA 171

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 43/77 (55%)
Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           ++LF G L N +NDD + +  + F       +V+D  TG +KGY F  + + +    A+ 
Sbjct: 97  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 156
Query: 199 EMNGKYVGNRPIKLRKS 215
            +NG  +G++ + ++++
Sbjct: 157 GLNGMQLGDKKLLVQRA 173

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 36/72 (50%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G L  EV+D VL  AF  F      ++  D  T K +G+ F+ F    D AAA+  M
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 201 NGKYVGNRPIKL 212
           N   +  R I++
Sbjct: 65  NESELFGRTIRV 76

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 36/63 (57%)
Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PE   +LF G L  E  D+ L   F ++ +     V+RD  T +++G+GF+++A   ++ 
Sbjct: 10  PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 195 AAL 197
           AA+
Sbjct: 70  AAM 72

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 36/63 (57%)
Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PE   +LF G L  E  D+ L   F ++ +     V+RD  T +++G+GF+++A   ++ 
Sbjct: 9   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 68
Query: 195 AAL 197
           AA+
Sbjct: 69  AAM 71

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 36/63 (57%)
Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PE   +LF G L  E  D+ L   F ++ +     V+RD  T +++G+GF+++A   ++ 
Sbjct: 10  PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69
Query: 195 AAL 197
           AA+
Sbjct: 70  AAM 72

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ GDL  +V + +L + FS        +V RD  T ++ GY +++F  P+D   AL  M
Sbjct: 13  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 201 NGKYVGNRPIKLRKSKWQER 220
           N   +  +P+++    W +R
Sbjct: 73  NFDVIKGKPVRI---MWSQR 89

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ GDL  +V + +L + FS        +V RD  T ++ GY +++F  P+D   AL  M
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 201 NGKYVGNRPIKLRKSKWQER 220
           N   +  +P+++    W +R
Sbjct: 78  NFDVIKGKPVRI---MWSQR 94

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 36/63 (57%)
Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PE   +LF G L  E  D+ L   F ++ +     V+RD  T +++G+GF+++A   ++ 
Sbjct: 8   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 67
Query: 195 AAL 197
           AA+
Sbjct: 68  AAM 70

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 36/63 (57%)
Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PE   +LF G L  E  D+ L   F ++ +     V+RD  T +++G+GF+++A   ++ 
Sbjct: 3   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 195 AAL 197
           AA+
Sbjct: 63  AAM 65

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 159 FSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
           F         K+VRDK TG++ GYGF+++++P+D   A+  +NG  +  + IK+
Sbjct: 25  FGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKV 78

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 36/63 (57%)
Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PE   +LF G L  E  D+ L   F ++ +     V+RD  T +++G+GF+++A   ++ 
Sbjct: 11  PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 70
Query: 195 AAL 197
           AA+
Sbjct: 71  AAM 73

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L  +  +D L + F ++ +    K+++D  TG+++G+GF+SF  PS +   +K 
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 200 ---MNGKYV 205
              ++GK +
Sbjct: 65  QHILDGKVI 73

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 43/77 (55%)
Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           ++LF G L N +NDD + +  + F       +V+D  TG +KGY F  + + +    A+ 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Query: 199 EMNGKYVGNRPIKLRKS 215
            +NG  +G++ + ++++
Sbjct: 62  GLNGMQLGDKKLLVQRA 78

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 34/60 (56%)
Query: 153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
           D     F         K+VRDK TG++ GYGF+++++P+D   A+  +NG  +  + IK+
Sbjct: 19  DEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKV 78

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/85 (28%), Positives = 40/85 (47%)
Query: 131 LAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANP 190
           LAE      R++   +  +++DD +   F  F       + RD  TGK KGYGFI +   
Sbjct: 103 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 162
Query: 191 SDIAAALKEMNGKYVGNRPIKLRKS 215
                A+  MN   +G + +++ K+
Sbjct: 163 QSSQDAVSSMNLFDLGGQYLRVGKA 187

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 41/85 (48%)
Query: 131 LAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANP 190
           LAE      R++   +  +++DD +   F  F     A + RD  TGK KGYGFI +   
Sbjct: 118 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKA 177
Query: 191 SDIAAALKEMNGKYVGNRPIKLRKS 215
                A+  MN   +G + +++ K+
Sbjct: 178 QSSQDAVSSMNLFDLGGQYLRVGKA 202

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 31/54 (57%)
Query: 159 FSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
           F         K+VRDK TG++ GYGF+++ +P D   A+  +NG  +  + IK+
Sbjct: 23  FGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV 76

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 34/62 (54%)
Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L     D  L K F  F     A V+ D++TGK++GYGF++ A+ +    A K+
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 200 MN 201
            N
Sbjct: 79  PN 80

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 38/72 (52%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F G++  E  ++ L   FS        ++V D+ TGK KGYGF  + +     +A++ +
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 201 NGKYVGNRPIKL 212
           NG+    R +++
Sbjct: 71  NGREFSGRALRV 82

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 153 DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
           D L   FS       AK++RDK  G + GYGF+++    D   A+  +NG  + ++ IK+
Sbjct: 34  DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKV 93

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF  +L N V +++L KAFS+F           +R  K K Y FI F        A++EM
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKL--------ERVKKLKDYAFIHFDERDGAVKAMEEM 65
Query: 201 NGKYVGNRPIKL 212
           NGK +    I++
Sbjct: 66  NGKDLEGENIEI 77

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           D +++ G+LGN  N   L +AF  +       V R+       G+ F+ F +P D A A+
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 127
Query: 198 KEMNGKYVGNRPIKLRKSKWQER 220
           +E++G+ +    +++  S  ++R
Sbjct: 128 RELDGRTLCGCRVRVELSNGEKR 150

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 35/72 (48%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L    L   +  D L   FS       AK++RDK  G + GYGF+++    D   A+  +
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 201 NGKYVGNRPIKL 212
           NG  + ++ IK+
Sbjct: 65  NGLRLQSKTIKV 76

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 35/72 (48%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L    L   +  D L   FS       AK++RDK  G + GYGF+++    D   A+  +
Sbjct: 7   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 201 NGKYVGNRPIKL 212
           NG  + ++ IK+
Sbjct: 67  NGLRLQSKTIKV 78

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 35/72 (48%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L    L   +  D L   FS       AK++RDK  G + GYGF+++    D   A+  +
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 201 NGKYVGNRPIKL 212
           NG  + ++ IK+
Sbjct: 65  NGLRLQSKTIKV 76

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDI 193
           +F G +   +++  +   F+R+ S    K++ D RTG +KGYGF+SF N  D+
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDV 63

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDI 193
           +F G +   +++  +   F+R+ S    K++ D RTG +KGYGF+SF N  D+
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDV 63

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 36/72 (50%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L    L  ++ D  L   F      N  +++RD +TG + GY F+ F +  D   A+K +
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 201 NGKYVGNRPIKL 212
           NG  V N+ +K+
Sbjct: 66  NGITVRNKRLKV 77

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 36/72 (50%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L    L  ++ D  L   F      N  +++RD +TG + GY F+ F +  D   A+K +
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 201 NGKYVGNRPIKL 212
           NG  V N+ +K+
Sbjct: 66  NGITVRNKRLKV 77

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 33/68 (48%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF   +  +  +  L + F  +       +V  KR+GK +GY FI + +  D+ +A K  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 201 NGKYVGNR 208
           +GK +  R
Sbjct: 165 DGKKIDGR 172

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           D +++ G+LGN  N   L +AF  +       V R+       G+ F+ F +P D A A+
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 127
Query: 198 KEMNGKYVGNRPIKLRKSKWQER 220
           ++++G+ +    +++  S  ++R
Sbjct: 128 RDLDGRTLCGCRVRVELSNGEKR 150

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDI 193
           +F G +   +++  +   F+R+ S    K++ D RTG +KGYGF+SF N  D+
Sbjct: 13  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDV 64

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 37/75 (49%)
Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R++ G +  E+ +D + +AF+ F          D  T K KG+ F+ +  P     AL++
Sbjct: 14  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 200 MNGKYVGNRPIKLRK 214
            N   +G R IK+ +
Sbjct: 74  XNSVXLGGRNIKVGR 88

>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna Selenocysteine Associated Protein Length = 99

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/64 (32%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMA-KVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           L+ GDL   ++++ +S+AF+      M+ K++R++ TG   GY F+ FA+ +     L +
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 200 MNGK 203
           +NGK
Sbjct: 72  INGK 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	247
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-42
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-36
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-34
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-33
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-32
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-28
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-18
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	8e-25
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-24
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-24
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-15
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-24
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-24
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-13
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-24
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-14
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-23
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-20
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-22
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-20
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	8e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-20
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-20
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-16
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-20
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-20
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-19
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-19
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-19
2div_A	99	TRNA selenocysteine associated protein; structural	4e-19
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-19
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-19
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-19
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	9e-19
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-18
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-18
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-18
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-18
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-18
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-18
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-18
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-18
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-18
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-18
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-18
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-17
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-17
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-17
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-17
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-17
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-14
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-17
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-17
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-17
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-17
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-17
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-13
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-16
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-16
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-16
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	6e-16
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-15
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-15
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-15
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-15
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-15
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-15
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-15
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-15
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-15
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-15
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-15
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-15
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-15
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	8e-15
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-14
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-14
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-14
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-14
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	6e-14
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-14
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	8e-14
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	9e-14
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-13
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-13
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-13
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	7e-13
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-12
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-12
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-12
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-12
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-12
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-12
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-12
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-12
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-12
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-12
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-12
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-08
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-11
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	9e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-09
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-08
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	5e-08
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	6e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	8e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	7e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-05
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	3e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-04

>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 =  138 bits (350), Expect = 3e-42
 Identities = 30/99 (30%), Positives = 43/99 (43%), Gaps = 2/99 (2%)

Query: 123 GQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGY 182
               EDP         + LF G+L    +   L  A S   + N    V D RTG  + +
Sbjct: 2   SHMLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKF 60

Query: 183 GFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERT 221
           G++ F +  D+  AL E+ G  V    IKL K K ++ T
Sbjct: 61  GYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGT 98

>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 =  123 bits (312), Expect = 1e-36
 Identities = 30/83 (36%), Positives = 50/83 (60%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             + + +F GDL  E+    ++ AF+ F   + A+VV+D  TGK+KGYGF+SF N  D  
Sbjct: 3   LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 195 AALKEMNGKYVGNRPIKLRKSKW 217
            A+++M G+++G R I+   +  
Sbjct: 63  NAIQQMGGQWLGGRQIRTNWATR 85

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score =  118 bits (298), Expect = 2e-34
 Identities = 31/88 (35%), Positives = 49/88 (55%), Gaps = 3/88 (3%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFS-RFPSFNMAKVVRDKRTGKTKGYGFISFANPSDI 193
              +Y LF GDL  +V+D +L + F   +PS    KVV D+ TG +KGYGF+ F +  + 
Sbjct: 6   SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQ 64

Query: 194 AAALKEMNGKY-VGNRPIKLRKSKWQER 220
             AL E  G   +G++P++L  +  +  
Sbjct: 65  KRALTECQGAVGLGSKPVRLSVAIPKAS 92

>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 =  115 bits (290), Expect = 2e-33
 Identities = 30/81 (37%), Positives = 47/81 (58%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + LF GDL   V+D+ L  AF  FPS+    V+ D +TG ++GYGF+SF +  D   A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 199 EMNGKYVGNRPIKLRKSKWQE 219
            M G+ +  RP+++  +   E
Sbjct: 62  SMQGQDLNGRPLRINWAAKLE 82

>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 =  114 bits (287), Expect = 1e-32
 Identities = 32/99 (32%), Positives = 54/99 (54%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             N + +F GDL  E+  + +  AF+ F   + A+VV+D  TGK+KGYGF+SF N  D  
Sbjct: 12  TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 71

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHN 233
            A+++M G+++G R I+   +  +        E +   +
Sbjct: 72  NAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110

>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 =  103 bits (260), Expect = 6e-28
 Identities = 29/77 (37%), Positives = 47/77 (61%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
           ++ + LF GDL   V+D+ L  AF  FPS+    V+ D +TG ++GYGF+SF +  D   
Sbjct: 85  DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144

Query: 196 ALKEMNGKYVGNRPIKL 212
           A+  M G+ +  RP+++
Sbjct: 145 AMDSMQGQDLNGRPLRI 161

>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 = 78.3 bits (194), Expect = 3e-18
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G+L   + +D+L + F         K++ D +  K   Y F+ +    D   AL+ +
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 201 NGKYVGNRPIKLRKSKWQERTDFE 224
           NGK + N  +K+  +   +++  +
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSD 85

>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 = 94.9 bits (236), Expect = 8e-25
 Identities = 28/141 (19%), Positives = 56/141 (39%), Gaps = 8/141 (5%)

Query: 83  QRDAQTITPEALESVKAALASS---DIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDY 139
           +   + +     E V    A+    D E   +   K+                +    D 
Sbjct: 15  ETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDC 74

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +++ G+LGN  N   L +AF  +       V R+       G+ F+ F +P D A A++E
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRE 129

Query: 200 MNGKYVGNRPIKLRKSKWQER 220
           ++G+ +    +++  S  ++R
Sbjct: 130 LDGRTLCGCRVRVELSNGEKR 150

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 96.6 bits (241), Expect = 1e-24
 Identities = 30/126 (23%), Positives = 51/126 (40%), Gaps = 2/126 (1%)

Query: 90  TPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNE 149
            PEA +     + S  +  +     +      A        LAE      R++   +  +
Sbjct: 79  VPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQP--IIDQLAEEARAFNRIYVASVHQD 136

Query: 150 VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRP 209
           ++DD +   F  F     A + RD  TGK KGYGFI +        A+  MN   +G + 
Sbjct: 137 LSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQY 196

Query: 210 IKLRKS 215
           +++ K+
Sbjct: 197 LRVGKA 202

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 79.3 bits (196), Expect = 4e-18
 Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 4/98 (4%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R++ G +  E+ +D + +AF+ F       +  D  T K KG+ F+ +  P     AL++
Sbjct: 30  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89

Query: 200 MNGKYVGNRPIK----LRKSKWQERTDFEALERSKNHN 233
           MN   +G R IK        + Q   D  A E    + 
Sbjct: 90  MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR 127

>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 = 95.0 bits (237), Expect = 2e-24
 Identities = 21/80 (26%), Positives = 42/80 (52%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
               ++LF G L N +NDD + +  + F       +V+D  TG +KGY F  + + +   
Sbjct: 91  LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 150

Query: 195 AALKEMNGKYVGNRPIKLRK 214
            A+  +NG  +G++ + +++
Sbjct: 151 QAIAGLNGMQLGDKKLLVQR 170

>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 = 70.3 bits (173), Expect = 3e-15
 Identities = 12/88 (13%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRF-----PSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           RL+ G++   + ++ +   F+        +      V   +  + K + F+ F +  +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTD 222
            A+   +G     + +K+R+    +   
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLP 92

>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 = 91.9 bits (229), Expect = 3e-24
 Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRF-PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
               +F G+L  E+++ +L   FS F       K++RD  TG +KGY FI+FA+     A
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 196 ALKEMNGKYVGNRPIK 211
           A++ MNG+Y+ NRPI 
Sbjct: 64  AIEAMNGQYLCNRPIT 79

>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 = 97.0 bits (242), Expect = 3e-24
 Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 2/99 (2%)

Query: 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSD 192
           +    D  L   +L   +      +    F S     +V  +RTG++KGYGF  +     
Sbjct: 90  QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149

Query: 193 IAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKN 231
            A A  ++ GK +G R + +  +         AL  S+ 
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHWT--DAGQLTPALLHSRC 186

>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 = 76.6 bits (189), Expect = 1e-16
 Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 2/78 (2%)

Query: 140 RLFCGDLGNEVND-DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
            L    L    ND D L +A S   S    ++   +  G+ KG+  + +        A +
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQ 244

Query: 199 EMNGKYVGNRPIKLRKSK 216
           + +G  +G   +++    
Sbjct: 245 QADGLSLGGSHLRVSFCA 262

>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 = 66.2 bits (162), Expect = 4e-13
 Identities = 12/82 (14%), Positives = 28/82 (34%), Gaps = 7/82 (8%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             N  ++    L  +V +  +    S +        ++     K KG  F++  N     
Sbjct: 19  FRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAE 71

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
           AA+   +   +  R + ++   
Sbjct: 72  AAINAFHQSRLRERELSVQLQP 93

>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 = 94.3 bits (235), Expect = 5e-24
 Identities = 22/81 (27%), Positives = 46/81 (56%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           P++ ++LF G L N +NDD + +  + F       +V+D  TG +KGY F  + + +   
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170

Query: 195 AALKEMNGKYVGNRPIKLRKS 215
            A+  +NG  +G++ + ++++
Sbjct: 171 QAIAGLNGMQLGDKKLLVQRA 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 = 67.7 bits (166), Expect = 4e-14
 Identities = 14/109 (12%), Positives = 38/109 (34%), Gaps = 6/109 (5%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRF-----PSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           RL+ G++   + ++ +   F+        +      V   +  + K + F+ F +  +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKS 243
            A+   +G     + +K+R+    +     +   S         +   S
Sbjct: 66  QAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDS 113

>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 = 90.7 bits (226), Expect = 1e-23
 Identities = 26/72 (36%), Positives = 46/72 (63%), Gaps = 2/72 (2%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L+  +L + ++D+ L KAFS F +   AKV+ +   G++KG+GF+ F++P +   A+ E
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74

Query: 200 MNGKYVGNRPIK 211
           MNG+ V  +P+ 
Sbjct: 75  MNGRIVATKPLY 86

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 90.5 bits (225), Expect = 2e-23
 Identities = 29/71 (40%), Positives = 38/71 (53%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF   L  E  D  L+  F  F +   AKV  DK+T  +K +GF+SF NP     A+K M
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 201 NGKYVGNRPIK 211
           NG  VG + +K
Sbjct: 103 NGFQVGTKRLK 113

>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 = 91.6 bits (228), Expect = 8e-23
 Identities = 25/103 (24%), Positives = 45/103 (43%), Gaps = 2/103 (1%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
                +F  +L   +++  L   FS F +    KVV D     +KGYGF+ F        
Sbjct: 101 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAER 158

Query: 196 ALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPK 238
           A+++MNG  + +R + + + K ++  + E   R+K        
Sbjct: 159 AIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVP 201

>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 = 85.8 bits (213), Expect = 1e-20
 Identities = 23/80 (28%), Positives = 40/80 (50%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
                L+ GDL  +V + +L + FS        +V RD  T ++ GY +++F  P+D   
Sbjct: 13  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72

Query: 196 ALKEMNGKYVGNRPIKLRKS 215
           AL  MN   +  +P+++  S
Sbjct: 73  ALDTMNFDVIKGKPVRIMWS 92

>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 = 87.8 bits (218), Expect = 2e-22
 Identities = 27/71 (38%), Positives = 39/71 (54%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           LF   L  E  D  L + F  F +   AKV  DK+T  +K +GF+S+ NP    AA++ M
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 201 NGKYVGNRPIK 211
           NG  +G + +K
Sbjct: 88  NGFQIGMKRLK 98

>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 = 85.8 bits (213), Expect = 1e-21
 Identities = 28/81 (34%), Positives = 49/81 (60%), Gaps = 1/81 (1%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
           ++  +LF G L  E N+ +L   F +    +   +++D RT K++G+ FI+F NP+D   
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKN 63

Query: 196 ALKEMNGKYVGNRPIKLRKSK 216
           A K+MNGK +  + IK+ ++K
Sbjct: 64  AAKDMNGKSLHGKAIKVEQAK 84

>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 = 86.9 bits (216), Expect = 2e-21
 Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
             D  L+  +L   + DD L   F ++ S     ++RDK TG+ +G  F+ +    +   
Sbjct: 87  IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146

Query: 196 ALKEMNGKYV--GNRPI 210
           A+  +N      G++P+
Sbjct: 147 AISALNNVIPEGGSQPL 163

>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 = 84.2 bits (209), Expect = 2e-20
 Identities = 25/97 (25%), Positives = 44/97 (45%), Gaps = 7/97 (7%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           ++  L    L  ++ D  L   F      N  +++RD +TG + GY F+ F +  D   A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 197 LKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHN 233
           +K +NG  V N+ +K+  ++          E  K+ N
Sbjct: 62  IKVLNGITVRNKRLKVSYAR-------PGGESIKDTN 91

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 84.4 bits (209), Expect = 8e-21
 Identities = 25/77 (32%), Positives = 35/77 (45%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                 L+ G L  EV+D VL  AF  F      ++  D  T K +G+ F+ F    D A
Sbjct: 60  ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119

Query: 195 AALKEMNGKYVGNRPIK 211
           AA+  MN   +  R I+
Sbjct: 120 AAIDNMNESELFGRTIR 136

>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 = 82.7 bits (205), Expect = 1e-20
 Identities = 26/82 (31%), Positives = 48/82 (58%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             ++ +LF G L  + N+  L + FS++   +   VV+D+ T +++G+GF++F N  D  
Sbjct: 9   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            A+  MNGK V  R I++ ++ 
Sbjct: 69  DAMMAMNGKSVDGRQIRVDQAG 90

>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 = 85.0 bits (211), Expect = 1e-20
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 5/78 (6%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                 L   +L   + +D L + F         ++    + GK+KG  +I F + +D  
Sbjct: 96  VRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAE 150

Query: 195 AALKEMNGKYVGNRPIKL 212
             L+E  G  +  R + L
Sbjct: 151 KNLEEKQGAEIDGRSVSL 168

>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 = 71.9 bits (177), Expect = 7e-16
 Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
               + LF G+L    +   L  A S   + N   VV D RTG  + +G++ F +  D+ 
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLE 68

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            AL E+ G  V    IKL K K
Sbjct: 69  KAL-ELTGLKVFGNEIKLEKPK 89

>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 = 81.8 bits (203), Expect = 2e-20
 Identities = 21/82 (25%), Positives = 29/82 (35%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                 L+   L     D  L K    +      K + DK T K KGYGF+ F +PS   
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            A+  +    V  +  K     
Sbjct: 62  KAVTALKASGVQAQMAKQSGPS 83

>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 = 81.8 bits (203), Expect = 2e-20
 Identities = 26/81 (32%), Positives = 38/81 (46%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
                L+ G L  EV+D VL  AF  F      ++  D  T K +G+ F+ F    D AA
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 196 ALKEMNGKYVGNRPIKLRKSK 216
           A+  MN   +  R I++  +K
Sbjct: 65  AIDNMNESELFGRTIRVNLAK 85

>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 = 82.7 bits (205), Expect = 2e-20
 Identities = 19/77 (24%), Positives = 32/77 (41%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L+  +L   V +  L   F+RF       +     TG+ +G  FI+F N      AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 200 MNGKYVGNRPIKLRKSK 216
           +NG  +  + + +   K
Sbjct: 87  VNGYKLYGKILVIEFGK 103

>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 = 81.5 bits (202), Expect = 3e-20
 Identities = 18/82 (21%), Positives = 37/82 (45%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           P+ +  L    L     +  L + FS++       +V D+++ +++G+ F+ F N  D  
Sbjct: 12  PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAK 71

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            A +  NG  +  R I++    
Sbjct: 72  EAKERANGMELDGRRIRVSGPS 93

>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 = 83.0 bits (206), Expect = 5e-20
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 4/87 (4%)

Query: 126 WEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFI 185
           +  P+ A     D  L+   L   +    L + FS++     ++++ D+ TG ++G GFI
Sbjct: 78  YARPSSAS--IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFI 135

Query: 186 SFANPSDIAAALKEMNGKYV--GNRPI 210
            F    +   A+K +NG+       PI
Sbjct: 136 RFDKRIEAEEAIKGLNGQKPSGATEPI 162

>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 = 81.9 bits (203), Expect = 1e-19
 Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 7/93 (7%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L    L   +  +     F         K+VRDK TG++ GYGF+++ +P D   A+  +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 201 NGKYVGNRPIKLRKSKWQERTDFEALERSKNHN 233
           NG  +  + IK+  ++        +    ++ N
Sbjct: 65  NGLRLQTKTIKVSYAR-------PSSASIRDAN 90

>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 = 80.0 bits (198), Expect = 1e-19
 Identities = 20/82 (24%), Positives = 41/82 (50%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            +++  +   +L  +  +  L + F  F S +   + +DK TG++KG+ FISF    D A
Sbjct: 12  ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 71

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            A+  ++G    +  + +  +K
Sbjct: 72  RAIAGVSGFGYDHLILNVEWAK 93

>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 = 79.6 bits (197), Expect = 2e-19
 Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 3/84 (3%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKT---KGYGFISFANPSDIAAA 196
            LF  +L     ++ L   FS+  +     + + K         G+GF+ +  P     A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 197 LKEMNGKYVGNRPIKLRKSKWQER 220
           LK++ G  V    +++R S+   +
Sbjct: 67  LKQLQGHTVDGHKLEVRISERATK 90

>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 = 78.5 bits (194), Expect = 4e-19
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 5/77 (6%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNM-AKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           L+ GDL   ++++ +S+AF+      M  K++R++ TG   GY F+ FA+ +     L +
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 200 MNGKYVGN----RPIKL 212
           +NGK +      +  KL
Sbjct: 72  INGKPLPGATPAKRFKL 88

>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 = 78.8 bits (195), Expect = 4e-19
 Identities = 26/81 (32%), Positives = 38/81 (46%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
                L+ G L  EV+D VL  AF  F      ++  D  T K +G+ F+ F    D AA
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69

Query: 196 ALKEMNGKYVGNRPIKLRKSK 216
           A+  MN   +  R I++  +K
Sbjct: 70  AIDNMNESELFGRTIRVNLAK 90

>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 = 79.8 bits (197), Expect = 4e-19
 Identities = 21/77 (27%), Positives = 39/77 (50%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           P+    L    +   V++  L + F R+      K+V D+ T +++GYGF+ F + S   
Sbjct: 39  PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQ 98

Query: 195 AALKEMNGKYVGNRPIK 211
            A+  +NG  + N+ +K
Sbjct: 99  QAIAGLNGFNILNKRLK 115

>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 = 78.8 bits (195), Expect = 5e-19
 Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 2/93 (2%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +F  +L   +++  L   FS F +    KVV D     +KGYGF+ F        A+++M
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65

Query: 201 NGKYVGNRPIKLRKSKWQERTDFEALERSKNHN 233
           NG  + +R + + + K ++  + E   R+K   
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGARAKEFT 98

>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 = 77.3 bits (191), Expect = 9e-19
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            E D  +F G+L   V +++L + F +        + +D R GK K +GF+ F +P  ++
Sbjct: 13  EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESVS 71

Query: 195 AALKEMNGKYVGNRPIK 211
            A+  +NG  +  RPI 
Sbjct: 72  YAIALLNGIRLYGRPIN 88

>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 = 77.7 bits (192), Expect = 1e-18
 Identities = 21/86 (24%), Positives = 44/86 (51%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
              D  ++ G L  +V++ +L + F +        + +D+ TG+ +GYGF+ F +  D  
Sbjct: 12  RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQER 220
            A+K M+   +  +PI++ K+    +
Sbjct: 72  YAIKIMDMIKLYGKPIRVNKASAHNK 97

>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 = 76.9 bits (190), Expect = 2e-18
 Identities = 23/94 (24%), Positives = 48/94 (51%), Gaps = 1/94 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            ++ G +  +  ++ +    S        K++ D +TG++KGY FI F +    A+A++ 
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 200 MNGKYVGNRPIKLRKSKWQERTDFEALERSKNHN 233
           +NG  +G+R +K   S   + +   +LE   +H+
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISG-VSLEHHHHHH 96

>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 = 77.8 bits (192), Expect = 2e-18
 Identities = 19/82 (23%), Positives = 38/82 (46%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           P+ +  L    L     +  L + FS++       +V D+++ +++G+ F+ F N  D  
Sbjct: 43  PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAK 102

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            A +  NG  +  R I++  S 
Sbjct: 103 EAKERANGMELDGRRIRVDFSI 124

>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 = 78.3 bits (193), Expect = 2e-18
 Identities = 22/147 (14%), Positives = 52/147 (35%), Gaps = 9/147 (6%)

Query: 79  QQLFQRDAQTITPEALESVKAALASSDIEHKAE---------TKKKSIPRKAAGQTWEDP 129
           Q     + +T+  E       A  +  +  +           T   +       +     
Sbjct: 2   QYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHH 61

Query: 130 TLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFAN 189
                 E    L   +L    + D L + F ++       + RD+ T +++G+ F+ F +
Sbjct: 62  HHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121

Query: 190 PSDIAAALKEMNGKYVGNRPIKLRKSK 216
             D   A+  M+G  +  R ++++ ++
Sbjct: 122 KRDAEDAMDAMDGAVLDGRELRVQMAR 148

>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 = 76.6 bits (189), Expect = 3e-18
 Identities = 31/116 (26%), Positives = 51/116 (43%), Gaps = 10/116 (8%)

Query: 107 EHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFN 166
            H       +       Q      +        RL+ G L   + +D+L   F  F    
Sbjct: 3   HHHHHHSHMAAAMANNLQKGSAGPM--------RLYVGSLHFNITEDMLRGIFEPFGRIE 54

Query: 167 MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTD 222
             +++ D  TG++KGYGFI+F++      AL+++NG  +  RP+K+      ERTD
Sbjct: 55  SIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV--TERTD 108

>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 = 76.1 bits (188), Expect = 3e-18
 Identities = 26/83 (31%), Positives = 46/83 (55%), Gaps = 2/83 (2%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L+ G L   + +D+L   F  F   +   +++D  TG++KGYGFI+F++      AL++
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 200 MNGKYVGNRPIKLRKSKWQERTD 222
           +NG  +  RP+++      ER D
Sbjct: 67  LNGFELAGRPMRVGHVT--ERLD 87

>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 = 80.8 bits (200), Expect = 3e-18
 Identities = 8/94 (8%), Positives = 29/94 (30%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L+  +         +           ++  +   R   ++ + +I   +  D    +++
Sbjct: 119 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 178

Query: 200 MNGKYVGNRPIKLRKSKWQERTDFEALERSKNHN 233
           +NG  +    +  + S   E++        +   
Sbjct: 179 LNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGRE 212

>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 = 68.9 bits (169), Expect = 6e-14
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 141 LFCGDLGNEVND-DVLSKAFSRFPSFNMAKVVRDKR-TGKTKGYGFISFANPSDIAAALK 198
           +   +L  E+ D ++L ++F  F S     +   ++         F+ F N      AL 
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 271

Query: 199 EMNGKYVGNRPIKL 212
           +MN   +GNR I +
Sbjct: 272 QMNRSLLGNREISV 285

>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 = 56.9 bits (138), Expect = 7e-10
 Identities = 17/110 (15%), Positives = 30/110 (27%), Gaps = 6/110 (5%)

Query: 110 AETKKKSIPRKAAGQTWEDPTLAEWPENDYR---LFCGDLGNEVNDDVLSKAFSRFPSFN 166
            ++K+       A          E    +     +   +L    N + + K F       
Sbjct: 10  PDSKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPII 69

Query: 167 MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
              V       K   +  I FA      AA+ + +   VG   I +    
Sbjct: 70  HVDVADS--LKKNFRFARIEFARYDGALAAITKTHK-VVGQNEIIVSHLT 116

>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 = 76.5 bits (189), Expect = 4e-18
 Identities = 21/110 (19%), Positives = 42/110 (38%), Gaps = 10/110 (9%)

Query: 107 EHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFN 166
              +  K   +  + A Q  +DPT          L+  +L   +++  L      F    
Sbjct: 3   SGSSGLKASGVQAQMAKQQEQDPT---------NLYISNLPLSMDEQELENMLKPFGQVI 53

Query: 167 MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
             +++RD  +G ++G GF    +     A +   NGK++   P     ++
Sbjct: 54  STRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 102

>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 = 75.8 bits (187), Expect = 5e-18
 Identities = 24/103 (23%), Positives = 47/103 (45%), Gaps = 2/103 (1%)

Query: 112 TKKKSIPRKAAGQTWEDPTL-AEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170
           ++ K +P K     ++         E   +L   +L   V+D  + + F+ F +   A V
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

Query: 171 VRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR 213
             D R+G++ G   + F   +D   A+K+ NG  +  RP+ ++
Sbjct: 62  HYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 103

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 77.3 bits (190), Expect = 5e-18
 Identities = 22/142 (15%), Positives = 52/142 (36%), Gaps = 2/142 (1%)

Query: 91  PEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEV 150
              ++     L    +E     +++  P+          T +        ++ G      
Sbjct: 8   SSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWT 67

Query: 151 NDDVLSKAFSRFPSFNM--AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNR 208
            D  L +       +++   K   ++  G++KGY  +  A+ + +   L+ + GK +   
Sbjct: 68  TDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGE 127

Query: 209 PIKLRKSKWQERTDFEALERSK 230
            + +R +  Q  + FEA  R +
Sbjct: 128 KVDVRPATRQNLSQFEAQARKR 149

>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 = 75.4 bits (186), Expect = 7e-18
 Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 5/93 (5%)

Query: 124 QTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYG 183
              EDP  ++       L   +L   + +D L + F         ++    + GK+KG  
Sbjct: 2   HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIA 56

Query: 184 FISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
           +I F + +D    L+E  G  +  R + L  + 
Sbjct: 57  YIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 89

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 75.1 bits (185), Expect = 1e-17
 Identities = 11/72 (15%), Positives = 24/72 (33%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            +    L + V +  L     ++      +++   RT K  G   + F +       +K 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 200 MNGKYVGNRPIK 211
           ++   V    I 
Sbjct: 68  LHLTSVMGNIIH 79

>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 = 75.1 bits (185), Expect = 1e-17
 Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            E   +L   +L   V+D  + + F+ F +   A V  D R+G++ G   + F   +D  
Sbjct: 32  VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADAL 90

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTDFEA 225
            A+K+  G  +  RP+ ++      + D E 
Sbjct: 91  KAMKQYKGVPLDGRPMDIQLV--ASQIDLEH 119

>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 = 74.6 bits (184), Expect = 1e-17
 Identities = 21/77 (27%), Positives = 35/77 (45%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RLF  +L    +++ L K FS +   +      D  T K KG+ F++F  P     A  E
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 200 MNGKYVGNRPIKLRKSK 216
           ++G+    R + +  S 
Sbjct: 70  VDGQVFQGRMLHVLPST 86

>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 = 74.6 bits (184), Expect = 2e-17
 Identities = 21/96 (21%), Positives = 43/96 (44%), Gaps = 9/96 (9%)

Query: 121 AAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTK 180
           ++G   +D            L+ G+L  +V + ++ + FS+       K++ +  +    
Sbjct: 5   SSGMMEDDGQPR-------TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND-- 55

Query: 181 GYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
            Y F+ F    D AAAL  MNG+ +  + +K+  + 
Sbjct: 56  PYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT 91

>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 = 78.2 bits (193), Expect = 2e-17
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSD 192
            +  +   L   +L   V++++L +AFS+F     A VV D   G+  G GF+ FA    
Sbjct: 91  RFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPP 149

Query: 193 IAAALKEMNGK-YVGNRPIK 211
              AL+      ++     +
Sbjct: 150 ARKALERCGDGAFLLTTTPR 169

>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 = 70.5 bits (173), Expect = 1e-14
 Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                RLF G+L  ++ ++   + F R+   +   + RD+      G+GFI   + +   
Sbjct: 19  YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAE 72

Query: 195 AALKEMNGKYVGNRPIKLRKS 215
            A  E++G  + +RP+++R +
Sbjct: 73  IAKAELDGTILKSRPLRIRFA 93

>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 = 74.2 bits (183), Expect = 2e-17
 Identities = 16/87 (18%), Positives = 37/87 (42%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            +    L   +L    + D L + F ++       + R+  T   +G+ F+ F +  D  
Sbjct: 10  VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ 69

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERT 221
            A   M+G  +  R ++++ +++  R 
Sbjct: 70  DAEAAMDGAELDGRELRVQVARYGRRD 96

>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 = 73.8 bits (182), Expect = 2e-17
 Identities = 18/77 (23%), Positives = 36/77 (46%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             +   ++  +L   + ++ L + FS++       +++DK T K+KG  FI F +     
Sbjct: 13  APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72

Query: 195 AALKEMNGKYVGNRPIK 211
              + +N K +  R IK
Sbjct: 73  NCTRAINNKQLFGRVIK 89

>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 = 74.7 bits (184), Expect = 2e-17
 Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 2/100 (2%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + LF   +  E  ++ +   F+ +       +  D+RTG  KGY  + +    +  AA++
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 199 EMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPK 238
            +NG+ +  +PI +       R   +   R      + P 
Sbjct: 83  GLNGQDLMGQPISVDWCF--VRGPPKGKRRGGRRRSRSPD 120

>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 = 73.4 bits (181), Expect = 3e-17
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            LF   L  +  ++ L ++F        A++V D+ TG +KG+GF+ F +  D  AA + 
Sbjct: 17  TLFVKGLSEDTTEETLKESFDGSVR---ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 200 MNGKYVGNRPIKLRKSK 216
           M    +    + L  +K
Sbjct: 74  MEDGEIDGNKVTLDWAK 90

>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 = 73.5 bits (181), Expect = 4e-17
 Identities = 22/104 (21%), Positives = 45/104 (43%), Gaps = 8/104 (7%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                 +F  +L  +V    L + FS       A ++ D + GK++G G ++F    +  
Sbjct: 12  GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAV 70

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPK 238
            A+   NG+ + +RP+ ++        D  AL +      ++P+
Sbjct: 71  QAISMFNGQLLFDRPMHVKM-------DERALPKGDFFPPERPQ 107

>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 = 74.6 bits (184), Expect = 8e-17
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
            D +LF G +  +  ++ +   FS F      +++R    G ++G  F++F   +    A
Sbjct: 94  EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTA 152

Query: 197 LKEMNGKYV---GNRPIK 211
           +K M+        + P+ 
Sbjct: 153 IKAMHQAQTMEGCSSPMV 170

>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 = 65.7 bits (161), Expect = 1e-13
 Identities = 16/95 (16%), Positives = 35/95 (36%), Gaps = 5/95 (5%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTG--KTKGYGFISFANPSDIAAALK 198
           +F G +    ++  L + F ++ +     V+RD+     ++KG  F++F        A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 199 EMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHN 233
            ++   V        + K     D E     ++  
Sbjct: 66  ALHNMKVLPGMHHPIQMKP---ADSEKNNAVEDRK 97

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 72.3 bits (178), Expect = 1e-16
 Identities = 17/78 (21%), Positives = 36/78 (46%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + LF   +  E  ++ +   F+ +       +  D+RTG  KGY  + +    +  AA++
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 199 EMNGKYVGNRPIKLRKSK 216
            +NG+ +  +PI +    
Sbjct: 84  GLNGQDLMGQPISVDWCF 101

>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 = 75.1 bits (184), Expect = 2e-16
 Identities = 20/168 (11%), Positives = 55/168 (32%), Gaps = 10/168 (5%)

Query: 79  QQLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPEND 138
            + F ++A+    + ++     ++ S   +    + +           +D      P   
Sbjct: 3   GEEFNQEAEYGGHDQIDLYDDVISPSA-NNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVV 61

Query: 139 Y-------RLFCGDLGNEVNDDVLSKAFSRF--PSFNMAKVVRDKRTGKTKGYGFISFAN 189
           Y        L+ G+L     D+ L++A            K   ++  G++KG+  +   +
Sbjct: 62  YTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGS 121

Query: 190 PSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKP 237
            +     +  +  + +  +   +     Q  + FE   R    + +  
Sbjct: 122 EASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMS 169

>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 = 70.7 bits (174), Expect = 3e-16
 Identities = 12/83 (14%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRF--PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
             L+ G+L     D+ L++A            K   ++  G++KG+  +   + +     
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 197 LKEMNGKYVGNRPIKLRKSKWQE 219
           +  +  + +  +   +  S   E
Sbjct: 62  MDLLPKRELHGQNPVVTPSNKLE 84

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 70.8 bits (174), Expect = 4e-16
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           ++LF   L      + L +      +    ++V + R GK KG  ++ + N S  + A+ 
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVM 76

Query: 199 EMNGKYVGNRPIKLRKSK 216
           +M+G  +    IK+  S 
Sbjct: 77  KMDGMTIKENIIKVAISN 94

>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 = 72.2 bits (177), Expect = 5e-16
 Identities = 17/77 (22%), Positives = 33/77 (42%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            LF   +  E  +D + + F  +       +  D+RTG +KGY  + +       AA + 
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 200 MNGKYVGNRPIKLRKSK 216
           +NG  +  + I++    
Sbjct: 134 LNGAEIMGQTIQVDWCF 150

>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 = 70.4 bits (173), Expect = 5e-16
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 7/83 (8%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                +L+ G+L   V  D L + F         K+    +     GY F+ + + +   
Sbjct: 5   SSGMNKLYIGNLSPAVTADDLRQLFGDR------KLPLAGQVLLKSGYAFVDYPDQNWAI 58

Query: 195 AALKEMNGKY-VGNRPIKLRKSK 216
            A++ ++GK  +  + +++  S 
Sbjct: 59  RAIETLSGKVELHGKIMEVDYSV 81

>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 = 69.9 bits (172), Expect = 6e-16
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKR-TGKTKGYGFISFANPSDIAAALK 198
           ++  G L   V  D + + FS +    M  +  ++     +KGY ++ F NP +   ALK
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 199 EMNGKYVGNRPIK 211
            M+G  +  + I 
Sbjct: 66  HMDGGQIDGQEIT 78

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 70.5 bits (173), Expect = 1e-15
 Identities = 17/82 (20%), Positives = 39/82 (47%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            E    L   +L    + D L + F ++       + RD+ T +++G+ F+ F +  D  
Sbjct: 44  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 103

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            A+  M+G  +  R ++++ ++
Sbjct: 104 DAMDAMDGAVLDGRELRVQMAR 125

>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 = 69.7 bits (171), Expect = 1e-15
 Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 3/89 (3%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             +  +LF G +   +++  L   F  F       V++D+ TG  KG  F+++       
Sbjct: 10  DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69

Query: 195 AALKEMNGKYV---GNRPIKLRKSKWQER 220
            A   ++ +      NRPI+++ +  + R
Sbjct: 70  KAQSALHEQKTLPGMNRPIQVKPADSESR 98

>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 = 69.2 bits (170), Expect = 1e-15
 Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 8/90 (8%)

Query: 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSD 192
             P     L+    G ++   +L  AFS F        + D      +   F+++     
Sbjct: 10  RAPRKGNTLYVY--GEDMTPTLLRGAFSPF------GNIIDLSMDPPRNCAFVTYEKMES 61

Query: 193 IAAALKEMNGKYVGNRPIKLRKSKWQERTD 222
              A+ E+NG  V +  +K+  ++ Q   D
Sbjct: 62  ADQAVAELNGTQVESVQLKVNIARKQPMLD 91

>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 = 69.2 bits (170), Expect = 1e-15
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+  +L    +++++ K F+        K    +R  K + Y F+ F+N  D   A+K +
Sbjct: 18  LYVRNLMLSTSEEMIEKEFNNI------KPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 71

Query: 201 NGKYVGNRPIKLRKSK 216
           NGK +   PI++  +K
Sbjct: 72  NGKVLDGSPIEVTLAK 87

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 68.9 bits (169), Expect = 2e-15
 Identities = 13/82 (15%), Positives = 37/82 (45%), Gaps = 6/82 (7%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNM--AKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           +   ++      D +  A S + S  +   ++++DK+T + +G+ F+  ++  D +  L+
Sbjct: 12  IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71

Query: 199 EMNGK----YVGNRPIKLRKSK 216
            +        +  + I +  +K
Sbjct: 72  ILQSLHPPLKIDGKTIGVDFAK 93

>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 = 68.9 bits (169), Expect = 2e-15
 Identities = 17/78 (21%), Positives = 34/78 (43%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + LF   +  E  +D + + F  +       +  D+RTG +KGY  + +       AA +
Sbjct: 27  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 86

Query: 199 EMNGKYVGNRPIKLRKSK 216
            +NG  +  + I++    
Sbjct: 87  ALNGAEIMGQTIQVDWCF 104

>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 = 70.2 bits (172), Expect = 2e-15
 Identities = 15/77 (19%), Positives = 34/77 (44%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L+ G+L     ++ + + FS+        +  DK      G+ F+ + + +D   A++ 
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100

Query: 200 MNGKYVGNRPIKLRKSK 216
           +NG  + +R I+     
Sbjct: 101 INGTRLDDRIIRTDWDA 117

>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 = 67.9 bits (167), Expect = 3e-15
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 135 PENDYR-LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDI 193
            E D R ++ G++      + L   F    S N   ++ DK +G  KG+ +I F++   +
Sbjct: 2   MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61

Query: 194 AAALKEMNGKYVGNRPIKLRKSK 216
             +L  ++      R IK+   +
Sbjct: 62  RTSL-ALDESLFRGRQIKVIPKR 83

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 68.0 bits (167), Expect = 3e-15
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 2/86 (2%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                ++F  +L  +    +L   F+       A +  +   GK+KG G + F +P    
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQER 220
            A + MNG  +  R I +R  +    
Sbjct: 63  RACRMMNGMKLSGREIDVRIDRNASG 88

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 68.5 bits (168), Expect = 3e-15
 Identities = 24/104 (23%), Positives = 44/104 (42%), Gaps = 9/104 (8%)

Query: 108 HKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNM 167
           H        +PR +   T       E      RL   ++     D  L + F +F     
Sbjct: 6   HHHHHSSGLVPRGSHMNT-------ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD 58

Query: 168 AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK 211
            +++ ++R  K  G+GF++F N +D   A ++++G  V  R I+
Sbjct: 59  VEIIFNERGSK--GFGFVTFENSADADRAREKLHGTVVEGRKIE 100

>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 = 70.8 bits (174), Expect = 3e-15
 Identities = 26/108 (24%), Positives = 48/108 (44%), Gaps = 11/108 (10%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PE   +LF G L  E  D+ L   F ++ +     V+RD  T +++G+GF+++A   ++ 
Sbjct: 10  PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 69

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKK 242
           AA+       V  R ++ ++          A+ R  +         KK
Sbjct: 70  AAM-NARPHKVDGRVVEPKR----------AVSREDSQRPGAHLTVKK 106

>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 = 64.6 bits (158), Expect = 6e-13
 Identities = 23/125 (18%), Positives = 53/125 (42%), Gaps = 14/125 (11%)

Query: 95  ESVKAALASSDIEHKAETK----KKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEV 150
           E V AA+ +    HK + +    K+++ R       ED           ++F G +  + 
Sbjct: 66  EEVDAAMNAR--PHKVDGRVVEPKRAVSR-------EDSQRPGAHLTVKKIFVGGIKEDT 116

Query: 151 NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPI 210
            +  L   F ++    + +++ D+ +GK +G+ F++F +   +   +       V     
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNC 175

Query: 211 KLRKS 215
           ++RK+
Sbjct: 176 EVRKA 180

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 70.3 bits (172), Expect = 3e-15
 Identities = 27/123 (21%), Positives = 52/123 (42%), Gaps = 8/123 (6%)

Query: 113 KKKSIPRKAAGQTWED-PTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVV 171
           + K +P K     ++      E  E   +L   +L   V+D  + + F+ F +   A V 
Sbjct: 62  RPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVD 121

Query: 172 RDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKN 231
            D R+G++ G   + F   +D   A+K+  G  +  RP+ ++      + D E      +
Sbjct: 122 YD-RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV--ASQIDLEH----HH 174

Query: 232 HNQ 234
           H+ 
Sbjct: 175 HHH 177

>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 = 68.1 bits (167), Expect = 4e-15
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 6/89 (6%)

Query: 128 DPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISF 187
           +  + +    +  ++CG + + + D ++ + FS F      +V  +K      GY F+ F
Sbjct: 15  EDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRF 68

Query: 188 ANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
           +     A A+  +NG  +    +K    K
Sbjct: 69  STHESAAHAIVSVNGTTIEGHVVKCYWGK 97

>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 = 68.1 bits (167), Expect = 4e-15
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 2/83 (2%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RL   ++     D  L + F +F      +++ ++R  K  G+GF++F N +D   A ++
Sbjct: 17  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRAREK 74

Query: 200 MNGKYVGNRPIKLRKSKWQERTD 222
           ++G  V  R I++  +  +  T+
Sbjct: 75  LHGTVVEGRKIEVNNATARVMTN 97

>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 = 68.5 bits (168), Expect = 4e-15
 Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 2/102 (1%)

Query: 116 SIPRKAAGQTWEDPTLAEWPENDYR-LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDK 174
           S          E        E D R +FC  L   +    L   FS        +++ D+
Sbjct: 2   SSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61

Query: 175 RTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
            + ++KG  ++ F     +  A+  + G+ +   PI ++ S+
Sbjct: 62  NSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ 102

>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 = 68.1 bits (167), Expect = 4e-15
 Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 4/77 (5%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L   +L     ++ L + F +         V   + GK+KGY FI FA+  D   AL  
Sbjct: 17  TLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 200 MNGKYVGNRPIKLRKSK 216
            N + +  R I+L    
Sbjct: 73  CNKREIEGRAIRLELQG 89

>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 = 68.1 bits (167), Expect = 4e-15
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 6/82 (7%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                RLF G+L  ++ ++ + K F ++       + +DK      G+GFI     +   
Sbjct: 12  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAE 65

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            A  E++   +  + +++R + 
Sbjct: 66  IAKVELDNMPLRGKQLRVRFAC 87

>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 = 69.5 bits (171), Expect = 5e-15
 Identities = 25/125 (20%), Positives = 59/125 (47%), Gaps = 21/125 (16%)

Query: 95  ESVKAALASSDIEHKAETK----KKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEV 150
            SV   + +   +H  + K    K++IPR    +T              ++F G +G +V
Sbjct: 56  SSVDEVVKT---QHILDGKVIDPKRAIPRDEQDKT-------------GKIFVGGIGPDV 99

Query: 151 NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPI 210
                 + FS++ +   A+++ DK TG+++G+GF+++ +   +     +       +R I
Sbjct: 100 RPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKI 158

Query: 211 KLRKS 215
           +++++
Sbjct: 159 EIKRA 163

>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 = 68.3 bits (168), Expect = 1e-14
 Identities = 22/101 (21%), Positives = 48/101 (47%), Gaps = 12/101 (11%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
           +   ++F G L  +  +D L + F ++ +    K+++D  TG+++G+GF+SF  PS +  
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

Query: 196 ALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKK 236
            +K  +   +  + I  ++          A+ R +     K
Sbjct: 61  VVKTQH--ILDGKVIDPKR----------AIPRDEQDKTGK 89

>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 = 67.8 bits (166), Expect = 6e-15
 Identities = 17/101 (16%), Positives = 33/101 (32%), Gaps = 8/101 (7%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                 +F  +L  +  ++ L +   +F      +VV    T  +KG  F  F       
Sbjct: 12  VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 71

Query: 195 AALKEMN------GKYVGNRPIKLRKSKWQERTDFEALERS 229
             L   +      G  +  R +K+  +    R +  +   S
Sbjct: 72  KCLAAASLEAEGGGLKLDGRQLKVDLAV--TRDEAASGPSS 110

>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 = 67.3 bits (165), Expect = 8e-15
 Identities = 20/83 (24%), Positives = 42/83 (50%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            +F G++  E  ++ L   FS        ++V D+ TGK KGYGF  + +     +A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 200 MNGKYVGNRPIKLRKSKWQERTD 222
           +NG+    R +++  +  ++  +
Sbjct: 70  LNGREFSGRALRVDNAASEKNKE 92

>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 = 66.9 bits (164), Expect = 1e-14
 Identities = 25/99 (25%), Positives = 45/99 (45%), Gaps = 10/99 (10%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            +F G +   +++  +   F+R+ S    K++ D RTG +KGYGF+SF N  D+   +  
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV-- 67

Query: 200 MNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPK 238
            +      + +KL  +    +        S  H Q +P 
Sbjct: 68  ESQINFHGKKLKLGPA--IRKQ-----NLSTYHVQPRPL 99

>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 = 67.1 bits (164), Expect = 2e-14
 Identities = 24/110 (21%), Positives = 41/110 (37%), Gaps = 5/110 (4%)

Query: 107 EHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFN 166
            H   T            + E+    +       ++ G++        L   FS   S N
Sbjct: 9   THSKMTAGAYTEGPPQPLSAEEKKEID----KRSVYVGNVDYGSTAQDLEAHFSSCGSIN 64

Query: 167 MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
              ++ DK +G  KGY +I FA  + + AA+  M+      R IK+   +
Sbjct: 65  RITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR 113

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 66.1 bits (162), Expect = 2e-14
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           Y  + G+L        +   F      +  ++VRDK T K KG+ ++ F     +  AL 
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLSIRS-VRLVRDKDTDKFKGFCYVEFDEVDSLKEAL- 73

Query: 199 EMNGKYVGNRPIKLRKSK 216
             +G  +G+R +++  ++
Sbjct: 74  TYDGALLGDRSLRVDIAE 91

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 65.4 bits (160), Expect = 3e-14
 Identities = 13/85 (15%), Positives = 26/85 (30%), Gaps = 6/85 (7%)

Query: 128 DPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISF 187
           D  +   P      + G++ +   +  L   F  F        + D +    KG  FI +
Sbjct: 17  DHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNF------GFILDFKHYPEKGCCFIKY 70

Query: 188 ANPSDIAAALKEMNGKYVGNRPIKL 212
                 A  +  +       R ++ 
Sbjct: 71  DTHEQAAVCIVALANFPFQGRNLRT 95

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 65.5 bits (160), Expect = 5e-14
 Identities = 26/98 (26%), Positives = 41/98 (41%), Gaps = 11/98 (11%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRF--------PSFNMAKVVRDKRTGKTKGYGFIS 186
            +N+  +F   LG  V  + ++  F +             M  +  D+ TGK KG   +S
Sbjct: 5   SDNN-TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 187 FANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFE 224
           F +P    AA+   +GK     PIK+  +    R DF 
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNPIKVSFA--TRRADFN 99

>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 = 66.0 bits (161), Expect = 6e-14
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV-----VRDKRTGKTKGYGFISFANPSDIA 194
           R++  +L   V +  L   F R+  F+         +R  + G+ KG  FI   N    A
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            ALKE NG  +  +P+ ++ ++
Sbjct: 107 KALKEANGYVLFGKPMVVQFAR 128

>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 = 64.5 bits (158), Expect = 6e-14
 Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            E+  ++F G L  + +   L   F++F       +  D  TG+++G+GFI F + + + 
Sbjct: 8   EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVE 67

Query: 195 AALKEMNGKYVGNRPIKLRK 214
             L +   + +  R I  +K
Sbjct: 68  KVLDQKEHR-LDGRVIDPKK 86

>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 = 64.1 bits (157), Expect = 8e-14
 Identities = 19/94 (20%), Positives = 46/94 (48%), Gaps = 6/94 (6%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            ++ G+L      + + + FS+F      K++ D+ T K KG+GF+       ++ A+ +
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 200 MNGKYVGNRPIKLRKSKWQERTDFEALERSKNHN 233
           ++      R I++ ++    +   ++LE   +H+
Sbjct: 62  LDNTDFMGRTIRVTEAN--PK---KSLEHHHHHH 90

>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 = 64.6 bits (158), Expect = 9e-14
 Identities = 25/104 (24%), Positives = 42/104 (40%), Gaps = 11/104 (10%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                ++F G L     D  L K F  F     A V+ D++TGK++GYGF++ A+ +   
Sbjct: 14  DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPK 238
            A K+ N   +  R   +            A   +K  + +   
Sbjct: 74  RACKDPNPI-IDGRKANVNL----------AYLGAKPRSLQTGF 106

>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 = 63.5 bits (155), Expect = 2e-13
 Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 10/96 (10%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            LF  +L N V +++L KAFS+F      K+ R K   K K Y FI F        A++E
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQF-----GKLERVK---KLKDYAFIHFDERDGAVKAMEE 64

Query: 200 MNGKYVGNRPIK--LRKSKWQERTDFEALERSKNHN 233
           MNGK +    I+    K   Q+R + +A  ++ +  
Sbjct: 65  MNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100

>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 = 62.6 bits (153), Expect = 4e-13
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 8/86 (9%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             N +++F G++        L   F R        VV        K Y F+     +D  
Sbjct: 6   SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAK 57

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQER 220
           AA+ ++NGK V  + I +  S   ++
Sbjct: 58  AAIAQLNGKEVKGKRINVELSTKGQK 83

>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 = 62.6 bits (153), Expect = 4e-13
 Identities = 19/85 (22%), Positives = 41/85 (48%), Gaps = 5/85 (5%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRT-GKTKGYGFISFANPSDIAAAL 197
           Y  F G+L  +V ++ + + F         ++ R+     + KG+G+  F +   + +AL
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78

Query: 198 KEMNGKYVGNRPIKLRKSKWQERTD 222
             +N + +GNR I++  +   +  D
Sbjct: 79  -SLNEESLGNRRIRVDVAD--QAQD 100

>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 = 62.3 bits (152), Expect = 5e-13
 Identities = 14/85 (16%), Positives = 34/85 (40%), Gaps = 2/85 (2%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKR-TGKTKGYGFISFANPSDIAAALK 198
           ++   ++  + N   + + FS F      ++ +    TG  +G+GF+ F    D   A  
Sbjct: 17  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76

Query: 199 EM-NGKYVGNRPIKLRKSKWQERTD 222
            + +  ++  R + L  +  +    
Sbjct: 77  ALCHSTHLYGRRLVLEWADSEVTVQ 101

>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 = 62.3 bits (152), Expect = 6e-13
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            +   +LF G L      + L   FS++       +++DK T +++G+GF+ F +P+ + 
Sbjct: 13  ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVG 72

Query: 195 AALKEMNGKYVGNRPI 210
             L       +  R I
Sbjct: 73  TVL-ASRPHTLDGRNI 87

>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 = 61.9 bits (151), Expect = 7e-13
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 8/79 (10%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           P    RL+ G LG   +   L++ F RF S      V+         + +I + +     
Sbjct: 16  PTT--RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQ 67

Query: 195 AALKEMNGKYVGNRPIKLR 213
           AA  +M G  +G    +LR
Sbjct: 68  AACAKMRGFPLGGPDRRLR 86

>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 = 61.9 bits (151), Expect = 7e-13
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            +    L    L  +  +  L + FS F    M +V +D +TG +KG+GF+ F       
Sbjct: 12  VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71

Query: 195 AALKEM---NGKYV 205
             + +    +G++ 
Sbjct: 72  KVMSQRHMIDGRWC 85

>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 = 61.6 bits (150), Expect = 1e-12
 Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRF--------PSFNMAKVVRDKRTGKTKGYGFISFANPS 191
            +F   LG  V  + ++  F +             M  +  D+ TGK KG   +SF +P 
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 192 DIAAALKEMNGKYVGNRPIK 211
              AA+   +GK     PIK
Sbjct: 75  SAKAAIDWFDGKEFSGNPIK 94

>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 = 61.4 bits (150), Expect = 1e-12
 Identities = 13/80 (16%), Positives = 37/80 (46%), Gaps = 1/80 (1%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                ++F G + +   +  L + F +F       ++ D    + +G+GFI+F +   + 
Sbjct: 7   GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVD 66

Query: 195 AALKEMNGKYVGNRPIKLRK 214
            A+  M+   +  + +++++
Sbjct: 67  QAV-NMHFHDIMGKKVEVKR 85

>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 = 61.6 bits (150), Expect = 1e-12
 Identities = 21/110 (19%), Positives = 47/110 (42%), Gaps = 10/110 (9%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV--VRDKRTGKTKGYGFISFANPSD 192
           PE +  L+  +L  ++  + +   F ++       +  +R   T +T+G  ++ + +  D
Sbjct: 5   PEVNRILYIRNLPYKITAEEMYDIFGKY-----GPIRQIRVGNTPETRGTAYVVYEDIFD 59

Query: 193 IAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKK 242
              A+  ++G  V NR + +          F+ ++  K   Q K  L +K
Sbjct: 60  AKNAVDHLSGFNVSNRYLVVLYY--NANRAFQKMDTKKKEEQLK-LLKEK 106

>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 = 61.1 bits (149), Expect = 1e-12
 Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKR-TGKTKGYGFISFANPSDIAAAL 197
           Y  F G+L  +V ++ + + F         ++ R+     + KG+G+  F +   + +AL
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

Query: 198 KEMNGKYVGNRPIKLRKSK 216
             +N + +GN+ I++  + 
Sbjct: 75  S-LNEESLGNKRIRVDVAD 92

>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 = 61.1 bits (149), Expect = 1e-12
 Identities = 12/87 (13%), Positives = 30/87 (34%), Gaps = 8/87 (9%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            +   +L  G++     +  L   F  +       +V+         Y F+      D  
Sbjct: 7   GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAV 58

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERT 221
            A++ ++      + + ++ S  + RT
Sbjct: 59  EAIRGLDNTEFQGKRMHVQLSTSRLRT 85

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 61.3 bits (149), Expect = 1e-12
 Identities = 19/86 (22%), Positives = 31/86 (36%), Gaps = 6/86 (6%)

Query: 144 GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK 203
                 V    L+  FS+       +   D+ TGKTKG+ F+   + +D    +K  +GK
Sbjct: 18  PSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77

Query: 204 YV-GNRPIKLRKSKWQERTDFEALER 228
            +     + L         D E    
Sbjct: 78  RLDLKHRLFLYTM-----KDVERYNS 98

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 60.2 bits (147), Expect = 2e-12
 Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L  +   + L + F +F       V+RD  T +++G+GF++F + + +   L  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60

Query: 200 MNGKYVGNRPI 210
            +   + ++ I
Sbjct: 61  QSRHELDSKTI 71

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 60.8 bits (148), Expect = 2e-12
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +++ G+LG       L +AFS +       + R+       G+ F+ F +P D   A++ 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRG 56

Query: 200 MNGKYVGNRPIKLRKSKWQERTD 222
           ++GK +    +++  S    R  
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRS 79

>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 = 60.4 bits (147), Expect = 2e-12
 Identities = 13/82 (15%), Positives = 33/82 (40%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                 +   ++   V+ D +   F  +     +  ++    G   G   ++F +  +  
Sbjct: 12  KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
           AA+ ++N + +G+R +KL    
Sbjct: 72  AAVIDLNDRPIGSRKVKLVLGS 93

>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 = 60.7 bits (148), Expect = 2e-12
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 4/82 (4%)

Query: 128 DPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISF 187
            P  +    +  ++F G L  +   + L + F +F       V+RD  T +++G+GF++F
Sbjct: 15  VPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74

Query: 188 ANPSDIAAALK----EMNGKYV 205
            + + +   L     E++ K +
Sbjct: 75  MDQAGVDKVLAQSRHELDSKTI 96

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 60.8 bits (148), Expect = 3e-12
 Identities = 24/109 (22%), Positives = 46/109 (42%), Gaps = 13/109 (11%)

Query: 108 HKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNM 167
           H        +PR +     ++  L     ++ RLF      +V +  L++ F  F     
Sbjct: 6   HHHHHSSGLVPRGSHMHHRQEGEL-----SNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60

Query: 168 AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
            K++         G+ F+ F      A A++E++GK   N+P+++  SK
Sbjct: 61  VKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK 101

>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 = 60.3 bits (147), Expect = 3e-12
 Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKA-FSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
            ++  +L  ++  D L K+  + F  F     +   R+ K +G  F+ F   S    AL+
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 69

Query: 199 EMNGKYVGNRPIKLRKSK 216
            M G    ++P++++ +K
Sbjct: 70  SMQGFPFYDKPMRIQYAK 87

>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 = 60.8 bits (148), Expect = 3e-12
 Identities = 13/88 (14%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             ND R++ G+L  ++    +   F ++ +     +   +       + F+ F +P D  
Sbjct: 19  GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAE 75

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTD 222
            A+   +G       +++   +    T 
Sbjct: 76  DAVYGRDGYDYDGYRLRVEFPRSGRGTG 103

>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 = 60.0 bits (146), Expect = 3e-12
 Identities = 13/81 (16%), Positives = 33/81 (40%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                 +   ++   V+ D +   F  +     +  ++    G   G   ++F +  +  
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 195 AALKEMNGKYVGNRPIKLRKS 215
           AA+ ++N + +G+R +KL   
Sbjct: 72  AAVIDLNDRPIGSRKVKLSGP 92

>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 = 60.8 bits (148), Expect = 3e-12
 Identities = 20/99 (20%), Positives = 48/99 (48%), Gaps = 13/99 (13%)

Query: 111 ETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170
           E   +++P +   +           E   +LF G L  E  ++ L   + ++       V
Sbjct: 9   EKTLETVPLERKKRE---------KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV 59

Query: 171 VRDKRTGKTKGYGFISFANPSDIAAALK----EMNGKYV 205
           +RD  + +++G+GF++F++ +++ AA+      ++G+ V
Sbjct: 60  MRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVV 98

>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 = 64.5 bits (156), Expect = 4e-12
 Identities = 29/170 (17%), Positives = 59/170 (34%), Gaps = 16/170 (9%)

Query: 46  QYPPPAAYPAPVVPSVYAAPVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSD 105
            Y PP           +  P   +    +       F+       P   E+        +
Sbjct: 20  PYLPPLEKLPH--EKHHNQPYCGIAPYIRE------FEDPRDAPPPTRAET---REERME 68

Query: 106 IEHKAETKKKSIPRKAAGQTW---EDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRF 162
            + + + +++    +   + W    DP           LF   +  +  +  L + F  +
Sbjct: 69  RKRREKIERRQQEVETELKMWDPHNDPNAQGDAFK--TLFVARVNYDTTESKLRREFEVY 126

Query: 163 PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL 212
                  +V  KR+GK +GY FI + +  D+ +A K  +GK +  R + +
Sbjct: 127 GPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 59.0 bits (144), Expect = 4e-12
 Identities = 16/75 (21%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L      + +   F +F   + A ++ DK T + +G+GF++F +   +     E
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 200 MNGKYVGNRPIKLRK 214
           ++   + N+ ++ +K
Sbjct: 60  IHFHEINNKMVECKK 74

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 60.7 bits (147), Expect = 4e-12
 Identities = 16/108 (14%), Positives = 32/108 (29%), Gaps = 2/108 (1%)

Query: 110 AETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKA-FSRFPSFNMA 168
            ET      R+         T      +   +   ++  EV  + L    ++   S    
Sbjct: 2   KETAAAKFERQHMDSPDLGSTPPHTEPSQ-VVLITNINPEVPKEKLQALLYALASSQGDI 60

Query: 169 KVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
             +    +    G  +I FA      A ++   G      P+ +  S+
Sbjct: 61  LDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSE 108

>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 = 60.1 bits (146), Expect = 4e-12
 Identities = 20/97 (20%), Positives = 40/97 (41%), Gaps = 8/97 (8%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRF--------PSFNMAKVVRDKRTGKTKGYGFIS 186
             ++  ++   L + V  D L+  F +             M  +  DK TGK KG   +S
Sbjct: 12  DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 71

Query: 187 FANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDF 223
           + +P    AA++  +GK      +K+  ++ +   + 
Sbjct: 72  YEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108

>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 = 61.5 bits (149), Expect = 7e-12
 Identities = 18/96 (18%), Positives = 35/96 (36%), Gaps = 6/96 (6%)

Query: 141 LFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           L   +L  E V    L   F  +      K++ +K     K    +  A+ +    A+  
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60

Query: 200 MNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQK 235
           +NG  +  +PI++  SK Q        +  +   + 
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKD 96

>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 = 54.9 bits (132), Expect = 2e-09
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 5/78 (6%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L   ++   V+++ L   FS         V   K   K +    I   +  +   AL +
Sbjct: 122 TLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALID 177

Query: 200 MNGKYVGN-RPIKLRKSK 216
           ++   +G    +++  SK
Sbjct: 178 LHNHDLGENHHLRVSFSK 195

>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 = 59.2 bits (144), Expect = 7e-12
 Identities = 17/77 (22%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
            D +LF G L  + +++ + + F  F   +   V+R    G +KG  F+ F++ ++  AA
Sbjct: 14  RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAA 72

Query: 197 LKEMNGKYV---GNRPI 210
           +  ++G       +  +
Sbjct: 73  IHALHGSQTMPGASSSL 89

>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 = 62.6 bits (151), Expect = 9e-12
 Identities = 24/113 (21%), Positives = 46/113 (40%), Gaps = 5/113 (4%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSR-FPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
            ++  +L  ++  D L K+    F  F     +   R+ K +G  F+ F   S    AL+
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 70

Query: 199 EMNGKYVGNRPIKL----RKSKWQERTDFEALERSKNHNQKKPKLSKKSVLHK 247
            M G    ++P+++      S    +     +ER +   ++KPK  +     K
Sbjct: 71  SMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKK 123

>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 = 53.7 bits (128), Expect = 1e-08
 Identities = 28/193 (14%), Positives = 54/193 (27%), Gaps = 9/193 (4%)

Query: 21  APTTANSSYFPLPFHLQQTDPTAVSQYPPPAAYPAPVVPSVYAAPVAPVYSLPQYHQAQQ 80
                  ++       ++  P +        A        V  A   PV  +P   QA +
Sbjct: 93  IIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPR 152

Query: 81  LFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYR 140
           +               +      +  +                   +  +        + 
Sbjct: 153 IMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILF- 211

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
               +L  E N+ +LS  F++FP F   ++V  +         F+ F N     AA   +
Sbjct: 212 --LTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDAL 264

Query: 201 NG-KYVGNRPIKL 212
            G K   N  +K+
Sbjct: 265 QGFKITQNNAMKI 277

>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 = 57.9 bits (141), Expect = 1e-11
 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L  +  ++ + + F  F      ++  D +T K +G+ FI+F     +   + E
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-E 59

Query: 200 MNGKYVGNRPIKLRK 214
                VG    +++ 
Sbjct: 60  KKYHNVGLSKCEIKV 74

>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 = 58.7 bits (142), Expect = 2e-11
 Identities = 21/102 (20%), Positives = 37/102 (36%), Gaps = 1/102 (0%)

Query: 118 PRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTG 177
                GQ     + +    ND  +    L      + + + FS          +     G
Sbjct: 22  ASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEG 81

Query: 178 KTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE 219
           K  G  F+ FA+      AL   + + +G+R I++ KS  +E
Sbjct: 82  KITGEAFVQFASQELAEKAL-GKHKERIGHRYIEVFKSSQEE 122

>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 = 2e-11
 Identities = 10/76 (13%), Positives = 20/76 (26%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
               L   +   EV ++   +            V       +    G + + + SD    
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181

Query: 197 LKEMNGKYVGNRPIKL 212
           L  +N   + N     
Sbjct: 182 LGFLNHYQMKNPNGPY 197

>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 = 54.7 bits (131), Expect = 2e-09
 Identities = 14/108 (12%), Positives = 34/108 (31%), Gaps = 6/108 (5%)

Query: 141 LFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           L    L    +N D +   F  + +    K ++ K      G   +  A+   +  A+  
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVEMADGYAVDRAITH 61

Query: 200 MNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSVLHK 247
           +N  ++  + + +  SK       ++          K     ++    
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFS 109

>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 = 57.6 bits (140), Expect = 3e-11
 Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 8/81 (9%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +LF G+L  E  +  +   F ++       ++        K YGF+   + +    A++ 
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61

Query: 200 MNGKYVGNRPIKLRKSKWQER 220
           ++   +    I +  SK + +
Sbjct: 62  LHHYKLHGVNINVEASKNKSK 82

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 56.7 bits (137), Expect = 5e-11
 Identities = 10/72 (13%), Positives = 27/72 (37%), Gaps = 3/72 (4%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +L   ++   +  +VL     ++      + V             +++++      AL +
Sbjct: 17  KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQALDK 73

Query: 200 MNGKYVGNRPIK 211
           +NG  + N  +K
Sbjct: 74  LNGFQLENFTLK 85

>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 = 56.7 bits (137), Expect = 7e-11
 Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             ND  +    L    + + + + FS          +     G++ G  F+ FA+     
Sbjct: 12  TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE 71

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQE 219
            AL + + + +G+R I++ KS   E
Sbjct: 72  KAL-KKHKERIGHRYIEIFKSSRAE 95

>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 = 55.7 bits (135), Expect = 1e-10
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 7/74 (9%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ G LG+ + +  L   F +F       VV+ +         FI FA       A ++ 
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAAEKS 68

Query: 201 -NGKYVGNRPIKLR 213
            N   V  R + ++
Sbjct: 69  FNKLIVNGRRLNVK 82

>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 = 55.1 bits (133), Expect = 2e-10
 Identities = 12/80 (15%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRF-----PSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           RL+ G++   + ++ +   F+        +      V   +  + K + F+ F +  +  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 195 AALKEMNGKYVGNRPIKLRK 214
            A+   +G     + +K+R+
Sbjct: 68  QAM-AFDGIIFQGQSLKIRR 86

>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 = 55.1 bits (133), Expect = 3e-10
 Identities = 12/90 (13%), Positives = 27/90 (30%), Gaps = 3/90 (3%)

Query: 149 EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNR 208
            +    + +     P    A  V     G+  G   + F N  D   + + ++ K +  R
Sbjct: 26  SITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGR 84

Query: 209 PIKLRKSKWQERTDFEALERSKNHNQKKPK 238
              +     ++  + E         +  P 
Sbjct: 85  EAFVHVVTLEDMREIEK--NPPAQGKSGPS 112

>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 = 56.9 bits (137), Expect = 5e-10
 Identities = 18/96 (18%), Positives = 35/96 (36%), Gaps = 6/96 (6%)

Query: 141 LFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           L   +L  E V    L   F  +      K++ +K     K    +  A+ +    A+  
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 91

Query: 200 MNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQK 235
           +NG  +  +PI++  SK Q        +  +   + 
Sbjct: 92  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKD 127

>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 = 52.7 bits (126), Expect = 1e-08
 Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 5/77 (6%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L   ++   V+++ L   FS             K     +    I   +  +   AL ++
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDL 209

Query: 201 NGKYVGN-RPIKLRKSK 216
           +   +G    +++  SK
Sbjct: 210 HNHDLGENHHLRVSFSK 226

>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 = 54.4 bits (131), Expect = 6e-10
 Identities = 13/103 (12%), Positives = 36/103 (34%), Gaps = 4/103 (3%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRF-PSFNMAKVVRDKR-TGKTKGYGFISFANPSDI 193
             + RLF G +      + + +  ++         V        K +G+ F+ + +    
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 194 AAALKEMNGK--YVGNRPIKLRKSKWQERTDFEALERSKNHNQ 234
           A A +++      +    I +  ++ +   D + +E     + 
Sbjct: 66  AMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPSS 108

>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 = 53.9 bits (130), Expect = 9e-10
 Identities = 17/83 (20%), Positives = 33/83 (39%), Gaps = 9/83 (10%)

Query: 140 RLFCGDLG-NEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           R+F G+L    V    +   FS++       V         KGY F+ ++N     AA+ 
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVL 80

Query: 199 EMNGKYVGNRPIKLRKSKWQERT 221
             NG+ +  + + +  +   +  
Sbjct: 81  GENGRVLAGQTLDINMAGEPKPD 103

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 53.2 bits (128), Expect = 1e-09
 Identities = 10/80 (12%), Positives = 24/80 (30%), Gaps = 1/80 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           ++      +   D + +           ++ R       KG  F+ F +       ++  
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP 72

Query: 201 NGKYVGNRPIKLRKSKWQER 220
             KY     + L K  +  +
Sbjct: 73  GQKYKETDLLILFKDDYFAK 92

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 53.4 bits (128), Expect = 1e-09
 Identities = 21/111 (18%), Positives = 40/111 (36%), Gaps = 5/111 (4%)

Query: 129 PTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVR--DKRTGKTKGYGFIS 186
             L       Y +    L    + + +    S     +    V     R G+  G  F+ 
Sbjct: 8   MMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVE 67

Query: 187 FANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKP 237
             +  D+  AL + + + +G+R I++ KS   E      L+ S  ++   P
Sbjct: 68  LESEDDVKLAL-KKDRESMGHRYIEVFKSHRTEMD--WVLKHSGPNSASGP 115

>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 = 53.3 bits (128), Expect = 2e-09
 Identities = 23/103 (22%), Positives = 43/103 (41%), Gaps = 3/103 (2%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            E  + ++   L  E  +  +   F +      +  +     GK  G GF+ F N +D  
Sbjct: 22  HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK 81

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKP 237
           AAL   + +Y+GNR I++      ++   E ++  +   Q  P
Sbjct: 82  AAL-CRHKQYMGNRFIQVHPI--TKKGMLEKIDMIRKRLQSGP 121

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.4 bits (126), Expect = 3e-09
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 149 EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV-GN 207
           E   +V+ K FS+F    +      +  GKTKGY F+ +A+P+    A+K  +G  +   
Sbjct: 32  EKLKNVIHKIFSKF--GKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

Query: 208 RPIKLRKSKWQERTDFE 224
              ++        TDF+
Sbjct: 90  HTFRVNLF-----TDFD 101

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 51.6 bits (124), Expect = 3e-09
 Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 154 VLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK 203
           V+ K FS+F    +      +  GKTKGY F+ +A+P+    A+K  +G 
Sbjct: 23  VIHKIFSKF--GKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGY 70

>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 = 51.3 bits (123), Expect = 4e-09
 Identities = 6/80 (7%), Positives = 23/80 (28%), Gaps = 7/80 (8%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
               +   +L  + N   +      +        ++     + K   F++  N      A
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDY-------DLKYCYVDRNKRTAFVTLLNGEQAQNA 56

Query: 197 LKEMNGKYVGNRPIKLRKSK 216
           ++  +      + + ++   
Sbjct: 57  IQMFHQYSFRGKDLIVQLQP 76

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 51.8 bits (124), Expect = 6e-09
 Identities = 14/80 (17%), Positives = 26/80 (32%), Gaps = 3/80 (3%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           P   YR+   +L    +   L K        ++        T    G G + F +   + 
Sbjct: 25  PAKRYRITMKNLPEGCSWQDL-KDL--ARENSLETTFSSVNTRDFDGTGALEFPSEEILV 81

Query: 195 AALKEMNGKYVGNRPIKLRK 214
            AL+ +N        I + +
Sbjct: 82  EALERLNNIEFRGSVITVER 101

>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 = 51.0 bits (122), Expect = 9e-09
 Identities = 12/77 (15%), Positives = 28/77 (36%), Gaps = 6/77 (7%)

Query: 141 LFCGDLGNEVNDDVLSK---AFSRFPSFNMAKVVRDKRTGKTK---GYGFISFANPSDIA 194
           +F   L   + D  + K    F +F   +   +        ++      ++++    D  
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 195 AALKEMNGKYVGNRPIK 211
            A++ +N   V  R +K
Sbjct: 78  RAIQCVNNVVVDGRTLK 94

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 22/99 (22%), Positives = 37/99 (37%), Gaps = 21/99 (21%)

Query: 140 RLFCGDL-GNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKT------KGYGFISFANPSD 192
           RLF G+L    V+ + L + FS +              G          +GFI F NP  
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPY--------------GHIMQINIKNAFGFIQFDNPQS 57

Query: 193 IAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKN 231
           +  A++  + +    + + L  S    R  F+  +   N
Sbjct: 58  VRDAIECESQEMNFGKKLILEVSSSNARPQFDHGDHGTN 96

>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 Length = 136

 Score = 50.4 bits (120), Expect = 2e-08
 Identities = 18/101 (17%), Positives = 35/101 (34%), Gaps = 3/101 (2%)

Query: 121 AAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVR--DKRTGK 178
                     L       + +    L    + + +    S     + A  V     R G+
Sbjct: 27  GQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR 86

Query: 179 TKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE 219
             G  F+   +  D+  AL + + + +G+R I++ KS   E
Sbjct: 87  QSGEAFVELGSEDDVKMAL-KKDRESMGHRYIEVFKSHRTE 126

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 49.9 bits (119), Expect = 3e-08
 Identities = 20/100 (20%), Positives = 34/100 (34%), Gaps = 6/100 (6%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRF-PSFNMAKVVR--DKRTGKTKGYGFISFANPS 191
            EN   +    L      + +   F +  P     + +       G+  G  F+ FA   
Sbjct: 20  KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEE 79

Query: 192 DIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKN 231
               AL   +   +G R I+L +S   E    + L R  +
Sbjct: 80  YAQNAL-RKHKDLLGKRYIELFRSTAAEVQ--QVLNRFSS 116

>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 = 48.8 bits (117), Expect = 4e-08
 Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 2/48 (4%)

Query: 169 KVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
           ++VR+   G   GY F+ F+N  ++  ALK  N +Y+G R I++ + K
Sbjct: 40  RIVRNAH-GNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREK 85

>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 = 49.4 bits (118), Expect = 4e-08
 Identities = 14/93 (15%), Positives = 35/93 (37%), Gaps = 3/93 (3%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           +D  +    +     ++ +   F       +  +++D   G+  G G + F +P D   A
Sbjct: 15  DDLYVSVHGMPFSAMENDVRDFFHGLRVDAV-HLLKD-HVGRNNGNGLVKFLSPQDTFEA 72

Query: 197 LKEMNGKYVGNRPIKLRKSKWQERTDFEALERS 229
           L + N   +  R +++  +  ++         S
Sbjct: 73  L-KRNRMLMIQRYVEVSPATERQWVAAGGHITS 104

>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 = 51.0 bits (121), Expect = 4e-08
 Identities = 18/132 (13%), Positives = 39/132 (29%), Gaps = 1/132 (0%)

Query: 89  ITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGN 148
           +T +    V+A   S     +    K  I R  +    E     +    +  ++      
Sbjct: 60  LTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPT 119

Query: 149 EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNR 208
           +   D + +           ++ R       KG  F+ F +       ++    KY    
Sbjct: 120 DATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETD 178

Query: 209 PIKLRKSKWQER 220
            + L K  +  +
Sbjct: 179 LLILFKDDYFAK 190

>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 = 48.9 bits (117), Expect = 4e-08
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 9/82 (10%)

Query: 140 RLFCGDL-GNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           RLF G+L    V+ + L + FS +       +           +GFI F NP  +  A++
Sbjct: 24  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 75

Query: 199 EMNGKYVGNRPIKLRKSKWQER 220
             + +    + + L  S    R
Sbjct: 76  XESQEMNFGKKLILEVSSSNAR 97

>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} Length = 107

 Score = 48.7 bits (116), Expect = 5e-08
 Identities = 22/111 (19%), Positives = 41/111 (36%), Gaps = 7/111 (6%)

Query: 129 PTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVR--DKRTGKTKGYGFIS 186
             L E  ++ + +    L      + +   FS     N    +     R GK +G   I 
Sbjct: 2   SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIE 61

Query: 187 FANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKP 237
             +  D+  AL E +  Y+G R +++ +       D +AL +     +  P
Sbjct: 62  MESEQDVQKAL-EKHRMYMGQRYVEVYEIN---NEDVDALMK-SLQVKSSP 107

>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 = 48.6 bits (116), Expect = 6e-08
 Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 7/83 (8%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           + R+    L    +   L            A V RD       G G + F    D+  A+
Sbjct: 15  ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAV 67

Query: 198 KEMNGKYVGNRPIKLRKSKWQER 220
           ++++     +   +    + +  
Sbjct: 68  RKLDNTKFRSHEGETAYIRVKVD 90

>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 = 47.6 bits (114), Expect = 8e-08
 Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 8/76 (10%)

Query: 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSD 192
               +  ++F G    ++  + L + F ++       + +  R      + F++FA+   
Sbjct: 6   HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR-----AFAFVTFADDKV 60

Query: 193 IAAALKEM---NGKYV 205
             +   E     G  V
Sbjct: 61  AQSLCGEDLIIKGISV 76

>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 = 47.9 bits (114), Expect = 2e-07
 Identities = 15/94 (15%), Positives = 32/94 (34%), Gaps = 5/94 (5%)

Query: 127 EDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV-VRDKRTGKTKGYGFI 185
            D          + +    L  +  ++ +   FS     N  +V +     G+  G   +
Sbjct: 35  GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFS---PLNPVRVHIEIGPDGRVTGEADV 91

Query: 186 SFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE 219
            FA   +  AA+   +   + +R I+L  +    
Sbjct: 92  EFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG 124

>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 = 47.0 bits (112), Expect = 2e-07
 Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 2/55 (3%)

Query: 162 FPSFNMAKV-VRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS 215
           F   N  +V +     G+  G   + FA   D  AA+   +   + +R ++L  +
Sbjct: 36  FSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLN 89

>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 = 46.1 bits (110), Expect = 3e-07
 Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 8/69 (11%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            +F G    ++ +D L + FS++       + +  R      + F++FA+     +   E
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLCGE 61

Query: 200 M---NGKYV 205
                G  V
Sbjct: 62  DLIIKGISV 70

>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 = 46.7 bits (111), Expect = 4e-07
 Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 7/77 (9%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           + R+    L    +   L            A V RD       G G + F    D+  A+
Sbjct: 16  ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAV 68

Query: 198 KEMNGKYVGNRPIKLRK 214
           ++++     +   +   
Sbjct: 69  RKLDNTKFRSHEGETAY 85

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.9 bits (109), Expect = 5e-07
 Identities = 13/83 (15%), Positives = 26/83 (31%), Gaps = 8/83 (9%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +    L + V +  L +A   F   +   V+        K    + F +      A+   
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYA 77

Query: 201 NGK--YVGNRPIKLRKSKWQERT 221
                Y+   P  +  S  Q+ +
Sbjct: 78  ADNQIYIAGHPAFVNYSTSQKIS 100

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 45.6 bits (108), Expect = 7e-07
 Identities = 10/81 (12%), Positives = 30/81 (37%), Gaps = 5/81 (6%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            ++ G+L  +     L +A     S  +    +       +   F+ + + +    A+  
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ-----GPRRRAFLHYPDSAAAQQAVSC 75

Query: 200 MNGKYVGNRPIKLRKSKWQER 220
           + G  +G   +++  ++ Q  
Sbjct: 76  LQGLRLGTDTLRVALARQQRD 96

>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 = 45.6 bits (108), Expect = 9e-07
 Identities = 16/103 (15%), Positives = 34/103 (33%), Gaps = 9/103 (8%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +   +L        + + FSRF        +      +      + F  P +   A + +
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRF------GSLGRVLLPEGGITAIVEFLEPLEARKAFRHL 66

Query: 201 NGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKS 243
                 + P+ L   +W     F A  + K+   ++P    +S
Sbjct: 67  AYSKFHHVPLYL---EWAPIGVFGAAPQKKDSQHEQPAEKAES 106

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 15/98 (15%), Positives = 29/98 (29%), Gaps = 14/98 (14%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK-- 198
           +    L  +V +  +      F        V +    K K   FI           +   
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGK------VTNLLMLKGKNQAFIEMNTEEAANTMVNYY 72

Query: 199 EMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKK 236
                 +  +PI ++ S  +E      L+   + NQ +
Sbjct: 73  TSVTPVLRGQPIYIQFSNHKE------LKTDSSPNQAR 104

>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 = 44.9 bits (106), Expect = 2e-06
 Identities = 19/98 (19%), Positives = 32/98 (32%), Gaps = 12/98 (12%)

Query: 114 KKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRD 173
           K ++ R    +T    T +        +  G LGN V+ + L     +         V  
Sbjct: 9   KHTLLRHEGIETVSYATQSLV------VANGGLGNGVSRNQLLPVLEKCGL------VDA 56

Query: 174 KRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK 211
                 K Y F  +    +   A   +NGK V +   +
Sbjct: 57  LLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ 94

>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 = 44.0 bits (104), Expect = 3e-06
 Identities = 13/96 (13%), Positives = 26/96 (27%), Gaps = 14/96 (14%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +    L   V +  L +A  +F +     ++  KR         + F N       +   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVTFA 71

Query: 201 --NGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQ 234
                Y+  +      S  +       + R  N   
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKR------ITRPGNSGP 101

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 20/102 (19%), Positives = 37/102 (36%), Gaps = 18/102 (17%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKR--TGKTKGYGFISFANPSD 192
                ++F G L  ++++D ++ +F RF    +    + +       KGY F+ F   S 
Sbjct: 5   SSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESS 64

Query: 193 IAAAL----------------KEMNGKYVGNRPIKLRKSKWQ 218
           + A +                  +  K V  RP  L  S + 
Sbjct: 65  VQALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSDSDFV 106

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            +F       V+   LS+ F  F    +A VV DK  G    +  +   +     A L  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFG--PVASVVMDKDKGV---FAIVEMGDVGAREAVL-S 63

Query: 200 MNGKYVGNRPIKLRKSKWQE 219
            +   +G   +++R  + +E
Sbjct: 64  QSQHSLGGHRLRVRPREQKE 83

>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 Length = 104

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 9/42 (21%), Positives = 17/42 (40%)

Query: 170 VVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK 211
            V D       G  ++ F    D   A+ ++N ++   +PI 
Sbjct: 58  NVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 38.5 bits (89), Expect = 5e-04
 Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 4/74 (5%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R+   +L   V  DVL + FS+F +             +      + +A+P     A   
Sbjct: 48  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLS 103

Query: 200 MNGKYVGNRPIKLR 213
           ++G+ + N    LR
Sbjct: 104 LDGQNIYNACCTLR 117

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	247
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.91
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.89
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.89
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.89
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.89
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.88
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.88
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.88
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.87
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.87
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.87
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.87
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.87
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.87
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.87
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.87
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.86
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.86
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.86
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.86
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.86
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.86
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.86
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.86
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.86
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.86
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.86
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.86
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.86
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.86
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.85
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.85
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.85
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.85
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.85
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.85
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.85
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.85
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.85
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.85
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.85
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.85
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.85
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.84
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.84
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.84
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.84
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.84
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.84
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.84
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.84
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.84
2div_A	99	TRNA selenocysteine associated protein; structural	99.84
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.84
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.84
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.84
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.84
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.84
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.84
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.84
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.83
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.83
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.83
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.83
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.83
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.83
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.83
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.83
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.83
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.83
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.83
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.83
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.83
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.83
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.83
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.83
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.83
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.83
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.83
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.83
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.83
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.83
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.83
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.83
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.82
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.82
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.82
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.82
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.82
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.82
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.82
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.82
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.82
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.82
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.82
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.82
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.82
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.82
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.82
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.81
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.81
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.81
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.81
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.81
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.81
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.81
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.81
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.81
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.81
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.8
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.8
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.8
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.8
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.8
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.8
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.8
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.8
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.8
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.8
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.79
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.79
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.79
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.79
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.79
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.79
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.79
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.79
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.79
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.79
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.79
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.79
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.78
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.78
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.78
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.78
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.78
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.78
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.78
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.78
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.78
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.78
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.78
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.78
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.65
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.78
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.78
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.77
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.77
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.77
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.77
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.77
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.77
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.76
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.76
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.76
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.76
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.76
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.76
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.76
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.76
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.75
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.75
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.75
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.75
1x5p_A	97	Negative elongation factor E; structure genomics,	99.75
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.75
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.75
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.74
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.74
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.74
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.73
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.73
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.72
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.72
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.72
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.72
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.71
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.71
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.71
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.71
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.7
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.7
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.69
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.69
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.69
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.69
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.68
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.64
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.63
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.62
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.62
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.61
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.6
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.58
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.58
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.57
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.54
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.53
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.47
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.46
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.4
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.39
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.32
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.25
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.1
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.64
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	97.96
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.84
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.71
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.59
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.54
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.5
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.22
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	96.97
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.62
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.54
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.25
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	96.19
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.14
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	96.12
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.09
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	93.98
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	93.97
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	93.92
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	93.92
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	93.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	93.73
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	93.57
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	93.42
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	93.4
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	93.36
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	93.25
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	93.09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	92.99
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	92.95
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	92.91
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	92.31
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	92.26
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	92.13
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	92.11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	92.09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	92.08
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	92.07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	92.0
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	91.98
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	91.85
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	91.81
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	91.77
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	91.75
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	91.68
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	91.63
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	91.23
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	91.16
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	91.11
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	91.1
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	91.03
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	90.98
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	90.98
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	90.88
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	90.86
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	90.84
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	90.53
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	90.49
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	90.47
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	90.22
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	90.06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	89.87
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	89.8
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	89.74
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	89.72
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	89.55
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	89.5
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	89.26
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	89.23
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	89.22
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	89.19
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	89.14
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	88.9
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	88.83
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	88.65
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	88.59
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	88.4
1x4e_A	85	RNA binding motif, single-stranded interacting pro	88.39
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	88.3
2dis_A	109	Unnamed protein product; structural genomics, RRM	88.26
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	88.17
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	87.95
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	87.94
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	87.86
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	87.52
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	87.3
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	87.28
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	87.23
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	87.21
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	87.18
2div_A	99	TRNA selenocysteine associated protein; structural	87.15
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	87.08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	86.99
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	86.96
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	86.89
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	86.78
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	86.69
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	86.67
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	86.62
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	86.59
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	86.46
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	86.41
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	85.85
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	85.63
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	85.8
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	85.5
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	85.45
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	85.3
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	85.29
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	85.21
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	85.12
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	85.06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	84.9
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	84.89
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	84.88
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	84.81
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	84.75
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	84.63
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	84.61
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	84.51
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	84.47
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	84.32
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	83.92
1x5p_A	97	Negative elongation factor E; structure genomics,	83.42
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	83.38
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	83.27
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	83.11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	82.98
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	82.95
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	82.51
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	82.3
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	82.17
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	81.96
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	81.9
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	81.83
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	81.52
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	80.57
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	80.52
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	80.39

>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=99.91  E-value=5.9e-24  Score=153.72  Aligned_cols=83  Identities=27%  Similarity=0.444  Sum_probs=79.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..++++|||+|||+++++++|+++|+.||.|.+|+|++|+.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            44567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 025814          215 SKW  217 (247)
Q Consensus       215 a~~  217 (247)
                      |++
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>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=99.89  E-value=4.8e-23  Score=160.98  Aligned_cols=137  Identities=13%  Similarity=0.235  Sum_probs=103.6

Q ss_pred             cCCCceeeCccCHHHHHHHHhcCc----cchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHH
Q 025814           82 FQRDAQTITPEALESVKAALASSD----IEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSK  157 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~al~~~~----~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L~~  157 (247)
                      ..+|++||.|.+.+.+.+++....    +++... ..........................++|||+|||+++++++|++
T Consensus        11 ~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~   89 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWT-YDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRR   89 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEE-EETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCHHHHHH
T ss_pred             cccchhHHHHHHHHhHHHHHHhhcccCCCCCccc-ccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHH
Confidence            478999999999999999985421    111111 000000000000011111112234567999999999999999999


Q ss_pred             HhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          158 AFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       158 ~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      +|+.||.|.+|+|++|+.+|.++|||||+|.+.++|++||+.|||..|+|+.|+|.+++.+.
T Consensus        90 ~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           90 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             HHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             HHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            99999999999999999899999999999999999999999999999999999999998654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.89  E-value=1.4e-22  Score=149.30  Aligned_cols=84  Identities=13%  Similarity=0.144  Sum_probs=79.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .+.++|||+||++++++++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|++|++.|||..|+|+.|+|.++
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            44569999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          216 KWQE  219 (247)
Q Consensus       216 ~~k~  219 (247)
                      ....
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            7543

>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=99.89  E-value=1.8e-23  Score=163.99  Aligned_cols=139  Identities=19%  Similarity=0.348  Sum_probs=119.7

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc-CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS-SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCG  144 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~-~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~  144 (247)
                      +|.+..+....+..+..++|++||.|.+.++|.+|+.. ..++++.+.+.....+..             ....++|||+
T Consensus        27 ~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~~~-------------~~~~~~l~V~   93 (167)
T 2cjk_A           27 YGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDE-------------QDKTGKIFVG   93 (167)
T ss_dssp             TCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCHHH-------------HHHCEEEEEE
T ss_pred             CCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccchhh-------------ccCCCeEEEC
Confidence            36777776677767788999999999999999999985 357777777665544322             1234589999


Q ss_pred             CCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          145 DLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       145 nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      |||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++ +||..++|+.|+|.++.++
T Consensus        94 nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A           94 GIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             EECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             CCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            999999999999999999999999999998899999999999999999999996 8999999999999999876

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.89  E-value=2.8e-23  Score=170.15  Aligned_cols=140  Identities=21%  Similarity=0.288  Sum_probs=114.9

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      |.|..+....+..+..+++++||+|++.+++..|+..   ..+.++.+.+..........           .....+|||
T Consensus        40 G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~~-----------~~~~~~l~v  108 (213)
T 4f02_A           40 GPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLR-----------KSGVGNIFI  108 (213)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCTHHH-----------HHCTTEEEE
T ss_pred             CCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccccccccc-----------ccccccceE
Confidence            6777776767777788899999999999999998853   45666666554433221110           123458999


Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          144 GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      +||++++++++|+++|+.||.|.+|+|++|.  +.++|||||+|.+.++|++||+.|||..|+|+.|+|.+++.+.
T Consensus       109 ~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          109 KNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             ESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             CCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            9999999999999999999999999999984  5689999999999999999999999999999999999998754

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.88  E-value=2.1e-22  Score=157.25  Aligned_cols=138  Identities=25%  Similarity=0.468  Sum_probs=114.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      |.+..+....+.. ..+++++||+|.+.+++.+|+.   +..+.++.+.+........           ......++|||
T Consensus        25 G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~-----------~~~~~~~~l~v   92 (166)
T 3md3_A           25 GPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQ-----------SSSDDTFNLFV   92 (166)
T ss_dssp             SCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCC-----------CCCTTCEEEEE
T ss_pred             CCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCC-----------CCCCCCceEEE
Confidence            5555554444432 4478999999999999999884   4567777777765543322           11445679999


Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          144 GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      +|||..+++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..|||..++|+.|+|.+++
T Consensus        93 ~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A           93 GDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             ESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.88  E-value=1.9e-22  Score=162.07  Aligned_cols=147  Identities=14%  Similarity=0.312  Sum_probs=116.1

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCG  144 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~  144 (247)
                      |.+..+....+.....++|++||.|.+.++|.+|++.  ..+.++.+.+.....+......       ......++|||+
T Consensus        38 G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~~~~~~~-------~~~~~~~~l~V~  110 (196)
T 1l3k_A           38 GTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------GAHLTVKKIFVG  110 (196)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC------------------CCSEEEEE
T ss_pred             CCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCccccccc-------ccCCCcceEEEe
Confidence            6666666666666777899999999999999999976  3577777777665544322111       112345699999


Q ss_pred             CCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccccc
Q 025814          145 DLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQERT  221 (247)
Q Consensus       145 nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~~  221 (247)
                      |||+++++++|+++|+.||.|..|.|++++.+|.++|||||+|.+.++|.+||.. +|..|+|+.|.|+++.++...
T Consensus       111 nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          111 GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             CCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             CCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            9999999999999999999999999999998999999999999999999999965 899999999999999877643

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.88  E-value=2.3e-22  Score=157.14  Aligned_cols=94  Identities=19%  Similarity=0.342  Sum_probs=84.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCC--CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFP--SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G--~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..++|||+||++++++++|+++|+.||  .|.+|+|++|+.+|.++|||||+|.+.++|++||..|||..|+|+.|+|++
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            456999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccccHHHHHhhh
Q 025814          215 SKWQERTDFEALERSK  230 (247)
Q Consensus       215 a~~k~~~~~~~~~~~~  230 (247)
                      +..+.....+...+++
T Consensus       134 a~~~~~~~~e~~~rkr  149 (156)
T 3n9u_C          134 ATRQNLSQFEAQARKR  149 (156)
T ss_dssp             CCHHHHHHHHHHHHHH
T ss_pred             cCCCcchhhhhhcccc
Confidence            9877665555444443

>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=99.87  E-value=8.7e-22  Score=137.16  Aligned_cols=81  Identities=37%  Similarity=0.735  Sum_probs=78.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      ++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|++++.+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             c
Q 025814          219 E  219 (247)
Q Consensus       219 ~  219 (247)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.87  E-value=8.1e-22  Score=154.51  Aligned_cols=136  Identities=17%  Similarity=0.315  Sum_probs=116.5

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      |.+..+....+.....+++++||.|.+.++|..|+.   +..+.++.+.+........             ....++|||
T Consensus        28 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~-------------~~~~~~l~v   94 (168)
T 1b7f_A           28 GPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGE-------------SIKDTNLYV   94 (168)
T ss_dssp             SCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCSS-------------TTTTCEEEE
T ss_pred             CCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCCcc-------------cCCCCCEEE
Confidence            666666666666677889999999999999999885   4567777777765543321             234569999


Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EeEEEEEc
Q 025814          144 GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN--RPIKLRKS  215 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~a  215 (247)
                      +|||..+++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|||..++|  +.|+|++|
T Consensus        95 ~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A           95 TNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             ESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             eCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999999999999999999999999998899999999999999999999999999999988  99999875

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.87  E-value=5.3e-23  Score=146.39  Aligned_cols=83  Identities=12%  Similarity=0.261  Sum_probs=76.9

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhC-CceeCCEeEEEEEcc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFP-SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN-GKYVGNRPIKLRKSK  216 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G-~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~-g~~i~g~~l~V~~a~  216 (247)
                      ++|||+|||+++++++|+++|+.|| .|.+|+|++|+.||.++|||||+|.+.++|++||+.|+ +..++|+.|+|++++
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            4899999999999999999999999 89999999999999999999999999999999998874 568999999999998


Q ss_pred             ccccc
Q 025814          217 WQERT  221 (247)
Q Consensus       217 ~k~~~  221 (247)
                      ++.+.
T Consensus        82 ~~~~~   86 (91)
T 2lxi_A           82 PKPKI   86 (91)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            76543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.87  E-value=9.3e-23  Score=166.36  Aligned_cols=151  Identities=22%  Similarity=0.304  Sum_probs=118.1

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      |.+..+....+......++++||.|.+.++|.+|+.   +..+.++.+.+..............  .........++|||
T Consensus        53 G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~--~~~~~~~~~~~l~v  130 (216)
T 2qfj_A           53 GPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIID--QLAEEARAFNRIYV  130 (216)
T ss_dssp             SCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHHHHH--HHHHHHTTSCEEEE
T ss_pred             CCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCccccchhhh--hhhcccCCCcEEEE
Confidence            666666666665667789999999999999999986   4567787777755433221100000  00001234569999


Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          144 GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      +||+.++++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|.+|++.|||..|+|+.|+|.++..+.
T Consensus       131 ~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          131 ASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             ECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             eCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999998654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.87  E-value=1.4e-21  Score=157.35  Aligned_cols=141  Identities=18%  Similarity=0.324  Sum_probs=113.8

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhc--CccchhhhhhcccccccccCCCCCCC-------CCCCCCCCCcEEEEcCCCCCC
Q 025814           80 QLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRKAAGQTWEDP-------TLAEWPENDYRLFCGDLGNEV  150 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~~~~~~~~~~-------~~~~~~~~~~~lfV~nLp~~~  150 (247)
                      ...+++++||+|.+.++|.+|+..  ..+.++.+.+................       .........++|||+|||+++
T Consensus        47 ~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~  126 (198)
T 2yh0_A           47 INQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYL  126 (198)
T ss_dssp             EETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTC
T ss_pred             ecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCC
Confidence            455699999999999999999842  35677777776654432211110000       111123566899999999999


Q ss_pred             cHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccccc
Q 025814          151 NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQER  220 (247)
Q Consensus       151 ~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~  220 (247)
                      ++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|||..|+|+.|+|++++++.+
T Consensus       127 ~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          127 NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             CHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            9999999999999999999999988999999999999999999999999999999999999999987654

>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=99.87  E-value=9.5e-22  Score=138.18  Aligned_cols=83  Identities=36%  Similarity=0.690  Sum_probs=77.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .+.++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            34669999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             ccc
Q 025814          216 KWQ  218 (247)
Q Consensus       216 ~~k  218 (247)
                      +.+
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            764

>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=99.87  E-value=1.2e-21  Score=154.15  Aligned_cols=123  Identities=19%  Similarity=0.337  Sum_probs=105.7

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhc--CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHH
Q 025814           80 QLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSK  157 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L~~  157 (247)
                      ...+++++||+|.+.++|.+|+..  ..+.++.+.+........             ....++|||+|||.++++++|++
T Consensus        47 ~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~~~~~-------------~~~~~~l~v~nlp~~~t~~~l~~  113 (172)
T 2g4b_A           47 INQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQP-------------LPGAHKLFIGGLPNYLNDDQVKE  113 (172)
T ss_dssp             EETTTTEEEEEESSHHHHHHHGGGTTCEETTEECEEECCSSCCC-------------CTTTTCEEEECCCTTCCHHHHHH
T ss_pred             ecCCCCEEEEEeCCHHHHHHHHHhCCcEecCceeeecCCcccCC-------------CCCCCEEEEEcCCCcCCHHHHHH
Confidence            345699999999999999999842  356677666654322211             23356899999999999999999


Q ss_pred             HhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          158 AFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       158 ~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|||..++|+.|+|++|
T Consensus       114 ~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          114 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             HHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            9999999999999999889999999999999999999999999999999999999987

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.87  E-value=2.3e-22  Score=144.11  Aligned_cols=79  Identities=18%  Similarity=0.354  Sum_probs=74.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCC--eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCc----eeCCEeEEE
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPS--FNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK----YVGNRPIKL  212 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~--i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~----~i~g~~l~V  212 (247)
                      .+|||+||++++|+++|+++|++||.  |.+|++++|+.||.++|||||+|.+.++|++|++.|||.    .|+||.|.|
T Consensus        10 ~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V   89 (95)
T 2lkz_A           10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV   89 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEE
Confidence            38999999999999999999999995  679999999999999999999999999999999999997    599999999


Q ss_pred             EEccc
Q 025814          213 RKSKW  217 (247)
Q Consensus       213 ~~a~~  217 (247)
                      ++|+.
T Consensus        90 ~~Aks   94 (95)
T 2lkz_A           90 DFAKS   94 (95)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            99864

>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=99.86  E-value=1.2e-21  Score=145.23  Aligned_cols=81  Identities=27%  Similarity=0.504  Sum_probs=75.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      ..+|||+|||+++++++|+++|+.||.|.+|+|++|+  +.++|||||+|.+.++|++||+.|||..|+|+.|+|.++..
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4489999999999999999999999999999999995  55899999999999999999999999999999999999986


Q ss_pred             ccc
Q 025814          218 QER  220 (247)
Q Consensus       218 k~~  220 (247)
                      +..
T Consensus        83 ~~~   85 (115)
T 4f25_A           83 RKE   85 (115)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.86  E-value=1.9e-21  Score=140.16  Aligned_cols=82  Identities=26%  Similarity=0.448  Sum_probs=78.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE--------EEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNM--------AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG  206 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~--------v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~  206 (247)
                      ....++|||+||++++++++|+++|+.||.|.+        +++++++.+|.++|||||+|.+.++|++|++.|||..|+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            566789999999999999999999999999999        999999999999999999999999999999999999999


Q ss_pred             CEeEEEEEcc
Q 025814          207 NRPIKLRKSK  216 (247)
Q Consensus       207 g~~l~V~~a~  216 (247)
                      |+.|+|++++
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999874

>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=99.86  E-value=1.1e-21  Score=153.21  Aligned_cols=136  Identities=18%  Similarity=0.252  Sum_probs=114.5

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      |.+..+....+.....+++++||+|.+.++|..|+.   +..+.++.+.+........             ....++|||
T Consensus        27 G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~-------------~~~~~~l~v   93 (167)
T 1fxl_A           27 GEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSA-------------SIRDANLYV   93 (167)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCG-------------GGTTCEEEE
T ss_pred             CCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCCcc-------------cCCCCcEEE
Confidence            666666666666667788999999999999999875   4567787777765543321             233458999


Q ss_pred             cCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEe--EEEEEc
Q 025814          144 GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRP--IKLRKS  215 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~--l~V~~a  215 (247)
                      +|||.++++++|+++|+.||.|.+++++++..+|.++|||||+|.+.++|.+|++.|||..++|+.  |+|++|
T Consensus        94 ~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A           94 SGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             ESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            999999999999999999999999999999889999999999999999999999999999999975  888765

>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=99.86  E-value=2e-21  Score=135.96  Aligned_cols=82  Identities=32%  Similarity=0.492  Sum_probs=78.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34567999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             cc
Q 025814          215 SK  216 (247)
Q Consensus       215 a~  216 (247)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.86  E-value=3.3e-21  Score=141.41  Aligned_cols=92  Identities=28%  Similarity=0.532  Sum_probs=83.8

Q ss_pred             CCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q 025814          128 DPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN  207 (247)
Q Consensus       128 ~~~~~~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g  207 (247)
                      ...........++|||+|||.++++++|+++|+.||.|.+|.+++++.+|.++|||||+|.+.++|.+|++.|||..|+|
T Consensus        16 ~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g   95 (108)
T 2jrs_A           16 ANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG   95 (108)
T ss_dssp             CCSSCCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSS
T ss_pred             ccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            33334446677899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeEEEEEccccc
Q 025814          208 RPIKLRKSKWQE  219 (247)
Q Consensus       208 ~~l~V~~a~~k~  219 (247)
                      +.|+|++++.+.
T Consensus        96 ~~l~V~~a~~k~  107 (108)
T 2jrs_A           96 RPMKVGHVTERT  107 (108)
T ss_dssp             SCCEEECSCSSC
T ss_pred             EEEEEEEcccCC
Confidence            999999997653

>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=99.86  E-value=2.5e-22  Score=142.39  Aligned_cols=81  Identities=15%  Similarity=0.245  Sum_probs=73.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCC--CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFP--SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G--~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      .+|||+||++++++++|+++|+.||  .|.++++++|+.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|.++.
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            3799999999999999999999999  99999999999999999999999999999999999999999999999999987


Q ss_pred             ccc
Q 025814          217 WQE  219 (247)
Q Consensus       217 ~k~  219 (247)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            654

>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=99.86  E-value=2.3e-21  Score=139.00  Aligned_cols=84  Identities=24%  Similarity=0.393  Sum_probs=79.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||.++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|++++.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cccc
Q 025814          218 QERT  221 (247)
Q Consensus       218 k~~~  221 (247)
                      +...
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            7644

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=4.2e-21  Score=139.32  Aligned_cols=86  Identities=23%  Similarity=0.375  Sum_probs=81.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++||..|||..|+|+.|+|++
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            45567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        92 a~~~~~   97 (103)
T 2cq0_A           92 AKPSTN   97 (103)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.86  E-value=2.2e-22  Score=145.58  Aligned_cols=83  Identities=25%  Similarity=0.276  Sum_probs=79.0

Q ss_pred             CcEEEEcCCCC------CCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC-EeE
Q 025814          138 DYRLFCGDLGN------EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN-RPI  210 (247)
Q Consensus       138 ~~~lfV~nLp~------~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g-~~l  210 (247)
                      +++|||+|||+      ++++++|+++|++||.|.+|+|++|+.||.++|||||+|.+.++|++||+.|||..|+| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            56899999999      99999999999999999999999999999999999999999999999999999999999 999


Q ss_pred             EEEEcccccc
Q 025814          211 KLRKSKWQER  220 (247)
Q Consensus       211 ~V~~a~~k~~  220 (247)
                      +|.++.++++
T Consensus        86 ~V~~a~~~~~   95 (100)
T 3ns6_A           86 FLYTMKDVER   95 (100)
T ss_dssp             EEEESHHHHH
T ss_pred             EEEECchhhh
Confidence            9999976543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=5.3e-21  Score=136.35  Aligned_cols=82  Identities=22%  Similarity=0.356  Sum_probs=78.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.+++++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
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            45567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q 025814          215 SK  216 (247)
Q Consensus       215 a~  216 (247)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=2.7e-21  Score=138.14  Aligned_cols=85  Identities=27%  Similarity=0.539  Sum_probs=80.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+|||.++++++|+++|+.||.|.+|.+++++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            45569999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          216 KWQER  220 (247)
Q Consensus       216 ~~k~~  220 (247)
                      +.+..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=8.3e-21  Score=137.00  Aligned_cols=85  Identities=20%  Similarity=0.327  Sum_probs=79.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.|+.++ +|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++++..
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            987653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.86  E-value=7.3e-21  Score=140.79  Aligned_cols=86  Identities=36%  Similarity=0.672  Sum_probs=81.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+||++++++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|++||+.|||..|+|+.|+|++
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            45677999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        92 a~~~~~   97 (115)
T 2dgo_A           92 ATRKPP   97 (115)
T ss_dssp             SSCCCC
T ss_pred             ccCCCC
Confidence            987654

>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=99.86  E-value=5e-21  Score=141.75  Aligned_cols=86  Identities=31%  Similarity=0.461  Sum_probs=81.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|++||+.|||..|+|+.|+|++
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            34567999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus       102 a~~~~~  107 (115)
T 2cpz_A          102 KRSKND  107 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCc
Confidence            987654

>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=99.86  E-value=3.1e-21  Score=138.93  Aligned_cols=86  Identities=24%  Similarity=0.397  Sum_probs=81.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
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            44567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            987653

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3e-21  Score=139.76  Aligned_cols=86  Identities=30%  Similarity=0.438  Sum_probs=81.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
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 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            45667999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        89 a~~~~~   94 (102)
T 2cqb_A           89 AKPMRI   94 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=4.1e-21  Score=138.38  Aligned_cols=85  Identities=15%  Similarity=0.429  Sum_probs=79.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++||+ |||..|+|+.|+|++
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            4456799999999999999999999999999999999999999999999999999999999997 999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        86 a~~~~~   91 (99)
T 2dgs_A           86 AEPRDS   91 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCCcc
Confidence            987654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=7.7e-21  Score=135.72  Aligned_cols=83  Identities=22%  Similarity=0.368  Sum_probs=78.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.+++++.+|.++|||||+|.+.++|++|+..|||..|+|+.|+|++
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            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 025814          215 SKW  217 (247)
Q Consensus       215 a~~  217 (247)
                      ++.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            863

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=2.6e-21  Score=138.56  Aligned_cols=85  Identities=35%  Similarity=0.626  Sum_probs=80.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEE-EEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMA-KVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v-~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ...++|||+|||+++++++|+++|+.||.|.++ +|++++.+|.++|||||+|.+.++|++|+..|||..|+|+.|+|++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345699999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            987654

>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=99.85  E-value=1.4e-21  Score=151.45  Aligned_cols=131  Identities=18%  Similarity=0.328  Sum_probs=103.4

Q ss_pred             CCCceeeCccCHHHHHHHH----hcCccchhhhhhcccccccccCCC---CCCCCCCCCCCCCcEEEEcCCCCCCcHHHH
Q 025814           83 QRDAQTITPEALESVKAAL----ASSDIEHKAETKKKSIPRKAAGQT---WEDPTLAEWPENDYRLFCGDLGNEVNDDVL  155 (247)
Q Consensus        83 ~~~~~~v~~~~~~~a~~al----~~~~~~~~~~~~~~~~~r~~~~~~---~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L  155 (247)
                      -+|..++.+.+.+.|.+++    ++..+++ .+.......+......   .............++|||+|||+++++++|
T Consensus        12 l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l   90 (150)
T 2i2y_A           12 LKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTEL   90 (150)
T ss_dssp             SCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHHH
T ss_pred             ccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHH
Confidence            3677788888888888887    5667777 6666655443221111   111112223456789999999999999999


Q ss_pred             HHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          156 SKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       156 ~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      +++|+.||.|.+|+|+++     ++|||||+|.+.++|.+|+..|||..|+|+.|+|++++++.
T Consensus        91 ~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           91 ERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            999999999999999876     58999999999999999999999999999999999998764

>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=99.85  E-value=5.1e-21  Score=139.28  Aligned_cols=86  Identities=24%  Similarity=0.457  Sum_probs=81.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++|+..|||..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45567999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+.+
T Consensus        92 a~~~~~   97 (105)
T 1x5u_A           92 ASAHNK   97 (105)
T ss_dssp             TTTTSC
T ss_pred             CCCCCc
Confidence            987654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=4.8e-21  Score=137.68  Aligned_cols=85  Identities=21%  Similarity=0.443  Sum_probs=78.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCC---CCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKR---TGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~---tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      .+.++|||+|||+++++++|+++|+.||.|.+|.|++++.   |+.++|||||+|.+.++|++|+..|||..|+|+.|+|
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            3456899999999999999999999999999999999876   6699999999999999999999999999999999999


Q ss_pred             EEcccccc
Q 025814          213 RKSKWQER  220 (247)
Q Consensus       213 ~~a~~k~~  220 (247)
                      ++++.+..
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99986653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=4.4e-21  Score=139.88  Aligned_cols=85  Identities=20%  Similarity=0.391  Sum_probs=80.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++|+..|||..|+|+.|+|++
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            97653

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.85  E-value=7.9e-21  Score=141.24  Aligned_cols=82  Identities=37%  Similarity=0.524  Sum_probs=77.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+||++++++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            45567999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q 025814          215 SK  216 (247)
Q Consensus       215 a~  216 (247)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>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=99.85  E-value=9.1e-21  Score=139.28  Aligned_cols=86  Identities=17%  Similarity=0.329  Sum_probs=81.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhC------CceeCCE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN------GKYVGNR  208 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~------g~~i~g~  208 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++||..||      |..|+|+
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            4556799999999999999999999999999999999999999999999999999999999999999      9999999


Q ss_pred             eEEEEEcccccc
Q 025814          209 PIKLRKSKWQER  220 (247)
Q Consensus       209 ~l~V~~a~~k~~  220 (247)
                      .|+|+++..+..
T Consensus        92 ~l~v~~a~~~~~  103 (111)
T 1x4h_A           92 QLKVDLAVTRDE  103 (111)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCcc
Confidence            999999987654

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.85  E-value=1.6e-20  Score=136.24  Aligned_cols=84  Identities=23%  Similarity=0.484  Sum_probs=78.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.|| |.+|+|++++.+|.++|||||+|.+.++|++|| .|||..|+|+.|+|.+
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            44567999999999999999999999997 999999999999999999999999999999999 9999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        90 a~~~~~   95 (103)
T 2dng_A           90 AEGRKQ   95 (103)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            987654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.9e-21  Score=139.79  Aligned_cols=78  Identities=9%  Similarity=0.081  Sum_probs=73.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|++|+. |.++|||||+|.+.++|.+||. +||..|+|+.|.|.++.
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            456899999999999999999999999999999999986 9999999999999999999997 99999999999999865

>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=99.85  E-value=7.3e-21  Score=150.36  Aligned_cols=125  Identities=19%  Similarity=0.259  Sum_probs=104.6

Q ss_pred             hhhhcCCCceeeCccCHHHHHHHHhc--CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHH
Q 025814           78 AQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVL  155 (247)
Q Consensus        78 ~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L  155 (247)
                      .....+++++||+|.+.++|.+|++.  ..+.++.+.+.....+...           .....++|||+|||.++++++|
T Consensus        48 ~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~~~~-----------~~~~~~~l~v~nlp~~~t~~~l  116 (175)
T 1fje_B           48 VRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSK-----------KVRAARTLLAKNLSFNITEDEL  116 (175)
T ss_dssp             EEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCSSCS-----------TTGGGGEEEEESCCSSCCHHHH
T ss_pred             CCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCCcccc-----------ccccCCEEEEeCCCCCCCHHHH
Confidence            34566799999999999999999853  3567777777665443221           1335669999999999999999


Q ss_pred             HHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          156 SKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       156 ~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      +++|+.||.|..+     ..+|.++|||||+|.+.++|.+|+..|||..|+|+.|+|++++++
T Consensus       117 ~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          117 KEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            9999999988765     458999999999999999999999999999999999999999865

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=4.3e-21  Score=139.29  Aligned_cols=86  Identities=19%  Similarity=0.395  Sum_probs=80.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++||..|||..|+|+.|+|++
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            44567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        90 a~~~~~   95 (103)
T 2dnm_A           90 ARYGRR   95 (103)
T ss_dssp             CSSCCS
T ss_pred             CCcCCC
Confidence            986543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=5e-21  Score=138.63  Aligned_cols=86  Identities=30%  Similarity=0.597  Sum_probs=81.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.|++++.++.++|||||+|.+.++|.+|++.|||..|+|+.|+|++
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            45667999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            987654

>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=99.84  E-value=1.6e-20  Score=136.63  Aligned_cols=85  Identities=20%  Similarity=0.414  Sum_probs=79.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC---EeEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN---RPIK  211 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g---~~l~  211 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++ +|.++|||||+|.+.++|++||+.|||..+.|   +.|+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            4456799999999999999999999999999999999997 89999999999999999999999999999988   9999


Q ss_pred             EEEcccccc
Q 025814          212 LRKSKWQER  220 (247)
Q Consensus       212 V~~a~~k~~  220 (247)
                      |++++.+..
T Consensus        91 V~~a~~~~~   99 (105)
T 2dnh_A           91 VKFADTDKE   99 (105)
T ss_dssp             EEESCSSCC
T ss_pred             EEECccCcc
Confidence            999987653

>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=99.84  E-value=8.5e-21  Score=139.33  Aligned_cols=85  Identities=20%  Similarity=0.375  Sum_probs=80.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.++.++.+|.++|||||+|.+.++|++|+..|||..|+|+.|+|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            98654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.84  E-value=1.5e-20  Score=143.67  Aligned_cols=86  Identities=24%  Similarity=0.440  Sum_probs=81.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||++++++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|.+||+.|||..|+|+.|+|++
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+.+
T Consensus       119 a~~~~~  124 (139)
T 1u6f_A          119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1e-20  Score=139.50  Aligned_cols=86  Identities=23%  Similarity=0.368  Sum_probs=80.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCee--------EEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFN--------MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG  206 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~--------~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~  206 (247)
                      ....++|||+|||+++++++|+++|+.||.|.        .|+|++++.+|.++|||||+|.+.++|++||+.|||..|+
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            45567999999999999999999999999999        6999999999999999999999999999999999999999


Q ss_pred             CEeEEEEEcccccc
Q 025814          207 NRPIKLRKSKWQER  220 (247)
Q Consensus       207 g~~l~V~~a~~k~~  220 (247)
                      |+.|+|++++.+..
T Consensus        92 g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           92 GSKLKVSLARKKPP  105 (113)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CCEEEEEECCCCCC
Confidence            99999999987654

>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=99.84  E-value=2.3e-20  Score=131.22  Aligned_cols=80  Identities=24%  Similarity=0.489  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|++|+ .+++..|+|+.|+|++
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 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVL-DQKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHH-HSSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHH-HhCCCEECCEEEEEEe
Confidence            455679999999999999999999999999999999999999999999999999999999999 5688999999999987


Q ss_pred             c
Q 025814          215 S  215 (247)
Q Consensus       215 a  215 (247)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.84  E-value=1.3e-20  Score=132.95  Aligned_cols=80  Identities=20%  Similarity=0.418  Sum_probs=76.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|++|+ .|||..++|+.|+|++++.
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            348999999999999999999999999999999999989999999999999999999999 9999999999999999875


Q ss_pred             c
Q 025814          218 Q  218 (247)
Q Consensus       218 k  218 (247)
                      +
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=1.3e-20  Score=137.53  Aligned_cols=86  Identities=16%  Similarity=0.366  Sum_probs=80.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEec-CCCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRD-KRTGKTKGYGFISFANPSDIAAALKEM-NGKYVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~-~~tg~~kg~~FV~f~~~~~a~~Al~~l-~g~~i~g~~l~V  212 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|+++ +.+|.++|||||+|.+.++|++||..| ||..|+|+.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            445679999999999999999999999999999999999 789999999999999999999999999 999999999999


Q ss_pred             EEcccccc
Q 025814          213 RKSKWQER  220 (247)
Q Consensus       213 ~~a~~k~~  220 (247)
                      ++++.+..
T Consensus        92 ~~a~~~~~   99 (107)
T 2cph_A           92 EWADSEVT   99 (107)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99987653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1e-20  Score=136.19  Aligned_cols=85  Identities=26%  Similarity=0.470  Sum_probs=79.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCee-EEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEe----
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFN-MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRP----  209 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~-~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~----  209 (247)
                      ....++|||+|||+++++++|+++|+.||.|. +|+|++++.+|.++|||||+|.+.++|++|++.|||..|+|+.    
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            34567999999999999999999999999999 9999999999999999999999999999999999999999999    


Q ss_pred             EEEEEccccc
Q 025814          210 IKLRKSKWQE  219 (247)
Q Consensus       210 l~V~~a~~k~  219 (247)
                      |+|.+++...
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999997654

>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=99.84  E-value=7.1e-21  Score=138.76  Aligned_cols=86  Identities=22%  Similarity=0.445  Sum_probs=80.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee---CCEeEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV---GNRPIK  211 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i---~g~~l~  211 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|++|++.|||..+   +|+.|+
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            45677999999999999999999999999999999999999999999999999999999999999999987   899999


Q ss_pred             EEEcccccc
Q 025814          212 LRKSKWQER  220 (247)
Q Consensus       212 V~~a~~k~~  220 (247)
                      |++++.+.+
T Consensus        90 v~~a~~~~~   98 (106)
T 2dgp_A           90 VKPADSESR   98 (106)
T ss_dssp             EEECCCCSC
T ss_pred             EEECCcccc
Confidence            999987654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.9e-20  Score=135.81  Aligned_cols=84  Identities=32%  Similarity=0.643  Sum_probs=78.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.|+.+  +|.++|||||+|.+.++|++|+..|||..|+|+.|+|++
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 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            445679999999999999999999999999999999998  899999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        90 a~~~~~   95 (103)
T 2d9p_A           90 AQRKEE   95 (103)
T ss_dssp             CSSCCC
T ss_pred             eccccc
Confidence            987653

>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=99.84  E-value=1.7e-20  Score=159.55  Aligned_cols=143  Identities=10%  Similarity=0.061  Sum_probs=120.5

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      |.+..+....+.....++|++||.|.+.+++.+|+.   +..+.++.+.+...........          ....++|||
T Consensus       120 G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~----------~~~~~~l~v  189 (284)
T 3smz_A          120 GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPA----------LLHSRCLCV  189 (284)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCCTT----------TTSCSEEEE
T ss_pred             CCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCcc----------cCCccEEEE
Confidence            556555555556667789999999999999998874   5578888888877655433221          345669999


Q ss_pred             cCCCCCC-cHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccccc
Q 025814          144 GDLGNEV-NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQER  220 (247)
Q Consensus       144 ~nLp~~~-~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~  220 (247)
                      +|||+++ ++++|+++|+.||.|.++.|+.+. +|.++|||||+|.+.++|.+|+..|||..|+|+.|+|.++.++..
T Consensus       190 ~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          190 DRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             ECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             ecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            9999995 999999999999999999999996 899999999999999999999999999999999999999987764

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.84  E-value=1.1e-20  Score=138.72  Aligned_cols=87  Identities=18%  Similarity=0.384  Sum_probs=76.6

Q ss_pred             CCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       133 ~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      +...+.++|||+||++++++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|.+||..+ |..|+|+.|+|
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V   98 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDP   98 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEE
Confidence            33566789999999999999999999999999999999999999999999999999999999999875 59999999999


Q ss_pred             EEcccccc
Q 025814          213 RKSKWQER  220 (247)
Q Consensus       213 ~~a~~k~~  220 (247)
                      +++..+..
T Consensus        99 ~~a~~~~~  106 (109)
T 2rs2_A           99 KVAFPRRA  106 (109)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99987653

>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=99.84  E-value=1.3e-20  Score=136.95  Aligned_cols=83  Identities=20%  Similarity=0.485  Sum_probs=78.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRT-GKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~t-g~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ...++|||+|||+++++++|+++|+.|| |.+|.|++++.+ |.++|||||+|.+.++|++|| .|||..|+|+.|+|++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4567999999999999999999999999 999999999887 999999999999999999999 9999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        91 a~~~~~   96 (104)
T 1wi8_A           91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987654

>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=99.84  E-value=1.1e-20  Score=140.34  Aligned_cols=85  Identities=32%  Similarity=0.606  Sum_probs=79.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.|+.++ +|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456699999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            987654

>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=99.84  E-value=3.1e-20  Score=135.58  Aligned_cols=81  Identities=25%  Similarity=0.425  Sum_probs=77.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++ +|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        26 ~~~~~~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           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4557799999999999999999999999999999999998 999999999999999999999999999999999999998


Q ss_pred             cc
Q 025814          215 SK  216 (247)
Q Consensus       215 a~  216 (247)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.83  E-value=7.3e-21  Score=140.64  Aligned_cols=82  Identities=18%  Similarity=0.415  Sum_probs=77.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+||++++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++|| .|||..|+|+.|+|++++
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            3568999999999999999999999999999999999999999999999999999999999 999999999999999987


Q ss_pred             ccc
Q 025814          217 WQE  219 (247)
Q Consensus       217 ~k~  219 (247)
                      .+.
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            543

>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=99.83  E-value=1.5e-20  Score=132.28  Aligned_cols=81  Identities=23%  Similarity=0.443  Sum_probs=76.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCC-cceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGK-TKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~-~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      .++|||+|||.++++++|+++|+.||.|.++.++.++.++. ++|||||+|.+.++|++|++.|||..++|+.|+|+++.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   83 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL   83 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECC
Confidence            45899999999999999999999999999999999987766 89999999999999999999999999999999999987


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      +.
T Consensus        84 ~~   85 (88)
T 4a8x_A           84 AP   85 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=1.7e-20  Score=136.57  Aligned_cols=85  Identities=21%  Similarity=0.423  Sum_probs=80.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++||.. ||..|+|+.|+|++
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            45667999999999999999999999999999999999999999999999999999999999988 99999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      +..+..
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            987654

>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=99.83  E-value=1.6e-20  Score=134.89  Aligned_cols=84  Identities=15%  Similarity=0.234  Sum_probs=78.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34567899999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      ++.+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8754

>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=99.83  E-value=9.5e-21  Score=137.56  Aligned_cols=84  Identities=24%  Similarity=0.498  Sum_probs=79.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|+++..
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            45899999999999999999999999999999999998999999999999999999999999999999999999999987


Q ss_pred             cccc
Q 025814          218 QERT  221 (247)
Q Consensus       218 k~~~  221 (247)
                      +...
T Consensus        88 ~~~~   91 (104)
T 1p1t_A           88 EKNK   91 (104)
T ss_dssp             TTHH
T ss_pred             ccch
Confidence            6543

>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=99.83  E-value=9.4e-21  Score=143.35  Aligned_cols=84  Identities=23%  Similarity=0.358  Sum_probs=79.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|+|++++.+|.++|||||+|.+.++|++||+.|||..|+|+.|+|++
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      ++.+
T Consensus       123 a~~~  126 (129)
T 2kxn_B          123 SITK  126 (129)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            8764

>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=99.83  E-value=2.1e-20  Score=133.52  Aligned_cols=81  Identities=27%  Similarity=0.575  Sum_probs=76.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|+|++++. |.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            44567999999999999999999999999999999999974 99999999999999999999999999999999999998


Q ss_pred             cc
Q 025814          215 SK  216 (247)
Q Consensus       215 a~  216 (247)
                      ++
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=3.4e-20  Score=137.41  Aligned_cols=84  Identities=27%  Similarity=0.458  Sum_probs=78.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|+|++++.++.++|||||+|.+.++|++||+.||+ .|+|+.|+|++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            45567999999999999999999999999999999999999999999999999999999999999998 89999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +..+.
T Consensus        93 a~~~~   97 (116)
T 2cqd_A           93 AYLGA   97 (116)
T ss_dssp             STTTC
T ss_pred             cccCC
Confidence            97543

>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=99.83  E-value=3.8e-21  Score=139.00  Aligned_cols=83  Identities=22%  Similarity=0.492  Sum_probs=75.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecC-CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDK-RTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~-~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ....++|||+||++++++++|+++|+.|| |.+|+|++++ .+|.++|||||+|.+.++|.+|| .|||..|+|+.|+|+
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            45567999999999999999999999999 9999999998 68999999999999999999999 999999999999999


Q ss_pred             Eccccc
Q 025814          214 KSKWQE  219 (247)
Q Consensus       214 ~a~~k~  219 (247)
                      +++.+.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            998754

>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=99.83  E-value=8.7e-20  Score=132.33  Aligned_cols=85  Identities=24%  Similarity=0.429  Sum_probs=77.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|+|++++.  .++|||||+|.+.++|++|+..|||..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45567999999999999999999999999999999999853  3899999999999999999999999999999999999


Q ss_pred             ccccccc
Q 025814          215 SKWQERT  221 (247)
Q Consensus       215 a~~k~~~  221 (247)
                      ++.+...
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
Confidence            9876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=5.6e-20  Score=135.73  Aligned_cols=83  Identities=23%  Similarity=0.394  Sum_probs=77.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||++++++++|+++|+.||.|.+|.|++++ +|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            4456799999999999999999999999999999999997 699999999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      ++..
T Consensus        91 a~~~   94 (114)
T 2do0_A           91 DERA   94 (114)
T ss_dssp             CSCC
T ss_pred             cccC
Confidence            8754

>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=99.83  E-value=2.3e-20  Score=133.84  Aligned_cols=82  Identities=12%  Similarity=0.184  Sum_probs=76.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLS----KAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPI  210 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~----~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l  210 (247)
                      ..+.++|||+|||+++++++|+    ++|+.||.|.+|+|+.|+.+   +|||||+|.+.++|++|++.|||..|+|+.|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            3456799999999999999999    99999999999999999765   8999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 025814          211 KLRKSKWQE  219 (247)
Q Consensus       211 ~V~~a~~k~  219 (247)
                      +|++++.+.
T Consensus        83 ~V~~a~~~~   91 (96)
T 2dgx_A           83 LVSLATGAS   91 (96)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEcCCCC
Confidence            999997654

>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=99.83  E-value=2.4e-20  Score=146.90  Aligned_cols=137  Identities=18%  Similarity=0.282  Sum_probs=106.5

Q ss_pred             CCccccccccchhhh--cCCCceeeCccCHHHHHHHHhc---Cccc---hhhhhhcccccccccCCCCCCCCCCCCCCCC
Q 025814           67 APVYSLPQYHQAQQL--FQRDAQTITPEALESVKAALAS---SDIE---HKAETKKKSIPRKAAGQTWEDPTLAEWPEND  138 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~--~~~~~~~v~~~~~~~a~~al~~---~~~~---~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~  138 (247)
                      |.+..+....+....  .+++++||+|.+.++|.+|+..   ..+.   ++.+..........            .....
T Consensus        28 G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~   95 (175)
T 3nmr_A           28 GAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKN------------NAVED   95 (175)
T ss_dssp             SCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCC------------SCGGG
T ss_pred             CCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEcccccccc------------ccCCC
Confidence            666666555555544  7899999999999999999863   2222   22222222211111            12345


Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---CEeEEEEEc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG---NRPIKLRKS  215 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~---g~~l~V~~a  215 (247)
                      ++|||+|||+.+++++|+++|+.||.|.++.++++. +|.++|||||+|.+.++|.+|++.|||..+.   |+.|+|.++
T Consensus        96 ~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A           96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             CeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            689999999999999999999999999999999995 6999999999999999999999999998776   499999987


Q ss_pred             c
Q 025814          216 K  216 (247)
Q Consensus       216 ~  216 (247)
                      .
T Consensus       175 d  175 (175)
T 3nmr_A          175 D  175 (175)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=1.1e-20  Score=137.33  Aligned_cols=84  Identities=37%  Similarity=0.680  Sum_probs=78.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhcc-CCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCce-eCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSR-FPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKY-VGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~-~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~-i~g~~l~V  212 (247)
                      ....++|||+|||+++++++|+++|+. ||.|.+|.|++++ +|.++|||||+|.+.++|.+||+.|||.. |+|+.|+|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            345679999999999999999999999 9999999999998 99999999999999999999999999999 99999999


Q ss_pred             EEccccc
Q 025814          213 RKSKWQE  219 (247)
Q Consensus       213 ~~a~~k~  219 (247)
                      +++..+.
T Consensus        85 ~~a~~~~   91 (104)
T 2dhg_A           85 SVAIPKA   91 (104)
T ss_dssp             CBCCCCC
T ss_pred             EEccCCC
Confidence            9987654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.83  E-value=4.2e-21  Score=145.59  Aligned_cols=86  Identities=17%  Similarity=0.341  Sum_probs=79.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE--EEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCc----eeCCE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNM--AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK----YVGNR  208 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~--v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~----~i~g~  208 (247)
                      ....++|||+||++++++++|+++|+.||.|..  |+|++|+.+|.++|||||+|.+. +|.+|+..|||.    .|+|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            345679999999999999999999999999976  99999999999999999999999 999999999999    99999


Q ss_pred             eEEEEEccccccc
Q 025814          209 PIKLRKSKWQERT  221 (247)
Q Consensus       209 ~l~V~~a~~k~~~  221 (247)
                      .|+|++++++.+.
T Consensus        99 ~l~V~~a~~~~~~  111 (131)
T 2m2b_A           99 TINVEFAKGSKRD  111 (131)
T ss_dssp             CCCCEECCCSCCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999876543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.83  E-value=4.3e-21  Score=146.33  Aligned_cols=86  Identities=20%  Similarity=0.433  Sum_probs=80.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++||..|||..|+|+.|+|++
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34466899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus       124 a~~~~~  129 (135)
T 2lea_A          124 ARYGRP  129 (135)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            986543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=3.8e-21  Score=134.64  Aligned_cols=81  Identities=26%  Similarity=0.366  Sum_probs=76.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|.++
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            45569999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             c
Q 025814          216 K  216 (247)
Q Consensus       216 ~  216 (247)
                      +
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.83  E-value=1.4e-20  Score=134.43  Aligned_cols=81  Identities=16%  Similarity=0.275  Sum_probs=76.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            34579999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             c
Q 025814          216 K  216 (247)
Q Consensus       216 ~  216 (247)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.83  E-value=7.6e-21  Score=157.48  Aligned_cols=85  Identities=13%  Similarity=0.208  Sum_probs=79.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCC--CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFP--SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G--~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..++|||+||++++++++|+++|+.||  .|.+|+|++|+.+|+++|||||+|.+.++|++||+.|||..|+|+.|+|.+
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            566899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccc
Q 025814          215 SKWQERT  221 (247)
Q Consensus       215 a~~k~~~  221 (247)
                      ++.....
T Consensus       147 a~~~~~~  153 (229)
T 3q2s_C          147 VNKQFLS  153 (229)
T ss_dssp             CCHHHHH
T ss_pred             CCCCccc
Confidence            9866543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=7.6e-20  Score=129.66  Aligned_cols=82  Identities=22%  Similarity=0.331  Sum_probs=77.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.| .|.+|+|+++ .+|.++|||||+|.+.++|++||. |||..|+|+.|+|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            4456799999999999999999999999 9999999999 789999999999999999999998 999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +..+.
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98764

>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=99.83  E-value=3.3e-20  Score=158.40  Aligned_cols=143  Identities=19%  Similarity=0.233  Sum_probs=109.4

Q ss_pred             CccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEc
Q 025814           68 PVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCG  144 (247)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~  144 (247)
                      .+..+....+.. ..+++++||.|.+.+++..|+.   +..+.++.+.+....++......      .......++|||+
T Consensus       144 ~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~------~~~~~~~~~l~v~  216 (292)
T 2ghp_A          144 VALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRT------DSATLEGREIMIR  216 (292)
T ss_dssp             CCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC---------------CCTTTEEEEE
T ss_pred             CeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccc------cccCCCCceEEEE
Confidence            444444433333 4579999999999999998876   45788888887766544332211      0113456799999


Q ss_pred             CCCCC-CcHHHHHHHhccCCCeeEEEEEecCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          145 DLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKR-TGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       145 nLp~~-~~e~~L~~~F~~~G~i~~v~i~~~~~-tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      |||+. +++++|+++|+.||.|..|+|+++.. ||.++|||||+|.+.++|.+|+ .|||..|+|+.|+|.++.+|
T Consensus       217 nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          217 NLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             EECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             CCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            99999 99999999999999999999999875 5999999999999999999999 99999999999999999875

>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=99.83  E-value=7.9e-20  Score=132.54  Aligned_cols=83  Identities=23%  Similarity=0.413  Sum_probs=76.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++.  .++|||||+|.+.++|++|+..|||..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            45567999999999999999999999999999999999853  3689999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus        90 a~~~~   94 (103)
T 2cqi_A           90 ATTPS   94 (103)
T ss_dssp             CCCTT
T ss_pred             CCCCc
Confidence            98754

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.83  E-value=3e-20  Score=131.92  Aligned_cols=84  Identities=23%  Similarity=0.374  Sum_probs=78.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.++.|+++  +|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345679999999999999999999999999999999985  899999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++....
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            987543

>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=99.83  E-value=1.3e-20  Score=141.41  Aligned_cols=85  Identities=24%  Similarity=0.351  Sum_probs=77.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.++.++.+..+|.++|||||+|.+.++|++||. |||..|+|+.|+|.+
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            4456799999999999999999999999999987777777899999999999999999999998 999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      +..+..
T Consensus       101 a~~~~~  106 (124)
T 1wel_A          101 ITKKGM  106 (124)
T ss_dssp             ECHHHH
T ss_pred             CCHHHH
Confidence            976553

>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=99.82  E-value=5.9e-20  Score=144.61  Aligned_cols=86  Identities=20%  Similarity=0.367  Sum_probs=80.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|+|+.|.|.+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      +..+..
T Consensus       149 a~~~~~  154 (165)
T 1rk8_A          149 CFVKGP  154 (165)
T ss_dssp             SEECC-
T ss_pred             ecCCCC
Confidence            986653

>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=99.82  E-value=1.2e-19  Score=131.52  Aligned_cols=84  Identities=20%  Similarity=0.329  Sum_probs=78.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++||.  ++..|+|+.|+|++
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            4456789999999999999999999999999999999999999999999999999999999997  58899999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      +..+..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            987654

>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=99.82  E-value=2.7e-20  Score=139.87  Aligned_cols=86  Identities=20%  Similarity=0.383  Sum_probs=80.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||++++++++|+++|+.||.|.+|.|+.++.+|.++|||||+|.+.++|++||+.|||..|+|+.|+|.+
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            44567999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      +..+..
T Consensus        99 a~~~~~  104 (126)
T 3ex7_B           99 CFVRGP  104 (126)
T ss_dssp             SEESSS
T ss_pred             ecCCCC
Confidence            986554

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.82  E-value=2.4e-21  Score=140.15  Aligned_cols=93  Identities=30%  Similarity=0.432  Sum_probs=81.7

Q ss_pred             CCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 025814          126 WEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV  205 (247)
Q Consensus       126 ~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i  205 (247)
                      +..+.........++|||+|||+++++++|+++|+.||.|.. .++.++.+|.++|||||+|.+.++|++||+ |||..|
T Consensus         5 ~~~p~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~   82 (101)
T 1fj7_A            5 LEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKV   82 (101)
T ss_dssp             CCCSCCSTTCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCB
T ss_pred             CCCCCCcccCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEE
Confidence            444444444667789999999999999999999999999988 677777789999999999999999999998 999999


Q ss_pred             CCEeEEEEEcccccc
Q 025814          206 GNRPIKLRKSKWQER  220 (247)
Q Consensus       206 ~g~~l~V~~a~~k~~  220 (247)
                      +|+.|+|.+++.+..
T Consensus        83 ~g~~l~V~~a~~~~~   97 (101)
T 1fj7_A           83 FGNEIKLEKPKGRDG   97 (101)
T ss_dssp             TTBCCEEECCSCCCC
T ss_pred             CCcEEEEEEcCCCCC
Confidence            999999999987653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.6e-20  Score=136.45  Aligned_cols=81  Identities=12%  Similarity=0.121  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG--KYVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g--~~i~g~~l~V  212 (247)
                      +...++|||+|||+++++++|+++|++||.|.+|+|+++      ||||||+|.+.++|++|++.|++  ..|+|+.|+|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            455679999999999999999999999999999999876      68999999999999999998864  7899999999


Q ss_pred             EEccccccc
Q 025814          213 RKSKWQERT  221 (247)
Q Consensus       213 ~~a~~k~~~  221 (247)
                      .+++.+...
T Consensus        87 ~~A~~~~~~   95 (105)
T 1sjq_A           87 QFSNHKELK   95 (105)
T ss_dssp             CCCSSSSCC
T ss_pred             EEcCCCCCC
Confidence            999876543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.82  E-value=1e-19  Score=136.41  Aligned_cols=84  Identities=24%  Similarity=0.385  Sum_probs=79.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||++++++++|+++|+.||.|.+|+|++++ +|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        32 ~~~~~~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           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4567899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +....
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            97643

>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=99.82  E-value=8.3e-20  Score=142.35  Aligned_cols=85  Identities=18%  Similarity=0.286  Sum_probs=80.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|+.++.++.++|||||+|.+.++|++||..|||..|+|+.|+|++
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus       116 a~~~~  120 (156)
T 1h2v_Z          116 DAGFK  120 (156)
T ss_dssp             ESCCC
T ss_pred             CCCCC
Confidence            98654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=4.1e-20  Score=136.98  Aligned_cols=82  Identities=21%  Similarity=0.472  Sum_probs=77.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++||.. ||..|+|+.|+|+++..
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            46899999999999999999999999999999999999999999999999999999999977 99999999999999987


Q ss_pred             ccc
Q 025814          218 QER  220 (247)
Q Consensus       218 k~~  220 (247)
                      +..
T Consensus       106 ~~~  108 (116)
T 1x4b_A          106 REE  108 (116)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            654

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.82  E-value=9.8e-21  Score=129.37  Aligned_cols=75  Identities=20%  Similarity=0.449  Sum_probs=72.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|++|++ |||..|+|+.|+|++|
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            49999999999999999999999999999999998899999999999999999999996 9999999999999875

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=5.7e-20  Score=134.91  Aligned_cols=82  Identities=22%  Similarity=0.427  Sum_probs=76.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||+.++++++|+++|+.||.|.+|++++++  +.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        26 ~~~~~~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           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4556799999999999999999999999999999999984  45899999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      ++.+
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8765

>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=99.82  E-value=1.4e-20  Score=137.84  Aligned_cols=85  Identities=13%  Similarity=0.200  Sum_probs=78.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCC-eeEEEEE-ecCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCEeEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPS-FNMAKVV-RDKRTGKTKGYGFISFANPSDIAAALKEMN--GKYVGNRPIK  211 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~-i~~v~i~-~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~--g~~i~g~~l~  211 (247)
                      .+.++|||+|||+++++++|+++|+.||. |.+|.++ .++.+|.++|||||+|.+.++|.+|++.||  +..++|+.|+
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            45679999999999999999999999998 9999998 888899999999999999999999999996  5899999999


Q ss_pred             EEEcccccc
Q 025814          212 LRKSKWQER  220 (247)
Q Consensus       212 V~~a~~k~~  220 (247)
                      |++++++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.82  E-value=5.5e-20  Score=137.84  Aligned_cols=81  Identities=26%  Similarity=0.422  Sum_probs=76.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+||++++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|++|| .|||..|+|+.|+|++++.
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            348999999999999999999999999999999999999999999999999999999999 8999999999999999875


Q ss_pred             cc
Q 025814          218 QE  219 (247)
Q Consensus       218 k~  219 (247)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.82  E-value=3.7e-20  Score=136.35  Aligned_cols=84  Identities=13%  Similarity=0.211  Sum_probs=77.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHH---HHhccCCCeeEEEEEecCCCC---CcceEEEEEecCHHHHHHHHHHhCCceeCCEeE
Q 025814          137 NDYRLFCGDLGNEVNDDVLS---KAFSRFPSFNMAKVVRDKRTG---KTKGYGFISFANPSDIAAALKEMNGKYVGNRPI  210 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~---~~F~~~G~i~~v~i~~~~~tg---~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l  210 (247)
                      ..++|||+|||+++++++|+   ++|++||.|.+|.|++++.++   .++|||||+|.+.++|++||+.|||..|+|+.|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   93 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   93 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEE
Confidence            45589999999999999999   999999999999999987654   456999999999999999999999999999999


Q ss_pred             EEEEcccccc
Q 025814          211 KLRKSKWQER  220 (247)
Q Consensus       211 ~V~~a~~k~~  220 (247)
                      +|+++..+..
T Consensus        94 ~V~~a~~k~~  103 (111)
T 2cpi_A           94 KASLGTTKYC  103 (111)
T ss_dssp             EEESCCCCSC
T ss_pred             EEEecccccc
Confidence            9999987764

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.82  E-value=6.2e-20  Score=136.68  Aligned_cols=83  Identities=19%  Similarity=0.261  Sum_probs=77.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCC---eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPS---FNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~---i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      ....++|||+|||+++++++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|++||+ |||..|+|+.|+
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            455679999999999999999999999999   89999999976 9999999999999999999997 999999999999


Q ss_pred             EEEccccc
Q 025814          212 LRKSKWQE  219 (247)
Q Consensus       212 V~~a~~k~  219 (247)
                      |.++..++
T Consensus        92 V~~a~~~~   99 (118)
T 2db1_A           92 VFKSHRTE   99 (118)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99986544

>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=99.82  E-value=2.6e-20  Score=137.78  Aligned_cols=83  Identities=13%  Similarity=0.171  Sum_probs=77.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCe-eEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSF-NMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i-~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ..+.++|||+|||+++++++|+++|+.||.| .+|+|++|+ +|.++|||||+|.+.++|++||.. ||..|+|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            4566799999999999999999999999999 899999998 999999999999999999999966 9999999999999


Q ss_pred             Eccccc
Q 025814          214 KSKWQE  219 (247)
Q Consensus       214 ~a~~k~  219 (247)
                      ++..+.
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            997654

>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=99.81  E-value=6.2e-21  Score=134.96  Aligned_cols=80  Identities=21%  Similarity=0.453  Sum_probs=74.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      ++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.+ |.+|+..|||..++|+.|+|+++..+
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            48999999999999999999999999999999999999999999999999999 99999999999999999999999765


Q ss_pred             c
Q 025814          219 E  219 (247)
Q Consensus       219 ~  219 (247)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=1.6e-20  Score=128.77  Aligned_cols=76  Identities=21%  Similarity=0.480  Sum_probs=73.2

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ++|||+|||+++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|++|++.+| ..++|+.|+|+++
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            379999999999999999999999999999999999899999999999999999999999999 9999999999886

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.81  E-value=1.3e-19  Score=138.26  Aligned_cols=81  Identities=31%  Similarity=0.485  Sum_probs=76.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||.++++++|+++|+.||.|.+++|++++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45677999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             c
Q 025814          215 S  215 (247)
Q Consensus       215 a  215 (247)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

>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=99.81  E-value=1.8e-19  Score=153.23  Aligned_cols=120  Identities=21%  Similarity=0.285  Sum_probs=106.8

Q ss_pred             hcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHH
Q 025814           81 LFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSK  157 (247)
Q Consensus        81 ~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L~~  157 (247)
                      ..+++++||.|.+.++|..|+.   +..+.++.+.+..                   ....++|||+|||+++++++|++
T Consensus        54 ~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~-------------------~~~~~~l~v~nlp~~~t~~~l~~  114 (284)
T 3smz_A           54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL-------------------QPTDALLCVANLPPSLTQQQFEE  114 (284)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE-------------------CCCSCEEEEESCCTTCCHHHHHH
T ss_pred             ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEe-------------------cCCCCEEEEcCCCCcCCHHHHHH
Confidence            4568999999999999999884   4567777766643                   23445999999999999999999


Q ss_pred             HhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          158 AFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       158 ~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      +|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.++..+.
T Consensus       115 ~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGG
T ss_pred             HHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            99999999999999999999999999999999999999999999999999999999997654

>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=99.81  E-value=7.7e-20  Score=132.68  Aligned_cols=83  Identities=14%  Similarity=0.157  Sum_probs=75.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||. .+|+|++|+ +|+++|||||+|.+.++|++|| .+|+..|+|+.|+|..
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEE
Confidence            455679999999999999999999999994 599999997 8999999999999999999999 6899999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      +.....
T Consensus        89 ~~~~~~   94 (102)
T 1wez_A           89 NSTAGT   94 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            876553

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.81  E-value=6.9e-20  Score=133.53  Aligned_cols=83  Identities=22%  Similarity=0.340  Sum_probs=75.8

Q ss_pred             CCCcEEEEcCCCCCC------cHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCE-
Q 025814          136 ENDYRLFCGDLGNEV------NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNR-  208 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~------~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~-  208 (247)
                      ...++|||+|||+.+      ++++|+++|+.||.|.+|.|++  .+|.++|||||+|.+.++|.+|+..|||..|+|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            345699999999999      7899999999999999999883  5899999999999999999999999999999998 


Q ss_pred             eEEEEEcccccc
Q 025814          209 PIKLRKSKWQER  220 (247)
Q Consensus       209 ~l~V~~a~~k~~  220 (247)
                      .|+|.++...++
T Consensus        91 ~l~V~~a~~~~k  102 (105)
T 2nlw_A           91 TFRVNLFTDFDK  102 (105)
T ss_dssp             EEEEECSCCCCC
T ss_pred             eEEEEEcchHhh
Confidence            999999876543

>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=99.81  E-value=2.7e-19  Score=131.06  Aligned_cols=83  Identities=14%  Similarity=0.329  Sum_probs=75.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|..+   +.++|||||+|.+.++|++||+.|||..|+|+.|+|++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            445679999999999999999999999999999999654   56899999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+.+
T Consensus        96 a~~~~~  101 (109)
T 1x4a_A           96 PRSGRG  101 (109)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            986543

>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=99.81  E-value=2.7e-19  Score=132.09  Aligned_cols=83  Identities=19%  Similarity=0.419  Sum_probs=77.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--------C
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV--------G  206 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i--------~  206 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|+|++++ +|.++|||||+|.+.++|++|+..|||..|        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3456799999999999999999999999999999999998 999999999999999999999999999999        5


Q ss_pred             CEeEEEEEcccc
Q 025814          207 NRPIKLRKSKWQ  218 (247)
Q Consensus       207 g~~l~V~~a~~k  218 (247)
                      ++.|.|++++++
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            788999998754

>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=99.81  E-value=2.7e-19  Score=161.23  Aligned_cols=84  Identities=23%  Similarity=0.463  Sum_probs=79.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+||++++++++|..+|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|+|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            44569999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          216 KWQE  219 (247)
Q Consensus       216 ~~k~  219 (247)
                      ..+.
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            8654

>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=99.81  E-value=5.6e-20  Score=140.14  Aligned_cols=83  Identities=18%  Similarity=0.248  Sum_probs=77.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCC---eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPS---FNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~---i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      ..+.++|||+|||+++++++|+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|++||+ |||..|+||.|+
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            455679999999999999999999999999   89999999986 9999999999999999999998 999999999999


Q ss_pred             EEEccccc
Q 025814          212 LRKSKWQE  219 (247)
Q Consensus       212 V~~a~~k~  219 (247)
                      |.++..++
T Consensus       119 V~~a~~~e  126 (136)
T 2hgl_A          119 VFKSHRTE  126 (136)
T ss_dssp             EEECCHHH
T ss_pred             EEECChHH
Confidence            99986543

>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=99.80  E-value=1.4e-19  Score=131.72  Aligned_cols=83  Identities=24%  Similarity=0.278  Sum_probs=76.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE-EEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNM-AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~-v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+ |.|+.+ .+|+++|||||+|.+.++|++||.. |+..|+|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            345679999999999999999999999999987 889888 7999999999999999999999976 9999999999999


Q ss_pred             Eccccc
Q 025814          214 KSKWQE  219 (247)
Q Consensus       214 ~a~~k~  219 (247)
                      ++..++
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            886543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.80  E-value=1.6e-19  Score=129.95  Aligned_cols=79  Identities=15%  Similarity=0.164  Sum_probs=71.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCce--eCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKY--VGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~--i~g~~l~V  212 (247)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.++++      ||||||+|.+.++|.+|++.|||..  |+|+.|+|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            445679999999999999999999999999999999854      6899999999999999999999874  88999999


Q ss_pred             EEccccc
Q 025814          213 RKSKWQE  219 (247)
Q Consensus       213 ~~a~~k~  219 (247)
                      .+++.++
T Consensus        92 ~~S~~k~   98 (100)
T 3r27_A           92 NYSTSQK   98 (100)
T ss_dssp             EECSCSC
T ss_pred             Eeccccc
Confidence            9998654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=2.2e-19  Score=129.76  Aligned_cols=82  Identities=27%  Similarity=0.433  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|   +++++ .+|.++|||||+|.+.++|++||..|||..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            4567799999999999999999999999977   56666 6899999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+.+
T Consensus        88 a~~~~~   93 (101)
T 2fc9_A           88 QGPRGS   93 (101)
T ss_dssp             CSSCCC
T ss_pred             cCCCCC
Confidence            987643

>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=99.80  E-value=4.6e-19  Score=128.27  Aligned_cols=80  Identities=16%  Similarity=0.154  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM--NGKYVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l--~g~~i~g~~l~V  212 (247)
                      ....++|||+|||+++++++|+++|++||.|.+|.++++      ||||||+|.+.++|.+|++.|  ++..|+|+.|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            345679999999999999999999999999999988865      789999999999999999976  567899999999


Q ss_pred             EEcccccc
Q 025814          213 RKSKWQER  220 (247)
Q Consensus       213 ~~a~~k~~  220 (247)
                      .+++.+..
T Consensus        86 ~~a~~~~~   93 (101)
T 2cq1_A           86 QYSNHKEL   93 (101)
T ss_dssp             EECSCSSC
T ss_pred             EEcCcccC
Confidence            99986553

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.80  E-value=1.3e-19  Score=126.27  Aligned_cols=71  Identities=11%  Similarity=0.135  Sum_probs=68.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ..|||+||++.++|++|+++|.+||+|.+++++.      ++|||||+|.+.++|.+|++.|||..++|+.|+|+++
T Consensus         8 ~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            8 SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             ceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            4799999999999999999999999999999865      5899999999999999999999999999999999998

>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=1.3e-19  Score=131.28  Aligned_cols=79  Identities=16%  Similarity=0.151  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCc--eeCCEeEE
Q 025814          135 PENDYRLFCGDLGN-EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK--YVGNRPIK  211 (247)
Q Consensus       135 ~~~~~~lfV~nLp~-~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~--~i~g~~l~  211 (247)
                      ..+.++|||+|||+ ++++++|+++|++||.|.+|.|+++      +|||||+|.+.++|.+|++.||+.  .|+|+.|+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            34567999999999 9999999999999999999999876      479999999999999999998864  69999999


Q ss_pred             EEEccccc
Q 025814          212 LRKSKWQE  219 (247)
Q Consensus       212 V~~a~~k~  219 (247)
                      |.+++.+.
T Consensus        86 V~~a~~~~   93 (102)
T 1x4d_A           86 VHLSQKYK   93 (102)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCCC
Confidence            99998544

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=5.2e-19  Score=127.89  Aligned_cols=83  Identities=25%  Similarity=0.464  Sum_probs=76.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||++++++++|+++|+.|+   .+.+++++.+|.++|||||+|.+.++|++||+.|||..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45567999999999999999999999874   788889988999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++++..
T Consensus        89 a~~~~~   94 (102)
T 2fc8_A           89 AKPKGE   94 (102)
T ss_dssp             CCCCCS
T ss_pred             ecCCCC
Confidence            987654

>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=99.80  E-value=3.9e-19  Score=151.00  Aligned_cols=76  Identities=28%  Similarity=0.463  Sum_probs=71.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEeEEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG-NRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~-g~~l~V~~  214 (247)
                      ...++|||+||+.++++++|+++|+.||.|.+|+|+.++     +|||||+|.+.++|.+|++.|||..|+ |+.|+|++
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  279 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF  279 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEE
Confidence            356789999999999999999999999999999998764     589999999999999999999999999 99999999


Q ss_pred             cc
Q 025814          215 SK  216 (247)
Q Consensus       215 a~  216 (247)
                      ++
T Consensus       280 ak  281 (282)
T 3pgw_A          280 AK  281 (282)
T ss_pred             ec
Confidence            86

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=2e-19  Score=132.01  Aligned_cols=79  Identities=16%  Similarity=0.316  Sum_probs=73.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      +.++|||+|||+++++++|+++|+.| .|.+|.|++|+. |+++|||||+|.+.++|++|| .|||..|+||.|.|..+.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            35689999999999999999999999 899999999975 999999999999999999999 799999999999998876


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      .+
T Consensus        92 ~~   93 (109)
T 2dnn_A           92 ER   93 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            43

>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=99.80  E-value=3.2e-20  Score=135.77  Aligned_cols=83  Identities=17%  Similarity=0.257  Sum_probs=77.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCC---eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPS---FNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~---i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      ....++|||+|||+++++++|+++|+.||.   |.+|.|++++. |.++|||||+|.+.++|++||. |||..|+|+.|+
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            456779999999999999999999999998   89999999976 9999999999999999999997 999999999999


Q ss_pred             EEEccccc
Q 025814          212 LRKSKWQE  219 (247)
Q Consensus       212 V~~a~~k~  219 (247)
                      |.++..++
T Consensus        86 V~~a~~~~   93 (107)
T 2lmi_A           86 VYEINNED   93 (107)
T ss_dssp             CEECCHHH
T ss_pred             EEECCHHH
Confidence            99987543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.79  E-value=5.6e-20  Score=127.61  Aligned_cols=72  Identities=24%  Similarity=0.418  Sum_probs=67.7

Q ss_pred             cEEEEcCCCCCC------cHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCE-eEE
Q 025814          139 YRLFCGDLGNEV------NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNR-PIK  211 (247)
Q Consensus       139 ~~lfV~nLp~~~------~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~-~l~  211 (247)
                      ++|||+|||+.+      ++++|+++|++||.|.++.+.+  .+|.++|||||+|.+.++|++|++.|||..|+|+ .|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            589999999999      7899999999999999999873  5899999999999999999999999999999999 887


Q ss_pred             E
Q 025814          212 L  212 (247)
Q Consensus       212 V  212 (247)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            7

>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=99.79  E-value=2.2e-19  Score=133.39  Aligned_cols=81  Identities=12%  Similarity=0.121  Sum_probs=72.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG--KYVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g--~~i~g~~l~V  212 (247)
                      ....++|||+|||+++++++|+++|++||.|.+|+|+++      ||||||+|.+.++|.+|++.|++  ..|+|+.|+|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            345669999999999999999999999999999999876      68999999999999999998885  6899999999


Q ss_pred             EEccccccc
Q 025814          213 RKSKWQERT  221 (247)
Q Consensus       213 ~~a~~k~~~  221 (247)
                      .+++.+...
T Consensus       102 ~~a~~k~~~  110 (119)
T 2ad9_A          102 QFSNHKELK  110 (119)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.79  E-value=1e-19  Score=137.12  Aligned_cols=82  Identities=17%  Similarity=0.179  Sum_probs=73.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHH----HHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLS----KAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~----~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      ...++|||+||++.+++++|+    ++|++||.|.+|.+.+   +|.++|||||+|.+.++|..|+..|||..|.|+.|+
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            446799999999999999876    6999999999987753   688999999999999999999999999999999999


Q ss_pred             EEEcccccc
Q 025814          212 LRKSKWQER  220 (247)
Q Consensus       212 V~~a~~k~~  220 (247)
                      |.+++.+..
T Consensus       104 V~~a~~~~~  112 (127)
T 2a3j_A          104 ITFSETPQS  112 (127)
T ss_dssp             EEECCCCCH
T ss_pred             EEEccCcch
Confidence            999987653

>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=99.79  E-value=6.1e-19  Score=126.70  Aligned_cols=77  Identities=23%  Similarity=0.385  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          135 PENDYRLFCGDLGN-EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~-~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ....++|||+||++ ++++++|+++|+.||.|.++.+.        +|||||+|.+.++|.+|++.|||..++|+.|+|+
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            55677999999998 99999999999999999999883        6899999999999999999999999999999999


Q ss_pred             Eccccc
Q 025814          214 KSKWQE  219 (247)
Q Consensus       214 ~a~~k~  219 (247)
                      +++.+.
T Consensus        91 ~a~~~~   96 (97)
T 2xnq_A           91 VSSSNA   96 (97)
T ss_dssp             ECCCCC
T ss_pred             ecCCCC
Confidence            998654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.79  E-value=2.2e-19  Score=132.14  Aligned_cols=80  Identities=16%  Similarity=0.207  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFP-SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G-~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      +...++|||+|||+++++++|+++|+.|| .|..+.|..    +.++|||||+|.+.++|++||+.|||..|+|+.|+|+
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~  100 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE  100 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            55677999999999999999999999999 899998853    3478999999999999999999999999999999999


Q ss_pred             Ecccc
Q 025814          214 KSKWQ  218 (247)
Q Consensus       214 ~a~~k  218 (247)
                      +++..
T Consensus       101 ~a~~~  105 (111)
T 2jvr_A          101 RDDNP  105 (111)
T ss_dssp             ESCC-
T ss_pred             ECCCC
Confidence            98754

>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=99.79  E-value=5.6e-19  Score=129.32  Aligned_cols=79  Identities=16%  Similarity=0.236  Sum_probs=73.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC-----Ee
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN-----RP  209 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g-----~~  209 (247)
                      ....++|||+|||+++++++|+++|+.||.|..|.|+.+       |||||+|.+.++|++||+.|||..|+|     +.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            345679999999999999999999999999999999876       799999999999999999999999999     99


Q ss_pred             EEEEEcccccc
Q 025814          210 IKLRKSKWQER  220 (247)
Q Consensus       210 l~V~~a~~k~~  220 (247)
                      |+|+++..+.+
T Consensus        85 i~V~~a~~~~~   95 (108)
T 1x4c_A           85 IRVKVDGPRSP   95 (108)
T ss_dssp             EEEEESSCCSC
T ss_pred             EEEEeCCCCCC
Confidence            99999987654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.79  E-value=3.1e-19  Score=127.68  Aligned_cols=81  Identities=21%  Similarity=0.370  Sum_probs=73.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|..+     ..+|.++|||||+|.+.++|.+|+..|||..|+|+.|+|++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4556799999999999999999999999988766     24799999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+.+
T Consensus        88 a~~~~~   93 (96)
T 1fjc_A           88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             cCCCCC
Confidence            987654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=4.9e-19  Score=127.02  Aligned_cols=80  Identities=13%  Similarity=0.275  Sum_probs=72.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|. +.++.    +.++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            44567999999999999999999999999997 66664    46789999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98754

>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=99.79  E-value=2.4e-19  Score=132.58  Aligned_cols=82  Identities=17%  Similarity=0.314  Sum_probs=75.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++++   +.++|||||+|.+.++|.+|+..|||..++|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            345679999999999999999999999999999999876   55699999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +.++.
T Consensus        82 a~~~~   86 (115)
T 3lqv_A           82 YNANR   86 (115)
T ss_dssp             CCHHH
T ss_pred             ecCCh
Confidence            98643

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.79  E-value=2.9e-19  Score=129.06  Aligned_cols=77  Identities=16%  Similarity=0.153  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+||+.++++++|+++|+.||.|.++++.      .++|||||+|.+.++|.+|+..|||..|+|+.|+|+++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            345699999999999999999999999999999997      34789999999999999999999999999999999998


Q ss_pred             ccc
Q 025814          216 KWQ  218 (247)
Q Consensus       216 ~~k  218 (247)
                      +.+
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=6.4e-19  Score=124.62  Aligned_cols=78  Identities=18%  Similarity=0.392  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.++.++        +|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            4566799999999999999999999999999999987        57999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+.+
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987654

>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=99.79  E-value=5.4e-20  Score=125.57  Aligned_cols=75  Identities=19%  Similarity=0.432  Sum_probs=71.6

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|++|++ +++..++|+.|+|+++
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999996 5999999999999875

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.78  E-value=1.3e-19  Score=134.67  Aligned_cols=79  Identities=13%  Similarity=0.192  Sum_probs=72.0

Q ss_pred             cEEEEcCC----CCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecC----HHH----HHHHHH--HhCCce
Q 025814          139 YRLFCGDL----GNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFAN----PSD----IAAALK--EMNGKY  204 (247)
Q Consensus       139 ~~lfV~nL----p~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~----~~~----a~~Al~--~l~g~~  204 (247)
                      ..|||+||    ++.+++++|+.+|+.||.|.++.++.|+.||.++|||||+|.+    .++    |.+|+.  .|||..
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            37999999    9999999999999999999999999999999999999999995    322    888988  789999


Q ss_pred             eCCEeEEEEEccc
Q 025814          205 VGNRPIKLRKSKW  217 (247)
Q Consensus       205 i~g~~l~V~~a~~  217 (247)
                      |+|+.|+|.+.+-
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

>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=1e-18  Score=125.82  Aligned_cols=80  Identities=20%  Similarity=0.387  Sum_probs=73.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|.+|.+.++      +|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            455679999999999999999999999999999999865      68999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        86 a~~~~~   91 (99)
T 2cpj_A           86 ACHSAS   91 (99)
T ss_dssp             SSCCSC
T ss_pred             cCCCCC
Confidence            987654

>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=99.78  E-value=3.2e-19  Score=127.75  Aligned_cols=83  Identities=24%  Similarity=0.404  Sum_probs=75.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLS----KAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPI  210 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~----~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l  210 (247)
                      ....++|||+|||+++++++|+    ++|++||.|.+|.+.+   +|.++|||||+|.+.++|.+|+..|||..++|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3456799999999999999999    9999999999998874   58889999999999999999999999999999999


Q ss_pred             EEEEcccccc
Q 025814          211 KLRKSKWQER  220 (247)
Q Consensus       211 ~V~~a~~k~~  220 (247)
                      +|++++.+..
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999987653

>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=99.78  E-value=7e-19  Score=128.90  Aligned_cols=80  Identities=23%  Similarity=0.474  Sum_probs=74.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||+.++++++|+++|+.||.|.+|+|+++      +|||||+|.+.++|.+|+..|||..|+|+.|+|.+
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            445669999999999999999999999999999999876      68999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        96 a~~~~~  101 (109)
T 1x4g_A           96 GKESPD  101 (109)
T ss_dssp             CCCCCS
T ss_pred             cCCCCC
Confidence            987653

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.78  E-value=1e-18  Score=128.06  Aligned_cols=77  Identities=26%  Similarity=0.509  Sum_probs=71.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||++++++++|+++|++||.|.+|.++        +|||||+|.+.++|++|+..|||..|+|+.|+|.+
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            4456799999999999999999999999999999987        68999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus       100 a~~~~  104 (108)
T 2jvo_A          100 SKLPA  104 (108)
T ss_dssp             CSCCC
T ss_pred             ecCCC
Confidence            98654

>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=99.78  E-value=7.9e-19  Score=127.73  Aligned_cols=80  Identities=13%  Similarity=0.119  Sum_probs=71.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCc--eeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK--YVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~--~i~g~~l~V  212 (247)
                      ....++|||+|||+++++++|+++|++||.|.+|.++++      ||||||+|.+.++|.+|++.||+.  .|+|+.|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345679999999999999999999999999999998764      689999999999999999988764  599999999


Q ss_pred             EEcccccc
Q 025814          213 RKSKWQER  220 (247)
Q Consensus       213 ~~a~~k~~  220 (247)
                      .+++.+..
T Consensus        86 ~~a~~~~~   93 (104)
T 1wex_A           86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEccCccc
Confidence            99986543

>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=99.78  E-value=1.7e-19  Score=133.37  Aligned_cols=86  Identities=23%  Similarity=0.293  Sum_probs=74.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|..+.+..+..+|.++|||||+|.+.++|++||+.|||..|+|+.|+|++
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34567999999999999999999999999995443333323799999999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus       102 a~~~~~  107 (115)
T 2cpx_A          102 GKNKKQ  107 (115)
T ss_dssp             CCCCSC
T ss_pred             ccCCCC
Confidence            987654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=2e-18  Score=122.54  Aligned_cols=78  Identities=15%  Similarity=0.362  Sum_probs=72.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++++        ||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            456679999999999999999999999999999999744        999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+.+
T Consensus        79 a~~~~~   84 (92)
T 2dgt_A           79 STSRLR   84 (92)
T ss_dssp             SSCCCS
T ss_pred             ccCCCC
Confidence            987654

>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=99.78  E-value=1.1e-18  Score=142.17  Aligned_cols=142  Identities=13%  Similarity=0.047  Sum_probs=104.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHH---hcCccchhhhhhcccccccccCCC-----CCC----------
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAAL---ASSDIEHKAETKKKSIPRKAAGQT-----WED----------  128 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al---~~~~~~~~~~~~~~~~~r~~~~~~-----~~~----------  128 (247)
                      |.+..+....+     .+|++||.|++.++|..|+   ++..+.++.+.+..+.........     ...          
T Consensus        30 G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~  104 (205)
T 3tyt_A           30 GNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESR  104 (205)
T ss_dssp             SCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCT
T ss_pred             CCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCccCCCcccccccCCccccccCCCc
Confidence            55555544332     4899999999998888886   456788888887765432110000     000          


Q ss_pred             -CC--------CCCCCCCCcEEEEcCCCCCCcHHHHHHHhccCCCe--eEEEEEecCCCCCcceEEEEEecCHHHHHHHH
Q 025814          129 -PT--------LAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSF--NMAKVVRDKRTGKTKGYGFISFANPSDIAAAL  197 (247)
Q Consensus       129 -~~--------~~~~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i--~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al  197 (247)
                       ..        ......+.++|||+|||+++++++|+++|+.||.|  .+++++.++  |..+|||||+|.+.++|.+||
T Consensus       105 ~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai  182 (205)
T 3tyt_A          105 NNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETL  182 (205)
T ss_dssp             TCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHH
T ss_pred             cccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHH
Confidence             00        00112345689999999999999999999999999  899998874  666799999999999999999


Q ss_pred             HHhCCceeCCE----eEEEEEc
Q 025814          198 KEMNGKYVGNR----PIKLRKS  215 (247)
Q Consensus       198 ~~l~g~~i~g~----~l~V~~a  215 (247)
                      ..|||..|.|+    .+.|+++
T Consensus       183 ~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          183 GFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             HHHTTCEECCSSSSSCEECEEE
T ss_pred             HHhCCCCccCCCCCcceEEEec
Confidence            99999999886    4666554

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.78  E-value=3.9e-19  Score=128.62  Aligned_cols=81  Identities=25%  Similarity=0.494  Sum_probs=75.5

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+|||+++++++|+++|+.||.|.+|.+++++ +|.++|||||+|.+.++|++|+.  ||..++|+.|.|.++.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            45689999999999999999999999999999999998 99999999999999999999997  9999999999999987


Q ss_pred             cccc
Q 025814          217 WQER  220 (247)
Q Consensus       217 ~k~~  220 (247)
                      .+..
T Consensus        85 ~~~~   88 (102)
T 2xs2_A           85 RKQN   88 (102)
T ss_dssp             ECC-
T ss_pred             cCcc
Confidence            6543

>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=99.78  E-value=8e-19  Score=125.85  Aligned_cols=79  Identities=24%  Similarity=0.432  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--CEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG--NRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~--g~~l~V  212 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.+..+      +|||||+|.+.++|++|++.|||..|+  |+.|+|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            345579999999999999999999999999999998754      689999999999999999999999999  999999


Q ss_pred             EEccccc
Q 025814          213 RKSKWQE  219 (247)
Q Consensus       213 ~~a~~k~  219 (247)
                      ++++++.
T Consensus        88 ~~a~~~~   94 (97)
T 1why_A           88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998764

>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=99.78  E-value=1.5e-18  Score=121.24  Aligned_cols=76  Identities=22%  Similarity=0.390  Sum_probs=70.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCEeEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM-NGKYVGNRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l-~g~~i~g~~l~V~  213 (247)
                      ....++|||+|||.++++++|+++|++||.|.++.++++      +|||||+|.+.++|++|++.| ||..++|+.|+|+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            345668999999999999999999999999999999874      689999999999999999989 9999999999999


Q ss_pred             Ecc
Q 025814          214 KSK  216 (247)
Q Consensus       214 ~a~  216 (247)
                      +++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            874

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.65  E-value=1.4e-20  Score=139.50  Aligned_cols=85  Identities=25%  Similarity=0.435  Sum_probs=79.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeE--------EEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNM--------AKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN  207 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~--------v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g  207 (247)
                      .+.++|||+|||+++++++|+++|+.||.|..        |+|++++.+|.++|||||+|.+.++|++|+..|||..|+|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            44568999999999999999999999999998        9999998899999999999999999999999999999999


Q ss_pred             EeEEEEEcccccc
Q 025814          208 RPIKLRKSKWQER  220 (247)
Q Consensus       208 ~~l~V~~a~~k~~  220 (247)
                      +.|+|++++.+..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999987654

>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=99.78  E-value=1.5e-18  Score=146.23  Aligned_cols=118  Identities=24%  Similarity=0.326  Sum_probs=101.9

Q ss_pred             cCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCCCCcHHHHHHH
Q 025814           82 FQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKA  158 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~~e~~L~~~  158 (247)
                      ..++++||.|.+.++|..|+.   +..+.++.+.+....                   +..+|||+||++.+++++|+++
T Consensus        56 ~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~-------------------~~~~l~v~nl~~~~t~~~l~~~  116 (261)
T 3sde_A           56 RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT-------------------HGAALTVKNLSPVVSNELLEQA  116 (261)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC-------------------CSSEEEEESCCTTCCHHHHHHH
T ss_pred             CCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc-------------------cCCcccccCCCCCCCHHHHHHH
Confidence            358999999999999998875   456777777775532                   3458999999999999999999


Q ss_pred             hccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhC-CceeC---CEeEEEEEccccc
Q 025814          159 FSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN-GKYVG---NRPIKLRKSKWQE  219 (247)
Q Consensus       159 F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~-g~~i~---g~~l~V~~a~~k~  219 (247)
                      |+.||.|.+|.|+.| .+|.++|||||+|.+.++|.+|+..|| |..+.   |+.|.|.++....
T Consensus       117 F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          117 FSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             HGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             HHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            999999999999999 589999999999999999999999995 55555   9999999987653

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.78  E-value=1.4e-18  Score=142.01  Aligned_cols=83  Identities=28%  Similarity=0.468  Sum_probs=78.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      +.++|||+|||+++++++|+++|++||.|.+|+|++|+.+|.++|||||+|.+.++|.+||+.|||..+.|+.|+|.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            45699999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ccc
Q 025814          217 WQE  219 (247)
Q Consensus       217 ~k~  219 (247)
                      ...
T Consensus        94 ~~~   96 (213)
T 4f02_A           94 RDP   96 (213)
T ss_dssp             CCT
T ss_pred             ccc
Confidence            544

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.77  E-value=1.5e-18  Score=139.89  Aligned_cols=130  Identities=12%  Similarity=0.144  Sum_probs=101.8

Q ss_pred             CCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCC-------------------C---CCCCCCCCCCCC
Q 025814           84 RDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQT-------------------W---EDPTLAEWPEND  138 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~-------------------~---~~~~~~~~~~~~  138 (247)
                      ++++||.|.+.++|..|+.   +..+.++.+.+............                   .   ............
T Consensus        41 ~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~  120 (198)
T 1qm9_A           41 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS  120 (198)
T ss_dssp             SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCc
Confidence            7899999999999888875   45778888877655433111000                   0   000011123447


Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEeEEEEEcc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFP-SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG-NRPIKLRKSK  216 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G-~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~-g~~l~V~~a~  216 (247)
                      ++|||+||+.++++++|+++|+.|| .|.+++++.+     .+|||||+|.+.++|.+|+..|||..++ |+.|+|.+++
T Consensus       121 ~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~  195 (198)
T 1qm9_A          121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK  195 (198)
T ss_dssp             CEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeec
Confidence            7999999999999999999999999 9999999764     2789999999999999999999999999 9999999987


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      ++
T Consensus       196 ~~  197 (198)
T 1qm9_A          196 ST  197 (198)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>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=99.77  E-value=1.7e-19  Score=138.61  Aligned_cols=85  Identities=27%  Similarity=0.480  Sum_probs=73.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEE--E---EecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEe
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAK--V---VRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRP  209 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~--i---~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~  209 (247)
                      ....++|||+|||+++++++|+++|+.||.|..+.  +   ++...+|.++|||||+|.+.++|.+||..|||..|+|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            34556999999999999999999999999987641  1   111247999999999999999999999999999999999


Q ss_pred             EEEEEccccc
Q 025814          210 IKLRKSKWQE  219 (247)
Q Consensus       210 l~V~~a~~k~  219 (247)
                      |+|.+++...
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999997654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.77  E-value=3.9e-19  Score=128.39  Aligned_cols=77  Identities=23%  Similarity=0.548  Sum_probs=72.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      ++|||+|||+++++++|+++|+.||.|.+|.++++     ++|||||+|.+.++|++|++.|||..++|+.|+|++++.+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            37999999999999999999999999999999887     6899999999999999999999999999999999999876


Q ss_pred             cc
Q 025814          219 ER  220 (247)
Q Consensus       219 ~~  220 (247)
                      .+
T Consensus        76 ~~   77 (101)
T 2hvz_A           76 PR   77 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=3.7e-19  Score=133.31  Aligned_cols=82  Identities=22%  Similarity=0.240  Sum_probs=74.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCe----eEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSF----NMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i----~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      .+.++|||+|||+++++++|+++|+.||.|    .+|.|++| .+|+++|||||+|.+.++|++||+. |+..|+||.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            345699999999999999999999999975    68999999 4899999999999999999999975 99999999999


Q ss_pred             EEEccccc
Q 025814          212 LRKSKWQE  219 (247)
Q Consensus       212 V~~a~~k~  219 (247)
                      |..+..++
T Consensus        99 V~~a~~~e  106 (123)
T 2dha_A           99 LFRSTAAE  106 (123)
T ss_dssp             CEEECHHH
T ss_pred             EEECCHHH
Confidence            99886543

>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=99.77  E-value=3.6e-18  Score=141.13  Aligned_cols=130  Identities=13%  Similarity=0.166  Sum_probs=102.0

Q ss_pred             CCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCC-------------------CCCCC---CCCCCCCC
Q 025814           84 RDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQT-------------------WEDPT---LAEWPEND  138 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~-------------------~~~~~---~~~~~~~~  138 (247)
                      ++++||+|.+.++|.+|+.   +..+.++.+.+............                   ...+.   ........
T Consensus        72 ~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (229)
T 2adc_A           72 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS  151 (229)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCC
Confidence            7899999999999999875   45778888877665533111000                   00000   01123446


Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCC-CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CEeEEEEEcc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFP-SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG-NRPIKLRKSK  216 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G-~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~-g~~l~V~~a~  216 (247)
                      ++|||+||+.++++++|+++|+.|| .|..|+++.+     .+|||||+|.+.++|.+|++.|||..++ |+.|+|.+++
T Consensus       152 ~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~  226 (229)
T 2adc_A          152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK  226 (229)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEec
Confidence            8999999999999999999999999 9999999653     3689999999999999999999999999 9999999987


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      ++
T Consensus       227 ~~  228 (229)
T 2adc_A          227 ST  228 (229)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.77  E-value=9.6e-19  Score=125.28  Aligned_cols=79  Identities=24%  Similarity=0.370  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          135 PENDYRLFCGDLGN-EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~-~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ..+.++|||+|||+ ++++++|+++|+.||.|.+|.+.        +|||||+|.+.++|++|+..|||..++|+.|+|+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45577999999999 99999999999999999999984        6799999999999999999999999999999999


Q ss_pred             Eccccccc
Q 025814          214 KSKWQERT  221 (247)
Q Consensus       214 ~a~~k~~~  221 (247)
                      +++.+.+.
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99876554

>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=99.76  E-value=1.3e-18  Score=127.97  Aligned_cols=80  Identities=16%  Similarity=0.171  Sum_probs=71.1

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCEeEE
Q 025814          135 PENDYRLFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG--KYVGNRPIK  211 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~-~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g--~~i~g~~l~  211 (247)
                      ....++|||+|||++ +++++|+++|++||.|.+|.|+++      +|||||+|.+.++|..|++.||+  ..|+|+.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            445679999999998 999999999999999999999753      68999999999999999998864  569999999


Q ss_pred             EEEcccccc
Q 025814          212 LRKSKWQER  220 (247)
Q Consensus       212 V~~a~~k~~  220 (247)
                      |.+++.+.+
T Consensus        96 V~~a~~~~~  104 (112)
T 1x4f_A           96 VDLSEKYKK  104 (112)
T ss_dssp             EEEECSCSS
T ss_pred             EEECccccc
Confidence            999976554

>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=99.76  E-value=1.2e-18  Score=148.77  Aligned_cols=131  Identities=8%  Similarity=0.127  Sum_probs=101.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--CccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCG  144 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~  144 (247)
                      |.+..+....+...  +++++||.|.+.++|.+|+..  ..+.++.+.+...                    ..++|||+
T Consensus        66 G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~--------------------~~~~l~v~  123 (292)
T 2ghp_A           66 GPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL--------------------TECTLWMT  123 (292)
T ss_dssp             SCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC--------------------CSCEEEEE
T ss_pred             CCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEEC--------------------CCCEEEEE
Confidence            55555444433322  489999999999999999953  3455665555432                    34589999


Q ss_pred             CCCCCCcHHHHHHHhccCC-CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccccc
Q 025814          145 DLGNEVNDDVLSKAFSRFP-SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQER  220 (247)
Q Consensus       145 nLp~~~~e~~L~~~F~~~G-~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~~  220 (247)
                      |||+++++++|+++|+.|| .|.+|.+++++. |.++|||||+|.+.++|.+|+..|||..|+|+.|.|.++.++.+
T Consensus       124 nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          124 NFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             CCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC--
T ss_pred             CCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            9999999999999999999 999999999864 88999999999999999999999999999999999999987654

>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=99.76  E-value=4.2e-18  Score=132.83  Aligned_cols=82  Identities=26%  Similarity=0.494  Sum_probs=78.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|||..++|+.|+|.++..
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            45899999999999999999999999999999999988999999999999999999999999999999999999999876


Q ss_pred             cc
Q 025814          218 QE  219 (247)
Q Consensus       218 k~  219 (247)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=8.5e-19  Score=129.08  Aligned_cols=76  Identities=14%  Similarity=0.191  Sum_probs=70.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+|||+++++++|+++|++||.|.+|.|+.      .+|||||+|.+.++|++|++.|||..|+|+.|+|.++.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            356899999999999999999999999999998864      46899999999999999999999999999999999997


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      ..
T Consensus        83 ~~   84 (111)
T 1whx_A           83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=2.2e-18  Score=121.84  Aligned_cols=77  Identities=26%  Similarity=0.464  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.++.++++        ||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            445678999999999999999999999999999999744        999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98654

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.76  E-value=1.3e-18  Score=138.45  Aligned_cols=84  Identities=24%  Similarity=0.385  Sum_probs=79.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||++++++++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|++||+.|||..|+|+.|+|++
T Consensus        85 ~~~~~~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           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4556799999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            87643

>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=99.76  E-value=7.3e-19  Score=132.08  Aligned_cols=81  Identities=23%  Similarity=0.249  Sum_probs=73.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCee--EEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFN--MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~--~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      ....++|||+|||+++++++|+++|+.| .|.  +|+|++|+. |+++|||||+|.+.++|++||+ +++..|+||.|+|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            3456789999999999999999999999 576  899999976 9999999999999999999996 5889999999999


Q ss_pred             EEcccc
Q 025814          213 RKSKWQ  218 (247)
Q Consensus       213 ~~a~~k  218 (247)
                      ..+..+
T Consensus       116 ~~a~~~  121 (126)
T 2hgm_A          116 FKSSQE  121 (126)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            887543

>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=99.76  E-value=3.3e-18  Score=133.78  Aligned_cols=82  Identities=27%  Similarity=0.444  Sum_probs=78.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|||..++|+.|+|.++..
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   82 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   82 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCC
Confidence            46899999999999999999999999999999999998999999999999999999999999999999999999999876


Q ss_pred             cc
Q 025814          218 QE  219 (247)
Q Consensus       218 k~  219 (247)
                      +.
T Consensus        83 ~~   84 (168)
T 1b7f_A           83 GG   84 (168)
T ss_dssp             CS
T ss_pred             Cc
Confidence            54

>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=99.76  E-value=2.6e-19  Score=136.93  Aligned_cols=83  Identities=14%  Similarity=0.138  Sum_probs=75.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.|| |.+|.|++|+. |+++|||||+|.+.++|++|| .+|+..|+|+.|+|..
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            44567899999999999999999999999 77999999975 999999999999999999999 8999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      +..+..
T Consensus       120 a~~~~~  125 (139)
T 2hgn_A          120 NSTTGA  125 (139)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            876654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.1e-17  Score=120.40  Aligned_cols=78  Identities=23%  Similarity=0.444  Sum_probs=71.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccC--CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRF--PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~--G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      ....++|||+|||+++++++|+++|+.|  |.|.+|.+.        +|||||+|.+.++|++|+..|||..|+|+.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            4556799999999999999999999999  999988774        569999999999999999999999999999999


Q ss_pred             EEcccccc
Q 025814          213 RKSKWQER  220 (247)
Q Consensus       213 ~~a~~k~~  220 (247)
                      ++++.+.+
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99987654

>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=1.8e-18  Score=122.93  Aligned_cols=79  Identities=16%  Similarity=0.300  Sum_probs=69.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCC-eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCC-ceeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPS-FNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG-KYVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~-i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g-~~i~g~~l~V  212 (247)
                      ....++|||+|||+++++++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.||| ..|+|+.|+|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            345668999999999999999999999999 5555552       478999999999999999999999 9999999999


Q ss_pred             EEcccccc
Q 025814          213 RKSKWQER  220 (247)
Q Consensus       213 ~~a~~k~~  220 (247)
                      ++++.+..
T Consensus        78 ~~a~~~~~   85 (93)
T 2cqh_A           78 DYSVSKKL   85 (93)
T ss_dssp             EECCCCCC
T ss_pred             EEccCccc
Confidence            99987543

>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=4.7e-18  Score=123.21  Aligned_cols=78  Identities=31%  Similarity=0.503  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+|||+++++++|+++|+.||.|.+|.+++        |||||+|.+.++|++|++.|||..|+|+.|+|+++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            4456899999999999999999999999999999874        49999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          216 KWQERT  221 (247)
Q Consensus       216 ~~k~~~  221 (247)
                      +.+...
T Consensus        81 ~~~~~~   86 (103)
T 2dgu_A           81 KPPDQK   86 (103)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            876543

>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=99.75  E-value=7.1e-18  Score=123.72  Aligned_cols=75  Identities=23%  Similarity=0.436  Sum_probs=69.8

Q ss_pred             CCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          136 ENDYRLFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp~~-~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ...++|||+||+++ +++++|+++|+.||.|.+|.+        ++|||||+|.+.++|++|++.|||..|+|+.|+|++
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34579999999999 999999999999999999988        478999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      ++..
T Consensus        97 a~~~  100 (110)
T 1wf1_A           97 AGEP  100 (110)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            9743

>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=1.5e-17  Score=119.26  Aligned_cols=78  Identities=19%  Similarity=0.310  Sum_probs=70.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+||  ++++++|+++|+.||.|.+|.|.      .++|||||+|.+.++|++||..|||..|+|+.|+|.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            445679999996  89999999999999999999884      4678999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      ++.+..
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            987653

>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=99.75  E-value=6.5e-18  Score=118.99  Aligned_cols=75  Identities=9%  Similarity=0.177  Sum_probs=69.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+|||+++++++|+++|++| .|.++++.      .++|||||+|.+.++|++|++.|||..++|+.|+|+++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            45689999999999999999999999 99999884      578999999999999999999999999999999999986


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      ..
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=3.6e-18  Score=122.04  Aligned_cols=80  Identities=15%  Similarity=0.177  Sum_probs=72.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEE-EEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMA-KVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v-~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ...++|||+|||+++++++|+++|+.||.|.++ .|+.++.+|.    |||+|.+.++|.+|+..|||..|+|+.|+|++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345789999999999999999999999999999 5888765544    99999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +..++
T Consensus        89 a~~~~   93 (96)
T 2e44_A           89 IPDEM   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCccc
Confidence            98764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=6.5e-18  Score=120.41  Aligned_cols=77  Identities=19%  Similarity=0.320  Sum_probs=69.1

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+|||+++++++|+++|+.||.|.+|  +.++.+|.   ||||+|.+.++|++||. |||..|+|+.|+|+++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            34589999999999999999999999999987  66666666   99999999999999998 99999999999998876


Q ss_pred             ccc
Q 025814          217 WQE  219 (247)
Q Consensus       217 ~k~  219 (247)
                      .+.
T Consensus        81 ~~~   83 (94)
T 2e5g_A           81 QKE   83 (94)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            443

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.74  E-value=1.7e-17  Score=124.84  Aligned_cols=77  Identities=21%  Similarity=0.325  Sum_probs=70.4

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceE-EEEEecCHHHHHHHHHHhCCceeCC--EeEEEEE
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGY-GFISFANPSDIAAALKEMNGKYVGN--RPIKLRK  214 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~-~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~  214 (247)
                      --.|||+||++.+++++|+++|++||.|.+|.++.+     .+|| |||+|.+.++|++|++.|||..|.|  +.|+|++
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            347899999999999999999999999999988764     2688 9999999999999999999999988  9999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus       103 ak~~~  107 (130)
T 3zzy_A          103 SKLTS  107 (130)
T ss_dssp             CSCSS
T ss_pred             cCCCc
Confidence            98764

>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=99.74  E-value=9.1e-18  Score=118.64  Aligned_cols=76  Identities=11%  Similarity=0.308  Sum_probs=63.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCce--eCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKY--VGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~--i~g~~l~V  212 (247)
                      .....+|||+|||+++++++|+++|++||.|.+|+|+++     ++|||||+|.+.++|++    |+|..  +.|+.|.|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            445669999999999999999999999999999999875     68999999999999883    55654  56999999


Q ss_pred             EEccccc
Q 025814          213 RKSKWQE  219 (247)
Q Consensus       213 ~~a~~k~  219 (247)
                      .++.++.
T Consensus        79 ~~a~~k~   85 (89)
T 3d2w_A           79 SNAEPKH   85 (89)
T ss_dssp             EECC---
T ss_pred             EEcCCCC
Confidence            9998764

>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=99.73  E-value=8.1e-18  Score=131.23  Aligned_cols=79  Identities=20%  Similarity=0.273  Sum_probs=71.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EeEEEEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN--RPIKLRK  214 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~  214 (247)
                      ...+|||+||++.+++++|+++|++||.|.+|.|..+    ..+|||||+|.+.++|++|++.|||..|.|  +.|+|++
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEE
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEE
Confidence            3457999999999999999999999999999998754    257899999999999999999999999965  9999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus       121 Ak~~~  125 (164)
T 1sjr_A          121 SKLTS  125 (164)
T ss_dssp             CSSSS
T ss_pred             ecCCc
Confidence            98764

>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=99.73  E-value=1.3e-17  Score=133.65  Aligned_cols=84  Identities=27%  Similarity=0.540  Sum_probs=77.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|++++.+|.++|||||+|.+.++|.+||+. ++..++|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            45567999999999999999999999999999999999999999999999999999999999955 99999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +..+.
T Consensus        89 ~~~~~   93 (196)
T 1l3k_A           89 AVSRE   93 (196)
T ss_dssp             CCC--
T ss_pred             ccCcc
Confidence            87654

>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=99.72  E-value=5e-18  Score=125.68  Aligned_cols=75  Identities=17%  Similarity=0.271  Sum_probs=66.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEe-----EE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRP-----IK  211 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~-----l~  211 (247)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|+.+       |||||+|.+.++|++||+.|||..|+|+.     |+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            4568999999999999999999999999999999876       89999999999999999999999999998     77


Q ss_pred             EEEcccc
Q 025814          212 LRKSKWQ  218 (247)
Q Consensus       212 V~~a~~k  218 (247)
                      |..+..+
T Consensus        88 v~~~~~~   94 (115)
T 3beg_B           88 VKVDGPR   94 (115)
T ss_dssp             EEECC--
T ss_pred             eccCCCC
Confidence            7776553

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.2e-17  Score=117.48  Aligned_cols=74  Identities=16%  Similarity=0.115  Sum_probs=65.7

Q ss_pred             CCcEEEEcCCCCCCcHHH----HHHHhccC-CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          137 NDYRLFCGDLGNEVNDDV----LSKAFSRF-PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~----L~~~F~~~-G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      ..+.|||+|||+.+++++    |+++|++| |.|.+|       +|   |||||.|.+.++|++|++.|||..+.||.|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            333499999999999988    55899999 599988       44   9999999999999999999999999999999


Q ss_pred             EEEcccccc
Q 025814          212 LRKSKWQER  220 (247)
Q Consensus       212 V~~a~~k~~  220 (247)
                      |.+++.+..
T Consensus        78 v~~A~~~sd   86 (96)
T 2diu_A           78 VSFTPKNRE   86 (96)
T ss_dssp             EESSCCSCC
T ss_pred             EEecCCCcc
Confidence            999986643

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=1.2e-17  Score=123.44  Aligned_cols=78  Identities=19%  Similarity=0.337  Sum_probs=68.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCC---CCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRT---GKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~t---g~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      ...++|||+|||+++++++|+++|++||.|. +.++.++.+   |.++|||||+|.+.++|++||+.|+  .++|+.|.+
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            4456899999999999999999999999999 888888777   7999999999999999999999984  367777776


Q ss_pred             EEcc
Q 025814          213 RKSK  216 (247)
Q Consensus       213 ~~a~  216 (247)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6543

>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=99.72  E-value=2.5e-17  Score=134.12  Aligned_cols=78  Identities=15%  Similarity=0.264  Sum_probs=72.0

Q ss_pred             CCcEEEEcCCC-CCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          137 NDYRLFCGDLG-NEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       137 ~~~~lfV~nLp-~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +.++|||+||+ +.+++++|+++|+.||.|.+|+|+++     .+|||||+|.+.++|++||+.|||..+.|+.|+|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            45699999999 89999999999999999999999876     3799999999999999999999999999999999998


Q ss_pred             cccc
Q 025814          216 KWQE  219 (247)
Q Consensus       216 ~~k~  219 (247)
                      +.+.
T Consensus        78 ~~~~   81 (205)
T 3tyt_A           78 KQPA   81 (205)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            7543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.71  E-value=7.4e-17  Score=120.68  Aligned_cols=75  Identities=13%  Similarity=0.118  Sum_probs=68.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceE-EEEEecCHHHHHHHHHHhCCceeCC--EeEEEEEc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGY-GFISFANPSDIAAALKEMNGKYVGN--RPIKLRKS  215 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~-~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~a  215 (247)
                      ..|||+||++.+++++|+++|++||.|.+|.|+..      .|| |||+|.+.++|..|++.|||..|.|  +.|+|.++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            45789999999999999999999999999998652      276 9999999999999999999999987  69999999


Q ss_pred             cccc
Q 025814          216 KWQE  219 (247)
Q Consensus       216 ~~k~  219 (247)
                      +.+.
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            8765

>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=99.71  E-value=9.4e-18  Score=123.47  Aligned_cols=77  Identities=21%  Similarity=0.255  Sum_probs=68.8

Q ss_pred             CCCcEEEE--cCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-----CCE
Q 025814          136 ENDYRLFC--GDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV-----GNR  208 (247)
Q Consensus       136 ~~~~~lfV--~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i-----~g~  208 (247)
                      ...++|||  |||++++++++|+++|++||.|.+|.++.+      +|||||+|.+.++|++|++.|||..|     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            34568999  779999999999999999999999887542      78999999999999999999999998     789


Q ss_pred             eEEEEEcccc
Q 025814          209 PIKLRKSKWQ  218 (247)
Q Consensus       209 ~l~V~~a~~k  218 (247)
                      .|.|.+++..
T Consensus        97 ~l~v~~a~~~  106 (114)
T 2cq2_A           97 TLYLNFVEKV  106 (114)
T ss_dssp             ECEEEEESCC
T ss_pred             EEEEEecccC
Confidence            9999998643

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.71  E-value=2.1e-17  Score=134.46  Aligned_cols=83  Identities=27%  Similarity=0.469  Sum_probs=75.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||.++++++|+++|+.||.|.+|++++++.+|.++|||||+|.+.++|.+|++.|||..|+|+.|+|.++..
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            35899999999999999999999999999999999988999999999999999999999999999999999999998876


Q ss_pred             ccc
Q 025814          218 QER  220 (247)
Q Consensus       218 k~~  220 (247)
                      +..
T Consensus       108 ~~~  110 (216)
T 2qfj_A          108 IGQ  110 (216)
T ss_dssp             CGG
T ss_pred             ccc
Confidence            543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.71  E-value=3.2e-17  Score=127.67  Aligned_cols=80  Identities=25%  Similarity=0.441  Sum_probs=74.7

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      ++|||+|||.++++++|+++|+.||.|.++++++++ +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            489999999999999999999999999999999996 5889999999999999999999999999999999999998755


Q ss_pred             c
Q 025814          219 E  219 (247)
Q Consensus       219 ~  219 (247)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.70  E-value=2.4e-17  Score=115.49  Aligned_cols=71  Identities=17%  Similarity=0.443  Sum_probs=65.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccC----C-------CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRF----P-------SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV  205 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~----G-------~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i  205 (247)
                      ..++|||+|||+++++++|+++|+.|    |       .|.++++.++      +|||||+|.+.++|++|+ .|||..+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            45699999999999999999999999    8       8999988765      789999999999999999 9999999


Q ss_pred             CCEeEEEEE
Q 025814          206 GNRPIKLRK  214 (247)
Q Consensus       206 ~g~~l~V~~  214 (247)
                      +|+.|+|+.
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.70  E-value=1.6e-16  Score=115.67  Aligned_cols=82  Identities=12%  Similarity=0.144  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCC-----CCcHHHHHHHhccCCCeeEEEEEecCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCEe
Q 025814          136 ENDYRLFCGDLGN-----EVNDDVLSKAFSRFPSFNMAKVVRDKRT-GKTKGYGFISFANPSDIAAALKEMNGKYVGNRP  209 (247)
Q Consensus       136 ~~~~~lfV~nLp~-----~~~e~~L~~~F~~~G~i~~v~i~~~~~t-g~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~  209 (247)
                      ...++|+|.||-.     +-++++|+++|++||.|.+|.|++++.+ +.++|||||+|.+.++|.+|++.|||..++||.
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            3456899999963     2368999999999999999999998654 689999999999999999999999999999999


Q ss_pred             EEEEEccc
Q 025814          210 IKLRKSKW  217 (247)
Q Consensus       210 l~V~~a~~  217 (247)
                      |+|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999864

>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=99.69  E-value=8.3e-17  Score=126.45  Aligned_cols=83  Identities=18%  Similarity=0.395  Sum_probs=75.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCC--CcceEEEEEecCHHHHHHHHHHhCCceeC---CEeEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTG--KTKGYGFISFANPSDIAAALKEMNGKYVG---NRPIK  211 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg--~~kg~~FV~f~~~~~a~~Al~~l~g~~i~---g~~l~  211 (247)
                      +.++|||+|||+++++++|+++|+.||.|.+|++++++.+|  .++|||||+|.+.++|++|++.|||..+.   ++.|.
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            45699999999999999999999999999999999998877  89999999999999999999999998775   67888


Q ss_pred             EEEccccc
Q 025814          212 LRKSKWQE  219 (247)
Q Consensus       212 V~~a~~k~  219 (247)
                      +..+....
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88776543

>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=99.69  E-value=2.4e-17  Score=115.98  Aligned_cols=77  Identities=13%  Similarity=0.276  Sum_probs=65.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+|||+++++++|+++|+.||.|.+|+|+++     ++|||||+|.+.++|++++..  +..++|+.|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecC
Confidence            4569999999999999999999999999999999765     689999999999999764321  345699999999998


Q ss_pred             cccc
Q 025814          217 WQER  220 (247)
Q Consensus       217 ~k~~  220 (247)
                      ++..
T Consensus        77 ~~~~   80 (88)
T 1wf0_A           77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.69  E-value=8.4e-17  Score=136.54  Aligned_cols=82  Identities=23%  Similarity=0.397  Sum_probs=75.3

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHH----HHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLS----KAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPI  210 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~----~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l  210 (247)
                      ....++|||+||++++++++|+    ++|+.||.|.+|++++   +|.++|||||+|.+.++|.+||+.|||..|.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4556799999999999999976    8999999999999876   68899999999999999999999999999999999


Q ss_pred             EEEEccccc
Q 025814          211 KLRKSKWQE  219 (247)
Q Consensus       211 ~V~~a~~k~  219 (247)
                      +|.+++.+.
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999997654

>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=99.69  E-value=4.5e-17  Score=127.25  Aligned_cols=79  Identities=24%  Similarity=0.562  Sum_probs=73.7

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||+++++++|+++|+.||.|.+|++++++.+|.++|||||+|.+.++|.+|+..  +..++|+.|.|.++..
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccccc
Confidence            46899999999999999999999999999999999999999999999999999999999974  6789999999988865


Q ss_pred             c
Q 025814          218 Q  218 (247)
Q Consensus       218 k  218 (247)
                      +
T Consensus        81 ~   81 (167)
T 2cjk_A           81 R   81 (167)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.68  E-value=1.8e-16  Score=127.83  Aligned_cols=78  Identities=9%  Similarity=0.047  Sum_probs=71.6

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||+++++++|+++|+.||.|.+|+|.++. +|.++|||||+|.+.++|++|+..+ +..++|+.|.|.+++.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            4689999999999999999999999999999999986 6999999999999999999999665 4599999999988653

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.64  E-value=3.1e-16  Score=129.87  Aligned_cols=79  Identities=15%  Similarity=0.306  Sum_probs=70.9

Q ss_pred             CCCCcEEEEcCCCCCC---------cHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 025814          135 PENDYRLFCGDLGNEV---------NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV  205 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~---------~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i  205 (247)
                      ....++||||||+..+         ++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|+.|++.|||..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4456799999999998         79999999999999999999864      78999999999999999999999999


Q ss_pred             ------------CCEeEEEEEccccc
Q 025814          206 ------------GNRPIKLRKSKWQE  219 (247)
Q Consensus       206 ------------~g~~l~V~~a~~k~  219 (247)
                                  .|+.|.|++|+...
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             eccccccccccCCCCEEEEEEccCCC
Confidence                        89999999997543

>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=99.63  E-value=5.4e-16  Score=128.01  Aligned_cols=79  Identities=22%  Similarity=0.354  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          135 PENDYRLFCGDLGN-EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~-~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ....++|||+|||+ ++++++|+++|+.||.|.+|+|++++     +|||||+|.+.++|++|++.|||..|+|+.|+|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            45567999999999 99999999999999999999999885     7899999999999999999999999999999999


Q ss_pred             Ecccc
Q 025814          214 KSKWQ  218 (247)
Q Consensus       214 ~a~~k  218 (247)
                      +++.+
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            99755

>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=99.62  E-value=3.2e-15  Score=109.90  Aligned_cols=82  Identities=15%  Similarity=0.302  Sum_probs=70.2

Q ss_pred             CCCCcEEEEcCCCCCCc-----------HHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCc
Q 025814          135 PENDYRLFCGDLGNEVN-----------DDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK  203 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~-----------e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~  203 (247)
                      +...++|+|.||-....           +++|+++|++||.|.+|.| .++   .++|||||+|.+.++|.+|+..|||.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            45567999999944432           5899999999999999955 553   37999999999999999999999999


Q ss_pred             eeCCEeEEEEEcccccc
Q 025814          204 YVGNRPIKLRKSKWQER  220 (247)
Q Consensus       204 ~i~g~~l~V~~a~~k~~  220 (247)
                      .|+|+.|+|.++.++.+
T Consensus        88 ~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           88 WFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             EETTEECEEEECCSCCC
T ss_pred             EECCcEEEEEEeCCCCC
Confidence            99999999999987653

>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=99.62  E-value=1.8e-16  Score=124.93  Aligned_cols=83  Identities=31%  Similarity=0.462  Sum_probs=73.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|..||.+.. .++++..+|.++|||||+|.+.++|.+|+ .|||..|+|+.|+|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            556789999999999999999999999998766 34455568999999999999999999999 6999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +..+.
T Consensus        88 ~~~~~   92 (175)
T 1fje_B           88 PKGRD   92 (175)
T ss_dssp             CCCSS
T ss_pred             CCCcc
Confidence            87654

>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=6.7e-16  Score=124.20  Aligned_cols=76  Identities=22%  Similarity=0.373  Sum_probs=71.5

Q ss_pred             CcEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          138 DYRLFCGDLGN-EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       138 ~~~lfV~nLp~-~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      .++|||+|||+ ++++++|+++|+.||.|.+|++++++     +|||||+|.+.++|.+|+..|||..++|+.|+|.+++
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            45899999999 99999999999999999999998874     7899999999999999999999999999999999997


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      .+
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.60  E-value=6e-16  Score=112.44  Aligned_cols=72  Identities=17%  Similarity=0.350  Sum_probs=65.0

Q ss_pred             EcCCCCCCcHHHHHHHh------------ccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeE
Q 025814          143 CGDLGNEVNDDVLSKAF------------SRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPI  210 (247)
Q Consensus       143 V~nLp~~~~e~~L~~~F------------~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l  210 (247)
                      +.||++.+++++|+++|            ++||.|.+|.|+++. +|.++|||||+|.+.++|.+|+..|||..++||.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56788888888887776            999999999999986 58999999999999999999999999999999999


Q ss_pred             EEEEc
Q 025814          211 KLRKS  215 (247)
Q Consensus       211 ~V~~a  215 (247)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99875

>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=99.58  E-value=5.2e-15  Score=107.63  Aligned_cols=81  Identities=15%  Similarity=0.147  Sum_probs=69.7

Q ss_pred             CCcEEEEcCC--CCCCc--------HHHHHHHhccCCCeeEEEEEecCCC--CCcceEEEEEecCHHHHHHHHHHhCCce
Q 025814          137 NDYRLFCGDL--GNEVN--------DDVLSKAFSRFPSFNMAKVVRDKRT--GKTKGYGFISFANPSDIAAALKEMNGKY  204 (247)
Q Consensus       137 ~~~~lfV~nL--p~~~~--------e~~L~~~F~~~G~i~~v~i~~~~~t--g~~kg~~FV~f~~~~~a~~Al~~l~g~~  204 (247)
                      +.+.|.|.|+  +.++.        +++|++.|++||.|.+|.|++++.+  +.++||+||+|.+.++|.+|++.|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            3457899998  33333        3689999999999999999998754  4689999999999999999999999999


Q ss_pred             eCCEeEEEEEccc
Q 025814          205 VGNRPIKLRKSKW  217 (247)
Q Consensus       205 i~g~~l~V~~a~~  217 (247)
                      ++||.|+|.+...
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999999753

>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=99.58  E-value=6.1e-15  Score=124.06  Aligned_cols=78  Identities=24%  Similarity=0.520  Sum_probs=71.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.+.++      +|||||+|.+.++|.+|+..|||..|+|+.|+|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            455679999999999999999999999999999999654      68999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      +...
T Consensus        93 a~~~   96 (261)
T 3sde_A           93 ATHG   96 (261)
T ss_dssp             CCCS
T ss_pred             cccC
Confidence            8753

>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=99.57  E-value=1.4e-14  Score=107.42  Aligned_cols=79  Identities=13%  Similarity=0.257  Sum_probs=69.4

Q ss_pred             CcEEEEcCCCC--C---CcHHHHHHHhccCCCeeEEEEEecCC----CCCcceEEEEEecCHHHHHHHHHHhCCceeCCE
Q 025814          138 DYRLFCGDLGN--E---VNDDVLSKAFSRFPSFNMAKVVRDKR----TGKTKGYGFISFANPSDIAAALKEMNGKYVGNR  208 (247)
Q Consensus       138 ~~~lfV~nLp~--~---~~e~~L~~~F~~~G~i~~v~i~~~~~----tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~  208 (247)
                      .++|+|.|+-.  +   --+++|++.|++||.|.+|.|++++.    ++.++||+||+|.+.++|.+|++.|||..++||
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR   99 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR   99 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            44899999832  1   23689999999999999999999864    467889999999999999999999999999999


Q ss_pred             eEEEEEcc
Q 025814          209 PIKLRKSK  216 (247)
Q Consensus       209 ~l~V~~a~  216 (247)
                      .|+|.+..
T Consensus       100 ~i~v~~~~  107 (118)
T 3ue2_A          100 KVVAEVYD  107 (118)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEcC
Confidence            99999975

>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=99.54  E-value=1.4e-14  Score=113.42  Aligned_cols=75  Identities=15%  Similarity=0.372  Sum_probs=66.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccC----C-------CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRF----P-------SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV  205 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~----G-------~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i  205 (247)
                      +.++|||+|||+++++++|+++|+.|    |       .|.++.+.      .++|||||+|.+.++|.+|+ .|||..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            34699999999999999999999999    6       66666664      34789999999999999999 9999999


Q ss_pred             CCEeEEEEEcccc
Q 025814          206 GNRPIKLRKSKWQ  218 (247)
Q Consensus       206 ~g~~l~V~~a~~k  218 (247)
                      +|+.|+|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.53  E-value=1.5e-14  Score=115.97  Aligned_cols=74  Identities=15%  Similarity=0.385  Sum_probs=65.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccC----C-------CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRF----P-------SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG  206 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~----G-------~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~  206 (247)
                      .++|||+|||+++++++|+++|+.|    |       .|.++.+      +.++|||||+|.+.++|++|+ .|||..|+
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            4699999999999999999999999    4       4555544      456899999999999999999 89999999


Q ss_pred             CEeEEEEEcccc
Q 025814          207 NRPIKLRKSKWQ  218 (247)
Q Consensus       207 g~~l~V~~a~~k  218 (247)
                      |+.|+|.++...
T Consensus        77 g~~i~v~~~~~~   88 (198)
T 2yh0_A           77 GQSLKIRRPHDY   88 (198)
T ss_dssp             TEEEEEECCCCC
T ss_pred             CceEEEeCCCCC
Confidence            999999988754

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=3.2e-13  Score=97.13  Aligned_cols=65  Identities=18%  Similarity=0.260  Sum_probs=58.0

Q ss_pred             CCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          148 NEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       148 ~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      ..+++++|+++|++||.|.+|.|+     +.++|||||+|.+.++|+.|++.+++  +.|+.|+|.+++.+.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            468999999999999999999987     46799999999999999999988555  679999999987654

>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=99.46  E-value=1.3e-13  Score=119.90  Aligned_cols=76  Identities=20%  Similarity=0.262  Sum_probs=64.7

Q ss_pred             CCCCcEEEEcC--CCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---CE-
Q 025814          135 PENDYRLFCGD--LGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG---NR-  208 (247)
Q Consensus       135 ~~~~~~lfV~n--Lp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~---g~-  208 (247)
                      .....+|||||  |++.+++++|+++|++||.|.+|.+..      +||||||+|.+.++|++|++.|||.++.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            45566999999  588999999999999999999887643      4799999999999999999999999872   44 


Q ss_pred             -eEEEEEcc
Q 025814          209 -PIKLRKSK  216 (247)
Q Consensus       209 -~l~V~~a~  216 (247)
                       .|.|.+..
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             57777763

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=8.5e-13  Score=91.97  Aligned_cols=74  Identities=24%  Similarity=0.305  Sum_probs=63.7

Q ss_pred             CCCCcEEEEcCCC----CCCcH----HHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q 025814          135 PENDYRLFCGDLG----NEVND----DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG  206 (247)
Q Consensus       135 ~~~~~~lfV~nLp----~~~~e----~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~  206 (247)
                      ++++.||+|..++    ..+-+    .+|.+.|.+||.|..++++.|+        +||+|.+.++|.+||+ |||..++
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeC
Confidence            5566799998776    23333    5788999999999999999883        8999999999999997 9999999


Q ss_pred             CEeEEEEEccc
Q 025814          207 NRPIKLRKSKW  217 (247)
Q Consensus       207 g~~l~V~~a~~  217 (247)
                      ||.|+|+++++
T Consensus        75 Gr~LkV~lkt~   85 (91)
T 2dnr_A           75 NRTITIALKSP   85 (91)
T ss_dssp             TEEEEEEECCC
T ss_pred             CeEEEEEeCCC
Confidence            99999999874

>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=99.39  E-value=6.2e-13  Score=97.92  Aligned_cols=75  Identities=11%  Similarity=0.139  Sum_probs=62.9

Q ss_pred             CcEEEEcCCCCCC----------cHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q 025814          138 DYRLFCGDLGNEV----------NDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN  207 (247)
Q Consensus       138 ~~~lfV~nLp~~~----------~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g  207 (247)
                      .+.|.|.|+=..-          -+++|++.|++||.|.+|.|.++.    .+||+||+|.+.++|.+|++.|||..++|
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3467777762211          235889999999999999987663    48999999999999999999999999999


Q ss_pred             EeEEEEEcc
Q 025814          208 RPIKLRKSK  216 (247)
Q Consensus       208 ~~l~V~~a~  216 (247)
                      |.|+|.++.
T Consensus        83 R~i~v~~~~   91 (114)
T 3s6e_A           83 KMITAAYVP   91 (114)
T ss_dssp             EECEEEEEC
T ss_pred             EEEEEEEEc
Confidence            999999985

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.32  E-value=4.1e-12  Score=93.97  Aligned_cols=83  Identities=14%  Similarity=0.135  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecC-HHHHHHHHHHhC--CceeCCEeE
Q 025814          135 PENDYRLFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFAN-PSDIAAALKEMN--GKYVGNRPI  210 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~-~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~-~~~a~~Al~~l~--g~~i~g~~l  210 (247)
                      -..++.|||+||++. ++.++|+++|+.||.|..|.++++..      .|||.|.+ .++|..|++.||  |..|.|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            456779999999999 99999999999999999999998854      59999999 899999999995  778999999


Q ss_pred             EEEEccccccccH
Q 025814          211 KLRKSKWQERTDF  223 (247)
Q Consensus       211 ~V~~a~~k~~~~~  223 (247)
                      +++.-.......+
T Consensus        89 ~~evL~GeeE~~y  101 (121)
T 1owx_A           89 TWEVLEGEVEKEA  101 (121)
T ss_dssp             EEEECCHHHHHHH
T ss_pred             EEEECCCHHHHHH
Confidence            9998877665443

>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=99.25  E-value=1.4e-11  Score=86.25  Aligned_cols=73  Identities=12%  Similarity=0.256  Sum_probs=63.1

Q ss_pred             CCCCcEEEEcCCCCC------CcH---HHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 025814          135 PENDYRLFCGDLGNE------VND---DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV  205 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~------~~e---~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i  205 (247)
                      .+++.||+|..++..      ..+   .+|.+.|.+||.|..++++.|+        +||+|.+.++|.+||+ |||..+
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeee
Confidence            667779999988642      332   4688999999999999999984        9999999999999997 999999


Q ss_pred             CCEeEEEEEcc
Q 025814          206 GNRPIKLRKSK  216 (247)
Q Consensus       206 ~g~~l~V~~a~  216 (247)
                      +||.|+|++..
T Consensus        83 ~Gr~L~V~~k~   93 (95)
T 1ufw_A           83 KGRAVKISGPS   93 (95)
T ss_dssp             TTEEEEEECCC
T ss_pred             CCeEEEEeccC
Confidence            99999998754

>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=99.10  E-value=1.8e-10  Score=94.31  Aligned_cols=67  Identities=15%  Similarity=0.279  Sum_probs=60.9

Q ss_pred             CcHHHHHHHhccCCCeeEEEEEecC----CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          150 VNDDVLSKAFSRFPSFNMAKVVRDK----RTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       150 ~~e~~L~~~F~~~G~i~~v~i~~~~----~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      -.+++|.+.|++||.|.++.|.++.    .+|.++|++||+|.+.++|.+|++.|||..++||.|.|.+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            4568899999999999999998654    455899999999999999999999999999999999999975

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.64  E-value=1.5e-07  Score=67.26  Aligned_cols=74  Identities=16%  Similarity=0.140  Sum_probs=66.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccC-----CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRF-----PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPI  210 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~-----G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l  210 (247)
                      ++.++|-+-|||..+++..|+.+++.+     |.|..+.++.|.      |-|+|+|.+...|-+|.-.|||.+|.||+|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            345689999999999999999999999     999999998884      479999999999999998999999999999


Q ss_pred             EEEEc
Q 025814          211 KLRKS  215 (247)
Q Consensus       211 ~V~~a  215 (247)
                      ++.--
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            99654

>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=97.96  E-value=1.1e-06  Score=64.03  Aligned_cols=81  Identities=9%  Similarity=0.049  Sum_probs=39.2

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      |.+..+....+..  .+++++||+|++.++|.+|+.   +..++++.+.+.....+.......     ........+|||
T Consensus        30 G~v~~v~i~~d~~--~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~~~-----~~~~~~~~~lyv  102 (115)
T 4f25_A           30 GNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL-----GARAKEFTNVYI  102 (115)
T ss_dssp             SCEEEEEEEEETT--EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC----------------------
T ss_pred             CCEEEEEEeecCC--CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcccccccc-----ccccCCCCceEe
Confidence            6666655555433  368999999999999988874   567889988887766554332211     111334457999


Q ss_pred             cCCCCCCcHHH
Q 025814          144 GDLGNEVNDDV  154 (247)
Q Consensus       144 ~nLp~~~~e~~  154 (247)
                      +||++++|++.
T Consensus       103 ~Nl~~~~T~~a  113 (115)
T 4f25_A          103 KNFGPGSTRAA  113 (115)
T ss_dssp             -----------
T ss_pred             CCCCCCccccc
Confidence            99999999863

>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=97.84  E-value=5.9e-05  Score=53.50  Aligned_cols=73  Identities=16%  Similarity=0.149  Sum_probs=61.0

Q ss_pred             cEEEEcCCCCCC-cH----HHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          139 YRLFCGDLGNEV-ND----DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       139 ~~lfV~nLp~~~-~e----~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ++|+|.||+.++ ..    +.++.+|..|+.+......+.=     + =..|.|.+.++|.+|-..|++..++|+.|+|-
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF-----R-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~Y   79 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-----K-RVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT-----T-EEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc-----e-EEEEEeCChHHHHHHHHHhccceecCceeEEE
Confidence            489999998876 22    5678999999999887776541     1 35799999999999999999999999999999


Q ss_pred             Eccc
Q 025814          214 KSKW  217 (247)
Q Consensus       214 ~a~~  217 (247)
                      ++..
T Consensus        80 Fgq~   83 (104)
T 1wey_A           80 FAQT   83 (104)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9873

>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=97.71  E-value=0.00026  Score=49.44  Aligned_cols=57  Identities=21%  Similarity=0.340  Sum_probs=47.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN  201 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~  201 (247)
                      .....++| ++|.++...||.++|+.||.| .|+++.|.       -|||.|.+++.|..|+..++
T Consensus        14 ~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            33445666 999999999999999999954 57777773       89999999999999998663

>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=97.59  E-value=0.00036  Score=48.48  Aligned_cols=67  Identities=13%  Similarity=0.225  Sum_probs=56.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCc--ceEEEEEecCHHHHHHHHHHhCCceeC
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKT--KGYGFISFANPSDIAAALKEMNGKYVG  206 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~--kg~~FV~f~~~~~a~~Al~~l~g~~i~  206 (247)
                      +|-|++||+.++++++.+.++..+.+.....+..+.+.+.  -+-|||.|.+.+++..-.+.++|..+.
T Consensus         3 KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            3 KVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             EEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             EEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            7999999999999999999999988777777666544332  256899999999999999999999763

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.54  E-value=0.0006  Score=48.14  Aligned_cols=71  Identities=17%  Similarity=0.164  Sum_probs=57.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhcc-----CCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSR-----FPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~-----~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      +.+|.|.|||..++++.|.-+|+.     -|.|.+|....        +-|+|+|.+.+.+++.|+ -..+.|+|..|.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV   78 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLA-QADHELHGAQLSL   78 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhc-CCcceecCeEEEE
Confidence            458999999999999999999976     25777777643        368999999999999984 3466788888998


Q ss_pred             EEccc
Q 025814          213 RKSKW  217 (247)
Q Consensus       213 ~~a~~  217 (247)
                      .-.-.
T Consensus        79 ~P~~~   83 (104)
T 2dhx_A           79 RPAPP   83 (104)
T ss_dssp             EECCC
T ss_pred             EcCCC
Confidence            66443

>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=97.50  E-value=0.00019  Score=50.27  Aligned_cols=53  Identities=21%  Similarity=0.290  Sum_probs=46.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN  201 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~  201 (247)
                      .++| ++|.++...||.++|+.|| -..|+++.|.       -|||.|.+++.|..|+..++
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            4556 9999999999999999999 4567888773       89999999999999998765

>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=97.22  E-value=0.0019  Score=46.96  Aligned_cols=71  Identities=11%  Similarity=0.166  Sum_probs=56.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC-EeEEEEEc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN-RPIKLRKS  215 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g-~~l~V~~a  215 (247)
                      +.+.|.|.+.+... -+.+.+.|++||.|.+.....    +  ..+-.|.|.+..+|++|| ..||..|+| -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~----~--~NWihI~Y~s~~~A~rAL-~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN----T--GNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS----S--SSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC----C--CCeEEEEeCCHHHHHHHH-HhCCeEecCCEEEEEEEC
Confidence            35578898999985 556778899999999877621    1  238899999999999999 569999984 66777664

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=96.97  E-value=0.00072  Score=47.43  Aligned_cols=63  Identities=14%  Similarity=-0.014  Sum_probs=45.1

Q ss_pred             CCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEcCCCC
Q 025814           83 QRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGN  148 (247)
Q Consensus        83 ~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~nLp~  148 (247)
                      .++++||+|++.++|.+|+.   +..+.++.+.+..+..+.........+..   .....+||||||+.
T Consensus        36 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~~~~~~~~---~~~~~~ifvg~L~h  101 (101)
T 2hvz_A           36 PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPAR---RKLLEVLFNGPLEH  101 (101)
T ss_dssp             SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSSCCCSCCCS---CCCCSCCCSCCCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCcccCCCCCcc---ccCCCceecCCCCC
Confidence            68999999999999888875   56788999988887766544333222211   23355899999963

>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=96.62  E-value=0.0017  Score=49.35  Aligned_cols=35  Identities=11%  Similarity=0.121  Sum_probs=29.9

Q ss_pred             EEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCc
Q 025814          167 MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK  203 (247)
Q Consensus       167 ~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~  203 (247)
                      .++|+++.  ..++|||||+|.+.++|++|++.+++.
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            56788874  468999999999999999999888754

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.54  E-value=0.0031  Score=44.12  Aligned_cols=67  Identities=15%  Similarity=0.221  Sum_probs=48.9

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCc--ceEEEEEecCHHHHHHHHHHhCCceeC
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKT--KGYGFISFANPSDIAAALKEMNGKYVG  206 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~--kg~~FV~f~~~~~a~~Al~~l~g~~i~  206 (247)
                      +|-|++||+.+||+++.+.++..-.+.....+..+.+.+.  -+-|||.|.+.+++..-.+.++|..+.
T Consensus        11 KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A           11 MVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             eEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            7999999999999998888877655432222222222111  134899999999999999999999663

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.25  E-value=0.0051  Score=45.35  Aligned_cols=76  Identities=14%  Similarity=0.159  Sum_probs=53.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeE-EEEEec------------CCCC-CcceEEEEEecCHHHHHHHHHHhCCce
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNM-AKVVRD------------KRTG-KTKGYGFISFANPSDIAAALKEMNGKY  204 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~-v~i~~~------------~~tg-~~kg~~FV~f~~~~~a~~Al~~l~g~~  204 (247)
                      ..|.|-+.|.+.. ..+.+.|++||.|.+ +.+.++            +..+ ...++-.|.|++..+|.+|| ..||..
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTTCE
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCCeE
Confidence            3677888977655 456778999999865 221110            0001 12346789999999999999 679999


Q ss_pred             eCCEeEEEEEcc
Q 025814          205 VGNRPIKLRKSK  216 (247)
Q Consensus       205 i~g~~l~V~~a~  216 (247)
                      |+|..|-|..-+
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999988887654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=96.19  E-value=0.0043  Score=42.73  Aligned_cols=57  Identities=9%  Similarity=0.040  Sum_probs=44.9

Q ss_pred             CccccccccchhhhcCCCceeeCccCHHHHHHHHhcC----ccchhhhhhcccccccccCC
Q 025814           68 PVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS----DIEHKAETKKKSIPRKAAGQ  124 (247)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~----~~~~~~~~~~~~~~r~~~~~  124 (247)
                      .+..+....+..+..++|++||+|++.++|.+|++..    .+.++.+.+..+.++.....
T Consensus        28 ~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~~~~   88 (91)
T 2lxi_A           28 QAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPKINE   88 (91)
T ss_dssp             CCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCCCCSC
T ss_pred             EeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCCCCCC
Confidence            4666666677778889999999999999999998642    57899998888776655443

>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=96.14  E-value=0.003  Score=47.65  Aligned_cols=42  Identities=12%  Similarity=0.060  Sum_probs=37.8

Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHh-CCceeCCEeEEEEEcccc
Q 025814          176 TGKTKGYGFISFANPSDIAAALKEM-NGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       176 tg~~kg~~FV~f~~~~~a~~Al~~l-~g~~i~g~~l~V~~a~~k  218 (247)
                      ....+|+++|+|.+.++|++|++.| ||..++| .|.+.++..+
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            4567899999999999999999999 9999999 9999887654

>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=96.12  E-value=0.0012  Score=47.40  Aligned_cols=74  Identities=9%  Similarity=0.083  Sum_probs=53.9

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEE
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFC  143 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV  143 (247)
                      |.+..+....+   ...++++||+|.+.++|..|+.   +..+.++.+.+..+..+...                     
T Consensus        33 G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~---------------------   88 (115)
T 3lqv_A           33 GPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAF---------------------   88 (115)
T ss_dssp             SCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHHT---------------------
T ss_pred             CCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCChhh---------------------
Confidence            55544433332   2348999999999999888865   56788888888776554332                     


Q ss_pred             cCCCCCCcHHHHHHHhccCCC
Q 025814          144 GDLGNEVNDDVLSKAFSRFPS  164 (247)
Q Consensus       144 ~nLp~~~~e~~L~~~F~~~G~  164 (247)
                      .++....++++|+++|++||.
T Consensus        89 ~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           89 QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             TTSCHHHHHHHHHHHHHHHCC
T ss_pred             hhhhHhHhHHHHHHHHHHhCC
Confidence            456778899999999999984

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.09  E-value=0.0025  Score=57.22  Aligned_cols=53  Identities=15%  Similarity=0.257  Sum_probs=40.5

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHH
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK  198 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~  198 (247)
                      .|||. .+..+++.+|.++|++||.|.++....++  |   .|+.|+|.+.+++..++.
T Consensus        55 sv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           55 TVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             EEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHS
T ss_pred             eEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHh
Confidence            79997 79999999999999999999999887653  2   599999999999887763

>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=93.98  E-value=0.054  Score=38.82  Aligned_cols=54  Identities=17%  Similarity=0.080  Sum_probs=41.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      |.+..+....+. ....++++||+|++.++|.+|+.   +..+.++.+.+..+..+..
T Consensus        32 G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   88 (116)
T 2fy1_A           32 GPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF   88 (116)
T ss_dssp             SCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSSC
T ss_pred             CCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            666666555555 67789999999999999999886   4578898888887765543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.97  E-value=0.073  Score=36.31  Aligned_cols=56  Identities=7%  Similarity=0.059  Sum_probs=43.1

Q ss_pred             CCcccc-ccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccccc
Q 025814           67 APVYSL-PQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAA  122 (247)
Q Consensus        67 ~~~~~~-~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~  122 (247)
                      +.+..+ ....+......++++||+|++.++|.+|+.   +..+.++.+.+..+..+...
T Consensus        30 G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   89 (96)
T 1x5t_A           30 GVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK   89 (96)
T ss_dssp             SCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCC
T ss_pred             CCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCCC
Confidence            666666 566666677889999999999999999987   34678888888777665443

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=93.92  E-value=0.033  Score=39.44  Aligned_cols=55  Identities=20%  Similarity=0.173  Sum_probs=42.3

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhccccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETKKKSIPRK  120 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~~r~  120 (247)
                      +|.+..+....+..+..++|++||+|++.+++.+|+...  .++++.+.+..+..+.
T Consensus        49 ~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a~~~~  105 (109)
T 2rs2_A           49 FGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRR  105 (109)
T ss_dssp             TSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEECCCCC
T ss_pred             cCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEccCCC
Confidence            366767666666667888999999999999999999754  5677777776665443

>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=93.92  E-value=0.027  Score=38.29  Aligned_cols=52  Identities=6%  Similarity=0.022  Sum_probs=38.1

Q ss_pred             CccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           68 PVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      .+..+....+..+..++|++||+|++.+++.+|+.   +..+.++.+.+..+.+.
T Consensus        29 ~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~   83 (90)
T 3p5t_L           29 DILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKL   83 (90)
T ss_dssp             CCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC---
T ss_pred             ceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCC
Confidence            56666666666778889999999999999888874   56788888887665543

>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=93.79  E-value=0.039  Score=38.89  Aligned_cols=56  Identities=9%  Similarity=0.068  Sum_probs=42.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---------cCccchhhhhhccccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---------SSDIEHKAETKKKSIPRKAA  122 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---------~~~~~~~~~~~~~~~~r~~~  122 (247)
                      +.+..+....+..+...++++||+|++.++|.+|+.         ...+.++.+.+..+..+...
T Consensus        40 G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           40 GDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             SCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCC
T ss_pred             CCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCccC
Confidence            666666666666667789999999999999999886         44678888888777665443

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.73  E-value=0.061  Score=37.22  Aligned_cols=56  Identities=13%  Similarity=0.069  Sum_probs=43.0

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      ++.+..+....+......++++||+|++.++|.+|+.   +..+.++.+.+..+..+..
T Consensus        36 ~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2cqb_A           36 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI   94 (102)
T ss_dssp             TSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             cCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCC
Confidence            3666666666666677889999999999999999874   4578888888877665543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=93.57  E-value=0.047  Score=37.65  Aligned_cols=55  Identities=27%  Similarity=0.193  Sum_probs=42.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh--cCccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+..+..+++++||+|++.+++.+|++  ...+.++.+.+..+..+..
T Consensus        35 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a~~~~~   91 (99)
T 2dgs_A           35 GVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPRDS   91 (99)
T ss_dssp             SCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEECCCCCC
T ss_pred             CCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEECCCCcc
Confidence            666666666666677789999999999999999986  3467888888877765544

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.42  E-value=0.068  Score=38.01  Aligned_cols=57  Identities=16%  Similarity=0.195  Sum_probs=44.9

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhccccccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRKAA  122 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~~~  122 (247)
                      ++.+..+....+..+...++++||+|++.+++.+|+..  ..+.++.+.+..+..+...
T Consensus        51 ~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~~~~  109 (116)
T 1x4b_A           51 WGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREES  109 (116)
T ss_dssp             SCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSCCCC
T ss_pred             cCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCCCccC
Confidence            46777776666667778899999999999999999976  3578888888777666543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=93.40  E-value=0.024  Score=39.51  Aligned_cols=54  Identities=4%  Similarity=-0.092  Sum_probs=41.3

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccch-hhhhhcccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEH-KAETKKKSIPR  119 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~-~~~~~~~~~~r  119 (247)
                      +|.+..+....+..+..++|++||+|++.++|.+|+.   +..+.+ +.+.+..+.++
T Consensus        36 ~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           36 AGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDV   93 (100)
T ss_dssp             TSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHHH
T ss_pred             cCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECchh
Confidence            3777777777777778899999999999998888874   457777 77766655443

>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=93.36  E-value=0.019  Score=40.04  Aligned_cols=52  Identities=8%  Similarity=-0.040  Sum_probs=40.1

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSI  117 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~  117 (247)
                      +|.+..+....+..+..++|++||+|++.++|.+|+.   +..+.++.+.+..+.
T Consensus        43 ~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           43 IGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             TSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            3777777666777778889999999999999988875   467788877776543

>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=93.25  E-value=0.049  Score=37.50  Aligned_cols=55  Identities=15%  Similarity=-0.017  Sum_probs=42.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+......++++||+|++.++|.+|+.   +..+.++.+.+..+..+..
T Consensus        33 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   90 (99)
T 1whw_A           33 GPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             SCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             CCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCcc
Confidence            666666666666677889999999999999999884   4467888888877766544

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=93.09  E-value=0.023  Score=40.55  Aligned_cols=53  Identities=6%  Similarity=-0.025  Sum_probs=42.0

Q ss_pred             CCCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccc
Q 025814           65 PVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSI  117 (247)
Q Consensus        65 P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~  117 (247)
                      .+|.+..+....+..+..++|++||+|++.++|.+|+.   +..+.++.+.+..+.
T Consensus        29 ~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A           29 KYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             hcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            34778777777777788899999999999999998875   557788877765543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=92.99  E-value=0.029  Score=38.97  Aligned_cols=48  Identities=13%  Similarity=0.026  Sum_probs=35.8

Q ss_pred             ccccccccchhhhcCCCceeeCccCHHHHHHHHhc---C----ccchhhhhhccc
Q 025814           69 VYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---S----DIEHKAETKKKS  116 (247)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~----~~~~~~~~~~~~  116 (247)
                      +..+....+..+..+||++||+|++.++|.+|+..   .    .++++.+.+..+
T Consensus        38 v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~A   92 (95)
T 2lkz_A           38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA   92 (95)
T ss_dssp             GGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEEC
T ss_pred             EEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEc
Confidence            45666667777889999999999999888888763   2    266776665543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=92.95  E-value=0.062  Score=36.62  Aligned_cols=58  Identities=12%  Similarity=0.084  Sum_probs=44.6

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccC
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAG  123 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~  123 (247)
                      ++.+..+....+..+..+++++||+|++.+++.+|+.   +..+.++.+.+..+..+...+
T Consensus        29 ~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   89 (95)
T 2dnz_A           29 FGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDGG   89 (95)
T ss_dssp             TSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCCCC
T ss_pred             cCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccCCC
Confidence            3666666666666677889999999999999988875   467889998888877665443

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=92.91  E-value=0.062  Score=34.87  Aligned_cols=47  Identities=15%  Similarity=0.018  Sum_probs=34.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhh
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETK  113 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~  113 (247)
                      |.+..+....+.....+++++||+|++.+++.+|+..  ..++++.+.+
T Consensus        24 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v   72 (75)
T 2mss_A           24 GKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVEC   72 (75)
T ss_dssp             SCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEE
T ss_pred             CCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEE
Confidence            6666666666666778899999999999999999863  3455555443

>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=92.31  E-value=0.067  Score=36.63  Aligned_cols=54  Identities=19%  Similarity=0.092  Sum_probs=40.9

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~  120 (247)
                      |.+..+....+.....+++++||+|++.++|.+|+.   +..+.++.+.+..+..+.
T Consensus        27 G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   83 (96)
T 2x1f_A           27 GPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD   83 (96)
T ss_dssp             SCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSS
T ss_pred             CCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCC
Confidence            666666666666667889999999999999988874   457888888777665443

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=92.26  E-value=0.12  Score=36.00  Aligned_cols=55  Identities=7%  Similarity=-0.046  Sum_probs=41.5

Q ss_pred             CCccccccccc-hhhhcCCCceeeCccCHHHHHHHHh----cCccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQ-AQQLFQRDAQTITPEALESVKAALA----SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~-~~~~~~~~~~~v~~~~~~~a~~al~----~~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+ ......++++||+|++.++|.+|+.    ...+.++.+.+..+..+..
T Consensus        40 G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~   99 (107)
T 2cph_A           40 GELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT   99 (107)
T ss_dssp             SCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCC
T ss_pred             CCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCC
Confidence            66666655555 4567789999999999999988875    4578888888877765543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.13  E-value=0.095  Score=36.21  Aligned_cols=54  Identities=9%  Similarity=0.102  Sum_probs=40.3

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~  120 (247)
                      +.+..+....+......++++||+|++.++|.+|+.   ...+.++.+.+..+..+.
T Consensus        37 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   93 (102)
T 1x5s_A           37 GQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSS   93 (102)
T ss_dssp             SCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCC
T ss_pred             CCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            555555555555566789999999999999988874   567888888887765544

>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=92.11  E-value=0.077  Score=34.36  Aligned_cols=47  Identities=17%  Similarity=0.038  Sum_probs=34.0

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhh
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETK  113 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~  113 (247)
                      |.+..+....+.....+++++||+|++.+++.+|+...  .+.++.+.+
T Consensus        24 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v   72 (75)
T 1iqt_A           24 GEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEI   72 (75)
T ss_dssp             SCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCE
T ss_pred             CCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEE
Confidence            55555555555556778999999999999999999753  455555444

>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=92.09  E-value=0.05  Score=38.68  Aligned_cols=55  Identities=15%  Similarity=0.065  Sum_probs=41.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+......++++||+|++.+++.+|+.   ...+.++.+.+..+..+..
T Consensus        50 G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~  107 (115)
T 2cpz_A           50 GNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  107 (115)
T ss_dssp             SCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             CCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCc
Confidence            566666555655567778999999999999998884   5678888888877665543

>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=92.08  E-value=0.13  Score=35.70  Aligned_cols=55  Identities=11%  Similarity=-0.023  Sum_probs=42.1

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+......++++||+|++.+++.+|+..   ..+.++.+.+..+..+..
T Consensus        40 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   97 (105)
T 1x5u_A           40 GPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK   97 (105)
T ss_dssp             SCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             CCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCc
Confidence            6666666666666777899999999999999999863   468888888877665543

>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=92.07  E-value=0.041  Score=36.45  Aligned_cols=54  Identities=9%  Similarity=-0.003  Sum_probs=40.5

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      +|.+..+....+.....+++++||+|++.++|.+|+.   +..+.++.+.+..+.++
T Consensus        25 ~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A           25 FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             STTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             cCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            3666666666666677789999999999999988875   45778887777665543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=92.00  E-value=0.4  Score=35.02  Aligned_cols=55  Identities=15%  Similarity=0.073  Sum_probs=38.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      |.+..+....+..+...++++||+|++.++|.+|+.   +..+.++.+.+..+..+..
T Consensus        67 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  124 (139)
T 1u6f_A           67 GPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             SCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             CCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            344444444444455668999999999999999886   3467888888877665543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.98  E-value=0.086  Score=36.57  Aligned_cols=56  Identities=11%  Similarity=-0.024  Sum_probs=41.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cc-cchhhhhhcccccccccC
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SD-IEHKAETKKKSIPRKAAG  123 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~-~~~~~~~~~~~~~r~~~~  123 (247)
                      +.+..+....+. ...+++++||+|++.++|.+|+..   .. +.++.+.+..+..+....
T Consensus        35 G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~~~~   94 (104)
T 2dhg_A           35 PSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRV   94 (104)
T ss_dssp             TTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCCSCC
T ss_pred             CCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCCcCC
Confidence            556565555555 666899999999999999999863   45 888888888876655443

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.85  E-value=0.041  Score=38.01  Aligned_cols=53  Identities=11%  Similarity=-0.033  Sum_probs=38.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~  120 (247)
                      +.+..+....+. ....++++||+|++.++|.+|+.   +..+.++.+.+..+.++.
T Consensus        42 G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   97 (100)
T 2do4_A           42 GTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGP   97 (100)
T ss_dssp             SCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCS
T ss_pred             CCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            556555555544 56678999999999999999884   456788888777665543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=91.81  E-value=0.09  Score=36.89  Aligned_cols=49  Identities=8%  Similarity=0.013  Sum_probs=37.4

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKK  115 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~  115 (247)
                      +|.+..+....+.. ..++|++||+|++.++|..|+..  ..+.++.+.+..
T Consensus        35 ~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~   85 (103)
T 1s79_A           35 KGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILF   85 (103)
T ss_dssp             SSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEE
T ss_pred             cCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            47777766666655 78899999999999999999973  356677666543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=91.77  E-value=0.076  Score=36.84  Aligned_cols=56  Identities=11%  Similarity=0.021  Sum_probs=43.1

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      ++.+..+....+.....+++++||+|++.++|.+|+.   +..+.++.+.+..+..+..
T Consensus        39 ~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   97 (103)
T 2cq0_A           39 FGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN   97 (103)
T ss_dssp             TCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCC
T ss_pred             CCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCC
Confidence            4777776666666667789999999999999999986   3467888888877665544

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=91.75  E-value=0.11  Score=36.88  Aligned_cols=56  Identities=4%  Similarity=-0.109  Sum_probs=42.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAA  122 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~  122 (247)
                      +.+..+....+......++++||+|++.++|.+|+.   +..+.++.+.+..+..+...
T Consensus        40 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   98 (115)
T 2dgo_A           40 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA   98 (115)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCC
T ss_pred             CCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCCC
Confidence            666666666655667778999999999999999885   45788888888877665443

>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=91.68  E-value=0.46  Score=43.14  Aligned_cols=56  Identities=23%  Similarity=0.321  Sum_probs=45.9

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNG  202 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g  202 (247)
                      ...++|+ ++..+...+|.+.|+.||.+ +|+++.+  |     .+||.|.+.+.|..+++.++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd--t-----~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD--T-----SAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS--S-----EEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC--C-----eEEEEECCHHHHHHHHHHHHh
Confidence            4467776 88899999999999999954 5666655  2     799999999999999998853

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=91.63  E-value=0.15  Score=35.87  Aligned_cols=52  Identities=13%  Similarity=0.107  Sum_probs=39.4

Q ss_pred             ccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccccc
Q 025814           71 SLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAA  122 (247)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~  122 (247)
                      .+....+..+...++++||+|++.++|.+|+.   +..+.++.+.+..+..+...
T Consensus        52 ~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           52 MIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             SEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCCS
T ss_pred             CEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCCC
Confidence            34555555677889999999999999998875   45788888888777665443

>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=91.23  E-value=0.12  Score=37.78  Aligned_cols=54  Identities=15%  Similarity=0.142  Sum_probs=40.5

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      +|.+..+....+......++++||+|++.++|.+|+.   +..+.++.+.+..+..+
T Consensus        70 ~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~  126 (129)
T 2kxn_B           70 YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK  126 (129)
T ss_dssp             TSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSS
T ss_pred             cCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            3666666666666667789999999999999988876   45678887777665443

>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=91.16  E-value=0.072  Score=35.38  Aligned_cols=48  Identities=13%  Similarity=0.047  Sum_probs=35.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKK  114 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~  114 (247)
                      |.+..+....+......++++||+|++.++|..|+.   +..+.++.+.+.
T Consensus        32 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A           32 GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             SCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            666666666666677789999999999999998874   456666665553

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.11  E-value=0.09  Score=36.43  Aligned_cols=55  Identities=7%  Similarity=-0.022  Sum_probs=41.4

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~  120 (247)
                      ++.+..+....+..+..+++++||+|++.++|.+|+.   +..+.++.+.+..+....
T Consensus        37 ~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dnm_A           37 YGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGR   94 (103)
T ss_dssp             TSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCC
T ss_pred             cCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCC
Confidence            3666666666666667789999999998887777765   567888888887766543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=91.10  E-value=0.22  Score=36.22  Aligned_cols=54  Identities=17%  Similarity=0.100  Sum_probs=41.6

Q ss_pred             CCccc--cccccchhhhcCCCceeeCccCHHHHHHHH---hcC----ccchhhhhhcccccccc
Q 025814           67 APVYS--LPQYHQAQQLFQRDAQTITPEALESVKAAL---ASS----DIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~--~~~~~~~~~~~~~~~~~v~~~~~~~a~~al---~~~----~~~~~~~~~~~~~~r~~  121 (247)
                      |.+..  +....+..+..++|++||+|++. ++.+|+   ++.    .+.++.+.+..+..+..
T Consensus        48 G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           48 AVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             CCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCC
T ss_pred             CCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCC
Confidence            66644  56667777888999999999998 777775   456    88999999887766543

>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=91.03  E-value=0.06  Score=37.38  Aligned_cols=55  Identities=7%  Similarity=-0.002  Sum_probs=41.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc-Cccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS-SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~-~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+..+..+++++||+|++.+++.+|+.. +.+.++.+.+..+..+..
T Consensus        40 G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~l~v~~a~~~~~   95 (103)
T 2cqg_A           40 GEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQS   95 (103)
T ss_dssp             SCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCTTCC
T ss_pred             CCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHcCCeeCCeEEEEEecCCCCc
Confidence            5666665555556677889999999999999999984 357788887777665544

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=90.98  E-value=0.11  Score=33.63  Aligned_cols=47  Identities=17%  Similarity=0.070  Sum_probs=35.3

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhh
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETK  113 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~  113 (247)
                      |.+..+....+.....+++++||+|++.+++.+|+...  .++++.+.+
T Consensus        25 G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v   73 (77)
T 1uaw_A           25 GEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDP   73 (77)
T ss_dssp             SCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEE
T ss_pred             CCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEE
Confidence            66666666666666788999999999999999998754  455555544

>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=90.98  E-value=0.073  Score=37.59  Aligned_cols=53  Identities=15%  Similarity=0.078  Sum_probs=39.9

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      |.+..+....+.....+++++||+|++.++|..|+.   +..+.++.+.+..+..+
T Consensus        51 G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k  106 (108)
T 2jrs_A           51 GRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER  106 (108)
T ss_dssp             SCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSS
T ss_pred             CCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccC
Confidence            666666666666667789999999999999998875   55778888777665443

>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=90.88  E-value=0.15  Score=35.17  Aligned_cols=51  Identities=10%  Similarity=0.033  Sum_probs=36.6

Q ss_pred             CCccccccccch-hhhcCCCceeeCccCHHHHHHHHh--cCccchhhhhhccccc
Q 025814           67 APVYSLPQYHQA-QQLFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSIP  118 (247)
Q Consensus        67 ~~~~~~~~~~~~-~~~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~~  118 (247)
                      | +..+....+. ....++|++||+|++.+++.+|+.  +..+.++.+.+..+..
T Consensus        44 G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~a~~   97 (100)
T 2j76_E           44 N-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQ   97 (100)
T ss_dssp             C-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEECCC
T ss_pred             C-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEeccC
Confidence            5 5555555554 467789999999999999999983  3467777777665543

>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=90.86  E-value=0.14  Score=36.84  Aligned_cols=55  Identities=9%  Similarity=0.108  Sum_probs=42.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+..+..+++++||+|++.++|.+|+.   +..+.++.+.+..+..+..
T Consensus        47 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  104 (126)
T 3ex7_B           47 GEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP  104 (126)
T ss_dssp             SCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSS
T ss_pred             CCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Confidence            666666666666677889999999999999988874   5678888888877765543

>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=90.84  E-value=0.047  Score=36.61  Aligned_cols=48  Identities=13%  Similarity=0.019  Sum_probs=36.0

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhh
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETK  113 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~  113 (247)
                      +|.+..+....+..+..+++++||+|++.+++.+|+...  .++++.+.+
T Consensus        35 ~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v   84 (87)
T 3s7r_A           35 FGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDP   84 (87)
T ss_dssp             TSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEE
T ss_pred             CCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEE
Confidence            367777666666667788999999999999999999753  355555444

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=90.53  E-value=0.19  Score=36.98  Aligned_cols=53  Identities=6%  Similarity=-0.085  Sum_probs=40.4

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      +.+..+....+......++++||+|++.+++.+|+.   +..+.++.+.+..+...
T Consensus        72 G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~  127 (135)
T 2lea_A           72 GRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  127 (135)
T ss_dssp             SCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCC
T ss_pred             CCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            666666565555667789999999999999999985   45688888877766544

>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=90.49  E-value=0.15  Score=35.34  Aligned_cols=54  Identities=11%  Similarity=0.040  Sum_probs=40.3

Q ss_pred             CCccccccccchhh-hcCCCceeeCccCHHHHHHHHh--cCccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQ-LFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~-~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~~r~~  121 (247)
                      + +..+....+..+ ..+++++||+|++.+++.+|+.  ...+.++.+.+..+..+..
T Consensus        40 G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~~   96 (104)
T 1wi8_A           40 N-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             C-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECCCCCC
T ss_pred             C-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEEccCCCC
Confidence            5 555555555554 7789999999999999999983  3467888888877766544

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=90.47  E-value=0.32  Score=34.35  Aligned_cols=53  Identities=9%  Similarity=-0.047  Sum_probs=41.2

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~~r  119 (247)
                      +.+..+....+..+..+++++||+|++.++|.+|+...  .+.++.+.+..+...
T Consensus        42 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           42 GDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLG   96 (116)
T ss_dssp             SCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTTT
T ss_pred             CCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEEEcccC
Confidence            66666666666667788999999999999999999753  577777777766543

>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=90.22  E-value=0.12  Score=36.27  Aligned_cols=53  Identities=9%  Similarity=0.054  Sum_probs=39.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      |.+..+....+.....+++++||+|++.+++..|+.   +..+.++.+.+..+..+
T Consensus        51 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  106 (110)
T 1oo0_B           51 GEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK  106 (110)
T ss_dssp             SCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEES
T ss_pred             CCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccC
Confidence            666666565666667789999999999999988875   45678887777665443

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=90.06  E-value=0.061  Score=37.48  Aligned_cols=55  Identities=16%  Similarity=0.115  Sum_probs=41.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+.....+++++||+|++.+++.+|+..  ..+.++.+.+..+..+..
T Consensus        41 G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~a~~~~~   97 (105)
T 2dh8_A           41 GEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGM   97 (105)
T ss_dssp             SCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCCSCCSSC
T ss_pred             CCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEccCCCC
Confidence            6666666666656677889999999999999999864  467788888877665543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=89.87  E-value=0.062  Score=40.82  Aligned_cols=50  Identities=10%  Similarity=0.011  Sum_probs=38.8

Q ss_pred             CccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccc
Q 025814           68 PVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSI  117 (247)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~  117 (247)
                      .+..+....+..+..++|++||+|++.++|.+|+..   ..+.++.+.+..+.
T Consensus        83 ~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~  135 (156)
T 3n9u_C           83 DVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPAT  135 (156)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECC
T ss_pred             cEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcC
Confidence            566666666667788899999999999999999864   56778777776554

>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=89.80  E-value=0.14  Score=36.27  Aligned_cols=50  Identities=0%  Similarity=-0.135  Sum_probs=35.6

Q ss_pred             CCc-cccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhcccc
Q 025814           67 APV-YSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETKKKSI  117 (247)
Q Consensus        67 ~~~-~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~  117 (247)
                      +.+ ..+....+. +...++++||+|++.++|.+||...  .+.++.+.+..+.
T Consensus        40 g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~a~   92 (114)
T 2cpy_A           40 PVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   92 (114)
T ss_dssp             CCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             CCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEECC
Confidence            555 445555555 6778999999999999999999753  4566665554443

>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=89.74  E-value=0.24  Score=34.29  Aligned_cols=54  Identities=13%  Similarity=0.079  Sum_probs=39.4

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCcc---chhhhhhccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDI---EHKAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~---~~~~~~~~~~~~r~  120 (247)
                      +.+..+....+..+..+++++||+|++.++|.+|+.   +..+   .++.+.+..+..+.
T Consensus        38 G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~   97 (106)
T 2dgp_A           38 GKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSES   97 (106)
T ss_dssp             SCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCS
T ss_pred             CCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccc
Confidence            556566555555667789999999999999988876   3344   67877777765544

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=89.72  E-value=0.12  Score=35.05  Aligned_cols=49  Identities=6%  Similarity=-0.023  Sum_probs=36.1

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKK  114 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~  114 (247)
                      ++.+..+....+......++++||+|++.+++.+|+..   ..+.++.+.+.
T Consensus        40 ~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           40 YGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             TSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             cCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            36676666666666677899999999999999999853   35666655543

>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=89.55  E-value=0.2  Score=35.12  Aligned_cols=47  Identities=13%  Similarity=0.013  Sum_probs=33.7

Q ss_pred             ccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhccc
Q 025814           69 VYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKS  116 (247)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~  116 (247)
                      +..+....+.. ..++|++||+|++.+++.+|+..  ..+.++.+.+..+
T Consensus        41 v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a   89 (107)
T 2lmi_A           41 ENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEI   89 (107)
T ss_dssp             TTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCEEC
T ss_pred             cceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEEEC
Confidence            55555555555 78899999999999999999873  3455665555443

>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=89.50  E-value=0.14  Score=35.02  Aligned_cols=51  Identities=8%  Similarity=-0.016  Sum_probs=37.2

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSI  117 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~  117 (247)
                      +.+..+....+..+...++++||+|++.+++.+|+..   ..+.++.+.+....
T Consensus        40 G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   93 (98)
T 2cqp_A           40 QVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGS   93 (98)
T ss_dssp             CCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcC
Confidence            5555554555555667789999999999999998853   46788877776544

>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=89.26  E-value=0.079  Score=35.36  Aligned_cols=51  Identities=2%  Similarity=-0.145  Sum_probs=37.3

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSI  117 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~  117 (247)
                      |.+..+....+.....+++++||+|++.++|.+|+.   +..+.++.+.+..+.
T Consensus        31 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A           31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            556565555555567778999999999999998876   456777777665543

>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=89.23  E-value=0.14  Score=35.40  Aligned_cols=52  Identities=12%  Similarity=0.065  Sum_probs=38.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIP  118 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~  118 (247)
                      |.+..+....+.....+++++||+|++.++|.+|+.   +..+.++.+.+..+..
T Consensus        33 G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A           33 GPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             SCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            666666666666677789999999999999999886   3466777766655543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=89.22  E-value=0.14  Score=35.23  Aligned_cols=43  Identities=14%  Similarity=0.147  Sum_probs=31.7

Q ss_pred             cccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhc
Q 025814           72 LPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKK  114 (247)
Q Consensus        72 ~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~  114 (247)
                      +....+..+..++|++||+|++.+++.+|+.   +..+.++.+.+.
T Consensus        51 v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   96 (99)
T 2la6_A           51 INLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS   96 (99)
T ss_dssp             EEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             EEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            5455555667789999999999999888875   456667666554

>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=89.19  E-value=0.31  Score=35.23  Aligned_cols=51  Identities=12%  Similarity=0.077  Sum_probs=36.5

Q ss_pred             CCCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc-----Cccchhhhhhcccccccc
Q 025814           65 PVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS-----SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        65 P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~-----~~~~~~~~~~~~~~~r~~  121 (247)
                      ++|.+..+....      .|+++||+|++.++|.+|+..     ..+.++.+.+..+..+..
T Consensus        54 ~fG~V~~v~i~~------~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~  109 (119)
T 2ad9_A           54 PFGKVTNLLMLK------GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL  109 (119)
T ss_dssp             TTSCCCEEEEEG------GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSC
T ss_pred             hcCCEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCC
Confidence            346555544332      389999999999999999863     358889888877765443

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=89.14  E-value=0.1  Score=36.37  Aligned_cols=52  Identities=8%  Similarity=0.089  Sum_probs=38.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIP  118 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~  118 (247)
                      |.+..+....+..+..+++++||+|++.++|.+|+.   +..+.++.+.+..+..
T Consensus        48 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~  102 (106)
T 1p27_B           48 GEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV  102 (106)
T ss_dssp             SCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEE
T ss_pred             CCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecC
Confidence            566666555566667779999999999999888875   4567787777765543

>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=88.90  E-value=0.3  Score=33.68  Aligned_cols=53  Identities=9%  Similarity=0.073  Sum_probs=38.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+...  .++++||+|++.++|.+|+.   +..+.++.+.+..+..+..
T Consensus        40 G~v~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   95 (103)
T 2cq3_A           40 GKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM   95 (103)
T ss_dssp             SCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCC
T ss_pred             CCeEEEEEEecCCC--CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCC
Confidence            55555554444332  79999999999999998875   4578888888877766544

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=88.83  E-value=0.75  Score=30.02  Aligned_cols=68  Identities=12%  Similarity=0.277  Sum_probs=42.6

Q ss_pred             EEEEc-CCCCCCcHHHHHHHhccCCCe-----eEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          140 RLFCG-DLGNEVNDDVLSKAFSRFPSF-----NMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       140 ~lfV~-nLp~~~~e~~L~~~F~~~G~i-----~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      +|||. +--..+...+|..++..-+.|     -.+.|..+        |.||+... +.+..++..|++..+.|+.++|+
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d~--------~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~   72 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMDN--------ASYVEILN-GKGPHVLKVMKNTTVKGKQLKVN   72 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEECSS--------CEEEEECT-TCHHHHHHHHTTCCC---CCCEE
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEeCC--------cEEEEECH-HHHHHHHHHhccccCcCceEEEE
Confidence            46664 223456677788887755543     44555333        88998865 56778899999999999999998


Q ss_pred             Ecc
Q 025814          214 KSK  216 (247)
Q Consensus       214 ~a~  216 (247)
                      .++
T Consensus        73 ~~~   75 (76)
T 2g0c_A           73 KAN   75 (76)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            764

>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=88.65  E-value=0.2  Score=34.83  Aligned_cols=50  Identities=18%  Similarity=-0.007  Sum_probs=35.6

Q ss_pred             CCccc-cccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcccc
Q 025814           67 APVYS-LPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSI  117 (247)
Q Consensus        67 ~~~~~-~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~  117 (247)
                      +.+.. +....+ ....++|++||+|++.+++.+|+..  ..+.++.+.+....
T Consensus        40 G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~~   92 (104)
T 1wg5_A           40 EIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEEC
T ss_pred             CCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEECC
Confidence            54443 333344 5677899999999999999999975  35677777665544

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=88.59  E-value=0.18  Score=36.10  Aligned_cols=52  Identities=12%  Similarity=0.008  Sum_probs=38.1

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh--cCccchhhhhhccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSIP  118 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~~  118 (247)
                      |.+..+....+.....+++++||+|++.+++..|+.  +..+.++.+.+.....
T Consensus        61 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           61 GSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             SCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSC
T ss_pred             CCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCC
Confidence            556666555555667779999999999999999983  2356777777765543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.40  E-value=0.15  Score=34.33  Aligned_cols=41  Identities=12%  Similarity=-0.063  Sum_probs=31.6

Q ss_pred             hhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcccccc
Q 025814           79 QQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPR  119 (247)
Q Consensus        79 ~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r  119 (247)
                      .....++++||+|++.+++.+|+..  ..+.++.+.+..+..+
T Consensus        45 ~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~~~   87 (91)
T 2dgw_A           45 AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREKSG   87 (91)
T ss_dssp             TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEESSC
T ss_pred             CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECCcC
Confidence            4556789999999999999999872  3577777777665544

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=88.39  E-value=0.23  Score=32.91  Aligned_cols=48  Identities=6%  Similarity=0.040  Sum_probs=35.4

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhh
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETK  113 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~  113 (247)
                      ++.+..+....+.....+++++||+|++.+++..|+.   +..+.++.+++
T Consensus        29 ~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   79 (85)
T 1x4e_A           29 YGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQ   79 (85)
T ss_dssp             TSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCS
T ss_pred             cCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEee
Confidence            4667666666666677889999999999999988876   34566655544

>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=88.30  E-value=0.19  Score=33.41  Aligned_cols=51  Identities=10%  Similarity=0.084  Sum_probs=36.0

Q ss_pred             CCccccccccchhhhc-CCCceeeCccCHHHHHHHHh---cCccchhhhhhcccc
Q 025814           67 APVYSLPQYHQAQQLF-QRDAQTITPEALESVKAALA---SSDIEHKAETKKKSI  117 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~-~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~  117 (247)
                      |.+..+....+..+.. .++++||+|++.++|.+|+.   +..+.++.+.+..+.
T Consensus        29 G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   83 (88)
T 4a8x_A           29 GKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL   83 (88)
T ss_dssp             SCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECC
Confidence            5555555544444434 79999999999999988875   456778777765543

>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=88.26  E-value=0.36  Score=33.58  Aligned_cols=53  Identities=13%  Similarity=0.070  Sum_probs=38.5

Q ss_pred             ccccccc-cchhhhcCCCceeeCccCHHHHHHHHhc-----Cccchhhhhhcccccccc
Q 025814           69 VYSLPQY-HQAQQLFQRDAQTITPEALESVKAALAS-----SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        69 ~~~~~~~-~~~~~~~~~~~~~v~~~~~~~a~~al~~-----~~~~~~~~~~~~~~~r~~  121 (247)
                      +..+... .+..+..+++++||+|++.++|..|+..     ..+.++.+.+..+..+..
T Consensus        36 v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~   94 (109)
T 2dis_A           36 VLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID   94 (109)
T ss_dssp             EEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCS
T ss_pred             ceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCC
Confidence            4444343 4445567899999999999999999863     357888888877765543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.17  E-value=0.3  Score=33.69  Aligned_cols=54  Identities=7%  Similarity=-0.046  Sum_probs=40.1

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      ++.+..+....+  ....++++||+|++.++|.+|+.   +..+.++.+.+..+..+..
T Consensus        39 ~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2d9p_A           39 FGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE   95 (103)
T ss_dssp             TSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCC
T ss_pred             cCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeccccc
Confidence            366666555544  55678999999999999998875   4578888888877765544

>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=87.95  E-value=0.13  Score=37.09  Aligned_cols=49  Identities=10%  Similarity=-0.096  Sum_probs=33.8

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKK  114 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~  114 (247)
                      ++.+..+....+..+...++++||+|++.+++.+||..  ..+.++.+.+.
T Consensus        49 ~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   99 (124)
T 1wel_A           49 LDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVH   99 (124)
T ss_dssp             SCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEE
T ss_pred             cCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEE
Confidence            36555544444555677899999999999999999873  24555554443

>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=87.94  E-value=0.28  Score=34.21  Aligned_cols=50  Identities=8%  Similarity=0.094  Sum_probs=35.4

Q ss_pred             CCCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc-----Cccchhhhhhccccccc
Q 025814           65 PVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS-----SDIEHKAETKKKSIPRK  120 (247)
Q Consensus        65 P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~-----~~~~~~~~~~~~~~~r~  120 (247)
                      ++|.+..+....      .|+++||+|++.++|.+|+..     ..+.++.+.+..+..+.
T Consensus        38 ~fG~v~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   92 (101)
T 2cq1_A           38 PFGKVTNILMLK------GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   92 (101)
T ss_dssp             TTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             hcCCEEEEEEEC------CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCccc
Confidence            346655543322      389999999999999999873     24788888887765543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.86  E-value=0.19  Score=34.64  Aligned_cols=47  Identities=17%  Similarity=0.151  Sum_probs=36.0

Q ss_pred             chhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccC
Q 025814           77 QAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAG  123 (247)
Q Consensus        77 ~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~  123 (247)
                      +.....+++++||+|++.++|.+|+.   +..+.++.+.+..+..+...+
T Consensus        47 ~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   96 (102)
T 2fc8_A           47 DRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGG   96 (102)
T ss_dssp             CSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCSSS
T ss_pred             cCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCCCC
Confidence            33455668999999999999988875   567889988888877665543

>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=87.52  E-value=0.24  Score=34.51  Aligned_cols=48  Identities=10%  Similarity=-0.011  Sum_probs=34.8

Q ss_pred             ccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcccccc
Q 025814           71 SLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPR  119 (247)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r  119 (247)
                      .+....+. ...+++++||+|++.+++.+||..  ..+.++.+.+......
T Consensus        43 ~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~~~   92 (102)
T 1wez_A           43 RVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTA   92 (102)
T ss_dssp             EEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECCC
T ss_pred             EEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECCCC
Confidence            44444444 677899999999999999999954  3677777777655443

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=87.30  E-value=0.17  Score=34.55  Aligned_cols=55  Identities=11%  Similarity=0.042  Sum_probs=39.4

Q ss_pred             CCccccccccchh---hhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQ---QLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~---~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+..   +...++++||+|++.++|.+|+..   ..+.++.+.+..+..+..
T Consensus        30 G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   90 (98)
T 2cpf_A           30 GAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK   90 (98)
T ss_dssp             SCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSC
T ss_pred             CCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCC
Confidence            5555555544443   446789999999999999999863   467888888877665543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.28  E-value=0.24  Score=35.15  Aligned_cols=45  Identities=4%  Similarity=-0.120  Sum_probs=30.8

Q ss_pred             ccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhccc
Q 025814           71 SLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKS  116 (247)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~  116 (247)
                      .+....+.. ..++|++||+|++.+++.+||..  ..+.++.+.+...
T Consensus        44 ~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           44 AVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             EEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             EEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEEC
Confidence            333333433 67899999999999999999853  3556665555443

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=87.23  E-value=0.14  Score=35.49  Aligned_cols=53  Identities=13%  Similarity=0.081  Sum_probs=38.5

Q ss_pred             ccccccccchhhhcCCCceeeCccCHHHHHHHHh--cCccchhhhhhcccccccc
Q 025814           69 VYSLPQYHQAQQLFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~~r~~  121 (247)
                      +..+....+..+...++++||+|++.+++.+|+.  +..+.++.+.+..+..+..
T Consensus        41 i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2dng_A           41 IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQ   95 (103)
T ss_dssp             EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEECCCCCC
T ss_pred             ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEecCCCC
Confidence            4444455555566778999999999999999983  3467788888877665543

>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=87.21  E-value=0.5  Score=33.72  Aligned_cols=50  Identities=12%  Similarity=-0.005  Sum_probs=36.0

Q ss_pred             CCCCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc-----Cccchhhhhhcccccc
Q 025814           64 APVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS-----SDIEHKAETKKKSIPR  119 (247)
Q Consensus        64 ~P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~-----~~~~~~~~~~~~~~~r  119 (247)
                      .++|.+..+...      ..++++||+|++.++|.+|+..     ..+.++.+.+..+..+
T Consensus        48 ~~fG~V~~v~i~------~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~  102 (112)
T 1x4f_A           48 EPYGKIKNYILM------RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY  102 (112)
T ss_dssp             TTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             HhcCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccc
Confidence            445666555432      3589999999999999999863     2478888888776544

>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=87.18  E-value=0.22  Score=33.69  Aligned_cols=49  Identities=8%  Similarity=0.011  Sum_probs=35.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKK  115 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~  115 (247)
                      +.+..+....+......++++||+|++.+++.+|+.   +..+.++.+.+..
T Consensus        40 G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           40 QVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             CBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            555555555555666789999999999999888875   4567777666544

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.15  E-value=0.23  Score=33.91  Aligned_cols=50  Identities=6%  Similarity=-0.055  Sum_probs=36.1

Q ss_pred             CCcc-ccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhh----hhhccc
Q 025814           67 APVY-SLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKA----ETKKKS  116 (247)
Q Consensus        67 ~~~~-~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~----~~~~~~  116 (247)
                      +.+. .+....+..+..+++++||+|++.+++.+|+..   ..+.++.    +.+..+
T Consensus        34 G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a   91 (99)
T 2div_A           34 GETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYA   91 (99)
T ss_dssp             TCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEET
T ss_pred             CCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeec
Confidence            5555 655556666677889999999999999999863   3566666    555443

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=87.08  E-value=0.35  Score=33.16  Aligned_cols=43  Identities=16%  Similarity=0.088  Sum_probs=31.9

Q ss_pred             chhhhcCCCceeeCccCHHHHHHHHh--cCccchhhhhhcccccc
Q 025814           77 QAQQLFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        77 ~~~~~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~~r  119 (247)
                      +.....+++++||+|++.+++.+|++  +..+.++.+.+..+..+
T Consensus        51 ~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~   95 (101)
T 1fj7_A           51 DVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGR   95 (101)
T ss_dssp             EEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCSCC
T ss_pred             cCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcCCC
Confidence            33456679999999999999999886  33567777777665544

>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=86.99  E-value=0.16  Score=33.92  Aligned_cols=51  Identities=16%  Similarity=0.020  Sum_probs=37.2

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh--cCccchhhhhhcccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSI  117 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~  117 (247)
                      |.+..+....+.....+++++||+|++.+++.+|+.  +..+.++.+.+..+.
T Consensus        31 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A           31 GSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             CCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETT
T ss_pred             CCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEcc
Confidence            556666555555677789999999999999999983  345677776665543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=86.96  E-value=0.16  Score=36.07  Aligned_cols=48  Identities=13%  Similarity=0.104  Sum_probs=34.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKK  114 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~  114 (247)
                      |.+..+....+......++++||+|++.+++.+|+..   ..+.++.+.+.
T Consensus        65 G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           65 GNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            5666665555556677899999999999999998863   45666655543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=86.89  E-value=0.31  Score=34.20  Aligned_cols=50  Identities=8%  Similarity=0.034  Sum_probs=34.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIP  118 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~  118 (247)
                      |.+..+....+..  ..++++||+|++.++|.+|+.   +..+.++.+.+..+..
T Consensus        54 G~i~~v~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  106 (109)
T 2err_A           54 GKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA  106 (109)
T ss_dssp             CCCSCEEECCBTT--BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEEEEECCC--CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            5555554444432  379999999999888888875   4567888777766543

>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=86.78  E-value=0.28  Score=33.51  Aligned_cols=50  Identities=14%  Similarity=0.038  Sum_probs=34.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      |.+..+....+...   ++++||+|++.++|.+|+.   +..+.++.+.+..+..+
T Consensus        38 G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   90 (96)
T 2dgx_A           38 GKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGA   90 (96)
T ss_dssp             SCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCS
T ss_pred             CcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            44444444333333   8899999999999888875   45788888888776544

>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=86.69  E-value=0.31  Score=34.30  Aligned_cols=42  Identities=19%  Similarity=-0.050  Sum_probs=33.6

Q ss_pred             hhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           80 QLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      ...+++++||+|++.++|..|+.   +..+.++.+.+..+..+..
T Consensus        63 ~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~  107 (115)
T 2cpx_A           63 TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  107 (115)
T ss_dssp             CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCC
Confidence            55678999999999999999885   4578888888877766544

>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=86.67  E-value=0.22  Score=33.37  Aligned_cols=52  Identities=12%  Similarity=0.155  Sum_probs=37.4

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      |.+..+....+..+..+++++||+|++.+ +.+|+.   +..+.++.+.+..+...
T Consensus        26 G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A           26 GKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             TCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             CCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            55656655666666788999999999999 888876   45678888877665543

>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=86.62  E-value=0.27  Score=34.01  Aligned_cols=53  Identities=9%  Similarity=-0.029  Sum_probs=37.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccch---hhhhhccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEH---KAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~---~~~~~~~~~~r~  120 (247)
                      +.+..+....+. ...+++++||+|++.++|.+|+.   +..+.+   +.+.+..+..+.
T Consensus        40 G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~   98 (105)
T 2dnh_A           40 GVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDK   98 (105)
T ss_dssp             SCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSC
T ss_pred             CCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCc
Confidence            666665555544 46668999999999999999875   445666   777776665544

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=86.59  E-value=0.21  Score=36.48  Aligned_cols=47  Identities=13%  Similarity=0.047  Sum_probs=34.1

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhh
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETK  113 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~  113 (247)
                      |.+..+....+......++++||+|++.++|.+|+..   ..+.++.+.+
T Consensus        88 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           88 GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            5565655555556677899999999999999999853   3455655544

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.46  E-value=0.19  Score=36.49  Aligned_cols=43  Identities=7%  Similarity=-0.143  Sum_probs=29.9

Q ss_pred             cccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhh
Q 025814           70 YSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETK  113 (247)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~  113 (247)
                      ..+....+ ....++|++||+|++.+++.+|+..+  .+.++.+++
T Consensus        55 ~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V   99 (123)
T 2dha_A           55 EGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIEL   99 (123)
T ss_dssp             GGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECC
T ss_pred             ceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEE
Confidence            34444444 46778999999999999999999642  344444443

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=86.41  E-value=0.48  Score=33.39  Aligned_cols=38  Identities=8%  Similarity=0.013  Sum_probs=30.8

Q ss_pred             CCceeeCccCHHHHHHHHhc-----Cccchhhhhhcccccccc
Q 025814           84 RDAQTITPEALESVKAALAS-----SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al~~-----~~~~~~~~~~~~~~~r~~  121 (247)
                      |+++||+|++.++|.+|+..     ..+.++.+.+..+..+..
T Consensus        52 kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~   94 (105)
T 1sjq_A           52 KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL   94 (105)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSC
T ss_pred             CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCC
Confidence            89999999999999999872     357888888877765543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=85.85  E-value=0.42  Score=32.70  Aligned_cols=30  Identities=7%  Similarity=0.013  Sum_probs=22.1

Q ss_pred             cCCCceeeCccCHHHHHHHHhc---Cccchhhh
Q 025814           82 FQRDAQTITPEALESVKAALAS---SDIEHKAE  111 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~  111 (247)
                      .++|++||+|.+.++|+.|+..   ..+.++.+
T Consensus        41 ~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I   73 (89)
T 2wbr_A           41 LNQGIALCKYTTREEANKAQMALNNCVLANTTI   73 (89)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEE
Confidence            3799999999988888877653   35555543

>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=85.63  E-value=0.31  Score=34.27  Aligned_cols=57  Identities=5%  Similarity=-0.025  Sum_probs=40.1

Q ss_pred             CCCCCccccccccchh---hhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccc
Q 025814           64 APVAPVYSLPQYHQAQ---QLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        64 ~P~~~~~~~~~~~~~~---~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~  120 (247)
                      ..++.+..+....+..   ....++++||+|++.++|.+|+.   +..++++.+.+..+..+.
T Consensus        40 ~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           40 GKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             TTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             hccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            3447776665554443   23456899999999999888876   457888888887766554

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=85.80  E-value=0.16  Score=36.09  Aligned_cols=51  Identities=14%  Similarity=0.111  Sum_probs=38.4

Q ss_pred             cccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccccc
Q 025814           72 LPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAA  122 (247)
Q Consensus        72 ~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~  122 (247)
                      +....+..+...++++||+|++.++|.+|+.   +..+.++.+.+..+..+...
T Consensus        45 v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           45 INLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF   98 (116)
Confidence            4445555567789999999999988888875   45788888888877665443

>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=85.50  E-value=0.87  Score=31.79  Aligned_cols=38  Identities=13%  Similarity=0.111  Sum_probs=30.5

Q ss_pred             CCCceeeCccCHHHHHHHHhc---C--ccchhhhhhccccccc
Q 025814           83 QRDAQTITPEALESVKAALAS---S--DIEHKAETKKKSIPRK  120 (247)
Q Consensus        83 ~~~~~~v~~~~~~~a~~al~~---~--~~~~~~~~~~~~~~r~  120 (247)
                      .|+++||+|++.++|.+|+..   .  .+.++.+.+..+..+.
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~   92 (104)
T 1wex_A           50 FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR   92 (104)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCcc
Confidence            489999999999999999863   2  4788888887776544

>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=85.45  E-value=0.12  Score=36.62  Aligned_cols=53  Identities=9%  Similarity=0.008  Sum_probs=38.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh--cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~~r  119 (247)
                      |.+..+....+..+...++++||+|++.+++.+|+.  +..+.++.+.+..+..+
T Consensus        50 G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~  104 (114)
T 2cq4_A           50 GKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE  104 (114)
T ss_dssp             SCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHHH
T ss_pred             CCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecCCC
Confidence            666666666666667889999999998888888873  34677777777665544

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=85.30  E-value=0.48  Score=31.05  Aligned_cols=41  Identities=2%  Similarity=-0.095  Sum_probs=29.3

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchh
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHK  109 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~  109 (247)
                      |.+..+...  ..+..++|++||+|++.++|.+|+..   ..+.++
T Consensus        32 G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   75 (81)
T 2krb_A           32 GKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   75 (81)
T ss_dssp             CCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSS
T ss_pred             CCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCc
Confidence            555554433  24567899999999999999999864   345555

>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=85.29  E-value=0.23  Score=36.79  Aligned_cols=44  Identities=14%  Similarity=0.040  Sum_probs=30.9

Q ss_pred             ccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhh
Q 025814           69 VYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETK  113 (247)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~  113 (247)
                      +..+....+.. ..++|++||+|++.+++.+|+..  ..+.++.+++
T Consensus        74 v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V  119 (136)
T 2hgl_A           74 AAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEV  119 (136)
T ss_dssp             STTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEE
T ss_pred             eeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEE
Confidence            45555555554 77899999999999999999872  2455554433

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=85.21  E-value=0.37  Score=34.51  Aligned_cols=51  Identities=4%  Similarity=-0.083  Sum_probs=36.9

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIP  118 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~  118 (247)
                      |.+..+....+. ....++++||+|++.+++.+|+.   +..+.++.+.+..+..
T Consensus        60 G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  113 (124)
T 2kt5_A           60 GTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS  113 (124)
T ss_dssp             SCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECC
T ss_pred             CCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCC
Confidence            555555555544 56689999999999999998876   4467777777766543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=85.12  E-value=0.19  Score=33.98  Aligned_cols=49  Identities=12%  Similarity=0.111  Sum_probs=35.4

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKK  115 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~  115 (247)
                      +.+..+....+......++++||+|++.++|.+|+..   ..+.++.+.+..
T Consensus        40 G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           40 GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             SCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            6666665655555667789999999999999998863   456666655543

>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=85.06  E-value=0.42  Score=35.47  Aligned_cols=48  Identities=8%  Similarity=-0.024  Sum_probs=34.9

Q ss_pred             ccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcccccc
Q 025814           71 SLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPR  119 (247)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r  119 (247)
                      .+....+.. ..+++++||+|++.+++.+||..  ..+.++.+.+.....+
T Consensus        74 ~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~~~  123 (139)
T 2hgn_A           74 RVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTT  123 (139)
T ss_dssp             EEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECCCS
T ss_pred             EEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECCCC
Confidence            444444443 67899999999999999999843  3677777777665543

>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=84.90  E-value=0.15  Score=41.24  Aligned_cols=50  Identities=4%  Similarity=0.005  Sum_probs=39.8

Q ss_pred             CccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccc
Q 025814           68 PVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSI  117 (247)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~  117 (247)
                      .|..+.+..+..+..+++++||+|++.++|.+||..   ..+.++.+.+..+.
T Consensus        96 ~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~  148 (229)
T 3q2s_C           96 DILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVN  148 (229)
T ss_dssp             CEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECC
T ss_pred             ceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECC
Confidence            666776777777888899999999999999999863   57888887776554

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=84.89  E-value=0.49  Score=32.38  Aligned_cols=36  Identities=6%  Similarity=-0.017  Sum_probs=27.5

Q ss_pred             cCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccc
Q 025814           82 FQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSI  117 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~  117 (247)
                      .+++++||+|++.+++..|+.   +..+.++.+.+..+.
T Consensus        61 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            468999999999998888874   456777777665543

>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=84.88  E-value=0.41  Score=32.95  Aligned_cols=52  Identities=15%  Similarity=-0.005  Sum_probs=36.3

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~  120 (247)
                      +.+..+....+..  ..++++||+|++.++|.+|+.   +..+.++.+.+..+..+.
T Consensus        40 G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2cqi_A           40 GPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPS   94 (103)
T ss_dssp             SCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTT
T ss_pred             CCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCc
Confidence            4444444444322  258999999999999988876   456788888887766544

>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=84.81  E-value=0.53  Score=32.75  Aligned_cols=39  Identities=8%  Similarity=-0.068  Sum_probs=31.1

Q ss_pred             CCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           83 QRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        83 ~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      .++++||+|++.++|.+|+.   ...+.++.+.+..+..+..
T Consensus        60 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~  101 (109)
T 1x4a_A           60 GPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG  101 (109)
T ss_dssp             SSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCC
T ss_pred             CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCCC
Confidence            68999999999999998874   4578888888877665443

>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=84.75  E-value=0.38  Score=42.75  Aligned_cols=54  Identities=13%  Similarity=0.066  Sum_probs=40.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~  120 (247)
                      |.|..+.+..+..+...++++||+|++.++|..||.   +..+.++.+.+..+..+.
T Consensus       127 G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          127 GPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRT  183 (437)
T ss_pred             CCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            555555555555566779999999999999999884   457888888887776543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=84.63  E-value=0.52  Score=34.32  Aligned_cols=39  Identities=13%  Similarity=-0.092  Sum_probs=30.7

Q ss_pred             hcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           81 LFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        81 ~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      ..++|++||+|++.++|..|+.   +..+.++.+.+..+..+
T Consensus        69 ~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~  110 (127)
T 2a3j_A           69 DDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP  110 (127)
T ss_dssp             CSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCC
T ss_pred             CCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCc
Confidence            4579999999999998888875   45788888877666544

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=84.61  E-value=0.57  Score=31.88  Aligned_cols=38  Identities=5%  Similarity=-0.051  Sum_probs=29.8

Q ss_pred             cCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           82 FQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      ..++++||+|++.+++..|+.   +..+.++.+.+..+..+
T Consensus        54 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           54 GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            568999999999998888874   56778888777665543

>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=84.51  E-value=0.23  Score=36.24  Aligned_cols=45  Identities=16%  Similarity=0.007  Sum_probs=32.5

Q ss_pred             cccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcccc
Q 025814           72 LPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSI  117 (247)
Q Consensus        72 ~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~  117 (247)
                      +....+.. ..++|++||+|++.+++.+|+..  ..+.++.+.+....
T Consensus        73 v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~a~  119 (126)
T 2hgm_A           73 ITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSS  119 (126)
T ss_dssp             EECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEEEC
T ss_pred             EEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            33344444 67899999999999999999974  35667776665543

>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=84.47  E-value=0.9  Score=30.47  Aligned_cols=41  Identities=10%  Similarity=0.062  Sum_probs=32.3

Q ss_pred             cCCCceeeCccCHHHHHHHHh---c-Cccchhhhhhccccccccc
Q 025814           82 FQRDAQTITPEALESVKAALA---S-SDIEHKAETKKKSIPRKAA  122 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~al~---~-~~~~~~~~~~~~~~~r~~~  122 (247)
                      ..++++||+|++.++|.+|+.   + ..+.++.+.+..+..+...
T Consensus        42 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~~   86 (93)
T 2cqh_A           42 LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   86 (93)
T ss_dssp             EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCcccc
Confidence            458999999999888888875   4 5688988888877665443

>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=84.32  E-value=0.26  Score=36.88  Aligned_cols=53  Identities=2%  Similarity=-0.108  Sum_probs=39.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      +.|..+....+..+...++++||+|++.++|.+|+.   ...+.++.+.+..+...
T Consensus        64 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  119 (156)
T 1h2v_Z           64 GDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGF  119 (156)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCC
T ss_pred             CCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            555555555555566678999999999999999886   35678888888776644

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=83.92  E-value=0.24  Score=35.43  Aligned_cols=46  Identities=20%  Similarity=0.092  Sum_probs=31.9

Q ss_pred             ccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhcc
Q 025814           69 VYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETKKK  115 (247)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~  115 (247)
                      +..+....+.. ..++|++||+|++.+++.+|+...  .+.++.+.+..
T Consensus        47 v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~   94 (118)
T 2db1_A           47 VAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFK   94 (118)
T ss_dssp             GGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEEE
T ss_pred             ceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEE
Confidence            45554444444 677999999999999999998732  45555554433

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=83.42  E-value=0.56  Score=31.91  Aligned_cols=39  Identities=21%  Similarity=0.198  Sum_probs=30.7

Q ss_pred             cCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccc
Q 025814           82 FQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~  120 (247)
                      ..++++||+|++.++|.+|+.   +..+.++.+.+..+..+.
T Consensus        47 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~   88 (97)
T 1x5p_A           47 PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   88 (97)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCC
T ss_pred             CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            568999999999999999885   446788888777665543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=83.38  E-value=1.8  Score=30.28  Aligned_cols=33  Identities=12%  Similarity=0.018  Sum_probs=26.2

Q ss_pred             hcCCCceeeCccCHHHHHHHHhcC-ccchhhhhh
Q 025814           81 LFQRDAQTITPEALESVKAALASS-DIEHKAETK  113 (247)
Q Consensus        81 ~~~~~~~~v~~~~~~~a~~al~~~-~~~~~~~~~  113 (247)
                      ..+++++||+|++.++|.+|+... .++++.+..
T Consensus        49 g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~   82 (114)
T 2dnl_A           49 FPPKGYAFLLFQEESSVQALIDACLEEDGKLYLC   82 (114)
T ss_dssp             SCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEE
T ss_pred             CCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEe
Confidence            578999999999999999999754 456655443

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=83.27  E-value=0.81  Score=31.99  Aligned_cols=52  Identities=13%  Similarity=-0.030  Sum_probs=37.5

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      +.+..+....+. ...+++++||+|++.+++.+|+.   +..+.++.+.+..+...
T Consensus        40 G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   94 (114)
T 2do0_A           40 GVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERA   94 (114)
T ss_dssp             SCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCC
T ss_pred             CCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccC
Confidence            556555554444 35668999999999998888875   45788888888766543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=83.11  E-value=0.7  Score=31.58  Aligned_cols=43  Identities=28%  Similarity=0.226  Sum_probs=33.7

Q ss_pred             hhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccccc
Q 025814           79 QQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        79 ~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~  121 (247)
                      .....++++||+|++.++|.+|+..   ..+.++.+.+..+..+..
T Consensus        48 ~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   93 (101)
T 2fc9_A           48 QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGS   93 (101)
T ss_dssp             SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCC
T ss_pred             CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCC
Confidence            3556799999999999999999863   467888888877765543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=82.98  E-value=0.51  Score=31.62  Aligned_cols=51  Identities=8%  Similarity=-0.044  Sum_probs=35.4

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      +.+..+....  .....++++||+|++.+++.+|+.   +..+.++.+.+..+...
T Consensus        33 G~v~~~~i~~--~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   86 (92)
T 2dgv_A           33 GHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA   86 (92)
T ss_dssp             SCEEEEEEEE--SSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCC
T ss_pred             CCEEEEEEEc--cCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            4444443333  244568999999999998888865   45788888877666544

>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=82.95  E-value=0.48  Score=31.93  Aligned_cols=36  Identities=17%  Similarity=0.145  Sum_probs=24.6

Q ss_pred             CCCceeeCccCHHHHHHHHhcCc--cchhhhhhcccccc
Q 025814           83 QRDAQTITPEALESVKAALASSD--IEHKAETKKKSIPR  119 (247)
Q Consensus        83 ~~~~~~v~~~~~~~a~~al~~~~--~~~~~~~~~~~~~r  119 (247)
                      ++|++||+|++.++|.+ +++..  +.++.+.+..+.++
T Consensus        47 srGfaFV~F~~~~~A~~-~~~~~~~~~g~~v~v~~a~~k   84 (89)
T 3d2w_A           47 FRAFAFVTFADDKVAQS-LCGEDLIIKGISVHISNAEPK   84 (89)
T ss_dssp             CCSEEEEEESCHHHHHH-HTTCEEEETTEEEEEEECC--
T ss_pred             CCCEEEEEECCHHHHHH-HcCCCcccCCEEEEEEEcCCC
Confidence            79999999999999985 44443  34666666555443

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=82.51  E-value=0.29  Score=34.41  Aligned_cols=51  Identities=10%  Similarity=-0.124  Sum_probs=36.2

Q ss_pred             CCCccccccccchh-hhcCCCceeeCccCHHHHHHHH---hcCccchhhhhhccc
Q 025814           66 VAPVYSLPQYHQAQ-QLFQRDAQTITPEALESVKAAL---ASSDIEHKAETKKKS  116 (247)
Q Consensus        66 ~~~~~~~~~~~~~~-~~~~~~~~~v~~~~~~~a~~al---~~~~~~~~~~~~~~~  116 (247)
                      +|.+..+....+.. ...++|++||+|++.++|.+|+   ++..+.++.+.+...
T Consensus        37 ~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a   91 (105)
T 2pe8_A           37 YGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFY   91 (105)
T ss_dssp             GSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             cCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEc
Confidence            47777776655443 2467999999999988888776   456777777666544

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=82.30  E-value=0.93  Score=31.48  Aligned_cols=47  Identities=6%  Similarity=-0.036  Sum_probs=33.1

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc-Cccchhhhhhccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS-SDIEHKAETKKKSIP  118 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~-~~~~~~~~~~~~~~~  118 (247)
                      |.+..+...     ...+|++||+|++.++|..|+.. ..+.++.+.+..+..
T Consensus        42 G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~~~g~~l~V~~a~~   89 (100)
T 2d9o_A           42 GEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLEG   89 (100)
T ss_dssp             SCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCBCSSSBCEEECSSC
T ss_pred             CCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCCCCCCeEEEEEccC
Confidence            655554433     25799999999999999999975 345566666655443

>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=82.17  E-value=0.35  Score=33.51  Aligned_cols=48  Identities=4%  Similarity=-0.071  Sum_probs=33.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKK  115 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~  115 (247)
                      +.+..+....+. ....++++||+|++.++|.+|+.   +..+.++.+.+..
T Consensus        54 G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           54 GTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             SCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            556555555554 66678999999999999888875   3466666665543

>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=81.90  E-value=0.4  Score=33.51  Aligned_cols=46  Identities=7%  Similarity=-0.087  Sum_probs=33.2

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhh
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETK  113 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~  113 (247)
                      |.+..+....+.. ..++|++||+|++.++|.+|+.   +..+.++.+.+
T Consensus        52 G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v  100 (104)
T 1jmt_A           52 GEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA  100 (104)
T ss_dssp             CCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCE
T ss_pred             CceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEE
Confidence            6666665555433 5679999999999888887764   55677776654

>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=81.83  E-value=0.92  Score=30.74  Aligned_cols=37  Identities=16%  Similarity=0.076  Sum_probs=28.6

Q ss_pred             CCceeeCccCHHHHHHHHh---cCccc--hhhhhhccccccc
Q 025814           84 RDAQTITPEALESVKAALA---SSDIE--HKAETKKKSIPRK  120 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al~---~~~~~--~~~~~~~~~~~r~  120 (247)
                      ++++||+|++.++|.+|+.   +..+.  ++.+.+..+..+.
T Consensus        53 ~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           53 DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            7899999999998888875   45677  7777776665543

>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=81.52  E-value=0.98  Score=31.36  Aligned_cols=38  Identities=13%  Similarity=0.019  Sum_probs=30.4

Q ss_pred             CCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           84 RDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      ++++||+|++.++|.+|+.   +..+.++.+.+..+..+..
T Consensus        61 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            8999999999999988874   5678888888877665543

>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=80.57  E-value=1.8  Score=29.55  Aligned_cols=40  Identities=15%  Similarity=0.130  Sum_probs=31.6

Q ss_pred             CCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccccC
Q 025814           84 RDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKAAG  123 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~~~  123 (247)
                      ++++||+|++.++|.+|+.   ...+.++.+.+..+..+....
T Consensus        45 ~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   87 (103)
T 2dgu_A           45 KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKR   87 (103)
T ss_dssp             SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCC
T ss_pred             CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcccc
Confidence            7899999999999998876   457888888888776655433

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=80.52  E-value=0.52  Score=31.87  Aligned_cols=40  Identities=8%  Similarity=0.032  Sum_probs=31.2

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccc
Q 025814           80 QLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPR  119 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r  119 (247)
                      ...+++++||+|++.++|..|+..   ..+.++.+.+..+..+
T Consensus        49 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           49 DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            455689999999999999999873   4678888777666544

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.39  E-value=1.2  Score=29.73  Aligned_cols=38  Identities=8%  Similarity=0.039  Sum_probs=30.6

Q ss_pred             CCceeeCccCHHHHHHHHh---cCccchhhhhhcccccccc
Q 025814           84 RDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        84 ~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~~  121 (247)
                      ++++||+|++.++|.+|+.   ...+.++.+.+..+..+..
T Consensus        42 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A           42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            7999999999999988875   4578888888877665543

---

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	247
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-16
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-16
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	7e-15
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-14
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-13
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	9e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-11
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-11
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-11
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-11
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	7e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	8e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	8e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-10
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	4e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-09
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:) 8e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	9e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	7e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-07
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	5e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	7e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	6e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.004

>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 = 70.3 bits (172), Expect = 1e-16
 Identities = 23/76 (30%), Positives = 41/76 (53%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+ GDL  +V + +L + FS        +V RD  T ++ GY +++F  P+D   AL  M
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 201 NGKYVGNRPIKLRKSK 216
           N   +  +P+++  S+
Sbjct: 63  NFDVIKGKPVRIMWSQ 78

>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 = 69.6 bits (170), Expect = 3e-16
 Identities = 14/84 (16%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKR-TGKTKGYGFISFANPSDIAAALK 198
           ++   ++  + N   + + FS F      ++ +    TG  +G+GF+ F    D   A  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 199 EM-NGKYVGNRPIKLRKSKWQERT 221
            + +  ++  R + L  +  +   
Sbjct: 70  ALCHSTHLYGRRLVLEWADSEVTV 93

>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 = 66.2 bits (161), Expect = 5e-15
 Identities = 21/82 (25%), Positives = 44/82 (53%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           ++LF G L N +NDD + +  + F       +V+D  TG +KGY F  + + +    A+ 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 199 EMNGKYVGNRPIKLRKSKWQER 220
            +NG  +G++ + ++++    +
Sbjct: 62  GLNGMQLGDKKLLVQRASVGAK 83

>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 = 65.4 bits (159), Expect = 7e-15
 Identities = 16/75 (21%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L  +   + L + F +F       V+RD  T +++G+GF++F + + +   L  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA- 60

Query: 200 MNGKYVGNRPIKLRK 214
            +   + ++ I  + 
Sbjct: 61  QSRHELDSKTIDPKV 75

>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 = 65.8 bits (160), Expect = 1e-14
 Identities = 20/90 (22%), Positives = 36/90 (40%), Gaps = 5/90 (5%)

Query: 127 EDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFIS 186
           EDP  ++       L   +L   + +D L + F       +       + GK+KG  +I 
Sbjct: 5   EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIE 59

Query: 187 FANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
           F + +D    L+E  G  +  R + L  + 
Sbjct: 60  FKSEADAEKNLEEKQGAEIDGRSVSLYYTG 89

>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 = 65.0 bits (158), Expect = 2e-14
 Identities = 15/77 (19%), Positives = 34/77 (44%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L+ G+L     ++ + + FS+        +  DK      G+ F+ + + +D   A++ 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 200 MNGKYVGNRPIKLRKSK 216
           +NG  + +R I+     
Sbjct: 69  INGTRLDDRIIRTDWDA 85

>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 = 63.9 bits (155), Expect = 4e-14
 Identities = 21/86 (24%), Positives = 44/86 (51%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
              D  ++ G L  +V++ +L + F +        + +D+ TG+ +GYGF+ F +  D  
Sbjct: 6   RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 65

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQER 220
            A+K M+   +  +PI++ K+    +
Sbjct: 66  YAIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 63.1 bits (153), Expect = 6e-14
 Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PE   +LF G L  E  D+ L   F ++ +     V+RD  T +++G+GF+++A   ++ 
Sbjct: 3   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62

Query: 195 AALKEMNGKYVGNRPIKLRK 214
           AA+       V  R ++ ++
Sbjct: 63  AAM-NARPHKVDGRVVEPKR 81

>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 = 63.5 bits (154), Expect = 1e-13
 Identities = 20/110 (18%), Positives = 45/110 (40%), Gaps = 5/110 (4%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PE +  L+  +L  ++  + +   F ++      + +R   T +T+G  ++ + +  D  
Sbjct: 4   PEVNRILYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDAK 60

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKSV 244
            A   ++G  V NR + +          F+ ++  K   Q K    K  +
Sbjct: 61  NACDHLSGFNVCNRYLVVLYY--NANRAFQKMDTKKKEEQLKLLKEKYGI 108

>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 = 62.3 bits (151), Expect = 1e-13
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +L   +L   V+D  + + F+ F +   A V  D R+G++ G   + F   +D   A+K+
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 60

Query: 200 MNGKYVGNRPIKLR 213
            NG  +  RP+ ++
Sbjct: 61  YNGVPLDGRPMNIQ 74

>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 = 62.4 bits (151), Expect = 1e-13
 Identities = 13/79 (16%), Positives = 33/79 (41%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                 +   ++   V+ D +   F  +     +  ++    G   G   ++F +  +  
Sbjct: 6   KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 65

Query: 195 AALKEMNGKYVGNRPIKLR 213
           AA+ ++N + +G+R +KL 
Sbjct: 66  AAVIDLNDRPIGSRKVKLV 84

>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 = 62.4 bits (151), Expect = 2e-13
 Identities = 18/87 (20%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
            E   +LF G L  E  ++ L   + ++       V+RD  + +++G+GF++F++ +++ 
Sbjct: 17  KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 76

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERT 221
           AA+       +  R ++ +++  +E +
Sbjct: 77  AAM-AARPHSIDGRVVEPKRAVAREES 102

>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 = 61.5 bits (149), Expect = 3e-13
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           D  L+  +L   + DD L   F ++ S     ++RDK TG+ +G  F+ +    +   A+
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 198 KEMNGKYV--GNRPIKLR 213
             +N      G++P+ +R
Sbjct: 66  SALNNVIPEGGSQPLSVR 83

>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 = 61.6 bits (149), Expect = 3e-13
 Identities = 22/80 (27%), Positives = 40/80 (50%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           ++  L    L  ++ D  L   F      N  +++RD +TG + GY F+ F +  D   A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 197 LKEMNGKYVGNRPIKLRKSK 216
           +K +NG  V N+ +K+  ++
Sbjct: 61  IKVLNGITVRNKRLKVSYAR 80

>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 = 60.0 bits (145), Expect = 9e-13
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 3/83 (3%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKR---TGKTKGYGFISFANPSDIAAAL 197
           LF  +L     ++ L   FS+  +     + + K       + G+GF+ +  P     AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 198 KEMNGKYVGNRPIKLRKSKWQER 220
           K++ G  V    +++R S+   +
Sbjct: 61  KQLQGHTVDGHKLEVRISERATK 83

>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 = 59.2 bits (143), Expect = 2e-12
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L  +     L   FS+F       +  D  TG+++G+GF+ F     +   + +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-D 59

Query: 200 MNGKYVGNRPIKLRK 214
                +  + I  ++
Sbjct: 60  QKEHKLNGKVIDPKR 74

>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 = 59.7 bits (144), Expect = 2e-12
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 3/82 (3%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             ND R++ G+L  ++    +   F ++ +    + +  K       + F+ F +P D  
Sbjct: 11  GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAI---RDIDLKNRRGGPPFAFVEFEDPRDAE 67

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            A+   +G       +++   +
Sbjct: 68  DAVYGRDGYDYDGYRLRVEFPR 89

>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 = 59.6 bits (144), Expect = 2e-12
 Identities = 17/89 (19%), Positives = 37/89 (41%), Gaps = 6/89 (6%)

Query: 128 DPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISF 187
           +  + +    +  ++CG + + + D ++ + FS F      +V  +K       Y F+ F
Sbjct: 8   EDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRF 61

Query: 188 ANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
           +     A A+  +NG  +    +K    K
Sbjct: 62  STHESAAHAIVSVNGTTIEGHVVKCYWGK 90

>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 = 59.0 bits (142), Expect = 2e-12
 Identities = 30/80 (37%), Positives = 49/80 (61%), Gaps = 1/80 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRF-PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +F G+L  E+++ +L   FS F       K++RD  TG +KGY FI+FA+     AA++ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 200 MNGKYVGNRPIKLRKSKWQE 219
           MNG+Y+ NRPI +  +  ++
Sbjct: 61  MNGQYLCNRPITVSYAFKKD 80

>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 = 59.0 bits (142), Expect = 3e-12
 Identities = 26/80 (32%), Positives = 48/80 (60%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           ++ +LF G L  + N+  L + FS++   +   VV+D+ T +++G+GF++F N  D   A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 197 LKEMNGKYVGNRPIKLRKSK 216
           +  MNGK V  R I++ ++ 
Sbjct: 64  MMAMNGKSVDGRQIRVDQAG 83

>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 = 58.1 bits (140), Expect = 3e-12
 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L  +  ++ + + F  F      ++  D +T K +G+ FI+F     +   + E
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-E 59

Query: 200 MNGKYVGNRPIKLRK 214
                VG    +++ 
Sbjct: 60  KKYHNVGLSKCEIKV 74

>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 = 58.6 bits (141), Expect = 4e-12
 Identities = 21/77 (27%), Positives = 37/77 (48%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L    L   +  +     F         K+VRDK TG++ GYGF+++ +P D   A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 200 MNGKYVGNRPIKLRKSK 216
           +NG  +  + IK+  ++
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>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 = 58.2 bits (140), Expect = 4e-12
 Identities = 18/77 (23%), Positives = 36/77 (46%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           P+ +  L    L     +  L + FS++       +V D+++ +++G+ F+ F N  D  
Sbjct: 6   PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAK 65

Query: 195 AALKEMNGKYVGNRPIK 211
            A +  NG  +  R I+
Sbjct: 66  EAKERANGMELDGRRIR 82

>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 = 57.8 bits (139), Expect = 6e-12
 Identities = 18/76 (23%), Positives = 35/76 (46%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           D  L+   L   +    L + FS++     ++++ D+ TG ++G GFI F    +   A+
Sbjct: 6   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 198 KEMNGKYVGNRPIKLR 213
           K +NG+        + 
Sbjct: 66  KGLNGQKPSGATEPIT 81

>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 = 57.4 bits (138), Expect = 1e-11
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 140 RLFCGDLGNEVNDDVLSK-AFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
            ++  +L  ++  D L K   + F  F     +   R+ K +G  F+ F   S    AL+
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 199 EMNGKYVGNRPIKLRKSK 216
            M G    ++P++++ +K
Sbjct: 65  SMQGFPFYDKPMRIQYAK 82

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {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: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (136), Expect = 2e-11
 Identities = 13/76 (17%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G +  +  +  L   F ++    + +++ D+ +GK +G+ F++F +   +   +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-I 62

Query: 200 MNGKYVGNRPIKLRKS 215
                V     ++RK+
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>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 = 57.0 bits (137), Expect = 2e-11
 Identities = 32/100 (32%), Positives = 48/100 (48%), Gaps = 7/100 (7%)

Query: 121 AAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTK 180
           AAG   E P           LF   L  E  D  L + F  F +   AKV  DK+T  +K
Sbjct: 8   AAGSQKEGPE-------GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 60

Query: 181 GYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQER 220
            +GF+S+ NP    AA++ MNG  +G + +K++  + +  
Sbjct: 61  CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 100

>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 = 56.6 bits (136), Expect = 2e-11
 Identities = 20/81 (24%), Positives = 41/81 (50%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
           +++  +   +L  +  +  L + F  F S +   + +DK TG++KG+ FISF    D A 
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 196 ALKEMNGKYVGNRPIKLRKSK 216
           A+  ++G    +  + +  +K
Sbjct: 66  AIAGVSGFGYDHLILNVEWAK 86

>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 = 56.6 bits (136), Expect = 2e-11
 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L+  +L    +++++ K F+             +R  K + Y F+ F+N  D   A+K 
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIK------PGAVERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 200 MNGKYVGNRPIKLRKSKWQER 220
           +NGK +   PI++  +K  ++
Sbjct: 64  LNGKVLDGSPIEVTLAKPVDK 84

>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 = 56.6 bits (136), Expect = 2e-11
 Identities = 20/91 (21%), Positives = 43/91 (47%), Gaps = 2/91 (2%)

Query: 132 AEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPS 191
           +E      RL   ++     D  L + F +F      +++ ++R  K   +GF++F N +
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG--FGFVTFENSA 62

Query: 192 DIAAALKEMNGKYVGNRPIKLRKSKWQERTD 222
           D   A ++++G  V  R I++  +  +  T+
Sbjct: 63  DADRAREKLHGTVVEGRKIEVNNATARVMTN 93

>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 = 56.5 bits (136), Expect = 2e-11
 Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 2/87 (2%)

Query: 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA 195
           +    L    L  +  +  L + FS F    M +V +D +TG +KG+GF+ F        
Sbjct: 6   QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 65

Query: 196 ALKEMNGKYVGNRPIKLRKSKWQERTD 222
            + + +   +  R    +    ++  D
Sbjct: 66  VMSQRHM--IDGRWCDCKLPNSKQSQD 90

>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 = 56.3 bits (135), Expect = 4e-11
 Identities = 21/86 (24%), Positives = 37/86 (43%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                RLF  +L    +++ L K FS +   +      D  T K KG+ F++F  P    
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQER 220
            A  E++G+    R + +  S  ++ 
Sbjct: 65  KAYAEVDGQVFQGRMLHVLPSTIKKE 90

>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 = 55.4 bits (133), Expect = 5e-11
 Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
               +F  +L   +++  L   FS F +    KVV D+   K   YGF+ F        A
Sbjct: 7   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERA 64

Query: 197 LKEMNGKYVGNRPIKLRKSKWQER 220
           +++MNG  + +R + + + K ++ 
Sbjct: 65  IEKMNGMLLNDRKVFVGRFKSRKE 88

>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 = 57.7 bits (138), Expect = 6e-11
 Identities = 19/152 (12%), Positives = 51/152 (33%), Gaps = 6/152 (3%)

Query: 68  PVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWE 127
            +              R    +T   +E V AA+ +   +      +             
Sbjct: 32  TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 91

Query: 128 DPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISF 187
                       ++F G +  +  +  L   F ++    + +++ D+ +GK +G+ F++F
Sbjct: 92  G-----AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146

Query: 188 ANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE 219
            +   +   +       V     ++RK+  ++
Sbjct: 147 DDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQ 177

>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 = 51.9 bits (123), Expect = 6e-09
 Identities = 25/97 (25%), Positives = 43/97 (44%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           PE   +LF G L  E  D+ L   F ++ +     V+RD  T +++G+GF+++A   ++ 
Sbjct: 3   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTDFEALERSKN 231
           AA+     K  G      R    ++     A    K 
Sbjct: 63  AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKK 99

>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 = 55.1 bits (132), Expect = 6e-11
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 7/78 (8%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           +L+ G+L   V  D L + F         K+    +     GY F+ + + +    A++ 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDR------KLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 200 MNGKY-VGNRPIKLRKSK 216
           ++GK  +  + +++  S 
Sbjct: 57  LSGKVELHGKIMEVDYSV 74

>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 = 55.0 bits (132), Expect = 7e-11
 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 131 LAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANP 190
           + E       L+ G+L  +V + ++ + FS+       K++ +        Y F+ F   
Sbjct: 1   MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEH 58

Query: 191 SDIAAALKEMNGKYVGNRPIKLRKSK 216
            D AAAL  MNG+ +  + +K+  + 
Sbjct: 59  RDAAAALAAMNGRKILGKEVKVNWAT 84

>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 = 54.7 bits (131), Expect = 8e-11
 Identities = 16/75 (21%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L      + +   F +F   + A ++ DK T + +G+GF++F +   +     E
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 200 MNGKYVGNRPIKLRK 214
           ++   + N+ ++ +K
Sbjct: 60  IHFHEINNKMVECKK 74

>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 = 55.1 bits (132), Expect = 8e-11
 Identities = 26/77 (33%), Positives = 38/77 (49%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L+ G L  EV+D VL  AF  F      ++  D  T K +G+ F+ F    D AAA+  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 200 MNGKYVGNRPIKLRKSK 216
           MN   +  R I++  +K
Sbjct: 67  MNESELFGRTIRVNLAK 83

>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 = 54.9 bits (132), Expect = 9e-11
 Identities = 15/86 (17%), Positives = 34/86 (39%), Gaps = 9/86 (10%)

Query: 136 ENDYRLFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             + R+F G+L    V    +   FS++       V         KG+ F+ + N  +  
Sbjct: 13  SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNAR 64

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQER 220
           AA+   +G+ +  + + +  +   + 
Sbjct: 65  AAVAGEDGRMIAGQVLDINLAAEPKV 90

>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 = 54.7 bits (131), Expect = 1e-10
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 136 ENDYR-LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           E D R +FC  L   +    L   FS        +++ D+ + ++KG  ++ F       
Sbjct: 15  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS-V 73

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
                + G+ +   PI ++ S+
Sbjct: 74  PLAIGLTGQRLLGVPIIVQASQ 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 = 54.4 bits (130), Expect = 1e-10
 Identities = 12/82 (14%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV-----VRDKRTGKTKGYGFISFANPSDIA 194
           RL+ G++   + ++ +   F+               V   +  + K + F+ F +  +  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            A+   +G     + +K+R+  
Sbjct: 63  QAMA-FDGIIFQGQSLKIRRPH 83

>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 = 54.0 bits (129), Expect = 2e-10
 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           ++F G L     D  L K F  F     A V+ D++TGK++GYGF++ A+ +    A K+
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 200 MNGKYVGNRPIKLRKSKWQER 220
            N   +  R   +  +    +
Sbjct: 72  PNP-IIDGRKANVNLAYLGAK 91

>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 = 53.7 bits (128), Expect = 3e-10
 Identities = 11/78 (14%), Positives = 26/78 (33%), Gaps = 6/78 (7%)

Query: 140 RLFCGDLGNEVNDDVLSKAF---SRFPSFNMAKVVRDKRTGKT---KGYGFISFANPSDI 193
            +F   L   + D  + K      +F   +   +        +       ++++    D 
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 194 AAALKEMNGKYVGNRPIK 211
             A++ +N   V  R +K
Sbjct: 70  LRAIQCVNNVVVDGRTLK 87

>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 = 52.8 bits (126), Expect = 5e-10
 Identities = 17/78 (21%), Positives = 34/78 (43%)

Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
           + LF   +  E  +D + + F  +       +  D+RTG +KGY  + +       AA +
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 199 EMNGKYVGNRPIKLRKSK 216
            +NG  +  + I++    
Sbjct: 68  ALNGAEIMGQTIQVDWCF 85

>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 = 51.7 bits (123), Expect = 9e-10
 Identities = 7/79 (8%), Positives = 26/79 (32%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           +  L+  +         +           ++  +   R   ++ + +I   +  D    +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 198 KEMNGKYVGNRPIKLRKSK 216
           +++NG  +    +  + S 
Sbjct: 61  EKLNGLKIEGYTLVTKVSN 79

>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 = 51.9 bits (124), Expect = 1e-09
 Identities = 15/77 (19%), Positives = 35/77 (45%), Gaps = 6/77 (7%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RLF G+L  ++ ++ + K F ++       + +DK       +GFI     +    A  E
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 200 MNGKYVGNRPIKLRKSK 216
           ++   +  + +++R + 
Sbjct: 64  LDNMPLRGKQLRVRFAC 80

>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 = 52.1 bits (124), Expect = 1e-09
 Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 11/100 (11%)

Query: 128 DPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRF--------PSFNMAKVVRDKRTGKT 179
           DP   +   ++  ++   L + V  D L+  F +             M  +  DK TGK 
Sbjct: 1   DP---DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 57

Query: 180 KGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE 219
           KG   +S+ +P    AA++  +GK      +K+  ++ + 
Sbjct: 58  KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 97

>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 = 51.8 bits (124), Expect = 1e-09
 Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 145 DLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKY 204
            + NE+ +D+  +  S+F       +          G   +SF +P +    ++ ++G++
Sbjct: 27  LVLNEIREDLRVE-CSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRW 81

Query: 205 VGNRPIKLRKSKWQERTDFE 224
            G R I      W   TD++
Sbjct: 82  FGGRQITA--QAWDGTTDYQ 99

>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 = 51.7 bits (123), Expect = 2e-09
 Identities = 20/81 (24%), Positives = 41/81 (50%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            +F G++  E  ++ L   FS        ++V D+ TGK KGYGF  + +     +A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 200 MNGKYVGNRPIKLRKSKWQER 220
           +NG+    R +++  +  ++ 
Sbjct: 70  LNGREFSGRALRVDNAASEKN 90

>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 = 50.6 bits (120), Expect = 4e-09
 Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L+  +L   V +  L   F+RF       +     TG+ +G  FI+F N      AL  
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 200 MNGKYVGNRPIKLRKSKWQ-ERT 221
           +NG  +  + + +   K + +R+
Sbjct: 80  VNGYKLYGKILVIEFGKNKKQRS 102

>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 = 50.8 bits (121), Expect = 4e-09
 Identities = 17/97 (17%), Positives = 38/97 (39%), Gaps = 6/97 (6%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R+   +L   V  DVL + FS+F +               +    + +A+P     A   
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVSAQHAKLS 64

Query: 200 MNGK--YVGNRPIKLRKSKWQERTDFEALERSKNHNQ 234
           ++G+  Y     +++  SK          ++S+++ +
Sbjct: 65  LDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTR 101

>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 = 50.5 bits (120), Expect = 4e-09
 Identities = 12/93 (12%), Positives = 35/93 (37%), Gaps = 4/93 (4%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRF--PSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
           RLF G +      + + +  ++      ++          K +G+ F+ + +    A A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 198 KEMNGKYV--GNRPIKLRKSKWQERTDFEALER 228
           +++    +      I +  ++ +   D + +E 
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>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 = 49.6 bits (118), Expect = 5e-09
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           P     L+      ++   +L  AFS F +        D      +   F+++       
Sbjct: 2   PRKGNTLYVYGE--DMTPTLLRGAFSPFGNII------DLSMDPPRNCAFVTYEKMESAD 53

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQ 218
            A+ E+NG  V +  +K+  ++ Q
Sbjct: 54  QAVAELNGTQVESVQLKVNIARKQ 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 = 50.1 bits (119), Expect = 6e-09
 Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 1/88 (1%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
               Y  F G+L  +V ++ + + F       +          + KG+G+  F +   + 
Sbjct: 12  KSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQERTD 222
           +AL  +N + +GN+ I++  +   +  D
Sbjct: 72  SALS-LNEESLGNKRIRVDVADQAQDKD 98

>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 = 50.0 bits (119), Expect = 8e-09
 Identities = 10/71 (14%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +   +  +E  ++V ++   ++       V  +       G  ++ F    D   A+ ++
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 201 NGKYVGNRPIK 211
           N ++   +PI 
Sbjct: 89  NNRWFNGQPIH 99

>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 = 49.8 bits (118), Expect = 9e-09
 Identities = 18/104 (17%), Positives = 40/104 (38%), Gaps = 10/104 (9%)

Query: 113 KKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVR 172
           K   +  + A Q  +DPT          L+  +L   +++  L +   +     ++  + 
Sbjct: 2   KASGVQAQMAKQQEQDPT---------NLYISNLPLSMDEQEL-ENMLKPFGQVISTRIL 51

Query: 173 DKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK 216
              +G ++G GF    +     A +   NGK++   P     ++
Sbjct: 52  RDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>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 = 48.2 bits (114), Expect = 1e-08
 Identities = 21/71 (29%), Positives = 29/71 (40%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           L+   L     D  L K    +      K + DK T K KGYGF+ F +PS    A+  +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 201 NGKYVGNRPIK 211
               V  +  K
Sbjct: 61  KASGVQAQMAK 71

>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 = 48.0 bits (113), Expect = 3e-08
 Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
               + LF G+L    +   L  A S   + N    V D RTG  + +G++ F +  D+ 
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLE 68

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            AL+ + G  V    IKL K K
Sbjct: 69  KALE-LTGLKVFGNEIKLEKPK 89

>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 = 47.0 bits (111), Expect = 7e-08
 Identities = 18/92 (19%), Positives = 31/92 (33%), Gaps = 12/92 (13%)

Query: 114 KKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRD 173
           K ++ R    +T    T          +  G LGN V+ + L     +    +   +  +
Sbjct: 2   KHTLLRHEGIETVSYAT------QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN 55

Query: 174 KRTGKTKGYGFISFANPSDIAAALKEMNGKYV 205
           K       Y F  +    +   A   +NGK V
Sbjct: 56  KP------YSFARYRTTEESKRAYVTLNGKEV 81

>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 = 46.1 bits (109), Expect = 1e-07
 Identities = 8/74 (10%), Positives = 22/74 (29%), Gaps = 8/74 (10%)

Query: 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAA 196
           +D  +            +L   F+++ +     +           +  I + +      A
Sbjct: 3   DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKA 55

Query: 197 LKEMNGKYVGNRPI 210
           L   +G+  G   +
Sbjct: 56  L-SKDGRIFGESIM 68

>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 = 46.3 bits (109), Expect = 2e-07
 Identities = 22/109 (20%), Positives = 38/109 (34%), Gaps = 16/109 (14%)

Query: 140 RLFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK 198
            L   +L  E V    L   F  +      K++ +K+         +  A+ +    A+ 
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAMS 58

Query: 199 EMNGKYVGNRPIKLRKSKWQERTDFEALER----------SKNHNQKKP 237
            +NG  +  +PI++  SK Q        +           S  H  KKP
Sbjct: 59  HLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKP 107

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {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: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (108), Expect = 2e-07
 Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 1/86 (1%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             ND  +    L    + + + + FS          +     G++ G  F+ FA+     
Sbjct: 12  TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE 71

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQER 220
            ALK  + + +G+R I++ KS   E 
Sbjct: 72  KALK-KHKERIGHRYIEIFKSSRAEV 96

>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 = 45.5 bits (107), Expect = 3e-07
 Identities = 11/82 (13%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
             +D+R+    L    +   L            A V +D         G + +    D+ 
Sbjct: 12  RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLRKEDME 64

Query: 195 AALKEMNGKYVGNRPIKLRKSK 216
            AL++++     +   +    +
Sbjct: 65  YALRKLDDTKFRSHEGETSYIR 86

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

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 = 44.7 bits (105), Expect = 3e-07
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 140 RLFCGDLGNEV-NDDVLSKAFSRFP-SFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
            +   +L  E+ ++++L ++F  F     +      K         F+ F N      AL
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 198 KEMNGKYVGNRPIKLRKSK 216
            +MN   +GNR I +  + 
Sbjct: 66  -QMNRSLLGNREISVSLAD 83

>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 = 45.7 bits (107), Expect = 5e-07
 Identities = 21/86 (24%), Positives = 42/86 (48%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
           P+    L    +   V++  L + F R+      K+V D+ T +++GYGF+ F + S   
Sbjct: 39  PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQ 98

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQER 220
            A+  +NG  + N+ +K+  +    +
Sbjct: 99  QAIAGLNGFNILNKRLKVALAASGHQ 124

>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 = 44.0 bits (103), Expect = 7e-07
 Identities = 15/92 (16%), Positives = 31/92 (33%), Gaps = 6/92 (6%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
                 +F  +L  +  ++ L +   +F      +VV    T  +KG  F  F       
Sbjct: 5   VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 64

Query: 195 AALKEMN------GKYVGNRPIKLRKSKWQER 220
             L   +      G  +  R +K+  +  ++ 
Sbjct: 65  KCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>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 = 43.5 bits (102), Expect = 1e-06
 Identities = 10/77 (12%), Positives = 29/77 (37%), Gaps = 7/77 (9%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            +F G    ++ +D L + FS++       V+        + + F++FA+     +    
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQY-----GDVMDVFIPKPFRAFAFVTFADDQIAQSLC-- 59

Query: 200 MNGKYVGNRPIKLRKSK 216
                +    + +  ++
Sbjct: 60  GEDLIIKGISVHISNAE 76

>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 = 43.0 bits (101), Expect = 2e-06
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 7/81 (8%)

Query: 148 NEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGF--ISFANPSDIAAALKEMNGKYV 205
            E+ +DV  +  S++      ++ R     +  G G   + F +  D   A++ + G+  
Sbjct: 25  EEIVEDVRDE-CSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF 83

Query: 206 GNRPIK---LRKSKWQERTDF 223
            NR +         +  R DF
Sbjct: 84  ANRVVVTKYCDPDSYHRR-DF 103

>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 = 42.4 bits (99), Expect = 3e-06
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           RL+ G LG   +   L++ F RF S      V+         + +I + +     AA  +
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAACAK 72

Query: 200 MNGKYVGNRPIKLR 213
           M G  +G    +LR
Sbjct: 73  MRGFPLGGPDRRLR 86

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {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: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 4e-06
 Identities = 12/86 (13%), Positives = 27/86 (31%), Gaps = 3/86 (3%)

Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIA 194
               + +    L     ++ +   FS      +         G+  G   + FA   D  
Sbjct: 12  STTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEADVEFATHEDAV 69

Query: 195 AALKEMNGKYVGNRPIKLRKSKWQER 220
           AA+   +   + +R ++L  +     
Sbjct: 70  AAM-AKDKANMQHRYVELFLNSTAGT 94

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 12/83 (14%), Positives = 27/83 (32%), Gaps = 1/83 (1%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L      ++V  +  ++       F         +  K+     I+F+NP   A A   
Sbjct: 7   GLIACVANDDVFSESETR-AKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLR 65

Query: 200 MNGKYVGNRPIKLRKSKWQERTD 222
           ++      + +KL  ++      
Sbjct: 66  LHKTEFLGKEMKLYFAQTLHIGS 88

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 20/97 (20%), Positives = 33/97 (34%), Gaps = 7/97 (7%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAA-ALKE 199
            F GDL ++   + L   FS          VR          G I F   +  A    K+
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALGKAKD 67

Query: 200 MNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKK 236
            N   +  R  ++     +   + EAL++     Q+ 
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQES 104

>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 = 40.5 bits (94), Expect = 1e-05
 Identities = 6/77 (7%), Positives = 23/77 (29%), Gaps = 7/77 (9%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            +   +L  + N   +      +        ++     + K   F++  N      A++ 
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 200 MNGKYVGNRPIKLRKSK 216
            +      + + ++   
Sbjct: 60  FHQYSFRGKDLIVQLQP 76

>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 = 39.9 bits (92), Expect = 3e-05
 Identities = 10/106 (9%), Positives = 27/106 (25%), Gaps = 6/106 (5%)

Query: 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAAL 197
              +   +L                 +F+    +      +      + F  P +   A 
Sbjct: 10  KTVILAKNLPAGTLAA------EIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAF 63

Query: 198 KEMNGKYVGNRPIKLRKSKWQERTDFEALERSKNHNQKKPKLSKKS 243
           + +      + P+ L  +           + S++    +   S  S
Sbjct: 64  RHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGPS 109

>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 = 36.7 bits (84), Expect = 4e-04
 Identities = 12/83 (14%), Positives = 24/83 (28%), Gaps = 8/83 (9%)

Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM 200
           +    L   V +  L +A  +F +     ++  KR         + F N       +   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVTFA 71

Query: 201 NGK--YVGNRPIKLRKSKWQERT 221
                Y+  +      S  +  T
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKRIT 94

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

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 = 36.0 bits (82), Expect = 6e-04
 Identities = 10/82 (12%), Positives = 22/82 (26%), Gaps = 7/82 (8%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
           R+    L    +   L            A V RD             F    D+  A+++
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVE-------FVRKEDMTYAVRK 54

Query: 200 MNGKYVGNRPIKLRKSKWQERT 221
           ++     +   +    + +   
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDG 76

>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 = 33.7 bits (76), Expect = 0.004
 Identities = 13/82 (15%), Positives = 27/82 (32%), Gaps = 8/82 (9%)

Query: 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKE 199
            L    L  EV +  +      F       +++ K         F+  A        +  
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN------QAFLELATEEAAITMVNY 63

Query: 200 MNGK--YVGNRPIKLRKSKWQE 219
            +    ++ N+PI ++ S  +E
Sbjct: 64  YSAVTPHLRNQPIYIQYSNHKE 85

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	247
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.9
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.9
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.9
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.9
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.9
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.9
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.9
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.89
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.89
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.89
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.88
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.88
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.88
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.88
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.88
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.88
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.88
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.88
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.87
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.87
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.87
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.87
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.87
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.87
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.87
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.87
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.86
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.86
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.86
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.85
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.85
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.85
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.84
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.83
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.83
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.83
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.83
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.82
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.82
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.82
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.82
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.81
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.81
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.81
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.81
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.81
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.8
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.8
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.8
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.8
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.8
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.79
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.79
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.78
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.78
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.77
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.77
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.76
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.76
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.76
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.75
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.75
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.74
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.72
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.7
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.7
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.69
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	99.67
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.62
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.56
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.55
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.52
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.42
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.09
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.59
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.5
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	96.02
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.01
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	95.62
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	95.45
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	95.41
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	94.93
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	94.93
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	94.51
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	94.49
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	94.32
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	94.29
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	94.05
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	93.98
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	93.86
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	93.62
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	93.5
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	93.46
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	93.46
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	93.36
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	92.89
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	92.78
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	92.58
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	92.55
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	92.25
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	92.24
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	92.08
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	91.56
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	91.4
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	91.39
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	91.35
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	90.62
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	90.41
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	90.13
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	89.9
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	89.79
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	89.73
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	89.69
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	89.55
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	89.04
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	88.46
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	88.43
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	87.49
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	86.32
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	86.24
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	85.65
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	84.97
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	84.82
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	83.68
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	83.66
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	83.36
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	83.18
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	83.08
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	82.99
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	82.87
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	82.62
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	82.44
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	81.27
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	81.18
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	80.57

>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=99.90  E-value=4.7e-24  Score=147.21  Aligned_cols=80  Identities=28%  Similarity=0.463  Sum_probs=77.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      +++|||+|||.++++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|++||+.|||..++|+.|+|++|++
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            45899999999999999999999999999999999999999999999999999999999999999999999999999875

>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=99.90  E-value=4.5e-24  Score=150.82  Aligned_cols=85  Identities=25%  Similarity=0.466  Sum_probs=80.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+|||.++++++|+++|++||.|.+|+|++|+.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|++|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          216 KWQER  220 (247)
Q Consensus       216 ~~k~~  220 (247)
                      +++.+
T Consensus        87 ~~~~~   91 (93)
T d1x5ua1          87 SAHNK   91 (93)
T ss_dssp             TTTSC
T ss_pred             CCCCC
Confidence            88764

>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=99.90  E-value=1.4e-23  Score=146.83  Aligned_cols=84  Identities=20%  Similarity=0.382  Sum_probs=79.2

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..++++|||+|||.++++++|+++|+.||.|.+|++++|+.+|.++|||||+|.+.++|++|+..|||..|+|+.|+|++
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            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      +..+
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9765

>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=99.90  E-value=1.6e-23  Score=150.44  Aligned_cols=85  Identities=32%  Similarity=0.473  Sum_probs=80.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +++++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|+.||+.|||..|+|+.|+|+++
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            45568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          216 KWQER  220 (247)
Q Consensus       216 ~~k~~  220 (247)
                      +++..
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            88764

>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=99.90  E-value=1.6e-23  Score=147.12  Aligned_cols=84  Identities=24%  Similarity=0.382  Sum_probs=79.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .+.++|||+|||.++++++|+++|+.||.|.+|+|+.|+.+|.++|||||+|.+.++|.+|++.|||..|+|+.|+|+++
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            44568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          216 KWQE  219 (247)
Q Consensus       216 ~~k~  219 (247)
                      +++.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8764

>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=99.90  E-value=7.7e-24  Score=148.43  Aligned_cols=83  Identities=31%  Similarity=0.463  Sum_probs=78.9

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|++|+.+|.++|||||+|.+.++|++|+..|||..|+|+.|+|++++
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            34589999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q 025814          217 WQE  219 (247)
Q Consensus       217 ~k~  219 (247)
                      ++.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.90  E-value=2.5e-23  Score=143.49  Aligned_cols=79  Identities=27%  Similarity=0.509  Sum_probs=76.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      ++|||+|||.++++++|+++|++||.|.++++++|..+|.++|||||+|.+.++|++|++.|||..|+|+.|+|++|++
T Consensus         3 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           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999999999875

>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=99.89  E-value=4e-23  Score=145.87  Aligned_cols=84  Identities=18%  Similarity=0.285  Sum_probs=79.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|.+++++.+|.++|||||+|.+.++|..|++.|||..|+|+.|+|++
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34566999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      +...
T Consensus        84 a~~~   87 (93)
T d1h2vz_          84 DAGF   87 (93)
T ss_dssp             ESCC
T ss_pred             cCCC
Confidence            8754

>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=99.89  E-value=8.7e-24  Score=146.88  Aligned_cols=81  Identities=26%  Similarity=0.528  Sum_probs=78.2

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      +|||+|||+++++++|+++|++||.|.+++|++|+.||.++|||||+|.+.++|..|++.|||..|+|+.|+|+++.+..
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~   82 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA   82 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             c
Q 025814          220 R  220 (247)
Q Consensus       220 ~  220 (247)
                      +
T Consensus        83 ~   83 (85)
T d2u2fa_          83 K   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.89  E-value=2.3e-23  Score=143.09  Aligned_cols=77  Identities=30%  Similarity=0.536  Sum_probs=75.3

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      +|||+|||+++++++|+++|+.||.|.+|+|++|+.+|.++|||||+|.+.++|..|++.|||..++|+.|+|.+++
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~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.89  E-value=4.7e-23  Score=147.23  Aligned_cols=85  Identities=25%  Similarity=0.400  Sum_probs=80.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|++||.|.+|+|++|+.+|.++|||||+|.+.++|++||+.|||..|+|+.|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus        85 a~~~~   89 (99)
T d1whwa_          85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98754

>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=99.88  E-value=1.1e-22  Score=154.08  Aligned_cols=85  Identities=24%  Similarity=0.416  Sum_probs=80.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+|||+++++++|+++|+.||.|.+|+|++|+.||.++|||||+|.+.++|.+||+.|||..|+|+.|+|+++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          216 KWQER  220 (247)
Q Consensus       216 ~~k~~  220 (247)
                      +.+..
T Consensus       120 ~~~~~  124 (139)
T d1u6fa1         120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.88  E-value=9.7e-23  Score=141.16  Aligned_cols=80  Identities=26%  Similarity=0.525  Sum_probs=75.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +..++|||+|||+++++++|+++|+.||.|.+++|++|+.+|.++|||||+|.+.++|++||+ ++|..|+|+.|+|+.|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            345689999999999999999999999999999999999999999999999999999999995 7999999999999887


Q ss_pred             c
Q 025814          216 K  216 (247)
Q Consensus       216 ~  216 (247)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.88  E-value=8.7e-23  Score=141.10  Aligned_cols=78  Identities=23%  Similarity=0.409  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V  212 (247)
                      +...++|||+|||+++++++|+++|++||.|.+|+|++|+.+|.++|||||+|.+.++|.+|++.|||..|+|+.|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            345678999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.88  E-value=1.5e-22  Score=141.90  Aligned_cols=83  Identities=20%  Similarity=0.344  Sum_probs=76.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+|||+++++++|+++|+.||.|.+|+|++|+.+|.++|||||+|.+.++|++||+.  +..|+|+.|.|+++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            3455899999999999999999999999999999999999999999999999999999999974  55899999999999


Q ss_pred             ccccc
Q 025814          216 KWQER  220 (247)
Q Consensus       216 ~~k~~  220 (247)
                      ..+..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87654

>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=99.88  E-value=4.6e-23  Score=141.87  Aligned_cols=80  Identities=9%  Similarity=0.195  Sum_probs=70.1

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      +++|||+|||+++++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||..++|+.|+|+++++
T Consensus         1 d~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           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            36999999999999999999999999999998888888999999999999999999999999999999999999999875

>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=99.88  E-value=1.1e-22  Score=141.17  Aligned_cols=78  Identities=26%  Similarity=0.509  Sum_probs=73.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EeEEEEEc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN--RPIKLRKS  215 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~a  215 (247)
                      +++|||+|||+++++++|+++|++||.|.+++|++|+.+|.++|||||+|.+.++|.+|++.|||..++|  ++|+|++|
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            4589999999999999999999999999999999999999999999999999999999999999999998  55898875

>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=99.88  E-value=1e-22  Score=146.39  Aligned_cols=82  Identities=21%  Similarity=0.470  Sum_probs=77.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||+++++++|+++|++||.|..+.|.+|+.++.++|||||+|.+.++|.+|| .++|..|+|+.|.|+++.+
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 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHH-TSCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHH-HhCCCeECCEEEEEEECcc
Confidence            358999999999999999999999999999999999999999999999999999999999 5899999999999999988


Q ss_pred             ccc
Q 025814          218 QER  220 (247)
Q Consensus       218 k~~  220 (247)
                      +++
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>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=99.88  E-value=2e-23  Score=142.19  Aligned_cols=76  Identities=21%  Similarity=0.473  Sum_probs=73.1

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      |+|||+|||+++++++|+++|++||.|.+++|++|+.||+++|||||+|.+.++|++||+ +|+..|+|+.|+|+.|
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            579999999999999999999999999999999999999999999999999999999995 7999999999999876

>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=99.88  E-value=1.8e-22  Score=140.12  Aligned_cols=79  Identities=24%  Similarity=0.522  Sum_probs=74.8

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EeEEEEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN--RPIKLRK  214 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~~  214 (247)
                      ..++|||+|||+++++++|+++|++||.|.++++++|+.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|+|++
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            34589999999999999999999999999999999999999999999999999999999999999999876  8899998


Q ss_pred             c
Q 025814          215 S  215 (247)
Q Consensus       215 a  215 (247)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.87  E-value=7.2e-23  Score=143.67  Aligned_cols=84  Identities=31%  Similarity=0.609  Sum_probs=79.2

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      +.++|||+|||+++++++|+++|++||.|..+.++++..+|.++|||||+|.+.++|+.|++.|||..|+|+.|+|+++.
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            45589999999999999999999999999999999998999999999999999999999999999999999999999987


Q ss_pred             cccc
Q 025814          217 WQER  220 (247)
Q Consensus       217 ~k~~  220 (247)
                      .+..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6553

>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=99.87  E-value=1.4e-22  Score=143.35  Aligned_cols=84  Identities=17%  Similarity=0.364  Sum_probs=77.7

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecC-CCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCEeEEEEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDK-RTGKTKGYGFISFANPSDIAAALKEM-NGKYVGNRPIKLRK  214 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~-~tg~~kg~~FV~f~~~~~a~~Al~~l-~g~~i~g~~l~V~~  214 (247)
                      ...+|||+|||+++++++|+++|+.||.|.+|+|+++. .+|.++|||||+|.+.++|.+||+.| ||..|+|+.|+|++
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            34589999999999999999999999999999999875 48999999999999999999999998 89999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      |+.+.+
T Consensus        87 A~~~~~   92 (94)
T d2cpha1          87 ADSEVT   92 (94)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987654

>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=99.87  E-value=9.3e-23  Score=146.95  Aligned_cols=81  Identities=25%  Similarity=0.531  Sum_probs=77.8

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      ++|||+|||+++++++|+++|++||.|.+|+|++++.+|.++|||||+|.+.++|++|++.|||..|+|+.|+|+++..+
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             c
Q 025814          219 E  219 (247)
Q Consensus       219 ~  219 (247)
                      .
T Consensus        89 ~   89 (104)
T d1p1ta_          89 K   89 (104)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.87  E-value=1.1e-22  Score=145.77  Aligned_cols=79  Identities=19%  Similarity=0.409  Sum_probs=75.3

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+||++++++++|+++|+.||.|.+|+|++|+.+|.++|||||+|.+.++|.+|+ .|||..|+|+.|+|+++..
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 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEECCC
Confidence            358999999999999999999999999999999999999999999999999999999999 5999999999999999754

>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=99.87  E-value=2.3e-22  Score=139.51  Aligned_cols=79  Identities=23%  Similarity=0.493  Sum_probs=73.6

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCC---CcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTG---KTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       141 lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg---~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      |||+|||+++++++|+++|++||.|.++.|++++.++   .++|||||+|.+.++|.+|++.|||..|+|+.|+|++++.
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            8999999999999999999999999999999987665   4789999999999999999999999999999999999865


Q ss_pred             cc
Q 025814          218 QE  219 (247)
Q Consensus       218 k~  219 (247)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.87  E-value=1.2e-22  Score=140.32  Aligned_cols=79  Identities=38%  Similarity=0.682  Sum_probs=74.9

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEE-EEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          141 LFCGDLGNEVNDDVLSKAFSRFPSFNMA-KVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       141 lfV~nLp~~~~e~~L~~~F~~~G~i~~v-~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      |||+|||+++++++|+++|++||.|.++ ++++++.+|+++|||||+|.+.++|.+||+.|||..++|+.|+|+++.+++
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            7999999999999999999999999764 789999999999999999999999999999999999999999999998765

>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=99.87  E-value=2.3e-22  Score=144.55  Aligned_cols=83  Identities=28%  Similarity=0.466  Sum_probs=76.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+|||+++++++|+++|+.||.|.+|+|++|+.||.++|||||+|.+.++|++||+.+|+ .|+|+.|+|+++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            3445899999999999999999999999999999999999999999999999999999999988876 799999999998


Q ss_pred             cccc
Q 025814          216 KWQE  219 (247)
Q Consensus       216 ~~k~  219 (247)
                      ..+.
T Consensus        87 ~~~~   90 (103)
T d2cqda1          87 YLGA   90 (103)
T ss_dssp             TTTC
T ss_pred             CCCC
Confidence            7543

>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=99.87  E-value=9.8e-22  Score=138.65  Aligned_cols=84  Identities=21%  Similarity=0.402  Sum_probs=77.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.+|+++.++  +.++|||||+|.+.++|.+|+..|||..|+|+.|+|++
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4445689999999999999999999999999999999985  44799999999999999999999999999999999999


Q ss_pred             cccccc
Q 025814          215 SKWQER  220 (247)
Q Consensus       215 a~~k~~  220 (247)
                      |+.+..
T Consensus        86 A~~r~~   91 (93)
T d2cq3a1          86 ATARVM   91 (93)
T ss_dssp             CCSSCC
T ss_pred             cCcCCC
Confidence            987654

>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=99.87  E-value=2.4e-22  Score=137.17  Aligned_cols=76  Identities=25%  Similarity=0.460  Sum_probs=73.6

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      +|||+|||+++++++|+++|+.||.|.+++|..++ +|+++|||||+|.+.++|++|++.|||..++|+.|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999995 89999999999999999999999999999999999999875

>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=99.87  E-value=1.2e-22  Score=137.62  Aligned_cols=75  Identities=20%  Similarity=0.453  Sum_probs=71.5

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +|||+|||+++++++|+++|++||.|.++.|++|+.+|+++|||||+|.+.++|++||+ +++..|+|+.|.|+.|
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            49999999999999999999999999999999999999999999999999999999995 8999999999999654

>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=99.87  E-value=7.4e-22  Score=138.44  Aligned_cols=83  Identities=23%  Similarity=0.418  Sum_probs=75.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|++++++.++  +|||||+|.+.++|++|++.|||..|+|+.|+|.+
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3445699999999999999999999999999999999986544  78999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++...
T Consensus        83 a~~~~   87 (90)
T d2cqia1          83 ATTPS   87 (90)
T ss_dssp             CCCTT
T ss_pred             cCCCC
Confidence            97643

>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=99.86  E-value=7.5e-22  Score=134.99  Aligned_cols=76  Identities=17%  Similarity=0.485  Sum_probs=73.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ++|||+|||+++++++|+++|+.||.|..+.+..++.++.++|||||+|.+.+++.+|+ .|||..|+|+.|+|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            48999999999999999999999999999999999999999999999999999999999 68999999999999876

>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=99.86  E-value=1e-21  Score=154.87  Aligned_cols=145  Identities=14%  Similarity=0.311  Sum_probs=116.0

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhcccccccccCCCCCCCCCCCCCCCCcEEEEc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCG  144 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~lfV~  144 (247)
                      |.+..+....+.....+++++||.|.+.+++..|+...  .+..+.+.......+.....       .......++|||+
T Consensus        31 G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~i~V~  103 (183)
T d1u1qa_          31 GTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQR-------PGAHLTVKKIFVG  103 (183)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCTTGGGS-------TTTTCCCSEEEEE
T ss_pred             CCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhcccccc-------cccccccceeEEc
Confidence            66666666666677888999999999999999999864  33344333333222221111       1123445699999


Q ss_pred             CCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          145 DLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       145 nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      |||+.+++++|+++|+.||.|..+.|+.++.+|.++|||||+|.+.++|.+||+ +++..|+|+.|+|.+|.+|.
T Consensus       104 ~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k~  177 (183)
T d1u1qa_         104 GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQ  177 (183)
T ss_dssp             CCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCHH
T ss_pred             cCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCcc
Confidence            999999999999999999999999999999999999999999999999999995 89999999999999987654

>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=99.86  E-value=5.2e-22  Score=138.95  Aligned_cols=79  Identities=28%  Similarity=0.513  Sum_probs=74.0

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      .+|||+|||+++++++|+++|+.||.|.+++|+.++  +.++|||||+|.+.++|++||+.|||..|+|+.|+|++++.+
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            389999999999999999999999999999999985  457899999999999999999999999999999999999865


Q ss_pred             c
Q 025814          219 E  219 (247)
Q Consensus       219 ~  219 (247)
                      .
T Consensus        87 ~   87 (89)
T d1cvja2          87 K   87 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.86  E-value=1.1e-21  Score=139.61  Aligned_cols=86  Identities=17%  Similarity=0.329  Sum_probs=79.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhC------CceeCCE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN------GKYVGNR  208 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~------g~~i~g~  208 (247)
                      ..++++|||+|||+++++++|+++|++||.|.++.++.+..++.++|||||+|.+.++|.+||+.||      |..|+|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3456689999999999999999999999999999999999999999999999999999999999886      6789999


Q ss_pred             eEEEEEcccccc
Q 025814          209 PIKLRKSKWQER  220 (247)
Q Consensus       209 ~l~V~~a~~k~~  220 (247)
                      .|+|+++.++.+
T Consensus        85 ~l~v~~a~~k~~   96 (98)
T d1x4ha1          85 QLKVDLAVTRDE   96 (98)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCCc
Confidence            999999987653

>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=99.86  E-value=1.7e-22  Score=136.85  Aligned_cols=75  Identities=20%  Similarity=0.442  Sum_probs=71.3

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +|||||||+++++++|+++|++||.|.+|+|++|+.+|+++|||||+|.+.++|++|| .+++..|+|+.|.|+.|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHT-TCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHH-hhCCCEECCEEeEEEEC
Confidence            5999999999999999999999999999999999999999999999999999999999 46888999999999865

>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=99.85  E-value=7.2e-22  Score=137.31  Aligned_cols=80  Identities=23%  Similarity=0.382  Sum_probs=70.2

Q ss_pred             CcEEEEcCCCCCCc-HHHHHHHhccCCCeeEEEEEec-CCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          138 DYRLFCGDLGNEVN-DDVLSKAFSRFPSFNMAKVVRD-KRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       138 ~~~lfV~nLp~~~~-e~~L~~~F~~~G~i~~v~i~~~-~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .++|||+|||++++ +++|+++|++||.|.+|+|.++ ..+|.++|||||+|.+.++|++|| .|||..|+|+.|+|+++
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al-~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHH-hcCCCEECCEEEEEEEc
Confidence            45999999999976 5679999999999999998764 578999999999999999999999 59999999999999999


Q ss_pred             ccc
Q 025814          216 KWQ  218 (247)
Q Consensus       216 ~~k  218 (247)
                      +++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.85  E-value=2.2e-21  Score=138.76  Aligned_cols=85  Identities=24%  Similarity=0.375  Sum_probs=77.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCee--------EEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFN--------MAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVG  206 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~--------~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~  206 (247)
                      ..+..+|||+|||+++++++|+++|+.||.|.        .+.+.+++.+|.++|||||+|.+.++|.+||+.|||..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            34566999999999999999999999999873        5677888889999999999999999999999999999999


Q ss_pred             CEeEEEEEccccc
Q 025814          207 NRPIKLRKSKWQE  219 (247)
Q Consensus       207 g~~l~V~~a~~k~  219 (247)
                      |+.|+|++++.+.
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999998654

>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=99.85  E-value=1.9e-21  Score=142.29  Aligned_cols=79  Identities=16%  Similarity=0.265  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +..++|||+|||+++++++|+++|++||.|.+|++..+   +.++|||||+|.+.++|..||+.|||..|+|+.|+|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            44569999999999999999999999999999998764   677999999999999999999999999999999999998


Q ss_pred             cc
Q 025814          216 KW  217 (247)
Q Consensus       216 ~~  217 (247)
                      ..
T Consensus        82 ~~   83 (114)
T d2f9da1          82 NA   83 (114)
T ss_dssp             CH
T ss_pred             CC
Confidence            64

>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=99.84  E-value=1e-21  Score=132.91  Aligned_cols=75  Identities=20%  Similarity=0.449  Sum_probs=72.1

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++ |||..|+|+.|+|++|
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            49999999999999999999999999999999999999999999999999999999995 9999999999999875

>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=99.83  E-value=6.4e-22  Score=139.01  Aligned_cols=82  Identities=32%  Similarity=0.455  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.|.++.|+.+ .+|+++|||||+|.+.++|++|| .|||..|+|+.|+|++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al-~~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHH-hcCCcEECCEEEEEEe
Confidence            445679999999999999999999999999999888765 58999999999999999999999 5999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      +++|
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8764

>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=99.83  E-value=6.7e-22  Score=141.83  Aligned_cols=85  Identities=24%  Similarity=0.303  Sum_probs=79.6

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .+.++|||+|||.++++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||..|+|+.|+|+++
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            34679999999999999999999999999999999988889999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 025814          216 KWQER  220 (247)
Q Consensus       216 ~~k~~  220 (247)
                      +.+..
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87653

>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=99.83  E-value=1.7e-20  Score=132.75  Aligned_cols=81  Identities=15%  Similarity=0.339  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.+..+   +..+|||||+|.+.++|+.||+.|||..|+|+.|+|++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            456678999999999999999999999999999887654   56789999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      ++..
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8753

>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=99.83  E-value=1.1e-20  Score=133.82  Aligned_cols=77  Identities=23%  Similarity=0.494  Sum_probs=71.7

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +..++|||+|||.++++++|+++|++||.|.+|+++++      +|||||+|.+.++|.+|+..|||..|+|+.|+|.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34468999999999999999999999999999999876      689999999999999999999999999999999998


Q ss_pred             ccc
Q 025814          216 KWQ  218 (247)
Q Consensus       216 ~~k  218 (247)
                      +.+
T Consensus        90 k~~   92 (96)
T d1x4ga1          90 KES   92 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.83  E-value=1.1e-20  Score=135.13  Aligned_cols=81  Identities=19%  Similarity=0.399  Sum_probs=75.1

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .+.++|||+|||+++++++|+++|+.||.|..+.+..+ .++.++|||||+|.+.++|.+|++.|||..|.|+.+.|..+
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            34568999999999999999999999999999999988 48999999999999999999999999999999999998776


Q ss_pred             cc
Q 025814          216 KW  217 (247)
Q Consensus       216 ~~  217 (247)
                      ++
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.82  E-value=3e-20  Score=128.68  Aligned_cols=76  Identities=11%  Similarity=0.076  Sum_probs=71.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ++|||+|||.++++++|+++|+.||.|.+|.+.++. +|.++|||||+|.+.++|++|| .++|..++|+.|.|.+++
T Consensus         7 rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al-~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           7 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHH-TCCCCEETTEECEEEEGG
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHH-HHCCCEECCEEEEEEEcC
Confidence            489999999999999999999999999999998885 8999999999999999999999 589999999999998753

>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=99.82  E-value=3.9e-21  Score=129.02  Aligned_cols=71  Identities=30%  Similarity=0.437  Sum_probs=69.0

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       141 lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      |||+|||+++++++|+++|+.||.|..+++.+++.++.++|||||+|.+.++|++|+..|||..|+|+.|+
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            79999999999999999999999999999999999999999999999999999999999999999999874

>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=99.82  E-value=1.9e-20  Score=132.73  Aligned_cols=82  Identities=21%  Similarity=0.351  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          134 WPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       134 ~~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ...+.++|||+|||+++++++|+++|+.||.|..+.     .+|.++|||||+|.+.++|++|++.|||..|+|+.|+|.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            355667999999999999999999999999876553     268899999999999999999999999999999999999


Q ss_pred             Ecccccc
Q 025814          214 KSKWQER  220 (247)
Q Consensus       214 ~a~~k~~  220 (247)
                      ++.++..
T Consensus        87 ~a~~k~~   93 (96)
T d1fjca_          87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EeCCCCC
Confidence            9987653

>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=99.82  E-value=1.4e-20  Score=131.46  Aligned_cols=76  Identities=14%  Similarity=0.284  Sum_probs=69.8

Q ss_pred             CcEEEEcCCCCCCcHHHH---HHHhccCCCeeEEEEEecCCCCCc---ceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          138 DYRLFCGDLGNEVNDDVL---SKAFSRFPSFNMAKVVRDKRTGKT---KGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L---~~~F~~~G~i~~v~i~~~~~tg~~---kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      .++|||+|||+++++++|   .++|++||.|.+|.+++++.++..   +|||||+|.+.++|.+|++.|||..++|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            347999999999999999   678999999999999999877655   49999999999999999999999999999999


Q ss_pred             EE
Q 025814          212 LR  213 (247)
Q Consensus       212 V~  213 (247)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            84

>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=99.81  E-value=1.4e-20  Score=133.40  Aligned_cols=83  Identities=13%  Similarity=0.196  Sum_probs=74.6

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCC-eeEEEEEecC-CCCCcceEEEEEecCHHHHHHHHHHhCCc--eeCCEeEEEEE
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPS-FNMAKVVRDK-RTGKTKGYGFISFANPSDIAAALKEMNGK--YVGNRPIKLRK  214 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~-i~~v~i~~~~-~tg~~kg~~FV~f~~~~~a~~Al~~l~g~--~i~g~~l~V~~  214 (247)
                      |+|||+|||.++++++|+++|+.||. |.++.++++. .+|.++|||||+|.+.++|..|++.|++.  .++|+.|+|.+
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999996 8999999885 46899999999999999999999998654  66899999999


Q ss_pred             ccccccc
Q 025814          215 SKWQERT  221 (247)
Q Consensus       215 a~~k~~~  221 (247)
                      |+++...
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9876543

>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=99.81  E-value=4.4e-20  Score=132.68  Aligned_cols=81  Identities=21%  Similarity=0.498  Sum_probs=72.6

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecC-CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDK-RTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~-~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +.++|||+|||+++++++|+++|+.|| |.++.++.+. .+|.++|||||+|.+.++|++|+ .|||..|+|+.|+|+++
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            457999999999999999999999999 7788877765 57899999999999999998777 69999999999999998


Q ss_pred             cccc
Q 025814          216 KWQE  219 (247)
Q Consensus       216 ~~k~  219 (247)
                      ..+.
T Consensus        92 ~~~~   95 (104)
T d1wi8a_          92 DQAQ   95 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.81  E-value=3.4e-20  Score=128.64  Aligned_cols=80  Identities=16%  Similarity=0.265  Sum_probs=71.2

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +...+|||+|||+++++++|+++|+.||.+....++.+..+|.++|||||+|.+.++|++|++.|||..|+||.|+|.++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34567999999999999999999999999976433444468999999999999999999999999999999999999874

>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=99.81  E-value=1e-19  Score=126.17  Aligned_cols=78  Identities=24%  Similarity=0.447  Sum_probs=71.2

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .++|||+|||+++++++|+++|+.||.|..+.+.      .++|||||+|.+.++|.+|+..|||..|+|+.|+|+++++
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            3589999999999999999999999999887764      3478999999999999999999999999999999999998


Q ss_pred             cccc
Q 025814          218 QERT  221 (247)
Q Consensus       218 k~~~  221 (247)
                      +.+.
T Consensus        82 ~~~~   85 (86)
T d2cpda1          82 VDKD   85 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.81  E-value=5.3e-20  Score=127.68  Aligned_cols=77  Identities=21%  Similarity=0.420  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+|||.++++++|+++|++||.|.+|++.++      +|||||+|.+.++|++|++.|||..|+|+.|+|++|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3458999999999999999999999999999999866      5799999999999999999999999999999999987


Q ss_pred             ccc
Q 025814          217 WQE  219 (247)
Q Consensus       217 ~k~  219 (247)
                      .+.
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            653

>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=8.5e-20  Score=125.82  Aligned_cols=77  Identities=25%  Similarity=0.437  Sum_probs=69.9

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-CCEeEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV-GNRPIKLR  213 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i-~g~~l~V~  213 (247)
                      .++.++|||+|||.++++++|.++|+.||.|.+|++++++     +|||||+|.+.++|..|++.|||..| +|+.|+|+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            3446799999999999999999999999999999997653     68999999999999999999999988 57899999


Q ss_pred             Ecc
Q 025814          214 KSK  216 (247)
Q Consensus       214 ~a~  216 (247)
                      +|+
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>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=99.80  E-value=2.5e-20  Score=127.63  Aligned_cols=75  Identities=20%  Similarity=0.344  Sum_probs=68.3

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCc-eeCCEeEEEEEcccc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGK-YVGNRPIKLRKSKWQ  218 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~-~i~g~~l~V~~a~~k  218 (247)
                      +|||+|||.++++++|+++|++||.|.++.+...      +|||||+|.+.++|.+|++.|||. .|+|+.|+|+++.++
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            6999999999999999999999999987766554      689999999999999999999996 699999999999876


Q ss_pred             cc
Q 025814          219 ER  220 (247)
Q Consensus       219 ~~  220 (247)
                      ..
T Consensus        77 ~~   78 (80)
T d2cqha1          77 KL   78 (80)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>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=99.80  E-value=1.3e-19  Score=128.71  Aligned_cols=75  Identities=20%  Similarity=0.403  Sum_probs=67.9

Q ss_pred             CCCcEEEEcCCC-CCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          136 ENDYRLFCGDLG-NEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp-~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ...++|||+||+ ..+++++|+++|++||.|.+|+|        ++|||||+|.+.++|++||+.|||..|+|+.|+|++
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345589999997 57889999999999999999988        368999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      ++.+
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            8754

>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=99.80  E-value=6.4e-20  Score=125.26  Aligned_cols=76  Identities=20%  Similarity=0.312  Sum_probs=69.1

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      +..+++|||+||+  +++++|+++|++||.|.++.+.++      +|||||+|.+.++|..|++.|||..|+|+.|+|++
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   73 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   73 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456699999985  899999999999999999998755      57999999999999999999999999999999999


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      ++.+
T Consensus        74 a~~~   77 (79)
T d2bz2a1          74 ARKQ   77 (79)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            9754

>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=99.80  E-value=1.5e-19  Score=122.07  Aligned_cols=73  Identities=21%  Similarity=0.237  Sum_probs=67.7

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      +|||+|||+++++++|+++|+.||.|.++++..++.  ..+|||||+|.+.++|.+|| .|||..|+|+.|.|+.+
T Consensus         2 tv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           2 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             EEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            799999999999999999999999999999999863  34679999999999999999 68999999999999764

>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=5.3e-20  Score=133.68  Aligned_cols=77  Identities=14%  Similarity=0.184  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+|||+++++++|+++|+.||.|..|.|.      ..+|||||+|.+.++|.+|++.|||..|.|+.|+|+++.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            34689999999999999999999999999998874      347899999999999999999999999999999999986


Q ss_pred             ccc
Q 025814          217 WQE  219 (247)
Q Consensus       217 ~k~  219 (247)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            543

>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=99.80  E-value=5.6e-20  Score=128.94  Aligned_cols=79  Identities=27%  Similarity=0.442  Sum_probs=71.5

Q ss_pred             CcEEEEcCCCCCCcHHHHHH----HhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          138 DYRLFCGDLGNEVNDDVLSK----AFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~----~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      .++|||+|||+++++++|++    +|++||.|.+|++..   ++.++|||||+|.+.++|.+|++.|||..++|+.|+|+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            46999999999999999864    689999999988754   57889999999999999999999999999999999999


Q ss_pred             Eccccc
Q 025814          214 KSKWQE  219 (247)
Q Consensus       214 ~a~~k~  219 (247)
                      +++.+.
T Consensus        80 ~ak~~~   85 (91)
T d1nu4a_          80 YAKTDS   85 (91)
T ss_dssp             ECSSCC
T ss_pred             EeCCCc
Confidence            998654

>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=99.79  E-value=5.8e-20  Score=131.81  Aligned_cols=82  Identities=12%  Similarity=0.104  Sum_probs=72.6

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .....+|||+|||+++++++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|++|| .|||..|+|+.|.|..
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al-~~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RLHRKKLNGREAFVHV   83 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHG-GGCSEEETTEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHH-hcCCCeECCcEEEEEE
Confidence            445568999999999999999999999999987555555568999999999999999999999 5999999999999988


Q ss_pred             ccc
Q 025814          215 SKW  217 (247)
Q Consensus       215 a~~  217 (247)
                      +..
T Consensus        84 ~~~   86 (103)
T d2cpya1          84 VTL   86 (103)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            754

>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=2.3e-19  Score=124.98  Aligned_cols=78  Identities=15%  Similarity=0.159  Sum_probs=69.9

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-CCEeEEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV-GNRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i-~g~~l~V~~  214 (247)
                      ++.++|||+|||+++++++|+++|+.||.|..+.+..    +..+|||||+|.+.++|.+|+..|||..| +|+.|+|++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            4466999999999999999999999999998887654    34578999999999999999999999988 589999999


Q ss_pred             ccc
Q 025814          215 SKW  217 (247)
Q Consensus       215 a~~  217 (247)
                      ++.
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            875

>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=99.79  E-value=3.1e-19  Score=128.15  Aligned_cols=83  Identities=22%  Similarity=0.241  Sum_probs=75.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .+...|||+|||+++++++|+++|..||.|..+.++.+..++.++|||||+|.+.++|++|+ .+|+..|+||.|+|..+
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~-~~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHH-TTTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHH-hhCCCEEcceEEEEEEC
Confidence            34557999999999999999999999999988777777789999999999999999999999 59999999999999998


Q ss_pred             cccc
Q 025814          216 KWQE  219 (247)
Q Consensus       216 ~~k~  219 (247)
                      ..++
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7654

>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=99.79  E-value=2.2e-19  Score=128.50  Aligned_cols=82  Identities=15%  Similarity=0.142  Sum_probs=73.5

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ...+.+|||+|||+++++++|+++|..|| +..|.++.+. +|..+|||||+|.+.++|++|+ .||+..|+||.|+|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al-~~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            45566999999999999999999999998 5578888884 6899999999999999999998 5899999999999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +..+.
T Consensus        89 s~~~~   93 (102)
T d1weza_          89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             cCCCC
Confidence            87654

>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=99.78  E-value=1.4e-19  Score=131.06  Aligned_cols=76  Identities=22%  Similarity=0.367  Sum_probs=70.0

Q ss_pred             cEEEEcCCCC-CCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          139 YRLFCGDLGN-EVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       139 ~~lfV~nLp~-~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .+|||+||++ .+++++|+++|+.||.|.+|.|++++     +|||||+|.+.++|.+|++.|||..|+|+.|+|++++.
T Consensus         3 ~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~   77 (109)
T d2adca1           3 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             SEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4899999965 59999999999999999999999874     78999999999999999999999999999999999875


Q ss_pred             cc
Q 025814          218 QE  219 (247)
Q Consensus       218 k~  219 (247)
                      +.
T Consensus        78 ~~   79 (109)
T d2adca1          78 QN   79 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.78  E-value=2e-19  Score=130.90  Aligned_cols=84  Identities=24%  Similarity=0.361  Sum_probs=74.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      ....++|||+|||+++++++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|+ .|||..|+||.|.|..
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 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHH-TSCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHH-HcCCCcCCCEEEEEEE
Confidence            345668999999999999999999999999987666666679999999999999999999999 5999999999999998


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      +..+.
T Consensus        94 ~~~~~   98 (112)
T d1wela1          94 ITKKG   98 (112)
T ss_dssp             ECHHH
T ss_pred             cChHH
Confidence            76544

>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=99.77  E-value=5.8e-19  Score=122.89  Aligned_cols=75  Identities=9%  Similarity=0.183  Sum_probs=65.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      ..+|||+|||+++++++|+++|++|| +..+.+      +..+|||||+|.+.++|++|++.|||..|+|+.|+|++++.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            34899999999999999999999999 333333      45688999999999999999999999999999999999865


Q ss_pred             cc
Q 025814          218 QE  219 (247)
Q Consensus       218 k~  219 (247)
                      +.
T Consensus        78 ~~   79 (88)
T d1wg1a_          78 DA   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=1.9e-19  Score=125.38  Aligned_cols=77  Identities=12%  Similarity=0.248  Sum_probs=68.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcc
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSK  216 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~  216 (247)
                      ..++|||+|||+++++++|+++|++||.|.+|++.     ..++|||||+|.+.++|++||.  ++..|+|+.|+|++++
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            34589999999999999999999999999998764     4468899999999999999984  8899999999999997


Q ss_pred             cccc
Q 025814          217 WQER  220 (247)
Q Consensus       217 ~k~~  220 (247)
                      ++..
T Consensus        77 ~k~~   80 (88)
T d1wf0a_          77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6553

>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=99.77  E-value=5.8e-20  Score=127.80  Aligned_cols=73  Identities=16%  Similarity=0.201  Sum_probs=67.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccccc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQE  219 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k~  219 (247)
                      +|||+|||+++++++|+++|++||.|.++++..+       |||||+|.+.++|++||..|||..|+|+.|+|.+++.+.
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 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            6999999999999999999999999999998654       799999999999999999999999999999998876543

>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=99.76  E-value=1.1e-18  Score=117.74  Aligned_cols=71  Identities=17%  Similarity=0.312  Sum_probs=63.9

Q ss_pred             EEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       141 lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      |||+|||+++++++|+++|++|| +..+.+      +..+|||||+|.+.++|++|++.|||..++|+.|+|+++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 444443      456899999999999999999999999999999999998643

>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=99.76  E-value=4.3e-19  Score=128.30  Aligned_cols=79  Identities=19%  Similarity=0.269  Sum_probs=71.4

Q ss_pred             CCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--CCEeEEEEE
Q 025814          137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV--GNRPIKLRK  214 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i--~g~~l~V~~  214 (247)
                      ...+|||+||++.+++++|+++|++||.|.++.+++++    .+|||||+|.+.++|++|+..|||..|  +|+.|+|.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            34589999999999999999999999999999998874    479999999999999999999999988  578999999


Q ss_pred             ccccc
Q 025814          215 SKWQE  219 (247)
Q Consensus       215 a~~k~  219 (247)
                      ++.+.
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            87654

>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=99.76  E-value=2.8e-18  Score=119.33  Aligned_cols=79  Identities=16%  Similarity=0.165  Sum_probs=70.7

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM--NGKYVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l--~g~~i~g~~l~V  212 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|.++++.++      +|||||+|.+.++|.+|++.|  ++..++|+.|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            456679999999999999999999999999999998865      469999999999999999865  577999999999


Q ss_pred             EEccccc
Q 025814          213 RKSKWQE  219 (247)
Q Consensus       213 ~~a~~k~  219 (247)
                      ++++.+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9997654

>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=99.75  E-value=1.5e-18  Score=123.04  Aligned_cols=78  Identities=24%  Similarity=0.428  Sum_probs=70.4

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--EeEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGN--RPIKLR  213 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g--~~l~V~  213 (247)
                      .+.++|||+|||+++++++|+++|++||.|..+++.++      +|||||+|.+.++|+.|++.|||..|+|  ++|+|+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            34569999999999999999999999999999998765      5799999999999999999999999986  589999


Q ss_pred             Eccccc
Q 025814          214 KSKWQE  219 (247)
Q Consensus       214 ~a~~k~  219 (247)
                      +++...
T Consensus        89 ~ak~~~   94 (97)
T d1whya_          89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            997643

>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=99.75  E-value=1.7e-18  Score=122.89  Aligned_cols=76  Identities=14%  Similarity=0.223  Sum_probs=69.8

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      ...++|||+|||+++++++|+++|+.||.|.++.|.+       +|||||+|.+.++|++||+.|||..++|+.|+|.+.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            3456899999999999999999999999999998864       479999999999999999999999999999999998


Q ss_pred             ccc
Q 025814          216 KWQ  218 (247)
Q Consensus       216 ~~k  218 (247)
                      +.+
T Consensus        86 ~~~   88 (98)
T d1wg4a_          86 RVY   88 (98)
T ss_dssp             EEE
T ss_pred             ecC
Confidence            654

>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=4.3e-18  Score=121.02  Aligned_cols=79  Identities=16%  Similarity=0.169  Sum_probs=70.3

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHH--HhCCceeCCEeEE
Q 025814          135 PENDYRLFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALK--EMNGKYVGNRPIK  211 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~-~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~--~l~g~~i~g~~l~  211 (247)
                      ...+++|||+|||.+ +++++|.++|+.||.|.++.++++      +|||||+|.+.++|.+|++  .+++..++|+.|+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            445679999999985 899999999999999999999866      5799999999999999997  5788899999999


Q ss_pred             EEEccccc
Q 025814          212 LRKSKWQE  219 (247)
Q Consensus       212 V~~a~~k~  219 (247)
                      |.+++.+.
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99996543

>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=99.72  E-value=1.9e-17  Score=118.71  Aligned_cols=79  Identities=13%  Similarity=0.115  Sum_probs=70.0

Q ss_pred             CCCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCEeEEE
Q 025814          135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM--NGKYVGNRPIKL  212 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l--~g~~i~g~~l~V  212 (247)
                      .....+|||+|||.++++++|.++|+.||.|.++.+.++      +|||||+|.+.++|++|+..|  ++..++|+.|+|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            345669999999999999999999999999999998765      579999999999999999977  566889999999


Q ss_pred             EEccccc
Q 025814          213 RKSKWQE  219 (247)
Q Consensus       213 ~~a~~k~  219 (247)
                      .+++.+.
T Consensus        86 ~~s~~~~   92 (104)
T d1wexa_          86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEcCCCc
Confidence            9997543

>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=99.70  E-value=2.4e-17  Score=114.78  Aligned_cols=78  Identities=17%  Similarity=0.135  Sum_probs=69.2

Q ss_pred             CCCCcEEEEcCCCCC-CcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCEeEE
Q 025814          135 PENDYRLFCGDLGNE-VNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEM--NGKYVGNRPIK  211 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~-~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l--~g~~i~g~~l~  211 (247)
                      .+..++|||+||+.. +++++|.++|+.||.|.++.++.+      +++|||+|++.++|..|++.|  ++..++|++|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            445668999999986 899999999999999999999876      358999999999999999965  67899999999


Q ss_pred             EEEcccc
Q 025814          212 LRKSKWQ  218 (247)
Q Consensus       212 V~~a~~k  218 (247)
                      |.+++..
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9998743

>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=99.70  E-value=8.2e-20  Score=127.81  Aligned_cols=76  Identities=16%  Similarity=0.377  Sum_probs=67.3

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEE-----EecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEE
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV-----VRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLR  213 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i-----~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~  213 (247)
                      ++|||+|||+++++++|+++|+.||.|..+.+     +.+..++.++|||||+|.+.++|++|+ .|||..++|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            48999999999999999999999998866554     345567889999999999999999999 599999999999996


Q ss_pred             Ec
Q 025814          214 KS  215 (247)
Q Consensus       214 ~a  215 (247)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=99.69  E-value=1.1e-17  Score=119.76  Aligned_cols=78  Identities=14%  Similarity=0.084  Sum_probs=68.8

Q ss_pred             CCcEEEEcCCCCCCcH-----HHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEE
Q 025814          137 NDYRLFCGDLGNEVND-----DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIK  211 (247)
Q Consensus       137 ~~~~lfV~nLp~~~~e-----~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~  211 (247)
                      ...+|||+||+.++.+     ++|+.+|+.||.|.++++++.      +|||||+|.+.++|.+|++.|||..|+|+.|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            3458999999998633     569999999999999999754      67999999999999999999999999999999


Q ss_pred             EEEcccccc
Q 025814          212 LRKSKWQER  220 (247)
Q Consensus       212 V~~a~~k~~  220 (247)
                      |.+++.+..
T Consensus        78 v~~a~~~~~   86 (104)
T d1weya_          78 LYFAQTLHI   86 (104)
T ss_dssp             EECCCCSSC
T ss_pred             EeecccCCC
Confidence            999976654

>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=99.67  E-value=5.9e-18  Score=121.26  Aligned_cols=75  Identities=15%  Similarity=0.278  Sum_probs=71.0

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEc
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKS  215 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a  215 (247)
                      .++|.++...++|++|+++|++||.|.+|+|+++ .+|.++|||||+|.+.++|.+|++.|||..++||.|+|+++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            5888999999999999999999999999999887 58999999999999999999999999999999999999875

>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=99.62  E-value=2.3e-16  Score=114.59  Aligned_cols=77  Identities=19%  Similarity=0.213  Sum_probs=66.0

Q ss_pred             CCCcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCH-HHHHHHHHHhCCceeCCEeEEEEE
Q 025814          136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANP-SDIAAALKEMNGKYVGNRPIKLRK  214 (247)
Q Consensus       136 ~~~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~-~~a~~Al~~l~g~~i~g~~l~V~~  214 (247)
                      .....+|||||++++|+++|+++|++||.|.+|.|+++      +|||||.|.+. ++|..|+..||+..+.++.+.|.+
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~   82 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   82 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEE
Confidence            33456799999999999999999999999999999865      68999999985 789999999999988877777766


Q ss_pred             cccc
Q 025814          215 SKWQ  218 (247)
Q Consensus       215 a~~k  218 (247)
                      +..+
T Consensus        83 ~~~~   86 (113)
T d1owxa_          83 EVLE   86 (113)
T ss_dssp             EECC
T ss_pred             eecc
Confidence            6543

>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=99.60  E-value=2.6e-15  Score=117.57  Aligned_cols=80  Identities=26%  Similarity=0.532  Sum_probs=73.5

Q ss_pred             cEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEcccc
Q 025814          139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKWQ  218 (247)
Q Consensus       139 ~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~k  218 (247)
                      ++|||+|||+++++++|+++|++||.|.++.++++..+|.++|||||+|.+.++|.+|+ .+++..++++.+.+.....+
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~-~~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HTCSCEETTEECEEEECCCT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHH-HhcCCcccccchhhhhhhhc
Confidence            58999999999999999999999999999999999999999999999999999999999 46777889999888876554


Q ss_pred             c
Q 025814          219 E  219 (247)
Q Consensus       219 ~  219 (247)
                      .
T Consensus        86 ~   86 (183)
T d1u1qa_          86 E   86 (183)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=99.56  E-value=2.9e-15  Score=106.43  Aligned_cols=64  Identities=22%  Similarity=0.304  Sum_probs=57.1

Q ss_pred             CCCcEEEEc--CCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 025814          136 ENDYRLFCG--DLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV  205 (247)
Q Consensus       136 ~~~~~lfV~--nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i  205 (247)
                      .+..+|||+  ||+.++++++|+++|++||.|..+.+..+      +|||||+|.+.++|.+|++.|||..|
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 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            334578885  59999999999999999999999988765      56999999999999999999999976

>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=4.1e-15  Score=101.21  Aligned_cols=73  Identities=14%  Similarity=0.174  Sum_probs=61.8

Q ss_pred             CcEEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEe-EEEEEcc
Q 025814          138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRP-IKLRKSK  216 (247)
Q Consensus       138 ~~~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~-l~V~~a~  216 (247)
                      ++.|||+|||++.+++.| ++|++||.|.++++.      ..+|||||+|.+.++|++|| .+||..|+|+. |.|....
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al-~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHH-hcCCCeECCcEEEEEEeCC
Confidence            457999999999987655 579999999999874      34689999999999999999 59999999974 6787765


Q ss_pred             cc
Q 025814          217 WQ  218 (247)
Q Consensus       217 ~k  218 (247)
                      .+
T Consensus        76 ~k   77 (81)
T d1wwha1          76 DK   77 (81)
T ss_dssp             CH
T ss_pred             Ch
Confidence            44

>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=99.52  E-value=3.2e-14  Score=100.54  Aligned_cols=80  Identities=14%  Similarity=0.304  Sum_probs=68.3

Q ss_pred             CCCcEEEEcCC--CCCCc---------HHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCce
Q 025814          136 ENDYRLFCGDL--GNEVN---------DDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKY  204 (247)
Q Consensus       136 ~~~~~lfV~nL--p~~~~---------e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~  204 (247)
                      ...++|+|.||  +.++.         +++|++.|++||.|..|.+..+    ..+||+||+|.+.++|.+|+..|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            44568999999  54332         2678999999999999988654    457999999999999999999999999


Q ss_pred             eCCEeEEEEEccccc
Q 025814          205 VGNRPIKLRKSKWQE  219 (247)
Q Consensus       205 i~g~~l~V~~a~~k~  219 (247)
                      ++||.|+|.+..++.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999988765

>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=99.42  E-value=1.1e-13  Score=98.69  Aligned_cols=80  Identities=15%  Similarity=0.170  Sum_probs=67.7

Q ss_pred             CCcEEEEcCC--CCCCc--------HHHHHHHhccCCCeeEEEEEecCCCC--CcceEEEEEecCHHHHHHHHHHhCCce
Q 025814          137 NDYRLFCGDL--GNEVN--------DDVLSKAFSRFPSFNMAKVVRDKRTG--KTKGYGFISFANPSDIAAALKEMNGKY  204 (247)
Q Consensus       137 ~~~~lfV~nL--p~~~~--------e~~L~~~F~~~G~i~~v~i~~~~~tg--~~kg~~FV~f~~~~~a~~Al~~l~g~~  204 (247)
                      +.+.|.|.||  +.++.        .++|++.|++||.|.+|.|.++..+.  ...|++||+|.+.++|.+|+..|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            3457999999  44432        35789999999999999998876443  356899999999999999999999999


Q ss_pred             eCCEeEEEEEcc
Q 025814          205 VGNRPIKLRKSK  216 (247)
Q Consensus       205 i~g~~l~V~~a~  216 (247)
                      ++||.|.|.+..
T Consensus        83 f~gR~v~v~f~~   94 (104)
T d1o0pa_          83 FANRVVVTKYCD   94 (104)
T ss_dssp             SSSSCCEEEEEC
T ss_pred             ECCeEEEEEEcC
Confidence            999999999975

>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=98.09  E-value=5e-06  Score=55.38  Aligned_cols=72  Identities=13%  Similarity=0.262  Sum_probs=57.9

Q ss_pred             CCCCcEEEEcCCCCCC------cH---HHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 025814          135 PENDYRLFCGDLGNEV------ND---DVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYV  205 (247)
Q Consensus       135 ~~~~~~lfV~nLp~~~------~e---~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i  205 (247)
                      .+.+.+|.|.=+..+.      +|   ++|.+.|..||+|.-|+++.|        --+|+|.+-++|.+|+ .++|.++
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al-~l~g~~v   82 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVL-DVDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHH-HGGGSEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHh-ccCCeEE
Confidence            4455588885444332      22   367888999999999999988        5799999999999999 7999999


Q ss_pred             CCEeEEEEEc
Q 025814          206 GNRPIKLRKS  215 (247)
Q Consensus       206 ~g~~l~V~~a  215 (247)
                      .|+.|+|...
T Consensus        83 ~G~~l~It~~   92 (95)
T d1ufwa_          83 KGRAVKISGP   92 (95)
T ss_dssp             TTEEEEEECC
T ss_pred             cceEEEEecC
Confidence            9999999754

>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=97.59  E-value=0.00018  Score=48.27  Aligned_cols=67  Identities=13%  Similarity=0.225  Sum_probs=56.8

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCc--ceEEEEEecCHHHHHHHHHHhCCceeC
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKT--KGYGFISFANPSDIAAALKEMNGKYVG  206 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~--kg~~FV~f~~~~~a~~Al~~l~g~~i~  206 (247)
                      +|-|++||+.++++++.+.++..|.+........+.+.+.  -.-|+|.|.+.+++..-.+.++|..+.
T Consensus         3 KvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           3 KVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             EEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             eEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            7999999999999999999999999887777776544332  246899999999999999999999763

>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=97.50  E-value=0.00027  Score=44.56  Aligned_cols=61  Identities=15%  Similarity=0.232  Sum_probs=50.9

Q ss_pred             HHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCEeEEEEEccc
Q 025814          154 VLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMNGKYVGNRPIKLRKSKW  217 (247)
Q Consensus       154 ~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~g~~i~g~~l~V~~a~~  217 (247)
                      .|...|..+|.|.++.|.... .|..  .|-|...+..+|..|+..|+...|++++|.|.++.+
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            455678999999999886552 2333  588999999999999999999999999999998753

>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=96.02  E-value=0.002  Score=44.02  Aligned_cols=57  Identities=16%  Similarity=0.195  Sum_probs=45.8

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhccccccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRKAA  122 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~~~  122 (247)
                      +|.+..+....+..+..++|++||+|.+.++|.+|+..  ..++++.+.++.+.++...
T Consensus        44 ~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~ke~~  102 (103)
T d1x4ba1          44 WGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREES  102 (103)
T ss_dssp             SCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSCCCC
T ss_pred             hCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECcccCCC
Confidence            47777776666777778899999999999999999974  3678888888887776554

>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=96.01  E-value=0.012  Score=39.27  Aligned_cols=54  Identities=20%  Similarity=0.346  Sum_probs=45.4

Q ss_pred             EEEEcCCCCCCcHHHHHHHhccCCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 025814          140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVVRDKRTGKTKGYGFISFANPSDIAAALKEMN  201 (247)
Q Consensus       140 ~lfV~nLp~~~~e~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~~FV~f~~~~~a~~Al~~l~  201 (247)
                      -||.-.+|..+...||.++|+.||.|. |..+.|  |     -|||...+.++++.++..++
T Consensus        17 HVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd--T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          17 HVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD--T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET--T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             eeEEEeCCcccchhHHHHHhcCCCceE-EEEecC--c-----eEEEEecCHHHHHHHHHHhc
Confidence            588889999999999999999999885 444555  3     79999999999999886544

>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=95.62  E-value=0.0033  Score=40.14  Aligned_cols=49  Identities=14%  Similarity=0.034  Sum_probs=39.2

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKK  115 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~  115 (247)
                      |.+..+....+..+..++|++||+|.+.+++.+|++.  ..+.|+.+.+++
T Consensus        24 G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_          24 GEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKR   74 (75)
T ss_dssp             SCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECC
T ss_pred             ccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeE
Confidence            6777777777777888999999999999999999974  356777666543

>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=95.45  E-value=0.003  Score=40.61  Aligned_cols=50  Identities=16%  Similarity=0.061  Sum_probs=40.0

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKK  115 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~  115 (247)
                      +|.+..+....+..+..++|++||+|++.+++.+|++.  +.++++.+.++.
T Consensus        24 ~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~   75 (77)
T d1uawa_          24 FGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKV   75 (77)
T ss_dssp             TSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEE
T ss_pred             hCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEE
Confidence            47777777777788888999999999999999999864  466777666543

>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=95.41  E-value=0.0016  Score=43.36  Aligned_cols=55  Identities=7%  Similarity=-0.008  Sum_probs=43.8

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC-ccchhhhhhccccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS-DIEHKAETKKKSIPRK  120 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~-~~~~~~~~~~~~~~r~  120 (247)
                      +|.+..+....+..+..++|++||+|.+.+++.+||... .++|+.+.++.+..++
T Consensus        32 ~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~l~Gr~i~v~~a~~k~   87 (90)
T d2cqga1          32 FGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQ   87 (90)
T ss_dssp             GSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCTTC
T ss_pred             hcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCCccCCEEeEEEeCCCCC
Confidence            377777777777778899999999999999999999753 5778888777665543

>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=94.93  E-value=0.0039  Score=39.86  Aligned_cols=48  Identities=19%  Similarity=0.057  Sum_probs=37.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKK  114 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~  114 (247)
                      |.+..+....+..+..++|++||+|++.+++.+||+.  +.++++.++++
T Consensus        24 G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk   73 (75)
T d1x0fa1          24 GEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIK   73 (75)
T ss_dssp             SCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEE
T ss_pred             CCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEE
Confidence            6666666677777888999999999999999999975  35666665543

>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=94.93  E-value=0.0087  Score=39.33  Aligned_cols=54  Identities=13%  Similarity=0.060  Sum_probs=42.4

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      +|.+..+....+..+..++|++||+|++.++|..|+.   +..+.++.+.+..+.++
T Consensus        29 ~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~   85 (89)
T d2cqba1          29 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPM   85 (89)
T ss_dssp             TSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            4777777777777778899999999999999888875   45688888887766543

>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=94.51  E-value=0.015  Score=37.45  Aligned_cols=54  Identities=7%  Similarity=0.062  Sum_probs=39.5

Q ss_pred             CCcccc-ccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhccccccc
Q 025814           67 APVYSL-PQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~-~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~  120 (247)
                      |.+... ....+..+..+++++||+|++.++|..|+..   ..++++.+.+..+.++.
T Consensus        23 G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1          23 GVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             SCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            444332 2445556677899999999999999999863   46788888887766543

>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=94.49  E-value=0.0095  Score=39.52  Aligned_cols=53  Identities=11%  Similarity=-0.024  Sum_probs=42.4

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      |.+..+....+..+..++|++||.|.+.++|..|+.   +..+.++.+.++.+..+
T Consensus        34 G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~   89 (93)
T d1x5ua1          34 GPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAH   89 (93)
T ss_dssp             SCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTT
T ss_pred             CCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            667777667777788899999999999999999885   35788888888776544

>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=94.32  E-value=0.012  Score=39.33  Aligned_cols=55  Identities=15%  Similarity=-0.018  Sum_probs=43.5

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~  121 (247)
                      +.+..+....+..+..+++++||+|++.+++.+|+..   ..+.++.+.+..+..+..
T Consensus        33 g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~   90 (99)
T d1whwa_          33 GPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             SCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             CCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCc
Confidence            6666666666777788999999999999999888753   478888888877766543

>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=94.29  E-value=0.0045  Score=40.43  Aligned_cols=50  Identities=14%  Similarity=0.173  Sum_probs=40.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKS  116 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~  116 (247)
                      |.+..+....+..+..++|++||+|.+.+.+.+|++.  ..+.|+.+.++++
T Consensus        31 G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1          31 GTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEEC
T ss_pred             ccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEee
Confidence            6777777777778888999999999999999999974  3677777776554

>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=94.05  E-value=0.0055  Score=43.88  Aligned_cols=54  Identities=15%  Similarity=0.075  Sum_probs=42.5

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~  120 (247)
                      |.+..+....+..+..++|++||+|.+.++|..|+..   ..+.++.+.+..+..+.
T Consensus        67 G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~  123 (139)
T d1u6fa1          67 GPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH  123 (139)
T ss_dssp             SCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCC
T ss_pred             ccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            6666666666666777899999999999999998863   57889999988776544

>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=93.98  E-value=0.022  Score=35.77  Aligned_cols=49  Identities=18%  Similarity=0.061  Sum_probs=36.9

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKK  115 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~  115 (247)
                      |.+..+....+......++++||+|++.+++.+|++.  ..++++.++++.
T Consensus        24 G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~   74 (75)
T d2msta_          24 GKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK   74 (75)
T ss_dssp             SCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEE
T ss_pred             CCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEE
Confidence            5555555556666778899999999999999999864  467777766643

>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=93.86  E-value=0.013  Score=38.99  Aligned_cols=53  Identities=8%  Similarity=0.058  Sum_probs=38.2

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---------Cccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---------SDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---------~~~~~~~~~~~~~~~r  119 (247)
                      |.+..+....+......+|++||+|.+.+++.+|+..         ..++++.+.+..+..+
T Consensus        33 G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k   94 (98)
T d1x4ha1          33 GDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTR   94 (98)
T ss_dssp             SCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCC
T ss_pred             ccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCC
Confidence            5555555555666777899999999999999999873         2456666666655444

>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=93.62  E-value=0.013  Score=37.58  Aligned_cols=51  Identities=6%  Similarity=0.046  Sum_probs=39.7

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKS  116 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~  116 (247)
                      +|.+..+....+......++++||+|++.++|..|+.   +..+.++.+.+..+
T Consensus        26 ~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a   79 (82)
T d1b7fa1          26 IGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA   79 (82)
T ss_dssp             TSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             hCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3667777677777778889999999999999998875   45677777766554

>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=93.50  E-value=0.023  Score=38.27  Aligned_cols=52  Identities=10%  Similarity=-0.026  Sum_probs=41.9

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhhcccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETKKKSI  117 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~~~~~  117 (247)
                      +|.+..+....+..+..+++++||+|++.++|.+|++..  .+.++.+.++.+.
T Consensus        34 ~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a~   87 (103)
T d2cqda1          34 FGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAY   87 (103)
T ss_dssp             TSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEEST
T ss_pred             cccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcC
Confidence            377777777777778889999999999999999999854  4677777776544

>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=93.46  E-value=0.0087  Score=39.40  Aligned_cols=54  Identities=11%  Similarity=0.023  Sum_probs=42.0

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPR  119 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r  119 (247)
                      +|.+..+....+.....++|++||+|++.++|..|+..   ..+.++.+.+..+.++
T Consensus        32 ~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~   88 (90)
T d2cq0a1          32 FGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS   88 (90)
T ss_dssp             TCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCC
T ss_pred             hcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCC
Confidence            47777776666667778899999999999999988764   4678888877766544

>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=93.46  E-value=0.0045  Score=41.96  Aligned_cols=52  Identities=12%  Similarity=0.025  Sum_probs=40.3

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh--cCccchhhhhhcccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSI  117 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~  117 (247)
                      +|.+..+....+..+..++|++||+|++.+++.+|++  +..+.++.+.++.+.
T Consensus        42 ~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          42 VGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             TSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             CCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            4777777777777788899999999999998888875  346777777665543

>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=93.36  E-value=0.017  Score=37.56  Aligned_cols=53  Identities=8%  Similarity=0.071  Sum_probs=42.4

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhccccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIP  118 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~  118 (247)
                      +|.+..+....+..+..+++++||+|.+.++|..|+..   ..+.++.+.+..+..
T Consensus        25 ~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~   80 (85)
T d2u2fa_          25 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             SSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCC
T ss_pred             cCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            47777777777777889999999999999999998863   467888777766543

>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=92.89  E-value=0.0096  Score=39.04  Aligned_cols=52  Identities=10%  Similarity=0.038  Sum_probs=40.2

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIP  118 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~  118 (247)
                      |.+..+....+..+..+++++||+|++.++|..|+.   +..+.++.+.+..+..
T Consensus        32 G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_          32 GEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             SCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             CCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            677777666777778889999999999999988875   4567787777765543

>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=92.78  E-value=0.013  Score=37.37  Aligned_cols=50  Identities=10%  Similarity=0.060  Sum_probs=39.4

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKS  116 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~  116 (247)
                      |.+..+....+.....++|++||+|++.+++.+++..  ..++|+.+.++++
T Consensus        27 G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          27 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             ccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            6666666667777888899999999999999999864  4678887776543

>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=92.58  E-value=0.016  Score=38.99  Aligned_cols=53  Identities=15%  Similarity=0.064  Sum_probs=40.4

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      |.+..+....+.....++|++||+|++.++|..|+.   +..+.++.+.+..+.++
T Consensus        43 G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k   98 (102)
T d2cpza1          43 GNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK   98 (102)
T ss_dssp             SCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCS
T ss_pred             ccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCC
Confidence            566666666666677889999999999999988875   45788888877665544

>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=92.55  E-value=0.033  Score=35.50  Aligned_cols=50  Identities=16%  Similarity=-0.009  Sum_probs=31.4

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKS  116 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~  116 (247)
                      |.+.......+.....+++++||+|.+.++|.+|+.   +..+.++.+.++.+
T Consensus        26 G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a   78 (81)
T d2ghpa1          26 NVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS   78 (81)
T ss_dssp             TCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            444444444455567789999999999999998875   45777877776554

>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=92.25  E-value=0.025  Score=38.07  Aligned_cols=51  Identities=14%  Similarity=0.094  Sum_probs=39.0

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhccc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKS  116 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~  116 (247)
                      +|.+..+....+..+..++|++||+|.+.+++..|+..   ..+.++.+.+..+
T Consensus        32 ~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a   85 (104)
T d1p1ta_          32 VGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             TSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             cccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            36777776767777788899999999999999999864   4666766665543

>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=92.24  E-value=0.031  Score=36.42  Aligned_cols=53  Identities=9%  Similarity=0.103  Sum_probs=39.5

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      |.+..+...........+|++||+|++.+++..|+.   +..+.++.+.+..+..+
T Consensus        30 G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~   85 (90)
T d1x5sa1          30 GQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS   85 (90)
T ss_dssp             SCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECC
T ss_pred             ccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            555555555555667789999999999999999874   56788888887765443

>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=92.08  E-value=0.033  Score=36.34  Aligned_cols=51  Identities=10%  Similarity=-0.007  Sum_probs=36.3

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPR  119 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r  119 (247)
                      |.+..+....+.  ..+++++||+|++.++|.+|+..   ..+.++.+.+..+..+
T Consensus        33 G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2          33 GNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             SCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            555554444443  23689999999999999999864   3677887777666544

>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=91.56  E-value=0.019  Score=36.76  Aligned_cols=50  Identities=14%  Similarity=0.045  Sum_probs=39.1

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKS  116 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~  116 (247)
                      |.+..+....+.++..+++++||+|.+.+++..|+..   ..+.++.+++..+
T Consensus        25 G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a   77 (80)
T d1cvja1          25 GPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   77 (80)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEEC
T ss_pred             CCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            6677777777777888899999999999999999864   4667776665443

>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=91.40  E-value=0.039  Score=34.30  Aligned_cols=47  Identities=9%  Similarity=0.083  Sum_probs=35.4

Q ss_pred             CCCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhh
Q 025814           65 PVAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAE  111 (247)
Q Consensus        65 P~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~  111 (247)
                      .+|.+..+....+......++++||+|++.++|.+|++   +..++++.+
T Consensus        21 ~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1          21 PYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             TTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             hhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            34777776666677778899999999999999998875   345555543

>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=91.39  E-value=0.057  Score=35.55  Aligned_cols=52  Identities=6%  Similarity=-0.060  Sum_probs=37.7

Q ss_pred             CCccccccccch-hhhcCCCceeeCccCHHHHHHHHhc----Cccchhhhhhccccc
Q 025814           67 APVYSLPQYHQA-QQLFQRDAQTITPEALESVKAALAS----SDIEHKAETKKKSIP  118 (247)
Q Consensus        67 ~~~~~~~~~~~~-~~~~~~~~~~v~~~~~~~a~~al~~----~~~~~~~~~~~~~~~  118 (247)
                      |.+..+....+. .+..++|++||+|.+.++|..|++.    ..+.|+.+.+..+..
T Consensus        33 G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~   89 (94)
T d2cpha1          33 GELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS   89 (94)
T ss_dssp             SCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCC
T ss_pred             CCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCC
Confidence            666655544443 3677899999999999999999853    457888777766543

>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=91.35  E-value=0.024  Score=36.21  Aligned_cols=50  Identities=6%  Similarity=-0.089  Sum_probs=37.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKS  116 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~  116 (247)
                      |.+..+....+......++++||+|++.+++..|+.   +..+.++.+.+..+
T Consensus        27 G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~A   79 (82)
T d1fxla1          27 GEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA   79 (82)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            666666666666677889999999999999988875   45777777766554

>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=90.62  E-value=0.062  Score=35.73  Aligned_cols=54  Identities=17%  Similarity=-0.053  Sum_probs=39.3

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~  120 (247)
                      |.+..+....+.....+++++||.|.+.++|..|+.   +..+.++.+.+..+..+.
T Consensus        43 G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~   99 (102)
T d2cpxa1          43 QEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK   99 (102)
T ss_dssp             HHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCS
T ss_pred             cceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCcc
Confidence            444444444455566779999999999999999985   457788888877766543

>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=90.41  E-value=0.042  Score=35.55  Aligned_cols=51  Identities=14%  Similarity=0.070  Sum_probs=34.5

Q ss_pred             CCcccccccc-chhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcccc
Q 025814           67 APVYSLPQYH-QAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSI  117 (247)
Q Consensus        67 ~~~~~~~~~~-~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~  117 (247)
                      |.+..+.... +......+|++||+|++.+++.+|+..  ..+.++.+.+..+.
T Consensus        30 G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a~   83 (86)
T d2ghpa3          30 GSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLAD   83 (86)
T ss_dssp             SCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEECC
T ss_pred             hhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEcC
Confidence            6665554433 345677899999999999999999853  35667777665544

>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=90.13  E-value=0.036  Score=36.49  Aligned_cols=50  Identities=2%  Similarity=-0.092  Sum_probs=39.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKS  116 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~  116 (247)
                      |.+..+....+..+..++|++||+|.+.++|..|+..   ..+.++.+.+..+
T Consensus        32 G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_          32 GDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            6777777777777788899999999999999999863   4677877777554

>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=89.90  E-value=0.045  Score=35.18  Aligned_cols=50  Identities=12%  Similarity=0.097  Sum_probs=35.5

Q ss_pred             CCccccccccchhh---hcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccc
Q 025814           67 APVYSLPQYHQAQQ---LFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKS  116 (247)
Q Consensus        67 ~~~~~~~~~~~~~~---~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~  116 (247)
                      |.+..+....+...   ..++|++||+|++.++|.+|+.   +..+.++.+.+..+
T Consensus        23 G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a   78 (85)
T d2cpfa1          23 GAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS   78 (85)
T ss_dssp             SCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECS
T ss_pred             CCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            55655544444332   3568999999999999999875   45778888877654

>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=89.79  E-value=0.14  Score=33.81  Aligned_cols=45  Identities=16%  Similarity=0.143  Sum_probs=35.4

Q ss_pred             ccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccccc
Q 025814           75 YHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPR  119 (247)
Q Consensus        75 ~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r  119 (247)
                      ..+.+....++++||+|.+.++|..|+.   +..+.++.+.+..+..+
T Consensus        49 ~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~   96 (101)
T d2cpea1          49 YLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK   96 (101)
T ss_dssp             CBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCC
T ss_pred             eeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            3444567789999999999999888865   56788999888777654

>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=89.73  E-value=0.09  Score=34.39  Aligned_cols=52  Identities=10%  Similarity=0.052  Sum_probs=38.2

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~r~  120 (247)
                      |.+..+....+..  .+++++||+|++.+++.+|+.   +..+.++.+.+..+.+|.
T Consensus        36 G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          36 GKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   90 (93)
T ss_dssp             SCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             ceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCC
Confidence            5555554444433  368999999999999999874   567888888887776553

>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=89.69  E-value=0.058  Score=35.33  Aligned_cols=40  Identities=15%  Similarity=0.061  Sum_probs=31.2

Q ss_pred             hhhhcCCCceeeCccCHHHHHHHHh--cCccchhhhhhcccc
Q 025814           78 AQQLFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSI  117 (247)
Q Consensus        78 ~~~~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~  117 (247)
                      .....+++++||+|++.+++.+||.  +..+.++.+.+..+.
T Consensus        48 ~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          48 VRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             EEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCC
T ss_pred             cCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecC
Confidence            3466789999999999999999975  346777777776554

>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=89.55  E-value=0.028  Score=36.07  Aligned_cols=45  Identities=13%  Similarity=0.142  Sum_probs=33.8

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchhhh
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHKAE  111 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~  111 (247)
                      |.+..+....+..+..+++++||+|.+.++|..|+..   ..+.++.+
T Consensus        34 G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i   81 (83)
T d2cqca1          34 GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   81 (83)
T ss_dssp             SCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEe
Confidence            6666666666666778899999999999999988753   35555543

>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=89.04  E-value=0.053  Score=34.87  Aligned_cols=38  Identities=8%  Similarity=0.022  Sum_probs=31.1

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHhc
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS  103 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~  103 (247)
                      +|.+..+....+.....+++++||+|++.++|.+|+..
T Consensus        30 ~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~   67 (85)
T d1b7fa2          30 YGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA   67 (85)
T ss_dssp             SSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             hCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHH
Confidence            36777776666667778899999999999999999864

>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=88.46  E-value=0.11  Score=32.86  Aligned_cols=41  Identities=12%  Similarity=0.108  Sum_probs=32.3

Q ss_pred             hcCCCceeeCccCHHHHHHHHh---cC-ccchhhhhhcccccccc
Q 025814           81 LFQRDAQTITPEALESVKAALA---SS-DIEHKAETKKKSIPRKA  121 (247)
Q Consensus        81 ~~~~~~~~v~~~~~~~a~~al~---~~-~~~~~~~~~~~~~~r~~  121 (247)
                      ...++++||+|.+.++|.+|++   +. .+.|+.+.+..+.+++.
T Consensus        34 ~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1          34 LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             EEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             ecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            4568999999999999999885   33 57888888887766543

>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=88.43  E-value=0.15  Score=33.85  Aligned_cols=42  Identities=14%  Similarity=0.044  Sum_probs=33.1

Q ss_pred             hhhcCCCceeeCccCHHHHHHHHh--cCccchhhhhhccccccc
Q 025814           79 QQLFQRDAQTITPEALESVKAALA--SSDIEHKAETKKKSIPRK  120 (247)
Q Consensus        79 ~~~~~~~~~~v~~~~~~~a~~al~--~~~~~~~~~~~~~~~~r~  120 (247)
                      .....++++||+|++.+++++++.  ...+.++.+++..+..+.
T Consensus        52 ~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~~~~   95 (104)
T d1wi8a_          52 NPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQ   95 (104)
T ss_dssp             CTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECCCCC
T ss_pred             cCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            356679999999999999988875  457888888887765543

>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=87.49  E-value=0.084  Score=34.17  Aligned_cols=40  Identities=10%  Similarity=-0.048  Sum_probs=32.5

Q ss_pred             cCCCceeeCccCHHHHHHHHhc-Cccchhhhhhcccccccc
Q 025814           82 FQRDAQTITPEALESVKAALAS-SDIEHKAETKKKSIPRKA  121 (247)
Q Consensus        82 ~~~~~~~v~~~~~~~a~~al~~-~~~~~~~~~~~~~~~r~~  121 (247)
                      ..++++||+|++.+.|.+|+.. +.++++.+.++.+.++..
T Consensus        40 ~~~gfafV~f~~~~~a~~a~~~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_          40 PFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCCCCC
T ss_pred             ccCceEEEEECCHHHHHHHHhCCCEECCEEeEEEeCCCCCC
Confidence            4689999999999999999864 468888888887765543

>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=86.32  E-value=0.14  Score=32.26  Aligned_cols=48  Identities=4%  Similarity=-0.071  Sum_probs=34.0

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKK  115 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~  115 (247)
                      |.+..+....+. ...+++++||+|++.++|..|+.   +..+.++.+.+..
T Consensus        25 G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~   75 (78)
T d1no8a_          25 GTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL   75 (78)
T ss_dssp             SCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            555555444443 56679999999999999988875   4567777666543

>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=86.24  E-value=0.072  Score=36.19  Aligned_cols=49  Identities=10%  Similarity=-0.004  Sum_probs=34.6

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIP  118 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~  118 (247)
                      |.|..+....   ....+|++||+|.+.++|..|+.   +..+.++.+.+..+..
T Consensus        32 G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1          32 GPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             SCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            5555543332   23458999999999999888874   5678888888766543

>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=85.65  E-value=0.21  Score=33.24  Aligned_cols=43  Identities=19%  Similarity=0.020  Sum_probs=33.8

Q ss_pred             hhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhccccccc
Q 025814           78 AQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRK  120 (247)
Q Consensus        78 ~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~  120 (247)
                      ......++++||.|++.+++.+++..  ..+.++.+.+.....++
T Consensus        51 ~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~~~~   95 (104)
T d1wg5a_          51 DFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             CSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECTTT
T ss_pred             CCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECCHHH
Confidence            34556799999999999999999863  47888888887665543

>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=84.97  E-value=0.2  Score=33.22  Aligned_cols=36  Identities=0%  Similarity=-0.096  Sum_probs=27.5

Q ss_pred             hhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhh
Q 025814           78 AQQLFQRDAQTITPEALESVKAALASS--DIEHKAETK  113 (247)
Q Consensus        78 ~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~  113 (247)
                      .....++|++||.|.+.++|.+||...  .+.++.+.+
T Consensus        44 ~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V   81 (103)
T d2cpya1          44 DNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFV   81 (103)
T ss_dssp             CTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEE
T ss_pred             CCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEE
Confidence            346678999999999999999999643  455555444

>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=84.82  E-value=0.12  Score=34.66  Aligned_cols=47  Identities=6%  Similarity=-0.096  Sum_probs=35.2

Q ss_pred             CCCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhh
Q 025814           66 VAPVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETK  113 (247)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~  113 (247)
                      +|.+..+....+ .+..++|++||.|++.++|.+|+.   +..++++.+.+
T Consensus        51 ~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v  100 (104)
T d1jmta_          51 YGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA  100 (104)
T ss_dssp             TCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCE
T ss_pred             CCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEE
Confidence            377777665443 467789999999999999988875   45677776655

>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=83.68  E-value=0.19  Score=32.42  Aligned_cols=49  Identities=16%  Similarity=0.020  Sum_probs=33.9

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhcccc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSI  117 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~  117 (247)
                      |.+..+....+...  .++++||+|++.++|..|+.   +..+.++.+++..+.
T Consensus        33 G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1          33 GPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45544444433332  38899999999999999875   346788887776654

>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=83.66  E-value=0.24  Score=31.54  Aligned_cols=39  Identities=13%  Similarity=0.023  Sum_probs=30.4

Q ss_pred             hcCCCceeeCccCHHHHHHHHhc---Cccchhhhhhcccccc
Q 025814           81 LFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPR  119 (247)
Q Consensus        81 ~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r  119 (247)
                      ...++++||+|.+.++|..|+..   ..+.++.+.+..+.++
T Consensus        41 ~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1          41 KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            45699999999999999998763   4678888877665543

>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=83.36  E-value=0.12  Score=33.21  Aligned_cols=46  Identities=9%  Similarity=0.063  Sum_probs=32.7

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhcC--ccchhhhhh
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASS--DIEHKAETK  113 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~~--~~~~~~~~~  113 (247)
                      |.+..+....+ .....+|++||+|++.++|.+||+..  .+.++.+.+
T Consensus        31 G~v~~v~l~~~-~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v   78 (85)
T d1zh5a2          31 GQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLI   78 (85)
T ss_dssp             CCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEE
T ss_pred             cccccceeeee-ccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEE
Confidence            66666554433 35667899999999999999999643  455555554

>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=83.18  E-value=0.44  Score=30.93  Aligned_cols=41  Identities=10%  Similarity=-0.010  Sum_probs=31.3

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhcC-----ccchhhhhhccccccc
Q 025814           80 QLFQRDAQTITPEALESVKAALASS-----DIEHKAETKKKSIPRK  120 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~~-----~~~~~~~~~~~~~~r~  120 (247)
                      ...++|++||+|++.++|..|+...     .+.++.+.+..+.++.
T Consensus        41 ~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~   86 (96)
T d2disa1          41 KMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI   86 (96)
T ss_dssp             TTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSC
T ss_pred             cccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCC
Confidence            5678999999999999999998643     3356777776665443

>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=83.08  E-value=0.15  Score=32.64  Aligned_cols=43  Identities=7%  Similarity=-0.044  Sum_probs=33.0

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHhc---Cccchh
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALAS---SDIEHK  109 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~~---~~~~~~  109 (247)
                      |.+..+....+......++++||+|++.+++.+|++.   ..+.++
T Consensus        31 G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~   76 (85)
T d1fxla2          31 GRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA   76 (85)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCC
Confidence            6777776666667778899999999999999998753   445443

>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=82.99  E-value=0.5  Score=31.39  Aligned_cols=43  Identities=9%  Similarity=-0.133  Sum_probs=33.3

Q ss_pred             hcCCCceeeCccCHHHHHHHHhc---CccchhhhhhcccccccccC
Q 025814           81 LFQRDAQTITPEALESVKAALAS---SDIEHKAETKKKSIPRKAAG  123 (247)
Q Consensus        81 ~~~~~~~~v~~~~~~~a~~al~~---~~~~~~~~~~~~~~~r~~~~  123 (247)
                      ..+++++||+|++.++|.+|+..   ..+.++.+.+..+..+....
T Consensus        43 ~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~~   88 (104)
T d1weya_          43 FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGS   88 (104)
T ss_dssp             ETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSSCCS
T ss_pred             ecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCCCCC
Confidence            34688999999998888888764   57889999888776554433

>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=82.87  E-value=0.34  Score=31.49  Aligned_cols=38  Identities=8%  Similarity=-0.154  Sum_probs=30.2

Q ss_pred             hcCCCceeeCccCHHHHHHHHh---cCccchhhhhhccccc
Q 025814           81 LFQRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIP  118 (247)
Q Consensus        81 ~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~  118 (247)
                      ...++++||+|++.+++..|+.   +..+.++.+.+..+..
T Consensus        50 ~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          50 RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            3458999999999999988864   5678888888876554

>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=82.62  E-value=0.26  Score=32.40  Aligned_cols=36  Identities=11%  Similarity=0.025  Sum_probs=29.8

Q ss_pred             CCCceeeCccCHHHHHHHHh---cCccchhhhhhccccc
Q 025814           83 QRDAQTITPEALESVKAALA---SSDIEHKAETKKKSIP  118 (247)
Q Consensus        83 ~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~~~~~  118 (247)
                      .++++||+|++.++|.+|+.   +..+.++.+.+..+..
T Consensus        49 ~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   87 (98)
T d1wf2a_          49 HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAE   87 (98)
T ss_dssp             ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTS
T ss_pred             eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            58999999999999999975   4578888888877643

>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=82.44  E-value=0.21  Score=32.23  Aligned_cols=49  Identities=6%  Similarity=-0.027  Sum_probs=33.1

Q ss_pred             CCCCCccccccccchhhhc---CCCceeeCccCHHHHHHHHh---cCccchhhhh
Q 025814           64 APVAPVYSLPQYHQAQQLF---QRDAQTITPEALESVKAALA---SSDIEHKAET  112 (247)
Q Consensus        64 ~P~~~~~~~~~~~~~~~~~---~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~  112 (247)
                      ..+|.+..+....+.....   .++++||+|++.++|.+|+.   +..+.++.++
T Consensus        33 ~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1          33 GKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             TTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            3457777766655544333   35789999999999998875   3456666554

>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=81.27  E-value=0.31  Score=32.14  Aligned_cols=47  Identities=15%  Similarity=0.063  Sum_probs=32.1

Q ss_pred             CCccccccccchhhhcCCCceeeCccCHHHHHHHHh---cCccchhhhhhc
Q 025814           67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALA---SSDIEHKAETKK  114 (247)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~a~~al~---~~~~~~~~~~~~  114 (247)
                      |.+..+....+ ....+++++||+|++.++|.+|+.   +..+.++.+.+.
T Consensus        43 G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~   92 (101)
T d1x5oa1          43 GQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   92 (101)
T ss_dssp             SCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccC
Confidence            55544433333 355678999999999999988864   456666666553

>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=81.18  E-value=0.21  Score=33.10  Aligned_cols=41  Identities=12%  Similarity=0.035  Sum_probs=32.4

Q ss_pred             hhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhccccccc
Q 025814           80 QLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKKSIPRK  120 (247)
Q Consensus        80 ~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~~~~r~  120 (247)
                      ....++++||.|++.++|.+|+..  ..+.++.+++.....+.
T Consensus        51 ~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s~~~~   93 (102)
T d1weza_          51 DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECCCC
T ss_pred             CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            456689999999999999999864  47888888887665443

>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=80.57  E-value=0.2  Score=33.89  Aligned_cols=42  Identities=10%  Similarity=-0.081  Sum_probs=30.0

Q ss_pred             cccchhhhcCCCceeeCccCHHHHHHHHhc--Cccchhhhhhcc
Q 025814           74 QYHQAQQLFQRDAQTITPEALESVKAALAS--SDIEHKAETKKK  115 (247)
Q Consensus        74 ~~~~~~~~~~~~~~~v~~~~~~~a~~al~~--~~~~~~~~~~~~  115 (247)
                      ..........+|++||.|.+.+++.+||..  ..+.++.+.+..
T Consensus        50 ~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~   93 (112)
T d1wela1          50 YIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHP   93 (112)
T ss_dssp             EEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEE
T ss_pred             eeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEE
Confidence            334445667799999999999999999853  356666655533