Citrus Sinensis ID: 011668

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480
Protein Sequence
MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKPPPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHDRPRDRDHRDDRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDKERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERDYDPTDQEDDRGWYDHHENYEHHRGYGDHDRYNQYHDDDNDRYDQMEEDDYRYDRATSESRDKERTRDLDREY
Secondary Structure (PSIPRED)
cccccHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHccccccccccccccccccccccccHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEEEEcccccccHHHHHHHHHHccccEEEEEcccccccccccEEEEEEEcHHHHHHHHHHHcccEEccEEEEEHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccHHHHHHHHHcccccccccHHHHHHHccccccccccccccccccccccHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccEEEEEEEEcccccHHHHHHHHHHccccEEEEEEEEcccccccEEEEEEEccHHHHHHHHHHccccEEcccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccc
Coil and Loop (DISEMBL)
MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKligqshptgLTANLLKlfeprapleykpppekrkcppltgmaQFVShfaepgdplyappvekaetpvERRARIHKLRLEKGAEKAAEELkkydphndpnvsgdpykTLFVARLSYETTESKIKREFesygpikrvrlvtdketnkprgYAFIEYMHTRDMKAAYKqadgrkldgrrvlvdvergrtvpnwrprrlggglgttrvggeevnqrysgreqepsrgpsrsaepriredrhgdrdrersrergrdREREREKSLElshdrprdrdhrddrhhrdrdrtrdrererdrgrerdrdrtrdrdrgrdrgrdherdrekdrdkerdrdrtrererdrdyevgdpdrdrgysrdrdsdydridskherdrhgerdydptdqeddrgwydhhenyehhrgygdhdrynqyhdddndrydqmeeddyrydratsesrdkertrdldrey
Flexible Loop (DISEMBL)
MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKPPPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEElkkydphndpnvsgdpYKTLFVARLSYETTeskikrefesygpikrvrlvtdketnkprGYAFIEYMHTRDMKAAykqadgrkldgrrvlvdvergrtvpnwrprrlggglgttrvggeevnqrysgreqepsrgpsrsaepriredrhgdrdrersrergrdrererekslelshdrprdrdhrddrhhrdrdrtrdrererdrgrerdrdrtrdrdrgrdrgrdherdrekdrdkerdrdrtrererdrdyevgdpdrdrgysrdrdsdydridskherdrhgerdydptdqeddrgWYDHHENYEHhrgygdhdrynqyHDDDNDRYdqmeeddyrydratsesrdkertrdldrey
Low Complexity Region (SEG)
MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKPPPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHklrlekgaekaaeelkkYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRrlggglgttrvggeevNQRYSGREQEPSRGPSRSAEPriredrhgdrdrersrergrdrerereKSLELShdrprdrdhrddrhhrdrdrtrdrererdrgrerdrdrtrdrdrgrdrgrdherdrekdrdkerdrdrtrererdrdYEVgdpdrdrgysrdrdsdydridSKHERDRHGERDYDPTDQEDDRGWYDHHENYEHHRGYGDHDRYNQYHDDDNDRYDQMEEDDYRYDRATSESRDKERTRDLDREY
Disordered region (IsUnstruct)
**************************NVLQLKLIGQSHPTGLTANLLKLF**************************************************************************************YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLG************************************************************************************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
***************************************TGLTANLLKLFEPRAPLEYKPPPEKR****LTGMAQFVSHFAEPG********************************************DPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGREQE*************************************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKPPPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEV*************************************************************************************************************************************VGDPDRDRGYSRDRDSDYDRIDS*****************EDDRGWYDHHENYEHHRGYGDHDRYNQYHDDDNDRYDQMEEDDYRY********************
Disordered Region (DISPRO)
*****DAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKPPPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETP*ERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRL*************************************************************************************************************************************************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKPPPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHDRPRDRDHRDDRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDKERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERDYDPTDQEDDRGWYDHHENYEHHRGYGDHDRYNQYHDDDNDRYDQMEEDDYRYDRATSESRDKERTRDLDREY
Positional Conservation
no confident homologs detected

---

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	480	2.2.26 [Sep-21-2011]
Q42404	427	U1 small nuclear ribonucl	yes	no	0.866	0.974	0.588	1e-132
Q62376	448	U1 small nuclear ribonucl	yes	no	0.425	0.455	0.584	1e-46
P08621	437	U1 small nuclear ribonucl	yes	no	0.427	0.469	0.582	2e-46
Q1RMR2	439	U1 small nuclear ribonucl	yes	no	0.427	0.466	0.582	2e-46
Q66II8	471	U1 small nuclear ribonucl	yes	no	0.425	0.433	0.580	6e-46
P09406	471	U1 small nuclear ribonucl	N/A	no	0.425	0.433	0.572	1e-44
Q55FQ0	459	U1 small nuclear ribonucl	yes	no	0.370	0.387	0.484	1e-42
P17133	448	U1 small nuclear ribonucl	yes	no	0.422	0.453	0.504	3e-39
O13829	261	U1 small nuclear ribonucl	yes	no	0.377	0.693	0.468	6e-35
Q00916	300	U1 small nuclear ribonucl	yes	no	0.347	0.556	0.331	1e-19

>sp|Q42404|RU17_ARATH U1 small nuclear ribonucleoprotein 70 kDa OS=Arabidopsis thaliana GN=RNU1 PE=1 SV=1

 Score =  473 bits (1217), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 280/476 (58%), Positives = 331/476 (69%), Gaps = 60/476 (12%)

Query: 1   MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKP 60
           MGD  D F+RN NAAVQAR K QNRANVLQLKL+GQSHPTGLT NLLKLFEPR PLEYKP
Sbjct: 1   MGDSGDPFLRNPNAAVQARAKVQNRANVLQLKLMGQSHPTGLTNNLLKLFEPRPPLEYKP 60

Query: 61  PPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEE 120
           PPEKRKCPP TGMAQFVS+FAEPGDP YAPP  + E P ++R RIHKLRLEKG EKAAE+
Sbjct: 61  PPEKRKCPPYTGMAQFVSNFAEPGDPEYAPPKPEVELPSQKRERIHKLRLEKGVEKAAED 120

Query: 121 LKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRG 180
           LKKYDP+NDPN +GDPYKTLFV+RL+YE++ESKIKREFESYGPIKRV LVTD+ TNKP+G
Sbjct: 121 LKKYDPNNDPNATGDPYKTLFVSRLNYESSESKIKREFESYGPIKRVHLVTDQLTNKPKG 180

Query: 181 YAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRV-GGE 239
           YAFIEYMHTRDMKAAYKQADG+K+DGRRVLVDVERGRTVPNWRPRRLGGGLGT+RV GGE
Sbjct: 181 YAFIEYMHTRDMKAAYKQADGQKIDGRRVLVDVERGRTVPNWRPRRLGGGLGTSRVGGGE 240

Query: 240 EVNQRYSGREQEPSRGPSRSAEP-RIREDRHGDRDRERSRERGRDREREREKSLELSHDR 298
           E+       EQ+P    S+S EP R RE      +RE+SRE+G++RER R    ELSH++
Sbjct: 241 EIVG-----EQQPQGRTSQSEEPSRPRE------EREKSREKGKERERSR----ELSHEQ 285

Query: 299 PRDRDH---RDDRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDR 355
           PR+R     R+D+HHRDRD+         R          DRD      R          
Sbjct: 286 PRERSRDRPREDKHHRDRDQGGRDRDRDSRRDRDRTRDRGDRD------RRDRDRGRDRT 339

Query: 356 DKERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERDYDPTDQE 415
            ++ DRDR+R++ERD +    +     G SR+RD++Y            GE        E
Sbjct: 340 SRDHDRDRSRKKERDYEGGEYE-HEGGGRSRERDAEY-----------RGE-------PE 380

Query: 416 DDRGWYDHHENYEHHRGYGDHDRYNQYHDDDNDRYDQMEEDDYRYDRATSESRDKE 471
           + RG+Y+  +        GD DRY+        RYD+MEEDD+RY+R    S+  E
Sbjct: 381 ETRGYYEDDQ--------GDTDRYSH-------RYDKMEEDDFRYEREYKRSKRSE 421

Mediates the splicing of pre-mRNA by binding to the loop I region of U1-snRNA.
Arabidopsis thaliana (taxid: 3702)

>sp|Q62376|RU17_MOUSE U1 small nuclear ribonucleoprotein 70 kDa OS=Mus musculus GN=Snrnp70 PE=1 SV=2

 Score =  187 bits (475), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 124/212 (58%), Positives = 151/212 (71%), Gaps = 8/212 (3%)

Query: 42  LTANLLKLFEPRAPLEYKPPPEKRK-----CPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
           L  NLL LF PR P+ Y PP EK         P  G+A ++  F +P D   APP  +AE
Sbjct: 5   LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query: 97  TPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
           T  ER  R  + ++E+  ++   ELK +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct: 62  TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121

Query: 157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
           EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct: 122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query: 217 RTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGR 248
           RTV  WRPRRLGGGLG TR GG +VN R+SGR
Sbjct: 182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGR 213

Mediates the splicing of pre-mRNA by binding to the loop I region of U1-snRNA. The truncated isoform cannot bind U1-snRNA.

Mus musculus (taxid: 10090)

>sp|P08621|RU17_HUMAN U1 small nuclear ribonucleoprotein 70 kDa OS=Homo sapiens GN=SNRNP70 PE=1 SV=2

 Score =  187 bits (475), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 124/213 (58%), Positives = 152/213 (71%), Gaps = 8/213 (3%)

Query: 42  LTANLLKLFEPRAPLEYKPPPEKRK-----CPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
           L  NLL LF PR P+ Y PP EK         P  G+A ++  F +P D   APP  +AE
Sbjct: 5   LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query: 97  TPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
           T  ER  R  + ++E+  ++   ELK +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct: 62  TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121

Query: 157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
           EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct: 122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query: 217 RTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGRE 249
           RTV  WRPRRLGGGLG TR GG +VN R+SGR+
Sbjct: 182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD 214

Mediates the splicing of pre-mRNA by binding to the loop I region of U1-snRNA. The truncated isoforms cannot bind U1-snRNA.

Homo sapiens (taxid: 9606)

>sp|Q1RMR2|RU17_BOVIN U1 small nuclear ribonucleoprotein 70 kDa OS=Bos taurus GN=SNRNP70 PE=2 SV=1

 Score =  186 bits (473), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 124/213 (58%), Positives = 152/213 (71%), Gaps = 8/213 (3%)

Query: 42  LTANLLKLFEPRAPLEYKPPPEKRK-----CPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
           L  NLL LF PR P+ Y PP EK         P  G+A ++  F +P D   APP  +AE
Sbjct: 5   LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query: 97  TPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
           T  ER  R  + ++E+  ++   ELK +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct: 62  TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121

Query: 157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
           EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct: 122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query: 217 RTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGRE 249
           RTV  WRPRRLGGGLG TR GG +VN R+SGR+
Sbjct: 182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD 214

Mediates the splicing of pre-mRNA by binding to the loop I region of U1-snRNA. The truncated isoforms cannot bind U1-snRNA.

Bos taurus (taxid: 9913)

>sp|Q66II8|RU17_XENTR U1 small nuclear ribonucleoprotein 70 kDa OS=Xenopus tropicalis GN=snrnp70 PE=2 SV=1

 Score =  185 bits (470), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 123/212 (58%), Positives = 150/212 (70%), Gaps = 8/212 (3%)

Query: 42  LTANLLKLFEPRAPLEYKPPP-----EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
           L  NLL LF PR P+ Y PP      EK    P  G+A ++  F +P D   APP  +AE
Sbjct: 5   LPPNLLALFAPRDPVPYLPPLDKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query: 97  TPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
           T  ER  R  + ++E+  +    ELK +DPHND N  GD +KTLFVAR++Y+TTESK++R
Sbjct: 62  TREERMERKRREKIERRQQDVENELKIWDPHNDQNAQGDAFKTLFVARVNYDTTESKLRR 121

Query: 157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
           EFE YGPIKR+ +V +K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct: 122 EFEVYGPIKRIHMVYNKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query: 217 RTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGR 248
           RTV  WRPRRLGGGLG TR GG +VN R+SGR
Sbjct: 182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGR 213

Mediates the splicing of pre-mRNA by binding to the stem loop I region of U1-snRNA.

Xenopus tropicalis (taxid: 8364)

>sp|P09406|RU17_XENLA U1 small nuclear ribonucleoprotein 70 kDa OS=Xenopus laevis GN=snrnp70 PE=2 SV=1

 Score =  181 bits (459), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 123/215 (57%), Positives = 150/215 (69%), Gaps = 11/215 (5%)

Query: 42  LTANLLKLFEPRAPLEYKPPP-----EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
           L  NLL LF PR P+ Y PP      EK    P  G+A ++  F +P D   APP  +AE
Sbjct: 5   LPPNLLALFAPRDPVPYLPPLDKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query: 97  TPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
           T  ER  R  + ++E+  +    ELK +DPHND N  GD +KTLFVAR++Y+TTESK++R
Sbjct: 62  TREERMERKRREKIERRQQDVENELKIWDPHNDQNAQGDAFKTLFVARVNYDTTESKLRR 121

Query: 157 EFESYGPIKRVRLVTDK---ETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV 213
           EFE YGPIKR+ +V +K    + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDV
Sbjct: 122 EFEVYGPIKRIHIVYNKGSEGSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV 181

Query: 214 ERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGR 248
           ERGRTV  WRPRRLGGGLG TR GG +VN R+SGR
Sbjct: 182 ERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGR 216

Mediates the splicing of pre-mRNA by binding to the stem loop I region of U1-snRNA.

Xenopus laevis (taxid: 8355)

>sp|Q55FQ0|RU17_DICDI U1 small nuclear ribonucleoprotein 70 kDa OS=Dictyostelium discoideum GN=snrnp70 PE=3 SV=1

 Score =  174 bits (442), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 91/188 (48%), Positives = 131/188 (69%), Gaps = 10/188 (5%)

Query: 71  TGMAQFVSHFAEPGDPLYAPPVEK--AETPVERRARIHKLRLEKGAEKAAEELKKYDPHN 128
           TG+  ++S F +P +     P +K   E   E+R +  KL++ +  E+ ++ LK +DP++
Sbjct: 33  TGLRDYLSIFTDPSN---EEPFKKEHIENLEEKREKKRKLKISENDERISKSLKAWDPYS 89

Query: 129 DPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKP---RGYAFIE 185
           +   +GDPYKT+FV+R+SY+TT+ K++ EF  +GPIK + LV  K++N P    GYAFIE
Sbjct: 90  NSETTGDPYKTIFVSRISYKTTQQKLEFEFGQFGPIKSLFLV--KDSNNPEKHTGYAFIE 147

Query: 186 YMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRY 245
           +   RDMKAAYKQADG K+D RR++VD+ERGR + NW+PR+ GGGLG TR GG +VNQ +
Sbjct: 148 FERERDMKAAYKQADGMKIDDRRIVVDIERGRVIKNWKPRKFGGGLGNTRAGGVDVNQTF 207

Query: 246 SGREQEPS 253
           SGRE   S
Sbjct: 208 SGREMSES 215

Mediates the splicing of pre-mRNA by binding to the stem loop I region of U1-snRNA.

Dictyostelium discoideum (taxid: 44689)

>sp|P17133|RU17_DROME U1 small nuclear ribonucleoprotein 70 kDa OS=Drosophila melanogaster GN=snRNP-U1-70K PE=1 SV=2

 Score =  163 bits (413), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 106/210 (50%), Positives = 143/210 (68%), Gaps = 7/210 (3%)

Query: 42  LTANLLKLFEPRAPLEYKPP----PEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAET 97
           L  NLL LF  R P+ + PP    P ++K     G+A+F++ F +P D    P  +  ET
Sbjct: 5   LPPNLLALFAAREPIPFMPPVDKLPHEKKSRGYLGVAKFMADFEDPKD---TPLPKTVET 61

Query: 98  PVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKRE 157
             ER  R  + + E+ A K   E+  +DP    N + DP++TLF+AR++Y+T+ESK++RE
Sbjct: 62  RQERLERRRREKAEQVAYKLEREIALWDPTEIKNATEDPFRTLFIARINYDTSESKLRRE 121

Query: 158 FESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           FE YGPIK++ L+ D+E+ KP+GYAFIEY H RDM AAYK ADG+K+D +RVLVDVER R
Sbjct: 122 FEFYGPIKKIVLIHDQESGKPKGYAFIEYEHERDMHAAYKHADGKKIDSKRVLVDVERAR 181

Query: 218 TVPNWRPRRLGGGLGTTRVGGEEVNQRYSG 247
           TV  W PRRLGGGLG TR GG +VN ++SG
Sbjct: 182 TVKGWLPRRLGGGLGGTRRGGNDVNIKHSG 211

Mediates the splicing of pre-mRNA by binding to the stem loop I region of U1-snRNA.

Drosophila melanogaster (taxid: 7227)

>sp|O13829|RU17_SCHPO U1 small nuclear ribonucleoprotein 70 kDa homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=usp101 PE=1 SV=1

 Score =  149 bits (375), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 89/190 (46%), Positives = 125/190 (65%), Gaps = 9/190 (4%)

Query: 42  LTANLLKLFEPRAPLEYK----PPPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAET 97
           L A LL LF PR PL Y      PPEKR  P ++G+A+++  +A+  D  Y P     E+
Sbjct: 5   LPAPLLALFAPRPPLRYLPPMDVPPEKRSTPRVSGIAKYLK-YAQSHDQQYHP----TES 59

Query: 98  PVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKRE 157
             E+R R+   + ++  E+    +K +DP +D +V GDPYKT+F++RLSY+T ES I+RE
Sbjct: 60  LEEKRLRLRDEKQKQQRERLRSMIKVWDPDHDRHVIGDPYKTMFLSRLSYDTKESDIERE 119

Query: 158 FESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           F  YGPI+R+R+V +K T K  GYAF+ +   RD+K AYK + G  L+GRR++VDVERGR
Sbjct: 120 FTRYGPIERIRVVRNKVTGKSMGYAFVVFERERDLKVAYKASAGLMLNGRRIVVDVERGR 179

Query: 218 TVPNWRPRRL 227
           TV  W PR+L
Sbjct: 180 TVKGWLPRKL 189

Involved in nuclear mRNA splicing (By similarity). Essential for growth.

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

>sp|Q00916|RU17_YEAST U1 small nuclear ribonucleoprotein 70 kDa homolog OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SNP1 PE=1 SV=1

 Score = 97.8 bits (242), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 64/193 (33%), Positives = 106/193 (54%), Gaps = 26/193 (13%)

Query: 48  KLFEPRAPLEYK-----PPPEKRKCPPLTGMAQFVS----HFAEPGDPLYAPPVEKAE-T 97
           +LF+PR PL YK     P  +++  P +TG+A  +S    H+ E          E  E +
Sbjct: 14  RLFKPRPPLSYKRPTDYPYAKRQTNPNITGVANLLSTSLKHYME----------EFPEGS 63

Query: 98  PVERRARIHKLRLEK--GAEKAAEELKKYDPHNDPNVS-GDPYKTLFVARLSYETTESKI 154
           P     R   ++L K   A+     L+ ++P+ DP++   DPY+T+F+ RL Y+  E ++
Sbjct: 64  PNNHLQRYEDIKLSKIKNAQLLDRRLQNWNPNVDPHIKDTDPYRTIFIGRLPYDLDEIEL 123

Query: 155 KREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD---GRKLDGRRVLV 211
           ++ F  +G I+++R+V DK T K +GYAFI +      K A+K+     G ++  R  +V
Sbjct: 124 QKYFVKFGEIEKIRIVKDKITQKSKGYAFIVFKDPISSKMAFKEIGVHRGIQIKDRICIV 183

Query: 212 DVERGRTVPNWRP 224
           D+ERGRTV  ++P
Sbjct: 184 DIERGRTVKYFKP 196

Involved in nuclear mRNA splicing.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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	480
356538166	482	PREDICTED: U1 small nuclear ribonucleopr	0.947	0.943	0.744	1e-162
356496753	481	PREDICTED: U1 small nuclear ribonucleopr	0.933	0.931	0.712	1e-159
255561192	506	U1 small nuclear ribonucleoprotein 70 kD	0.637	0.604	0.866	1e-152
356538168	465	PREDICTED: U1 small nuclear ribonucleopr	0.912	0.941	0.716	1e-152
449451513	505	PREDICTED: U1 small nuclear ribonucleopr	0.631	0.6	0.851	1e-147
297735173	504	unnamed protein product [Vitis vinifera]	0.577	0.549	0.880	1e-144
225430786	514	PREDICTED: U1 small nuclear ribonucleopr	0.577	0.538	0.880	1e-143
357518361	502	U1 small nuclear ribonucleoprotein 70 kD	0.575	0.549	0.877	1e-140
84468434	506	putative U1 snRNP 70K protein [Trifolium	0.566	0.537	0.879	1e-138
338762844	532	hypothetical protein 111O18.18 [Coffea c	0.641	0.578	0.804	1e-131

>gi|356538166|ref|XP_003537575.1| PREDICTED: U1 small nuclear ribonucleoprotein 70 kDa-like isoform 1 [Glycine max]

 Score =  577 bits (1488), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 368/494 (74%), Positives = 408/494 (82%), Gaps = 39/494 (7%)

Query: 1   MGDYN---DAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLE 57
           MGD N   DAFMRNQNAAVQARTKAQNR+NVLQLKLIGQSHPTGLTANLLKLFEPR PLE
Sbjct: 1   MGDNNSNNDAFMRNQNAAVQARTKAQNRSNVLQLKLIGQSHPTGLTANLLKLFEPRPPLE 60

Query: 58  YKPPPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKA 117
           YKPPPEKRKCPPL+GMAQFVS FAEPG+P YAPPV + ETP ++RARIHKLRLEKGA KA
Sbjct: 61  YKPPPEKRKCPPLSGMAQFVSKFAEPGEPEYAPPVPETETPAQKRARIHKLRLEKGAAKA 120

Query: 118 AEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNK 177
           AEEL+KYDPHNDPNVSGDPYKTLFVA+LSYETTES+IKREFESYGPIKRVRLV DK+ NK
Sbjct: 121 AEELEKYDPHNDPNVSGDPYKTLFVAKLSYETTESRIKREFESYGPIKRVRLVADKDINK 180

Query: 178 PRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVG 237
           PRGYAFIEY+HTRDMKAAYKQADGRK+DGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVG
Sbjct: 181 PRGYAFIEYLHTRDMKAAYKQADGRKIDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVG 240

Query: 238 GEEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHD 297
           GEEVNQR+SGREQ+     SRS EPR+REDRH DRDRE SRERGRD++RERE+S E SH+
Sbjct: 241 GEEVNQRHSGREQQ----QSRSEEPRVREDRHADRDREISRERGRDKDRERERSREHSHE 296

Query: 298 RPRDRDHRDDRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDK 357
           R RDRDHR+DRHHRDRDR RDR+R+R+R R+R RDR R RDR R+RGRD +RDRE DR +
Sbjct: 297 RVRDRDHREDRHHRDRDRNRDRDRDRERDRDRGRDRDRTRDRDRERGRDRDRDREYDRHR 356

Query: 358 ERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERDYDPTDQEDD 417
           ERDRD          YEVGDP  DRG SRDR+SDYDR++SK     HGER++D  + EDD
Sbjct: 357 ERDRD----------YEVGDP--DRGRSRDRESDYDRVESK-----HGERNHD-YEPEDD 398

Query: 418 RGWYDHHENYEHHRGYGDHD----RYNQYH--DDDNDRYDQM-----EEDDYRYDRATSE 466
           RG    H  YEH R + D D    RY+ Y+  DD  D Y+Q       EDDY   RATSE
Sbjct: 399 RG---RHNQYEHGRRHADPDHDPERYDHYNHGDDHGDHYNQYRDHDGMEDDYHAGRATSE 455

Query: 467 SRDKERTRDLDREY 480
           S +KER+ D+DREY
Sbjct: 456 SHEKERSHDVDREY 469

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496753|ref|XP_003517230.1| PREDICTED: U1 small nuclear ribonucleoprotein 70 kDa-like [Glycine max]

 Score =  567 bits (1461), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 356/500 (71%), Positives = 399/500 (79%), Gaps = 52/500 (10%)

Query: 1   MGDYN---DAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLE 57
           MGD N   DAFMRNQNAAVQARTKAQNR+NVLQLKLIGQSHPTGLTANLLKLFEPR PLE
Sbjct: 1   MGDNNSNNDAFMRNQNAAVQARTKAQNRSNVLQLKLIGQSHPTGLTANLLKLFEPRPPLE 60

Query: 58  YKPPPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKA 117
           YKPPPEKRKCPPL+GMAQFVS FA+PGDP YAPPV + ETP ++RARIHKLRLEKGA KA
Sbjct: 61  YKPPPEKRKCPPLSGMAQFVSKFAQPGDPEYAPPVPETETPAQKRARIHKLRLEKGAAKA 120

Query: 118 AEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNK 177
           AEEL+KYDPHNDPNVSGDPYKTLFVA+LSYETTES+IKREFESYGPIKRVRLV DK+TNK
Sbjct: 121 AEELEKYDPHNDPNVSGDPYKTLFVAKLSYETTESRIKREFESYGPIKRVRLVADKDTNK 180

Query: 178 PRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVG 237
           PRGYAFIEY+HTRDMKAAYKQADGRK+DGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVG
Sbjct: 181 PRGYAFIEYLHTRDMKAAYKQADGRKIDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVG 240

Query: 238 GEEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHD 297
           GEEVNQR+SGREQ+     SRS EPR+REDRH DRDRE SRER RD+++ERE+S E S++
Sbjct: 241 GEEVNQRHSGREQQ----QSRSEEPRVREDRHSDRDREISRERVRDKDKERERSREHSNE 296

Query: 298 RPRDRDHRDDRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDK 357
           R RDRD R+DR    RDR R R+R+R+R R+RDR R RDR R R+RGRD +RDRE DR +
Sbjct: 297 RVRDRDQREDR--HHRDRDRTRDRDRERDRDRDRGRDRDRARDRERGRDRDRDREYDRHR 354

Query: 358 ERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERDYDPTDQEDD 417
           ERDRD          YEVG  + DRG SRDR+S Y+R++SK     HGER++D  + EDD
Sbjct: 355 ERDRD----------YEVG--ETDRGRSRDRESHYNRVESK-----HGERNHD-YEPEDD 396

Query: 418 RG---WYDH--------HENYEHHRGY------GDHDRYNQYHDDDNDRYDQMEEDDYRY 460
           RG    Y+H        H+  EH+  Y      GDH  YNQY D D        EDDY  
Sbjct: 397 RGRQNQYEHGHRHADPDHDTTEHYDPYNHGDDRGDH--YNQYPDPDR------MEDDYHA 448

Query: 461 DRATSESRDKERTRDLDREY 480
            RATSES +KER+ D+DREY
Sbjct: 449 GRATSESHEKERSHDVDREY 468

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255561192|ref|XP_002521608.1| U1 small nuclear ribonucleoprotein 70 kDa, putative [Ricinus communis] gi|223539286|gb|EEF40879.1| U1 small nuclear ribonucleoprotein 70 kDa, putative [Ricinus communis]

 Score =  546 bits (1406), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 265/306 (86%), Positives = 286/306 (93%)

Query: 1   MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKP 60
           MGDYNDAFMRNQNAAV+  TK QNRANVLQLKLIGQSHPTGLTANLLKLFEPR PLEYKP
Sbjct: 1   MGDYNDAFMRNQNAAVRGATKGQNRANVLQLKLIGQSHPTGLTANLLKLFEPRPPLEYKP 60

Query: 61  PPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEE 120
           PPEKRKCPP TGMAQFV+ FAEPGDP YAPPV++AETP +RRARIH+LRLEKGAEKAAEE
Sbjct: 61  PPEKRKCPPYTGMAQFVTQFAEPGDPEYAPPVQEAETPTQRRARIHQLRLEKGAEKAAEE 120

Query: 121 LKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRG 180
           L+KYDP++DPN+SGDPYKTLFVARL+YETTES+IKREFESYGPIKRVRL+TDK  NKPRG
Sbjct: 121 LQKYDPNSDPNISGDPYKTLFVARLNYETTESRIKREFESYGPIKRVRLITDKAANKPRG 180

Query: 181 YAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE 240
           YAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE
Sbjct: 181 YAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE 240

Query: 241 VNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHDRPR 300
           VNQR SGRE + S G SRS EPR REDR+ +RDRE+SRERGRDRE+EREKS E SH+RPR
Sbjct: 241 VNQRNSGRELQQSGGSSRSEEPRPREDRYNERDREKSRERGRDREKEREKSREHSHERPR 300

Query: 301 DRDHRD 306
           DRDH++
Sbjct: 301 DRDHKE 306

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538168|ref|XP_003537576.1| PREDICTED: U1 small nuclear ribonucleoprotein 70 kDa-like isoform 2 [Glycine max]

 Score =  543 bits (1400), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 354/494 (71%), Positives = 392/494 (79%), Gaps = 56/494 (11%)

Query: 1   MGDYN---DAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLE 57
           MGD N   DAFMRNQNAAVQARTKAQNR+NVLQLKLIGQSHPTGLTANLLKLFEPR PLE
Sbjct: 1   MGDNNSNNDAFMRNQNAAVQARTKAQNRSNVLQLKLIGQSHPTGLTANLLKLFEPRPPLE 60

Query: 58  YKPPPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKA 117
           YKPPPEKRKCPPL+GMAQFVS FAEPG+P YAPPV + ETP ++RARIHKLRLEKGA KA
Sbjct: 61  YKPPPEKRKCPPLSGMAQFVSKFAEPGEPEYAPPVPETETPAQKRARIHKLRLEKGAAKA 120

Query: 118 AEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNK 177
           AEEL+KYDPHNDPNVSGDPYKTLFVA+LSYETTES+IKREFESYGPIKRVRLV DK+ NK
Sbjct: 121 AEELEKYDPHNDPNVSGDPYKTLFVAKLSYETTESRIKREFESYGPIKRVRLVADKDINK 180

Query: 178 PRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVG 237
           PRGYAFIEY+HTRDMKAAYKQADGRK+DGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVG
Sbjct: 181 PRGYAFIEYLHTRDMKAAYKQADGRKIDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVG 240

Query: 238 GEEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHD 297
           GEEVNQR+SGR                       RDRE SRERGRD++RERE+S E SH+
Sbjct: 241 GEEVNQRHSGRSS---------------------RDREISRERGRDKDRERERSREHSHE 279

Query: 298 RPRDRDHRDDRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDK 357
           R RDRDHR+DRHHRDRDR RDR+R+R+R R+R RDR R RDR R+RGRD +RDRE DR +
Sbjct: 280 RVRDRDHREDRHHRDRDRNRDRDRDRERDRDRGRDRDRTRDRDRERGRDRDRDREYDRHR 339

Query: 358 ERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERDYDPTDQEDD 417
           ERDRD          YEVGDP  DRG SRDR+SDYDR++SK     HGER++D  + EDD
Sbjct: 340 ERDRD----------YEVGDP--DRGRSRDRESDYDRVESK-----HGERNHD-YEPEDD 381

Query: 418 RGWYDHHENYEHHRGYGDHD----RYNQYH--DDDNDRYDQM-----EEDDYRYDRATSE 466
           RG    H  YEH R + D D    RY+ Y+  DD  D Y+Q       EDDY   RATSE
Sbjct: 382 RG---RHNQYEHGRRHADPDHDPERYDHYNHGDDHGDHYNQYRDHDGMEDDYHAGRATSE 438

Query: 467 SRDKERTRDLDREY 480
           S +KER+ D+DREY
Sbjct: 439 SHEKERSHDVDREY 452

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449451513|ref|XP_004143506.1| PREDICTED: U1 small nuclear ribonucleoprotein 70 kDa-like [Cucumis sativus] gi|449504870|ref|XP_004162317.1| PREDICTED: U1 small nuclear ribonucleoprotein 70 kDa-like [Cucumis sativus]

 Score =  528 bits (1361), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 258/303 (85%), Positives = 281/303 (92%)

Query: 1   MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKP 60
           MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPR PLE+KP
Sbjct: 1   MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRPPLEFKP 60

Query: 61  PPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEE 120
           PPEKRKCPPLTGMAQFVS+FAEP DP YAPPV+K ETP ERRARIH LR+EKGAEKAAEE
Sbjct: 61  PPEKRKCPPLTGMAQFVSNFAEPDDPEYAPPVQKGETPTERRARIHLLRIEKGAEKAAEE 120

Query: 121 LKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRG 180
           L KY   +DPNV+GDPYKTLFVARL+YETTES+IKREFESYGPIKRVRL+TDK T KP+G
Sbjct: 121 LPKYLERDDPNVTGDPYKTLFVARLNYETTESRIKREFESYGPIKRVRLITDKVTGKPKG 180

Query: 181 YAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE 240
           YAFIEYMH RDMKAAYKQADGRK+DGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE
Sbjct: 181 YAFIEYMHKRDMKAAYKQADGRKIDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE 240

Query: 241 VNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHDRPR 300
            +QR+SGREQ+ S  PSRS EPR+REDRHG+RDRE+S ++GRDRER+REKS E SH+R +
Sbjct: 241 NSQRHSGREQQQSGAPSRSEEPRVREDRHGERDREKSYDKGRDRERDREKSREHSHERSK 300

Query: 301 DRD 303
           +RD
Sbjct: 301 ERD 303

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297735173|emb|CBI17535.3| unnamed protein product [Vitis vinifera]

 Score =  516 bits (1330), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 244/277 (88%), Positives = 261/277 (94%)

Query: 1   MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKP 60
           MGDYNDA MRN NAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPR PLE+KP
Sbjct: 1   MGDYNDALMRNNNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRPPLEFKP 60

Query: 61  PPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEE 120
           PPEKRKCPP TGMAQF S+FAEPG+P Y+PPV+KAETP +RRARIHKLRLEKGAEKA EE
Sbjct: 61  PPEKRKCPPYTGMAQFASNFAEPGEPEYSPPVQKAETPAQRRARIHKLRLEKGAEKATEE 120

Query: 121 LKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRG 180
            +KYDP+NDPN+SGDPYKTLFVARL+YETTES+IKREFE+YGPIKRVRL+TDKET+KPRG
Sbjct: 121 FQKYDPNNDPNISGDPYKTLFVARLNYETTESRIKREFEAYGPIKRVRLITDKETSKPRG 180

Query: 181 YAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE 240
           YAFIEYMHTRDMKAAYKQADGRKLD RRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE
Sbjct: 181 YAFIEYMHTRDMKAAYKQADGRKLDNRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE 240

Query: 241 VNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERS 277
           VN +YSGREQ+P  GP RS EPR REDRHGDRDRE+S
Sbjct: 241 VNPKYSGREQQPVGGPPRSEEPRTREDRHGDRDREKS 277

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225430786|ref|XP_002270129.1| PREDICTED: U1 small nuclear ribonucleoprotein 70 kDa-like [Vitis vinifera]

 Score =  515 bits (1326), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 244/277 (88%), Positives = 261/277 (94%)

Query: 1   MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKP 60
           MGDYNDA MRN NAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPR PLE+KP
Sbjct: 1   MGDYNDALMRNNNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRPPLEFKP 60

Query: 61  PPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEE 120
           PPEKRKCPP TGMAQF S+FAEPG+P Y+PPV+KAETP +RRARIHKLRLEKGAEKA EE
Sbjct: 61  PPEKRKCPPYTGMAQFASNFAEPGEPEYSPPVQKAETPAQRRARIHKLRLEKGAEKATEE 120

Query: 121 LKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRG 180
            +KYDP+NDPN+SGDPYKTLFVARL+YETTES+IKREFE+YGPIKRVRL+TDKET+KPRG
Sbjct: 121 FQKYDPNNDPNISGDPYKTLFVARLNYETTESRIKREFEAYGPIKRVRLITDKETSKPRG 180

Query: 181 YAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE 240
           YAFIEYMHTRDMKAAYKQADGRKLD RRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE
Sbjct: 181 YAFIEYMHTRDMKAAYKQADGRKLDNRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEE 240

Query: 241 VNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERS 277
           VN +YSGREQ+P  GP RS EPR REDRHGDRDRE+S
Sbjct: 241 VNPKYSGREQQPVGGPPRSEEPRTREDRHGDRDREKS 277

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357518361|ref|XP_003629469.1| U1 small nuclear ribonucleoprotein 70 kDa [Medicago truncatula] gi|355523491|gb|AET03945.1| U1 small nuclear ribonucleoprotein 70 kDa [Medicago truncatula]

 Score =  506 bits (1302), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 243/277 (87%), Positives = 261/277 (94%), Gaps = 1/277 (0%)

Query: 6   DAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKPPPEKR 65
           D  +RNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPR PLEYKPPPEKR
Sbjct: 3   DPLLRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRPPLEYKPPPEKR 62

Query: 66  KCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEELKKYD 125
           KCPPLTGMAQFVS FAEPG+P Y+PPV   ETP ERRAR+HKLRLEKGA KAAEEL+KYD
Sbjct: 63  KCPPLTGMAQFVSKFAEPGEPEYSPPVPVVETPAERRARVHKLRLEKGAAKAAEELEKYD 122

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
           PHNDPN+SGDPYKTLFVARLSYETTES+IKREFESYG IKRVRLVTD E+NKPRGYAFIE
Sbjct: 123 PHNDPNISGDPYKTLFVARLSYETTESRIKREFESYGAIKRVRLVTDAESNKPRGYAFIE 182

Query: 186 YMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRY 245
           Y+HTRDMKAAYKQADGRK++GRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGG+EVNQR+
Sbjct: 183 YLHTRDMKAAYKQADGRKIEGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGDEVNQRH 242

Query: 246 SGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGR 282
           SGREQ+ S GPSRS EPR+RE+RH DRDRE+SRERG+
Sbjct: 243 SGREQQQS-GPSRSEEPRVREERHADRDREKSRERGK 278

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|84468434|dbj|BAE71300.1| putative U1 snRNP 70K protein [Trifolium pratense]

 Score =  498 bits (1282), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 240/273 (87%), Positives = 255/273 (93%), Gaps = 1/273 (0%)

Query: 5   NDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKPPPEK 64
           ND  +RNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLT NLLKLFEPR PLEYKPPPEK
Sbjct: 6   NDPLLRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTTNLLKLFEPRPPLEYKPPPEK 65

Query: 65  RKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEELKKY 124
           RKCPPLTGMAQFVS FAEPG+P Y+PPV   ETP ERRAR+HKLRLEKGA KAAEEL+KY
Sbjct: 66  RKCPPLTGMAQFVSKFAEPGEPEYSPPVPVVETPAERRARVHKLRLEKGAAKAAEELEKY 125

Query: 125 DPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
           DPH DPN+SGDPYKTLFVARLSYETTES+IKREFESYG IKRVRLVTD E+NKPRGYAFI
Sbjct: 126 DPHTDPNISGDPYKTLFVARLSYETTESRIKREFESYGAIKRVRLVTDTESNKPRGYAFI 185

Query: 185 EYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQR 244
           EY+HTRDMKAAYKQADGRK++GRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQR
Sbjct: 186 EYLHTRDMKAAYKQADGRKIEGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQR 245

Query: 245 YSGREQEPSRGPSRSAEPRIREDRHGDRDRERS 277
           +SGREQ+ S GPSRS EPR+REDRH DRDRE+S
Sbjct: 246 HSGREQQQS-GPSRSEEPRVREDRHVDRDREKS 277

Source: Trifolium pratense

Species: Trifolium pratense

Genus: Trifolium

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|338762844|gb|AEI98631.1| hypothetical protein 111O18.18 [Coffea canephora]

 Score =  475 bits (1223), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 263/327 (80%), Positives = 288/327 (88%), Gaps = 19/327 (5%)

Query: 1   MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKP 60
           MGDY+DA MRNQNAAVQARTKAQNRANV+QLKLIGQSHPTGLT NLLKLFEPR PLEYKP
Sbjct: 1   MGDYSDALMRNQNAAVQARTKAQNRANVMQLKLIGQSHPTGLTTNLLKLFEPRPPLEYKP 60

Query: 61  PPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEE 120
           PPEKRKCPP TGMAQFVS+FA+PGD  YAPPV+KAETPVERRARIHK+RLE+GA+KAAEE
Sbjct: 61  PPEKRKCPPYTGMAQFVSNFAQPGDAEYAPPVQKAETPVERRARIHKIRLEEGAKKAAEE 120

Query: 121 LKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRV------------- 167
           L+KYDP+NDPN+SGDPYKTLFVARL+YETTES+IKREFE+YG IKRV             
Sbjct: 121 LEKYDPNNDPNISGDPYKTLFVARLNYETTESRIKREFEAYGAIKRVGIKEHRECALVIG 180

Query: 168 ----RLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWR 223
               RLVTDK TNKPRGYAFIEY+HTRDMKAAYKQADG+K+D RRVLVDVERGRTVPNWR
Sbjct: 181 FWFVRLVTDKSTNKPRGYAFIEYVHTRDMKAAYKQADGKKIDNRRVLVDVERGRTVPNWR 240

Query: 224 PRRLGGGLGTTRVGGEEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRD 283
           PRRLGGGLGTTRVGGEE+NQRYSGREQ    G SRS EPR+R+DR  DR+RE+SRER RD
Sbjct: 241 PRRLGGGLGTTRVGGEELNQRYSGREQVQPGGASRSEEPRMRDDR--DREREKSRERVRD 298

Query: 284 REREREKSLELSHDRPRDRDHRDDRHH 310
           RERERE+S E S DR RDR+HR+DRHH
Sbjct: 299 RERERERSQERSQDRTRDREHREDRHH 325

Source: Coffea canephora

Species: Coffea canephora

Genus: Coffea

Family: Rubiaceae

Order: Gentianales

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	480
TAIR|locus:2101714	427	U1-70K "AT3G50670" [Arabidopsi	0.537	0.604	0.690	5.1e-104
ZFIN|ZDB-GENE-040825-2	495	snrnp70 "small nuclear ribonuc	0.443	0.430	0.5	1.4e-56
UNIPROTKB|Q66II8	471	snrnp70 "U1 small nuclear ribo	0.45	0.458	0.493	2.3e-56
UNIPROTKB|P09406	471	snrnp70 "U1 small nuclear ribo	0.45	0.458	0.491	2.9e-56
MGI|MGI:98341	448	Snrnp70 "small nuclear ribonuc	0.443	0.475	0.504	6.1e-56
UNIPROTKB|I3LNE5	452	SNRNP70 "Uncharacterized prote	0.443	0.471	0.504	1.3e-55
UNIPROTKB|P08621	437	SNRNP70 "U1 small nuclear ribo	0.443	0.487	0.504	1.3e-55
UNIPROTKB|F6V5G7	439	SNRNP70 "Uncharacterized prote	0.443	0.485	0.504	1.3e-55
UNIPROTKB|Q1RMR2	439	SNRNP70 "U1 small nuclear ribo	0.443	0.485	0.504	1.3e-55
UNIPROTKB|E2QRU8	386	SNRNP70 "Uncharacterized prote	0.443	0.551	0.504	1.3e-55

TAIR|locus:2101714 U1-70K "AT3G50670" [Arabidopsis thaliana (taxid:3702)]

 Score = 930 (332.4 bits), Expect = 5.1e-104, Sum P(2) = 5.1e-104
 Identities = 181/262 (69%), Positives = 200/262 (76%)

Query:     1 MGDYNDAFMRNQNAAVQARTKAQNRANVLQLKLIGQSHPTGLTANLLKLFEPRAPLEYKP 60
             MGD  D F+RN NAAVQAR K QNRANVLQLKL+GQSHPTGLT NLLKLFEPR PLEYKP
Sbjct:     1 MGDSGDPFLRNPNAAVQARAKVQNRANVLQLKLMGQSHPTGLTNNLLKLFEPRPPLEYKP 60

Query:    61 PPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHXXXXXXXXXXXXXX 120
             PPEKRKCPP TGMAQFVS+FAEPGDP YAPP  + E P ++R RIH              
Sbjct:    61 PPEKRKCPPYTGMAQFVSNFAEPGDPEYAPPKPEVELPSQKRERIHKLRLEKGVEKAAED 120

Query:   121 XXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRG 180
                YDP+NDPN +GDPYKTLFV+RL+YE++ESKIKREFESYGPIKRV LVTD+ TNKP+G
Sbjct:   121 LKKYDPNNDPNATGDPYKTLFVSRLNYESSESKIKREFESYGPIKRVHLVTDQLTNKPKG 180

Query:   181 YAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRXXXXXXXXXXXXXXX 240
             YAFIEYMHTRDMKAAYKQADG+K+DGRRVLVDVERGRTVPNWRPR               
Sbjct:   181 YAFIEYMHTRDMKAAYKQADGQKIDGRRVLVDVERGRTVPNWRPRRLGGGLGTSRVGG-- 238

Query:   241 XNQRYSGREQEPSRGPSRSAEP 262
               +   G EQ+P    S+S EP
Sbjct:   239 -GEEIVG-EQQPQGRTSQSEEP 258

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0005515 "protein binding" evidence=IPI

GO:0000398 "mRNA splicing, via spliceosome" evidence=IDA;RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

ZFIN|ZDB-GENE-040825-2 snrnp70 "small nuclear ribonucleoprotein 70 (U1)" [Danio rerio (taxid:7955)]

 Score = 526 (190.2 bits), Expect = 1.4e-56, Sum P(2) = 1.4e-56
 Identities = 111/222 (50%), Positives = 135/222 (60%)

Query:    42 LTANLLKLFEPRAPLEYKP-----PPEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
             L  NLL LF PR P+ + P     P EK    P  G+A F+ HF +P D   APP  +AE
Sbjct:     5 LPPNLLALFAPRDPIPFLPQLGKLPHEKHHNQPYCGIAPFIRHFEDPRD---APPPTRAE 61

Query:    97 TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
             T  ER  R                   +DPHND N  GD +KTLFVAR++Y+TTESK++R
Sbjct:    62 TREERLERKRREKMERRQVVVEGELKLWDPHNDANAQGDAFKTLFVARINYDTTESKLRR 121

Query:   157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
             EFE YGPIKR+ +V +K+T KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct:   122 EFEVYGPIKRIYIVYNKKTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query:   217 RTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGREQEPSRGPSR 258
             RTV  WRPR                N ++SGR+ + SR   R
Sbjct:   182 RTVKGWRPRRLGGGLGGTRRGGADVNIKHSGRD-DTSRYDDR 222

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0060218 "hematopoietic stem cell differentiation" evidence=IMP

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|Q66II8 snrnp70 "U1 small nuclear ribonucleoprotein 70 kDa" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 521 (188.5 bits), Expect = 2.3e-56, Sum P(2) = 2.3e-56
 Identities = 111/225 (49%), Positives = 135/225 (60%)

Query:    42 LTANLLKLFEPRAPLEYKPP----P-EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
             L  NLL LF PR P+ Y PP    P EK    P  G+A ++  F +P D   APP  +AE
Sbjct:     5 LPPNLLALFAPRDPVPYLPPLDKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query:    97 TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
             T  ER  R                   +DPHND N  GD +KTLFVAR++Y+TTESK++R
Sbjct:    62 TREERMERKRREKIERRQQDVENELKIWDPHNDQNAQGDAFKTLFVARVNYDTTESKLRR 121

Query:   157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
             EFE YGPIKR+ +V +K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct:   122 EFEVYGPIKRIHMVYNKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query:   217 RTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGREQEPSRGPSRSAE 261
             RTV  WRPR                N R+SGR+ + SR   R  +
Sbjct:   182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD-DTSRYDERDRD 225

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

GO:0003723 "RNA binding" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0043484 "regulation of RNA splicing" evidence=ISS

UNIPROTKB|P09406 snrnp70 "U1 small nuclear ribonucleoprotein 70 kDa" [Xenopus laevis (taxid:8355)]

 Score = 509 (184.2 bits), Expect = 2.9e-56, Sum P(2) = 2.9e-56
 Identities = 112/228 (49%), Positives = 135/228 (59%)

Query:    42 LTANLLKLFEPRAPLEYKPP----P-EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
             L  NLL LF PR P+ Y PP    P EK    P  G+A ++  F +P D   APP  +AE
Sbjct:     5 LPPNLLALFAPRDPVPYLPPLDKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query:    97 TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
             T  ER  R                   +DPHND N  GD +KTLFVAR++Y+TTESK++R
Sbjct:    62 TREERMERKRREKIERRQQDVENELKIWDPHNDQNAQGDAFKTLFVARVNYDTTESKLRR 121

Query:   157 EFESYGPIKRVRLVTDKETN---KPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV 213
             EFE YGPIKR+ +V +K +    KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDV
Sbjct:   122 EFEVYGPIKRIHIVYNKGSEGSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV 181

Query:   214 ERGRTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGREQEPSRGPSRSAE 261
             ERGRTV  WRPR                N R+SGR+ + SR   R  E
Sbjct:   182 ERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD-DTSRYDERDRE 228

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

GO:0003723 "RNA binding" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0043484 "regulation of RNA splicing" evidence=ISS

MGI|MGI:98341 Snrnp70 "small nuclear ribonucleoprotein 70 (U1)" [Mus musculus (taxid:10090)]

 Score = 529 (191.3 bits), Expect = 6.1e-56, Sum P(2) = 6.1e-56
 Identities = 112/222 (50%), Positives = 134/222 (60%)

Query:    42 LTANLLKLFEPRAPLEYKPP----P-EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
             L  NLL LF PR P+ Y PP    P EK    P  G+A ++  F +P D   APP  +AE
Sbjct:     5 LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query:    97 TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
             T  ER  R                   +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct:    62 TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121

Query:   157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
             EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct:   122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query:   217 RTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGREQEPSRGPSR 258
             RTV  WRPR                N R+SGR+ + SR   R
Sbjct:   182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD-DTSRYDER 222

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0043484 "regulation of RNA splicing" evidence=ISO

UNIPROTKB|I3LNE5 SNRNP70 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 529 (191.3 bits), Expect = 1.3e-55, Sum P(2) = 1.3e-55
 Identities = 112/222 (50%), Positives = 134/222 (60%)

Query:    42 LTANLLKLFEPRAPLEYKPP----P-EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
             L  NLL LF PR P+ Y PP    P EK    P  G+A ++  F +P D   APP  +AE
Sbjct:     5 LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query:    97 TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
             T  ER  R                   +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct:    62 TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121

Query:   157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
             EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct:   122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query:   217 RTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGREQEPSRGPSR 258
             RTV  WRPR                N R+SGR+ + SR   R
Sbjct:   182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD-DTSRYDER 222

GO:0043484 "regulation of RNA splicing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|P08621 SNRNP70 "U1 small nuclear ribonucleoprotein 70 kDa" [Homo sapiens (taxid:9606)]

 Score = 529 (191.3 bits), Expect = 1.3e-55, Sum P(2) = 1.3e-55
 Identities = 112/222 (50%), Positives = 134/222 (60%)

Query:    42 LTANLLKLFEPRAPLEYKPP----P-EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
             L  NLL LF PR P+ Y PP    P EK    P  G+A ++  F +P D   APP  +AE
Sbjct:     5 LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query:    97 TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
             T  ER  R                   +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct:    62 TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121

Query:   157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
             EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct:   122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query:   217 RTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGREQEPSRGPSR 258
             RTV  WRPR                N R+SGR+ + SR   R
Sbjct:   182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD-DTSRYDER 222

GO:0000166 "nucleotide binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0003723 "RNA binding" evidence=IMP

GO:0043484 "regulation of RNA splicing" evidence=IMP

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;IDA;TAS

GO:0006397 "mRNA processing" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

UNIPROTKB|F6V5G7 SNRNP70 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 529 (191.3 bits), Expect = 1.3e-55, Sum P(2) = 1.3e-55
 Identities = 112/222 (50%), Positives = 134/222 (60%)

Query:    42 LTANLLKLFEPRAPLEYKPP----P-EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
             L  NLL LF PR P+ Y PP    P EK    P  G+A ++  F +P D   APP  +AE
Sbjct:     5 LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query:    97 TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
             T  ER  R                   +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct:    62 TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121

Query:   157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
             EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct:   122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query:   217 RTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGREQEPSRGPSR 258
             RTV  WRPR                N R+SGR+ + SR   R
Sbjct:   182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD-DTSRYDER 222

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q1RMR2 SNRNP70 "U1 small nuclear ribonucleoprotein 70 kDa" [Bos taurus (taxid:9913)]

 Score = 529 (191.3 bits), Expect = 1.3e-55, Sum P(2) = 1.3e-55
 Identities = 112/222 (50%), Positives = 134/222 (60%)

Query:    42 LTANLLKLFEPRAPLEYKPP----P-EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
             L  NLL LF PR P+ Y PP    P EK    P  G+A ++  F +P D   APP  +AE
Sbjct:     5 LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query:    97 TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
             T  ER  R                   +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct:    62 TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121

Query:   157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
             EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct:   122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query:   217 RTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGREQEPSRGPSR 258
             RTV  WRPR                N R+SGR+ + SR   R
Sbjct:   182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD-DTSRYDER 222

GO:0043484 "regulation of RNA splicing" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0003723 "RNA binding" evidence=ISS

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

GO:0016607 "nuclear speck" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2QRU8 SNRNP70 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 529 (191.3 bits), Expect = 1.3e-55, Sum P(2) = 1.3e-55
 Identities = 112/222 (50%), Positives = 134/222 (60%)

Query:    42 LTANLLKLFEPRAPLEYKPP----P-EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
             L  NLL LF PR P+ Y PP    P EK    P  G+A ++  F +P D   APP  +AE
Sbjct:     5 LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61

Query:    97 TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
             T  ER  R                   +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct:    62 TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121

Query:   157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
             EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct:   122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query:   217 RTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGREQEPSRGPSR 258
             RTV  WRPR                N R+SGR+ + SR   R
Sbjct:   182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD-DTSRYDER 222

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" 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)
Q42404	RU17_ARATH	No assigned EC number	0.5882	0.8666	0.9742	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:
	GSVIVG00024956001	SubName- Full=Chromosome chr4 scaffold_32, whole genome shotgun sequence; (393 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00033465001	SubName- Full=Chromosome chr19 scaffold_66, whole genome shotgun sequence; (107 aa)				•	•	•	•		0.670
	GSVIVG00017697001	SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (86 aa)				•	•	•	•		0.668
	GSVIVG00025760001	SubName- Full=Chromosome chr19 scaffold_35, whole genome shotgun sequence; (411 aa)					•	•	•	•	0.638
	GSVIVG00021594001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (80 aa)					•	•	•		0.637
	GSVIVG00006250001	SubName- Full=Chromosome chr1 scaffold_166, whole genome shotgun sequence; (320 aa)					•	•	•		0.618
	GSVIVG00023992001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (234 aa)					•	•	•		0.580
	GSVIVG00002642001	SubName- Full=Putative uncharacterized protein (Chromosome undetermined scaffold_134, whole gen [...] (276 aa)				•	•	•	•		0.573
	GSVIVG00028024001	SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (245 aa)					•	•	•		0.573
	GSVIVG00000599001	SubName- Full=Chromosome chr8 scaffold_106, whole genome shotgun sequence; (357 aa)				•	•	•	•		0.564
	GSVIVG00030614001	SubName- Full=Chromosome chr1 scaffold_5, whole genome shotgun sequence; (104 aa)					•	•	•		0.560

---

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	480
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	8e-49
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-32
smart00360	73	smart00360, RRM, RNA recognition motif	4e-22
pfam12220	94	pfam12220, U1snRNP70_N, U1 small nuclear ribonucle	7e-22
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-18
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-18
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-17
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-15
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-15
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-15
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	5e-15
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	8e-15
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-14
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-14
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	5e-14
PRK12678	672	PRK12678, PRK12678, transcription termination fact	7e-14
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	8e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-13
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-13
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-13
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-13
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	5e-13
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-12
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-12
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	3e-12
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-12
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	5e-12
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-11
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-11
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-11
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-11
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-11
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-11
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-11
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	5e-11
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	7e-11
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-10
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	3e-10
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-10
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-10
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-10
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	4e-10
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-10
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	5e-10
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	6e-10
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-10
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	8e-10
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	9e-10
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-09
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-09
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-09
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-09
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-09
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-09
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	5e-09
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-09
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	5e-09
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	7e-09
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	7e-09
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	1e-08
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-08
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-08
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	3e-08
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-08
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	5e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-08
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	7e-08
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	8e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	9e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-07
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-07
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	2e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-07
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	4e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-07
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-07
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	5e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	5e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	7e-07
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	9e-07
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	9e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-06
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-06
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	1e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-06
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	2e-06
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	2e-06
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-06
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	4e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-06
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	4e-06
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	4e-06
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	5e-06
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	6e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	6e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	7e-06
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	7e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	7e-06
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	7e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	8e-06
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	8e-06
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	8e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	8e-06
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	8e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	8e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	9e-06
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	9e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-05
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	1e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	1e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-05
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	1e-05
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	1e-05
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	2e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-05
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	2e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-05
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	3e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-05
cd12465	88	cd12465, RRM_UHMK1, RNA recognition motif found in	3e-05
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	3e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	4e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	4e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	5e-05
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	5e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	5e-05
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	5e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	5e-05
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	6e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	6e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-05
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	7e-05
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	7e-05
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	8e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	8e-05
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	8e-05
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	8e-05
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	8e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	8e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	9e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	9e-05
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	1e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	1e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	1e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-04
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	2e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	2e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	3e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-04
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	3e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	3e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	4e-04
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	4e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	4e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-04
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	4e-04
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	5e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	5e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	5e-04
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	5e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	5e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	5e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	5e-04
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	5e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	6e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	6e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	6e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	6e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	7e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	7e-04
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	7e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	7e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	8e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	0.001
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.001
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	0.001
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.001
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.001
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	0.001
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.001
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	0.001
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	0.001
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.001
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.001
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.002
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	0.002
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.002
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	0.002
cd12461	81	cd12461, RRM_SCAF4, RNA recognition motif found in	0.002
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.002
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	0.002
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.002
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.002
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.002
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.003
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	0.003
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	0.003
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.003
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.003
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	0.003
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	0.004
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.004

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

 Score =  162 bits (411), Expect = 8e-49
 Identities = 72/91 (79%), Positives = 82/91 (90%)

Query: 137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
           +KTLFVARL+Y+TTESK++REFE YGPIKR+RLV DK+T KPRGYAFIE+ H RDMKAAY
Sbjct: 1   FKTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAY 60

Query: 197 KQADGRKLDGRRVLVDVERGRTVPNWRPRRL 227
           K ADG+K+DGRRVLVDVERGRTV  W PRRL
Sbjct: 61  KYADGKKIDGRRVLVDVERGRTVKGWLPRRL 91

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

 Score =  118 bits (298), Expect = 2e-32
 Identities = 49/93 (52%), Positives = 60/93 (64%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           DPY TLFV RLS +TTE  ++  F  YG I+R+RLV D  T   +GYAF+EY H RD   
Sbjct: 1   DPYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60

Query: 195 AYKQADGRKLDGRRVLVDVERGRTVPNWRPRRL 227
           AY+ A    +DG  + VD ER RT+P W PRRL
Sbjct: 61  AYRDAHKLVIDGSEIFVDFERERTLPGWIPRRL 93

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|214636 smart00360, RRM, RNA recognition motif

 Score = 89.6 bits (223), Expect = 4e-22
 Identities = 31/73 (42%), Positives = 48/73 (65%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TLFV  L  +TTE +++  F  +G ++ VRLV DKET K +G+AF+E+    D + A + 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 199 ADGRKLDGRRVLV 211
            +G++LDGR + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|221466 pfam12220, U1snRNP70_N, U1 small nuclear ribonucleoprotein of 70kDa MW N terminal

 Score = 89.6 bits (223), Expect = 7e-22
 Identities = 45/97 (46%), Positives = 58/97 (59%), Gaps = 7/97 (7%)

Query: 38  HPTGLTANLLKLFEPRAPLEYKPP----PEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVE 93
               L  NLL LF PR PL Y PP    PEKRK  P+TG+AQ++S F +  D    PP E
Sbjct: 1   MTDKLPPNLLALFAPRPPLPYLPPLDKAPEKRKTNPITGVAQYLSEFKDYKDE---PPPE 57

Query: 94  KAETPVERRARIHKLRLEKGAEKAAEELKKYDPHNDP 130
             ET +E+R R  + + EK  +K  EELK++DP+ DP
Sbjct: 58  PTETWLEKREREKREKKEKLEKKLEEELKEWDPNEDP 94

This domain is found in eukaryotes. This domain is about 90 amino acids in length. This domain is found associated with pfam00076. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition. Length = 94

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 90.3 bits (225), Expect = 3e-19
 Identities = 45/217 (20%), Positives = 64/217 (29%), Gaps = 13/217 (5%)

Query: 213 VERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDR 272
             R         R+             E            +   S     + RE R    
Sbjct: 76  AARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGE 135

Query: 273 DRERSRERGRDREREREKSLELSHDRPRDRDHRDDRHHRDRDRTRDRERERDRGRERDRD 332
              R   R      E+  +   +    R  +   D   R  DR  DR+ E +RG    R+
Sbjct: 136 AARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDR-EDRQAEAERGERGRRE 194

Query: 333 RTRDRDRGRDRGRDHERDREKDRDKERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSD- 391
                   RDR    E+   ++    RD    R R R RD      D +R    DRD D 
Sbjct: 195 ERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDD 254

Query: 392 -----------YDRIDSKHERDRHGERDYDPTDQEDD 417
                      +   D +  R   G  + +P  +EDD
Sbjct: 255 GEGRGGRRGRRFRDRDRRGRRGGDGGNEREPELREDD 291

Length = 672

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

 Score = 78.5 bits (194), Expect = 3e-18
 Identities = 28/73 (38%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  L  +TTE  ++  F  +G I+ VR+V DK   K +G+AF+E+    D + A +  
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 200 DGRKLDGRRVLVD 212
           +G++LDGR++ V 
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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 78.4 bits (194), Expect = 3e-18
 Identities = 27/70 (38%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  L  +TTE  +K  F  +GPI+ +R+V D ET + +G+AF+E+    D + A +  
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 200 DGRKLDGRRV 209
           +G++L GR +
Sbjct: 60  NGKELGGREL 69

(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|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 = 76.5 bits (189), Expect = 2e-17
 Identities = 26/77 (33%), Positives = 46/77 (59%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV+ LS  TTE +++  F  +G ++ V L+ D ET + RG+ F+ +    D  AA + 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 199 ADGRKLDGRRVLVDVER 215
            +G++L+GR + V+  +
Sbjct: 63  LNGKELEGRVIKVEKAK 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 71.3 bits (175), Expect = 1e-15
 Identities = 29/75 (38%), Positives = 47/75 (62%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TLFV  LS+   +  +K EFE +G +   R++TD+ET + RG+ ++++    D K A + 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 199 ADGRKLDGRRVLVDV 213
            DG++LDGR + VD 
Sbjct: 61  MDGKELDGRPINVDF 75

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

 Score = 70.3 bits (173), Expect = 3e-15
 Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 7/81 (8%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRD-----M 192
           +T+F+  L ++ TE ++K  F  +G +K  R+V DK T   +G AF+++  T++     +
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFK-TKESAQKCL 59

Query: 193 KAAYKQADGR-KLDGRRVLVD 212
           +AA    D    LDGRR++V 
Sbjct: 60  EAADNAEDSGLSLDGRRLIVT 80

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|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 = 69.6 bits (171), Expect = 4e-15
 Identities = 27/68 (39%), Positives = 39/68 (57%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  L + TTE +++  FE++G I  V L  DKET + +G+AF+ +M       AY + 
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 200 DGRKLDGR 207
           DG    GR
Sbjct: 62  DGSIFQGR 69

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|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 = 69.6 bits (171), Expect = 5e-15
 Identities = 26/72 (36%), Positives = 41/72 (56%)

Query: 141 FVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD 200
           FV  + Y+ TE ++   F   GP+   RLVTD++T KP+GY F E+       +A +  +
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 201 GRKLDGRRVLVD 212
           G + +GR + VD
Sbjct: 62  GYEFNGRALRVD 73

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

 Score = 69.0 bits (169), Expect = 8e-15
 Identities = 27/68 (39%), Positives = 38/68 (55%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  L+Y  TE  +++ F  YGP+  V L  DK T KP+G+AF+ YM       A+ + 
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 200 DGRKLDGR 207
           DG    GR
Sbjct: 65  DGTVFQGR 72

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

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

 Score = 68.1 bits (167), Expect = 1e-14
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  L Y+TT   +   F++ G    VRL+TDK+T K +G AF+E+     M  A K 
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61

Query: 199 ADGRKLDGRRVLVD 212
                L GR++ V+
Sbjct: 62  -HHTLLKGRKINVE 74

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

 Score = 74.9 bits (184), Expect = 2e-14
 Identities = 40/131 (30%), Positives = 57/131 (43%), Gaps = 8/131 (6%)

Query: 267 DRHGDRDRERSRERGRDREREREKSLELSHDRPRDRDHRD-DRHHRDRDRTRDRERERDR 325
           D   DR+RE+SR R RDR  ER +       R RDR  R  +R +R+  R RDR R   R
Sbjct: 2   DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSR 61

Query: 326 GRERDRDRTRDRDRGRDRGRDHERDREKDRDKERDRDRTRERERDRDYEVGDPDRDRGYS 385
                R  +  R R R R R        ++ + R RDR+   +  +D      D+ R   
Sbjct: 62  SPRSLRYSSVRRSRDRPRRRSRSVRSI-EQHRRRLRDRSPSNQWRKD------DKKRSLW 114

Query: 386 RDRDSDYDRID 396
             +   Y+ + 
Sbjct: 115 DIKPPGYELVT 125

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

 Score = 66.9 bits (164), Expect = 5e-14
 Identities = 27/75 (36%), Positives = 43/75 (57%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TLFV  L Y+TT+ +++  F   GPIKR  +V DK + K RG+ ++ +    D K A ++
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 199 ADGRKLDGRRVLVDV 213
               K  GR++ V+ 
Sbjct: 61  KKKTKFGGRKIHVEF 75

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|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 73.8 bits (182), Expect = 7e-14
 Identities = 37/232 (15%), Positives = 67/232 (28%), Gaps = 11/232 (4%)

Query: 250 QEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHDRPRDRDHRDDRH 309
           +E   G + +A           R   R+    R  E+   ++     +            
Sbjct: 56  KEARGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAA 115

Query: 310 HRDRDRTRDRERERDRGRER--DRDRTRDRDRGRDRGRDHERDREKDRDKERDRDRTRER 367
                     +    R R     R   R    G ++     R    +R +E +RD  R R
Sbjct: 116 AEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRR 175

Query: 368 ERDRDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERDYDPTDQEDDRGWYDHHENY 427
               D +      +RG   +R  D D  D +  R++   R+        DR         
Sbjct: 176 GDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRR-------- 227

Query: 428 EHHRGYGDHDRYNQYHDDDNDRYDQMEEDDYRYDRATSESRDKERTRDLDRE 479
              R   D        + ++      ++ + R  R     RD++R      +
Sbjct: 228 -GRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGD 278

Length = 672

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

 Score = 66.4 bits (163), Expect = 8e-14
 Identities = 31/83 (37%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYG--PIKRVRLVTDKETNKPRGYAFIEYMHTRD-- 191
           P  TL +  L   TTE  I +   +    PIK VRL+ DK T   RG+AF+E+    D  
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 192 --MKAAYKQADGRKLDGRRVLVD 212
             M A     D   +DGR V V 
Sbjct: 61  QWMDALNNL-DPFVIDGRVVRVS 82

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

 Score = 65.3 bits (160), Expect = 1e-13
 Identities = 25/77 (32%), Positives = 41/77 (53%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L+V  L Y  TE  +K  F  +G +   R++TD+ET + RG+ F+E     +  AA ++
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 199 ADGRKLDGRRVLVDVER 215
            +G    GR + V+  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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 71.8 bits (176), Expect = 2e-13
 Identities = 35/105 (33%), Positives = 43/105 (40%), Gaps = 3/105 (2%)

Query: 311 RDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDKERDRDRTRERERD 370
            + DR R++ R RDR R  +R R R RDR R R R         R+  R RDR R   R 
Sbjct: 3   EEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRS 62

Query: 371 RDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERDYDPTDQE 415
                         SRDR     R     E+ R   RD  P++Q 
Sbjct: 63  PR---SLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQW 104

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

 Score = 64.5 bits (158), Expect = 3e-13
 Identities = 28/72 (38%), Positives = 42/72 (58%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L V +L+    +  +K  F +YG +K V L  D+E N PRGYA++E+    D + A K  
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 200 DGRKLDGRRVLV 211
           DG ++DG+ V V
Sbjct: 61  DGGQIDGQEVTV 72

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 63.7 bits (156), Expect = 4e-13
 Identities = 28/70 (40%), Positives = 43/70 (61%), Gaps = 2/70 (2%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L    TE  ++  F  YG ++ VRLV +K  ++PRG+AF+E+    D +AA K+ 
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 200 DGRKLDGRRV 209
           +G  LDGR +
Sbjct: 59  NGLVLDGRTL 68

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

>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 = 64.0 bits (156), Expect = 5e-13
 Identities = 30/73 (41%), Positives = 44/73 (60%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  + YE TE ++K  F   GP+   RLV D+ET KP+GY F EY       +A +  
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 200 DGRKLDGRRVLVD 212
           +G +L+GR++ VD
Sbjct: 61  NGYELNGRQLRVD 73

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

 Score = 62.6 bits (153), Expect = 1e-12
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             +FV  L Y TT+  +++ F  +G I+   ++TD++T K RGY F+ +      + A K
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 198 QA----DGRKL 204
                 DGRK 
Sbjct: 61  DPNPIIDGRKA 71

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

 Score = 62.8 bits (153), Expect = 1e-12
 Identities = 22/68 (32%), Positives = 38/68 (55%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  L Y   E  +++ F  +G +  V +  DK++ K +G+A++ ++   D   AYK+ 
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 200 DGRKLDGR 207
           DG+   GR
Sbjct: 65  DGKVFQGR 72

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

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 28/77 (36%), Positives = 42/77 (54%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P   LFV +L+  TT+  ++  F  +G IK   ++ DK+T     YAFIE+    D + A
Sbjct: 2   PENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

Query: 196 YKQADGRKLDGRRVLVD 212
           Y + D   +D RR+ VD
Sbjct: 62  YFKMDNVLIDDRRIHVD 78

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

 Score = 61.8 bits (151), Expect = 3e-12
 Identities = 24/67 (35%), Positives = 37/67 (55%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T+ V  LS +  E  ++  F  +GPI RV L  DKET + RG+AF+ +    D + A ++
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 199 ADGRKLD 205
            +G   D
Sbjct: 61  LNGFGYD 67

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|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 = 61.4 bits (149), Expect = 5e-12
 Identities = 27/73 (36%), Positives = 45/73 (61%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  LS++T E  +++ F  YG I  V +V D+ET + RG+ F+ + +  D K A    
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 200 DGRKLDGRRVLVD 212
           +G+ +DGR++ VD
Sbjct: 63  NGKSVDGRQIRVD 75

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|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 66.9 bits (164), Expect = 1e-11
 Identities = 42/170 (24%), Positives = 56/170 (32%)

Query: 193 KAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGREQEP 252
                QA  R+  G        R       +P          R   EE ++R    ++E 
Sbjct: 121 APEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDRED 180

Query: 253 SRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHDRPRDRDHRDDRHHRD 312
            +  +   E   RE+R  D D    R+R    +R  E+      DR   R  RD R  R 
Sbjct: 181 RQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARG 240

Query: 313 RDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDKERDRD 362
            D   DR        E    R   R R RDR      D   +R+ E   D
Sbjct: 241 DDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNEREPELRED 290

Length = 672

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

 Score = 66.5 bits (162), Expect = 1e-11
 Identities = 40/117 (34%), Positives = 50/117 (42%), Gaps = 7/117 (5%)

Query: 282 RDREREREKSLELSHDRPRDRDHRDDRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGR 341
           RD E +RE+      ++ R RD RD    R R R+RDR R RDR R       R+  R R
Sbjct: 1   RDEEPDRER------EKSRGRD-RDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPR 53

Query: 342 DRGRDHERDREKDRDKERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRIDSK 398
           DR R   R     R     R R R R R R     +  R R   R   + + + D K
Sbjct: 54  DRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKK 110

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

 Score = 66.1 bits (161), Expect = 1e-11
 Identities = 37/120 (30%), Positives = 48/120 (40%), Gaps = 8/120 (6%)

Query: 244 RYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHDRPRDRD 303
               RE+E SRG  R        +R   R R R R R RDR R   +       RPRDR 
Sbjct: 3   EEPDREREKSRGRDRDRS----SERP--RRRSRDRSRFRDRHRRSRERSYREDSRPRDRR 56

Query: 304 HRDDRHHRDRDRT-RDRERERDRGRERDRDR-TRDRDRGRDRGRDHERDREKDRDKERDR 361
             D R  R    +   R R+R R R R      + R R RDR   ++  ++  +    D 
Sbjct: 57  RYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDI 116

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

 Score = 62.0 bits (150), Expect = 1e-11
 Identities = 30/99 (30%), Positives = 53/99 (53%), Gaps = 3/99 (3%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  LS+ T ++ ++  F  +G +   +++ D+ET + RG+ F+ +       AA  + 
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 200 DGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGG 238
           DG++L+GR + V+    R      PR  GGG G +  GG
Sbjct: 97  DGKELNGRHIRVNPANDRPSA---PRAYGGGGGYSGGGG 132

Length = 144

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

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 26/68 (38%), Positives = 40/68 (58%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L +  TE  ++  FE +G I+ V+L  D ET + +GY FI++    D K A +Q 
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 200 DGRKLDGR 207
           +G +L GR
Sbjct: 61  NGFELAGR 68

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

 Score = 59.5 bits (145), Expect = 2e-11
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPR-----GYAFIEYMHTRDM 192
            TLFV  L+++TTE  +K+ FE  G ++ V +   K+   P      GY F+E+      
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 193 KAAYKQADGRKLDGRRV 209
           + A K+  G  LDG  +
Sbjct: 61  QKALKRLQGTVLDGHAL 77

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

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 23/71 (32%), Positives = 40/71 (56%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T++V+ L +  T + + + F  YG + +V +V DKET K +G AFI ++   D     K 
Sbjct: 3   TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62

Query: 199 ADGRKLDGRRV 209
            + ++L GR +
Sbjct: 63  LNNKELFGRTL 73

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

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 27/68 (39%), Positives = 45/68 (66%)

Query: 145 LSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL 204
           LS  TTE  ++  F  YGPI++V++V D++T + RG+ F+ +    D K A ++ +G ++
Sbjct: 7   LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66

Query: 205 DGRRVLVD 212
           DGRR+ VD
Sbjct: 67  DGRRIRVD 74

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

 Score = 63.8 bits (154), Expect = 4e-11
 Identities = 46/213 (21%), Positives = 82/213 (38%), Gaps = 12/213 (5%)

Query: 127 HNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
                 S +   TLFV  L Y+ TE  ++  F+ +GP+KRVRLV D+ET K RG+AF+E+
Sbjct: 105 PKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEF 164

Query: 187 MHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRYS 246
                 + A ++ +G++L+GR + V     +  P  +PR             +    +  
Sbjct: 165 ESEESAEKAIEELNGKELEGRPLRVQ----KAQPASQPRSELSNNLDASFAKKLSRGKAL 220

Query: 247 GREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHDRPRDRDHRD 306
             E+  +            E+            + R                P+ R    
Sbjct: 221 LLEKSDNLYVGNLPLKTAEEEL-------ADLFKSRGDIVRASLPPSKDGKIPKSRSFVG 273

Query: 307 DRHHRDRDRTRDRERERDR-GRERDRDRTRDRD 338
           +   +D   +  R  ++   GR   +  ++ R 
Sbjct: 274 NEASKDALESNSRGNKKKILGRGPRKAFSQPRL 306

Length = 306

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

 Score = 58.3 bits (142), Expect = 5e-11
 Identities = 31/77 (40%), Positives = 43/77 (55%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  LS+ TTE +I   F   G IKR+ +  D+ T  P G+ F+EY    D + A K  
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 200 DGRKLDGRRVLVDVERG 216
           +G KLD R + VD + G
Sbjct: 61  NGTKLDDRIIRVDWDAG 77

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

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

 Score = 57.8 bits (139), Expect = 7e-11
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL+V  LS + TE  I + F   GP K  +++T+  +N P  Y F+E+   RD  AA   
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 58

Query: 199 ADGRKLDGRRVLVD 212
            +GRK+ G+ V V+
Sbjct: 59  MNGRKILGKEVKVN 72

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

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

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 23/74 (31%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             LFV+ L +  T+ ++++ F+ +G +K VRLVT++ + KP+G A++EY +      A  
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVL 61

Query: 198 QADGRKLDGRRVLV 211
           + DG ++  + + V
Sbjct: 62  KMDGTEIKEKTISV 75

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 29/73 (39%), Positives = 39/73 (53%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +++  L YE TE  I   F  YG I  + LV DK+T K +G+AF+ Y   R    A    
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 200 DGRKLDGRRVLVD 212
           +G KL GR + VD
Sbjct: 72  NGIKLLGRTIRVD 84

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

 Score = 55.8 bits (135), Expect = 3e-10
 Identities = 27/73 (36%), Positives = 39/73 (53%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  LS++  E  I   F  YG I  VRL TD ++ +P+G+ ++E+      +AA    
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 200 DGRKLDGRRVLVD 212
            G  L GR V +D
Sbjct: 61  GGTDLLGRPVRLD 73

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

 Score = 57.3 bits (138), Expect = 3e-10
 Identities = 19/61 (31%), Positives = 28/61 (45%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TLFV  L Y+ TE  +   F  +G ++    V DK T + +G  F+ +       A  K 
Sbjct: 3   TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKN 62

Query: 199 A 199
           A
Sbjct: 63  A 63

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 56.6 bits (136), Expect = 3e-10
 Identities = 33/78 (42%), Positives = 49/78 (62%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           DP   L V  LS  TTE  ++  F  YGPI  V +V D+++ + RG+AF+ + +  D K 
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 195 AYKQADGRKLDGRRVLVD 212
           A ++A+G +LDGRR+ VD
Sbjct: 67  AKERANGMELDGRRIRVD 84

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). 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. It 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. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 55.8 bits (135), Expect = 4e-10
 Identities = 21/72 (29%), Positives = 41/72 (56%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L V  L  + T+ +++  FE+ GPI+  ++V D+ T +  GY F++Y+   D + A    
Sbjct: 3   LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62

Query: 200 DGRKLDGRRVLV 211
           +G ++  +R+ V
Sbjct: 63  NGFEIRNKRLKV 74

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|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 = 55.7 bits (135), Expect = 4e-10
 Identities = 22/72 (30%), Positives = 36/72 (50%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +F+  L    +E ++K   ES+G +K   LV D  T   +GYAF EY+       A    
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 200 DGRKLDGRRVLV 211
           +G +L  +++ V
Sbjct: 63  NGMQLGDKKLTV 74

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

 Score = 61.1 bits (148), Expect = 5e-10
 Identities = 39/125 (31%), Positives = 47/125 (37%), Gaps = 14/125 (11%)

Query: 325 RGRERDRDRTRDRDRGRDRGRDHERDREKDRDKERDRDRTRERERDRDYEVGDPDRDRGY 384
           R  E DR+R + R R RDR  +  R R +DR + RDR R   R R+R Y      RDR  
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHR---RSRERSYREDSRPRDRRR 57

Query: 385 SRDRDSDYDRIDSKHERDRHGERDYDPTDQEDDRGWYDHHENYEHHRGYGDHDRYNQYHD 444
              R     R  S   R R              R         +H R   D    NQ+  
Sbjct: 58  YDSRSPRSLR-YSSVRRSRD----------RPRRRSRSVRSIEQHRRRLRDRSPSNQWRK 106

Query: 445 DDNDR 449
           DD  R
Sbjct: 107 DDKKR 111

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

 Score = 55.4 bits (133), Expect = 6e-10
 Identities = 29/68 (42%), Positives = 42/68 (61%)

Query: 145 LSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL 204
           LS  TTE  ++  F  YGP+  V +V D+ T + RG+AF+ +    D K A + A+G +L
Sbjct: 7   LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66

Query: 205 DGRRVLVD 212
           DGRR+ VD
Sbjct: 67  DGRRIRVD 74

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

 Score = 55.0 bits (133), Expect = 7e-10
 Identities = 25/72 (34%), Positives = 40/72 (55%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++VA +  + +E  IK  FE++G IK   L  D ET K +GY FIEY + +  + A    
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 200 DGRKLDGRRVLV 211
           +   L G+++ V
Sbjct: 63  NLFDLGGQQLRV 74

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|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 54.7 bits (132), Expect = 8e-10
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 4/73 (5%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH----TRDMKAA 195
           +FV  LS ETTE KI+  F  +G I  + L  DK+TNK RG+ FI +       + ++  
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQ 61

Query: 196 YKQADGRKLDGRR 208
           +    G+K++ ++
Sbjct: 62  FHVIGGKKVEVKK 74

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, 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. It 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 memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 54.7 bits (131), Expect = 9e-10
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL+V  LS + TE+ I + F   GP K  +++ D   N P  Y F+E+   R   A+   
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP--YCFVEFFEHRHAAASLAA 58

Query: 199 ADGRKLDGRRVLVD 212
            +GRK+ G+ V V+
Sbjct: 59  MNGRKIMGKEVKVN 72

This subgroup corresponds to the RRM1 of 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 functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 54.4 bits (131), Expect = 1e-09
 Identities = 25/72 (34%), Positives = 41/72 (56%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  +S+E  E  I++ F  +GPIK + +  D  T K +G+AF+EY      + A +Q 
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 200 DGRKLDGRRVLV 211
           +G  L GR + V
Sbjct: 63  NGVMLGGRNIKV 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 154 IKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV 213
           + + F  +G +++++L+  K      G+AF+E+      + A +  +G    GR + VD 
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

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

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 9/83 (10%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS E     ++  F  +G I   R+V D +T K +GY F+ ++   D + A +  
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 200 DGRKLDGRRVLVDVERGRTVPNW 222
           +G+ L GR +       RT  NW
Sbjct: 62  NGQWLGGRAI-------RT--NW 75

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

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 22/71 (30%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 141 FVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD 200
           FV  + Y TT  +++  F+S G I R+ ++ DK T +P+G+A+IE++    ++ A    +
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA-LLLN 61

Query: 201 GRKLDGRRVLV 211
             +  GR++ V
Sbjct: 62  ESEFRGRQIKV 72

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L V  L  E T+ + +     +G ++R  LV  + T + +GY F+EY  ++      K 
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYA-SKASALKAKN 59

Query: 199 A-DGRKLDGRRVLVD 212
             DG+++ GR++ VD
Sbjct: 60  QLDGKQIGGRKLQVD 74

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

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 23/79 (29%), Positives = 41/79 (51%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
            +L+V  ++  T    ++R F  YGPI  V +  D  T +PRG+A++++   RD + A  
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 198 QADGRKLDGRRVLVDVERG 216
             D  +  GR + +   +G
Sbjct: 61  YLDRTRFLGREIEIQFAQG 79

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

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

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  LS++TTE  ++  F  YG +    ++ D  T + RG+ F+ +     +       
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 200 DGRKLDGRRV 209
               LDGR +
Sbjct: 61  P-HVLDGREI 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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 52.9 bits (127), Expect = 5e-09
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  L+ +T++S ++R F  YG +    ++ D  T + RG+ FI +    +   A  +A
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM-EA 63

Query: 200 DGRKLDGRRV 209
               +DG ++
Sbjct: 64  QPHSIDGNQI 73

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

 Score = 52.7 bits (127), Expect = 5e-09
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P   LF+       TE  ++  F  +G I+ + +V DK+T + +G A++++        A
Sbjct: 2   PNSRLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60

Query: 196 YKQADGRKLDGR----RVLV 211
            ++ +G+ L G     +VL+
Sbjct: 61  MEEMNGKCLGGDTKPLKVLI 80

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

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  L +     ++K  F  +G +K   +  DKET   +GY F+ +  +RD      Q
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSF-SSRDGLENALQ 59

Query: 199 ADGRKLDGRRVLV 211
                L+G ++ V
Sbjct: 60  KQKHILEGNKLQV 72

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

 Score = 52.1 bits (125), Expect = 7e-09
 Identities = 19/75 (25%), Positives = 38/75 (50%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            +++  L +   E ++K+ F  +G +K VR+   K+T   + Y FI++++      A K 
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 199 ADGRKLDGRRVLVDV 213
            +   L G+ + V V
Sbjct: 61  MNNYLLMGKVLQVHV 75

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

 Score = 52.1 bits (125), Expect = 7e-09
 Identities = 27/79 (34%), Positives = 41/79 (51%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TLFV  L++  T+  +   F    PIK   +VTD ET + RGY F+ +    D + A  +
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 199 ADGRKLDGRRVLVDVERGR 217
              +KL GR + +D+   R
Sbjct: 61  LKNKKLHGRILRLDIAERR 79

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

 Score = 51.9 bits (125), Expect = 7e-09
 Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 12/83 (14%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L    TE  +   F   GPIK  +L+ +   N P  YAF+EY   R   AA +  
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE-HGNDP--YAFVEYYDHRSAAAALQTM 57

Query: 200 DGRKLDGRRVLVDVERGRTVPNW 222
           +GR + G+ + V         NW
Sbjct: 58  NGRLILGQEIKV---------NW 71

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

 Score = 51.3 bits (123), Expect = 1e-08
 Identities = 26/75 (34%), Positives = 48/75 (64%), Gaps = 3/75 (4%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  LS+ETTE +++  F   G I+RVR++T +++ K +G+AF+++    +++ A    
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF---EEIEFATNAL 57

Query: 200 DGRKLDGRRVLVDVE 214
            G+ L+GR + V+  
Sbjct: 58  KGKHLNGRALRVEYG 72

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

 Score = 51.2 bits (122), Expect = 2e-08
 Identities = 31/86 (36%), Positives = 43/86 (50%), Gaps = 9/86 (10%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS E T   IK  F  +G I   R+V D  T K +GY F+ + +  D + A +Q 
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 200 DGRKLDGRRVLVDVERGRTVPNWRPR 225
            G+ L GR++       RT  NW  R
Sbjct: 64  GGQWLGGRQI-------RT--NWATR 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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 15/48 (31%), Positives = 26/48 (54%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           TL++  L     E+ I   F   G +  V+++ +K+T K  GY F+E+
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEF 48

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|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 50.1 bits (120), Expect = 3e-08
 Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T++          S +KR FE+ GP+++V +++       + +AFI + +    + A + 
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTV----QPHAFITFENLEAAQLAIET 56

Query: 199 ADGRKLDGRRVLV 211
            +G  +DG  + V
Sbjct: 57  LNGASVDGNCIKV 69

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

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

 Score = 50.2 bits (121), Expect = 3e-08
 Identities = 22/73 (30%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           ++FV  L ++  E ++++ FE  G ++ VR+V D++T   +G+ ++ +  T+D  A   +
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLF-KTKDSVALALK 59

Query: 199 ADGRKLDGRRVLV 211
            +G KL GR++ V
Sbjct: 60  LNGIKLKGRKIRV 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|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 = 49.9 bits (120), Expect = 4e-08
 Identities = 19/72 (26%), Positives = 38/72 (52%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  L  E T+  + + F  +G +   ++  DK T + + + F+ Y +    +AA K  
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 200 DGRKLDGRRVLV 211
           +G ++ G+R+ V
Sbjct: 61  NGFQVGGKRLKV 72

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

 Score = 54.9 bits (132), Expect = 5e-08
 Identities = 35/112 (31%), Positives = 45/112 (40%), Gaps = 24/112 (21%)

Query: 272 RDRERSRERGRDREREREKSLELSHDRPRDRDHRDDRHHRDRDRTRDRERERDRG-RERD 330
           R R+R R R R+  R  +K                      R+R+R R R RDR  R RD
Sbjct: 1   RYRDRERGRLRNDTRRSDKG---------------------RERSRRRSRSRDRSRRRRD 39

Query: 331 RDRTRDRDRGRDRGRDHERDREKDRDKERDRDRTRERERDRDYEVGDPDRDR 382
           RD  R R RGR R R   R   + R     R   R   R+    + + +RD 
Sbjct: 40  RDYYRGR-RGRSRSRSPNR-YYRPRGDRSYRRDDRRSGRNTKEPLTEAERDD 89

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

 Score = 49.9 bits (120), Expect = 5e-08
 Identities = 24/73 (32%), Positives = 41/73 (56%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  +  E  E  +  +F  +G IK + L  D+ T   +GYA IEY   ++ +AA +  
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 200 DGRKLDGRRVLVD 212
           +G++L G+ + VD
Sbjct: 69  NGKELLGQTISVD 81

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

 Score = 49.6 bits (119), Expect = 6e-08
 Identities = 21/47 (44%), Positives = 30/47 (63%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           LFV  L  + TE  ++  F  YG ++ V +VTDKET K RG+AF+ +
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48

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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 49.0 bits (117), Expect = 7e-08
 Identities = 18/47 (38%), Positives = 30/47 (63%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           +FV  LS  TTE  +K+ F  +G ++   L+ DK+TN+ RG+ F+ +
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48

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

 Score = 49.2 bits (117), Expect = 8e-08
 Identities = 29/75 (38%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           KTLFV  LS +TTE  +K  F+  G I   R+VTD++T   +G+ F+++    D KAA +
Sbjct: 1   KTLFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKE 57

Query: 198 QADGRKLDGRRVLVD 212
             +  ++DG +V +D
Sbjct: 58  AMEDGEIDGNKVTLD 72

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

 Score = 49.1 bits (118), Expect = 8e-08
 Identities = 25/72 (34%), Positives = 38/72 (52%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L+ E  E  +   F  +G IK +++  D ET K RG+AF+E+    D  AA    
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 200 DGRKLDGRRVLV 211
           +  +L GR + V
Sbjct: 61  NESELFGRTIRV 72

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

 Score = 48.8 bits (117), Expect = 9e-08
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L V  L ++ TE+ +K+ F  +G +  V +       K +G+AF+++    D + A K  
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 200 DGRKLDGRRVLVD 212
           +G+K+ GR V VD
Sbjct: 61  NGKKIKGRPVAVD 73

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 28/73 (38%), Positives = 42/73 (57%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L V  L+Y TT   ++R FE YG +  V +  D+ T + RG+AF+ +   RD + A    
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 200 DGRKLDGRRVLVD 212
           DG++LDGR + V 
Sbjct: 61  DGKELDGRELRVQ 73

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

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

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 2/79 (2%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TLFV  LS+   +  ++  F+  G +  VR+  D +  + +G+  +E+      + A ++
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEK 59

Query: 199 ADGRKLDGRRVLVDVERGR 217
           + G +L GR + VD+   R
Sbjct: 60  S-GEELLGREIRVDLATER 77

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|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 = 48.7 bits (117), Expect = 1e-07
 Identities = 18/47 (38%), Positives = 30/47 (63%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           LFV +L    TE  ++  FE YG I+ V ++ DK+T + +G AF+++
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKF 48

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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T+FV+ L Y   E ++++ F   G I  VRLV + +  K +GYA++E+ +   ++ A K 
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKL 59

Query: 199 ADGRKLDGRRVLVD 212
            D   + GR + V 
Sbjct: 60  -DRELIKGRPMFVS 72

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), 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 = 72

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 24/59 (40%), Positives = 34/59 (57%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMK 193
           DP K +FV  L+ E TE KI+  F  +G I+ + L  D +TNK RG+ FI +     +K
Sbjct: 2   DPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVK 60

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), 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 = 80

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 20/69 (28%), Positives = 36/69 (52%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            +FV  L  +  ES + + F  +G +  V+++ D  TNK +GY F+   +  +  +A   
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 199 ADGRKLDGR 207
            +G +L GR
Sbjct: 63  LNGYRLGGR 71

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

 Score = 52.8 bits (126), Expect = 3e-07
 Identities = 29/85 (34%), Positives = 48/85 (56%), Gaps = 2/85 (2%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  +S+E  E  I+R F+ +GPIK + +  D  T K +G+AF+EY      + A +Q 
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 200 DGRKLDGRRVLVDVERGRTVPNWRP 224
           +G+ L GR   + V R   +P  +P
Sbjct: 170 NGQMLGGRN--IKVGRPSNMPQAQP 192

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

 Score = 47.2 bits (113), Expect = 4e-07
 Identities = 17/75 (22%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPR---GYAFIEYMHTRDMKAAY 196
           ++V  L ++  E  ++  F  +G ++ +R+   ++  + R   G+AF+ +      + A 
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 197 KQADGRKLDGRRVLV 211
            Q +G +L GR++ V
Sbjct: 63  -QLNGTELGGRKISV 76

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

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +TLFV  L    TE  +   F   GP++ V++  D    KP+ +AF+ + H   +  A +
Sbjct: 2   RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQ 60

Query: 198 QADGRKLDGRRVLVD 212
             +G +L GR + + 
Sbjct: 61  LLNGIRLFGRELRIK 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|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 = 46.8 bits (112), Expect = 5e-07
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T++V  L +  TE +++R F  +G I+ VR+  DK      GYAF+ +        A   
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVA 55

Query: 199 ADGRKLDGRRV 209
            +G  ++G+ V
Sbjct: 56  VNGTSINGQTV 66

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

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 6/80 (7%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
            TL++  LS + TE  +K  FE YG I+ + ++       PRG A++     +D   A +
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQ 56

Query: 198 QADGRKLDGRRVLVDVERGR 217
           +    KL G+++ V     +
Sbjct: 57  KLRNVKLAGKKIKVAWAPNK 76

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

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

 Score = 46.8 bits (112), Expect = 5e-07
 Identities = 21/70 (30%), Positives = 36/70 (51%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  L  E T+  + R F  Y   ++ ++V DK T K +GY F+ +    D   A K+ 
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 200 DGRKLDGRRV 209
           +G+ +  R +
Sbjct: 69  NGKYVGNRPI 78

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

 Score = 47.0 bits (112), Expect = 5e-07
 Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 5/81 (6%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  LSYETT+  +K  F  +G I    ++ D  T + RG+ F+ +    ++ AA   A
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMN-A 60

Query: 200 DGRKLDGRRVLVDVERGRTVP 220
              K+DGR    +VE  R VP
Sbjct: 61  RPHKVDGR----EVEPKRAVP 77

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

 Score = 46.5 bits (111), Expect = 7e-07
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             L V  + +E T+ +++  F  +G +K VRL   K     RG+AF+E++  ++ + A +
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRL-PKKFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 198 QADGRKLDGRRVLVD 212
                 L GR ++++
Sbjct: 60  ALKSTHLYGRHLVLE 74

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

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

 Score = 46.2 bits (110), Expect = 9e-07
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 3/78 (3%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P+ T FV  L + T +  +   F+    +K VRLV DKET+K +G+ ++E+     +K A
Sbjct: 1   PF-TAFVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEA 58

Query: 196 YKQADGRKLDGRRVLVDV 213
            +  DG   D R + VD+
Sbjct: 59  LE-YDGALFDDRSLRVDI 75

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

 Score = 46.1 bits (110), Expect = 9e-07
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +TLFV  ++    + +++  FE +G I+ +         K RG+  + Y   R  + A +
Sbjct: 2   RTLFVRNINSNVEDEELRALFEQFGDIRTLYTAC-----KHRGFIMVSYYDIRAARRAKR 56

Query: 198 QADGRKLDGRRVLV 211
              G +L GR++ +
Sbjct: 57  ALQGTELGGRKLDI 70

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

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

 Score = 46.2 bits (109), Expect = 1e-06
 Identities = 25/70 (35%), Positives = 36/70 (51%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS E T   IK  F  +G I   R+V D  T K +GY F+ + +  D + A    
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 200 DGRKLDGRRV 209
            G+ L GR++
Sbjct: 64  GGQWLGGRQI 73

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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L ++ +  ++   F  YG I+++R+   KET   RG AF+ Y    D K A    
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDHL 61

Query: 200 DGRKLDGRRVLV 211
            G  +  R ++V
Sbjct: 62  SGFNVANRYLVV 73

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is 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 has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T+++  L+++ TE  + REF     I  VRL TDKET + +G+  +++     + AA K 
Sbjct: 1   TVYIGNLAWDITEDDV-REFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALK- 58

Query: 199 ADGRKLDGRRVLVD 212
            DG  L GR + + 
Sbjct: 59  LDGTVLCGRPIRIA 72

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 8/78 (10%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           K L+V  L   TTE +++  F  YG ++RV+        K + YAF+ +    D   A +
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVK--------KIKDYAFVHFEERDDAVKAME 53

Query: 198 QADGRKLDGRRVLVDVER 215
           + +G++L+G  + V + +
Sbjct: 54  EMNGKELEGSPIEVSLAK 71

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

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 16/75 (21%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
           +  ++V  L  +  + K+K  F  YG I   +++ D +  K +G+ F+ + +    + A 
Sbjct: 1   FTNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAV 59

Query: 197 KQADGRKLDGRRVLV 211
           ++ +G++++G+++ V
Sbjct: 60  EELNGKEVNGKKLYV 74

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

 Score = 45.6 bits (108), Expect = 1e-06
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           + V  L +E T+  ++  F SYG +K VR V  K     RG+AF+E+   ++   A    
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMNAL 61

Query: 200 DGRKLDGRRVLVD 212
               L GRR+++ 
Sbjct: 62  KDTHLLGRRLVLQ 74

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

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L V+ L Y+ TE  ++  F   G +K+V++  D+ + +  G A + +    D + A KQ
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60

Query: 199 ADGRKLDGR 207
            +G  LDG+
Sbjct: 61  FNGVLLDGQ 69

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

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 139 TLFVARLSYETT-ESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           TLFV      TT E  I++ FE +GP+ R  +         + +AF+E+  + D   A +
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALE 52

Query: 198 QADGRKLDGRRVLVD 212
              G ++DG  + V+
Sbjct: 53  ALHGSRIDGSVLTVE 67

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

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

 Score = 50.3 bits (120), Expect = 2e-06
 Identities = 32/119 (26%), Positives = 38/119 (31%), Gaps = 10/119 (8%)

Query: 239 EEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHDR 298
           E+   R   R  E  R  SR         R       R   R RDR R   +S       
Sbjct: 10  EKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSP------ 63

Query: 299 PRDRDHRDDRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDK 357
              R  R     R RDR R R R      E+ R R RDR       +D ++    D   
Sbjct: 64  ---RSLRYSSVRRSRDRPRRRSRSVRSI-EQHRRRLRDRSPSNQWRKDDKKRSLWDIKP 118

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

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L    TE  +K+ F+  GP++ V+++ DK  NK   Y F+EY  + D + A +  
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 200 DGRKLDGRRVLVD 212
           +GR+++   + V+
Sbjct: 60  NGRQIENNEIRVN 72

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|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 46.6 bits (111), Expect = 2e-06
 Identities = 24/84 (28%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM--- 192
           P   + V      T+E  IK  F S+G I  +R   D  T  P G   I+Y  +      
Sbjct: 1   PPVEIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDR 60

Query: 193 --KAAYK---QADGRKLDGRRVLV 211
             KAA K   +A   ++ G    V
Sbjct: 61  AAKAALKAVRKAQDCRIGGAEFKV 84

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 110

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 20/47 (42%), Positives = 31/47 (65%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           +FV  LS +TTE +IK  F ++G I+ + L  D +TN+ RG+ F+ Y
Sbjct: 2   VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTY 48

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), 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. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T+FV +LS +  E  +   F   G ++ VR++ D+ + + +G A++E+     +  A   
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-G 59

Query: 199 ADGRKLDGRRVLV 211
             G++L G+ ++V
Sbjct: 60  LTGQRLLGQPIMV 72

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

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +TLF+  L   TT S ++  FE +G I  + +   K+      YAFI+Y     +  A +
Sbjct: 3   RTLFIGNLEKTTTYSDLREAFERFGEIIDIDI---KKQGGNPAYAFIQYADIASVVKAMR 59

Query: 198 QADGRKLDGRRV 209
           + DG  L   RV
Sbjct: 60  KMDGEYLGNNRV 71

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

 Score = 44.5 bits (105), Expect = 4e-06
 Identities = 24/68 (35%), Positives = 37/68 (54%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L  + TE ++++ FE+YG I +  L+ DK T  PRG AF+ Y    + +AA    
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 200 DGRKLDGR 207
           +G    G 
Sbjct: 63  NGTIPPGS 70

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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 17/48 (35%), Positives = 24/48 (50%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           T++V  L    T   +K  F  YG +  V L   K T   +G+AFIE+
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEF 48

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL +  L    +   ++  F+ YG +K +R     ET   R   F+E+   RD   A + 
Sbjct: 3   TLVIFNLDPTVSSETLRSIFQVYGDVKELR-----ETPCKREQRFVEFFDVRDAAKALRA 57

Query: 199 ADGRKLDGRRVLVD 212
            +G+++ G+ V+++
Sbjct: 58  MNGKEISGKPVVIE 71

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 7/75 (9%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  + Y +TE +I+  F   G I+ + L+T  +T + RG AFI    T   + A K+A
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFI----TFKTEEAAKRA 56

Query: 200 ---DGRKLDGRRVLV 211
              DG  + GR + V
Sbjct: 57  LALDGEDMGGRFLKV 71

This subfamily corresponds to the RRM1 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|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 44.1 bits (104), Expect = 5e-06
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           K L V  LSY  +E  ++  FE    I+       +   +P+GYAF+E+    D K A  
Sbjct: 2   KVLVVNNLSYSASEDSLQEVFEKATSIR-----IPQNNGRPKGYAFVEFESAEDAKEALN 56

Query: 198 QADGRKLDGRRV 209
             +  +++GR +
Sbjct: 57  SCNNTEIEGRSI 68

This subfamily corresponds to the RRM3 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 = 72

>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 44.2 bits (105), Expect = 6e-06
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 138 KTLFVARLSYETTE-SKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
           + LFV RL     + S +++ F   G     +L       +PRG+AF+EY    D + A 
Sbjct: 3   RCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIA-PNGQPRGFAFVEYATAEDAEEAQ 61

Query: 197 KQADGRKLDGRRVLV 211
           +  +G  L G  + V
Sbjct: 62  QALNGHSLQGSPIRV 76

This subfamily corresponds to the RRM3 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 = 92

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

 Score = 44.0 bits (103), Expect = 6e-06
 Identities = 25/81 (30%), Positives = 39/81 (48%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           D    L V  L    T+ ++K  F S G I+  +LV DK T +  GY F+ Y+  +D + 
Sbjct: 2   DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61

Query: 195 AYKQADGRKLDGRRVLVDVER 215
           A    +G +L  + + V   R
Sbjct: 62  AINTLNGLRLQTKTIKVSYAR 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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 43.7 bits (103), Expect = 7e-06
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +TLFV  L  + TE  I   F   GP+ +V++  DK+  KP+ +AF+ + H   +  A  
Sbjct: 2   RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAMN 60

Query: 198 QADGRKLDGRRV 209
             +G KL GR +
Sbjct: 61  LLNGIKLYGRPL 72

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|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 43.4 bits (103), Expect = 7e-06
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL V  L    ++ +++  F  +G +K +R    + + K     F+E+   R  +AA   
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQK-----FVEFYDIRAAEAALDA 57

Query: 199 ADGRKLDGRRVLVD 212
            +GR   G R+ V 
Sbjct: 58  LNGRPFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 43.5 bits (103), Expect = 7e-06
 Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 139 TLFVARLSYETTESKIKRE----FESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           T+FV        E  I+R     F S G I RV + TD+ET   +G+A+IE   + D   
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIE-FKSVDGVE 59

Query: 195 AYKQADGRKLDGRRVLVD 212
              + DG  L G  ++VD
Sbjct: 60  KALELDGSDLGGGNLVVD 77

This subfamily corresponds to the RRM2 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 = 79

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 43.5 bits (103), Expect = 7e-06
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FVA L Y+    K+K  F+  G + R  +  DKE  K RG   +++ H  +   A    
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 200 DGRKLDGRRVLV 211
           +G+ L  R + V
Sbjct: 60  NGQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is 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). MEF-2 is 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 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 43.9 bits (103), Expect = 8e-06
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS E  ES + + F  +G +  V+++ D  TNK +G+ F+   +  +   A    
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 200 DGRKLDGRRVL 210
           +G +L G RVL
Sbjct: 64  NGYRL-GDRVL 73

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 43.5 bits (102), Expect = 8e-06
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + LF+  LS+ETT+  ++  FE +G +    ++ D  T + RG+ F+ Y    ++ AA  
Sbjct: 3   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM- 61

Query: 198 QADGRKLDGRRV 209
            A   K+DGR V
Sbjct: 62  NARPHKVDGRVV 73

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|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 43.3 bits (102), Expect = 8e-06
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +TLFV  L Y  T  ++K  FE       +RL + K+    +G A+IE+    + + A +
Sbjct: 4   RTLFVKNLPYNITVDELKEVFED---AVDIRLPSGKD-GSSKGIAYIEFKTEAEAEKALE 59

Query: 198 QADGRKLDGRRVLVD 212
           +  G ++DGR ++VD
Sbjct: 60  EKQGAEVDGRSIVVD 74

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, 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.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 43.3 bits (103), Expect = 8e-06
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL+V        +S I+  FE YG I  +R  + +  NK R + ++++       AA   
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLR-FNKTRRFCYVQFTSPESAAAAVAL 60

Query: 199 ADGRKLDGRRVLVDV 213
            +G+  +G +++V +
Sbjct: 61  LNGKLGEGYKLVVKI 75

This subfamily corresponds to the RRM2 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|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 43.6 bits (103), Expect = 8e-06
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 7/78 (8%)

Query: 136 PYKTLFVARL----SYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRD 191
           P   +FVA L    S +  E+ +   F  YG +  V+++ D    + R YAF+++ +  D
Sbjct: 1   PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDD 57

Query: 192 MKAAYKQADGRKLDGRRV 209
            K A  +  G  LDGR +
Sbjct: 58  AKNALAKGQGTILDGRHI 75

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

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 5/77 (6%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  L    T+ +++ EFE YGP++ V +        P G+AF+E+   RD + A +  
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWV-----ARNPPGFAFVEFEDPRDAEDAVRAL 56

Query: 200 DGRKLDGRRVLVDVERG 216
           DGR++ G RV V++ RG
Sbjct: 57  DGRRICGNRVRVELSRG 73

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

 Score = 43.5 bits (103), Expect = 9e-06
 Identities = 21/77 (27%), Positives = 38/77 (49%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L +  L    T+ + +  F + GP+K  ++V DK T    G+ F++Y    D + A + 
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 199 ADGRKLDGRRVLVDVER 215
            +G +L  +R+ V   R
Sbjct: 62  LNGLQLQNKRIKVAYAR 78

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

 Score = 43.5 bits (102), Expect = 9e-06
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 5/77 (6%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  L     +++++R F  YGP++ V +  +     P G+AF+E+   RD   A ++ 
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 61

Query: 200 DGRKLDGRRVLVDVERG 216
           DGR L G RV V++  G
Sbjct: 62  DGRTLCGCRVRVELSNG 78

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

 Score = 47.6 bits (113), Expect = 1e-05
 Identities = 28/97 (28%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 311 RDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDKERDRDRTRERERD 370
           R+R R R+  R  D+GRER R R+R RDR R           + RD++  R R       
Sbjct: 5   RERGRLRNDTRRSDKGRERSRRRSRSRDRSR-----------RRRDRDYYRGRRGRSRSR 53

Query: 371 RDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGER 407
                  P  DR Y RD                  +R
Sbjct: 54  SPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDR 90

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|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 10/80 (12%)

Query: 138 KTLFVARLSYETTESKIKREFESYGP--IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           K L+V  L   TTE  IK EF  + P  ++RV+        K R YAF+ + +  D  AA
Sbjct: 2   KVLYVRNLMISTTEETIKAEFNKFKPGVVERVK--------KLRDYAFVHFFNREDAVAA 53

Query: 196 YKQADGRKLDGRRVLVDVER 215
               +G+ +DG  + V + +
Sbjct: 54  MSVMNGKCIDGASIEVTLAK 73

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>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 = 42.9 bits (102), Expect = 1e-05
 Identities = 15/48 (31%), Positives = 30/48 (62%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
            +++  L +   E ++++ F  +G + R+RL   K+T K +GYAF+E+
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEF 48

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

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 25/78 (32%), Positives = 45/78 (57%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           +LFV  ++ +T    ++REF  YGPI  V +  D  T +PRG+A++++   RD + A   
Sbjct: 2   SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61

Query: 199 ADGRKLDGRRVLVDVERG 216
            D + + GR++ +   +G
Sbjct: 62  LDRKWICGRQIEIQFAQG 79

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

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

 Score = 46.9 bits (111), Expect = 1e-05
 Identities = 24/81 (29%), Positives = 38/81 (46%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           +    L V  L    T+ +I+  F S G I+  +LV DK T +  GY F+ Y+   D + 
Sbjct: 1   ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 195 AYKQADGRKLDGRRVLVDVER 215
           A    +G +L  + + V   R
Sbjct: 61  AVNSLNGLRLQNKTIKVSYAR 81

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 20/68 (29%), Positives = 33/68 (48%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  L  + TE  +   F   GP+  V +  D+ T   +GY F+E++   D   A K  
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 200 DGRKLDGR 207
           +  KL G+
Sbjct: 61  NMIKLYGK 68

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|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 19/57 (33%), Positives = 35/57 (61%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           +++V  + Y +T  +++  F   GPI RV ++ DK +  P+GYA+IE+     ++AA
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAA 57

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 142 VARLSYETTESKIKREFES-YGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD 200
           V+ L  + TE++I+  F S  GPIKRV L  + E  K  G A I +    D   AY + +
Sbjct: 4   VSNLPKDVTEAQIREYFVSQIGPIKRVLLSYN-EGGKSTGIANITFKRAGDATKAYDKFN 62

Query: 201 GRKLDGRRVL 210
           GR  DG R +
Sbjct: 63  GRIDDGNRKM 72

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 20/54 (37%), Positives = 32/54 (59%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMK 193
           +FV  LS +T E KI+  F ++G ++ + L  D +TNK RG+ FI +     +K
Sbjct: 2   IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 55

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 8/72 (11%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V     +T+ES I+  F  YG +K V++++         +AF+E+        A    
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIRAKDSV 53

Query: 200 DGRKLDGRRVLV 211
            G+ L+   + V
Sbjct: 54  HGKVLNNNPLYV 65

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p 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 containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 42.5 bits (101), Expect = 2e-05
 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 158 FESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL 210
           FE  GPI  +RL+ D      RGYAF+ Y +    + A KQ    ++   + L
Sbjct: 22  FEKAGPIYELRLMMDFSGLN-RGYAFVTYTNKEAAQRAVKQLHNYEIRPGKRL 73

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It 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. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 19/76 (25%), Positives = 36/76 (47%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
            T+FV  +    ++  I++  E  G +   + V D  T K + + F E+        A +
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 198 QADGRKLDGRRVLVDV 213
             +G +L G+++LV V
Sbjct: 61  LLNGLELGGKKLLVKV 76

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

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + LF+  LS+ETT+  ++  FE +G +    ++ D +T + RG+ F+ Y    ++ AA  
Sbjct: 3   RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM- 61

Query: 198 QADGRKLDGRRV 209
            A   K+DGR V
Sbjct: 62  SARPHKVDGRVV 73

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|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 = 2e-05
 Identities = 16/67 (23%), Positives = 35/67 (52%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +++  L   TT+  +++  + +G I   + + DK+TNK +GY F+++        A +  
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 200 DGRKLDG 206
           +GR +  
Sbjct: 63  NGRGVQA 69

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|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           +++V  + Y  T  +++  F   G + RV ++ DK +  P+G+A+IE+     ++ A   
Sbjct: 1   SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTA-LA 59

Query: 199 ADGRKLDGRRVLVDVER 215
            D     GR++ V  +R
Sbjct: 60  LDESLFRGRQIKVMPKR 76

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L V  L    T+ +I+  F S G I+  +L+ DK T +  GY F+ Y+   D + A    
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 200 DGRKLDGRRVLVD 212
           +G +L  + + V 
Sbjct: 64  NGLRLQNKTIKVS 76

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 8/77 (10%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +++ RL Y   E  ++R F+ YG I+ + L          G+ F+E+   RD   A  + 
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYEL 53

Query: 200 DGRKLDGRRVLVDVERG 216
           +G++L G RV+V+  RG
Sbjct: 54  NGKELCGERVIVEHARG 70

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

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 42.4 bits (99), Expect = 3e-05
 Identities = 18/49 (36%), Positives = 29/49 (59%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           K +FV  LS  T    +K+ FE +G ++   L+ DK TN+ RG+ F+ +
Sbjct: 4   KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF 52

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

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 20/73 (27%), Positives = 41/73 (56%), Gaps = 3/73 (4%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLV---TDKETNKPRGYAFIEYMHTRDMKAAY 196
           L+V  L+ + TE  + +EF  +GP+  V+++   T++E  + R   F+ +M+  D + A 
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 197 KQADGRKLDGRRV 209
            + DG+ + G  +
Sbjct: 64  DELDGKDVMGYEL 76

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|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology motif kinase 1 (UHMK1) and similar proteins

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 27/64 (42%), Positives = 35/64 (54%), Gaps = 3/64 (4%)

Query: 147 YETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG 206
           YE     IK E + YGP+  V L+  KE N  +G  F+EY +  D KAA K   GR  DG
Sbjct: 23  YEDIIEDIKEECQKYGPV--VSLLIPKE-NPGKGQVFVEYANAGDSKAAQKLLTGRIFDG 79

Query: 207 RRVL 210
           + V+
Sbjct: 80  KFVV 83

This subgroup corresponds to the RRM of UHMK1. UHMK1, also termed kinase interacting with stathmin (KIS) or P-CIP2, is a serine/threonine protein kinase functionally related to RNA metabolism and neurite outgrowth. It contains an N-terminal kinase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), with high homology to the corresponding motif of the mammalian U2 small nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1 targets two key regulators of cell proliferation and migration, the cyclin-dependent kinase (CDK) inhibitor p27Kip1 and the microtubule-destabilizing protein stathmin. It plays a critical role during vascular wound repair by preventing excessive vascular smooth muscle cell (VSMC) migration into the vascular lesion. Moreover, UHMK1 may control cell migration and neurite outgrowth by interacting with and phosphorylating the splicing factor SF1, thereby probably contributing to the control of protein expression. Furthermore, UHMK1 may be functionally related to microtubule dynamics and axon development. It localizes to RNA granules, interacts with three proteins found in RNA granules (KIF3A, NonO, and eEF1A), and further enhances the local translation. UHMK1 is highly expressed in regions of the brain implicated in schizophrenia and may play a role in susceptibility to schizophrenia. Length = 88

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

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 23/76 (30%), Positives = 37/76 (48%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L V  L    T+ + +  F S G I+  +LV DK T +  GY F+ Y+  +D + A    
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 200 DGRKLDGRRVLVDVER 215
           +G +L  + + V   R
Sbjct: 65  NGLRLQTKTIKVSYAR 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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS ++ ES + + F  +G +  V+++ D  TNK +G+ F+   +  +   A    
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 200 DGRKLDGRRVL 210
           +G +L G RVL
Sbjct: 66  NGYRL-GDRVL 75

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

 Score = 41.4 bits (97), Expect = 4e-05
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +++ RLSY   E  I+R F  YG +  + L          GY F+E+  +RD   A  + 
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYEL 53

Query: 200 DGRKLDGRRVLVDVERG 216
           +G+ L G RV+V+  RG
Sbjct: 54  NGKDLCGERVIVEHARG 70

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

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

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 26/81 (32%), Positives = 36/81 (44%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           D    L V  L    T+ + K  F S G I+  +LV DK T +  GY F+ Y+   D   
Sbjct: 1   DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60

Query: 195 AYKQADGRKLDGRRVLVDVER 215
           A    +G KL  + + V   R
Sbjct: 61  AINTLNGLKLQTKTIKVSYAR 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|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 45.4 bits (107), Expect = 5e-05
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
           +  ++VA +  + +E+ IK  FE++G I + +L         +GY FIEY + +    A 
Sbjct: 204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAI 263

Query: 197 KQADGRKLDGRRVLVDVERGRTVPN 221
              +   L G+   + V +  T P+
Sbjct: 264 ASMNLFDLGGQ--YLRVGKCVTPPD 286

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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTD-KETNKPRGYAFIEYMHTRDMKAAYKQ 198
           + V  + +E T  +++  F ++G +K VRL      T   RG+ F++++  +D K A+K 
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 199 -ADGRKLDGRRVLVD 212
                 L GRR++++
Sbjct: 63  LCHSTHLYGRRLVLE 77

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 41.5 bits (97), Expect = 5e-05
 Identities = 25/78 (32%), Positives = 44/78 (56%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           +LFV  ++  T    ++REF  YGPI  V +  D  T +PRG+A+I++   RD + A   
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 199 ADGRKLDGRRVLVDVERG 216
            + + + GR++ +   +G
Sbjct: 62  LNRKWVCGRQIEIQFAQG 79

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

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

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 18/72 (25%), Positives = 39/72 (54%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  L  E T++ + + F  +G +   ++  DK+TN  + + F+ Y +    +AA +  
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 200 DGRKLDGRRVLV 211
           +G ++  +R+ V
Sbjct: 67  NGFQIGTKRLKV 78

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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 45.3 bits (107), Expect = 5e-05
 Identities = 24/144 (16%), Positives = 55/144 (38%), Gaps = 1/144 (0%)

Query: 248 REQEPSRGPSRSAEPRIRE-DRHGDRDRERSRERGRDREREREKSLELSHDRPRDRDHRD 306
             ++         +   +E ++  ++  E  R+R  +++RER ++       P+ +    
Sbjct: 127 EPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNK 186

Query: 307 DRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDKERDRDRTRE 366
            +   + ++ R   RE  +G+  + D   +R++  D G+D E       + E  +     
Sbjct: 187 KKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEIS 246

Query: 367 RERDRDYEVGDPDRDRGYSRDRDS 390
           R      +  DP         R+S
Sbjct: 247 RRSSSSLKKPDPSPSMASPETRES 270

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPI-KRVRLVTDKETNKPRGYAFIEYMHTRD 191
           P  T+ +  L    TE  I+    S+G   K VRL+  K T   RG+AF+E+M   +
Sbjct: 1   PNNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEE 57

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, 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. Both, RBM5 and RBM10, 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 = 81

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

 Score = 41.0 bits (96), Expect = 6e-05
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 4/69 (5%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T+FV  +     E++I+  F  YG +K V+++TD+ T   +GY F+ +    D++   + 
Sbjct: 7   TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVES 65

Query: 199 A---DGRKL 204
                G+KL
Sbjct: 66  QINFHGKKL 74

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

 Score = 41.1 bits (97), Expect = 7e-05
 Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLV---TDKETNKPRGYAFIEYMHTRDMKAA 195
            L++  L    TE  + + F  YG IK+   +   +     +PRGY F+ +    + + A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 196 YKQADGRKLDGRRVLVD 212
            K  +G+   G++++V 
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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 41.0 bits (96), Expect = 7e-05
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK-- 197
           LFV  LS+ETT+  ++R F  YG +    ++ DK TN+ RG+ F+++     +       
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 198 --QADGRKLD 205
               DGR +D
Sbjct: 62  PHTLDGRTID 71

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|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 40.9 bits (96), Expect = 7e-05
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 138 KTLFVARLSYETTES----KIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMK 193
           KTL+V  +S + TE      +   F  +G +  V++  +     P  YAF+++   R   
Sbjct: 1   KTLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAAS 60

Query: 194 AAYKQADGRKLDGRRVL 210
            A K  +G+ L     L
Sbjct: 61  RAQKACNGKWLFQGSPL 77

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 40.8 bits (96), Expect = 8e-05
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L V  L     E K+++ FE++G I  V+L   K+  K R + F+ Y    + + A K  
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKALKHF 61

Query: 200 DGRKLDGRRVLVD 212
           +   +D  ++ V+
Sbjct: 62  NNSFIDTSKITVE 74

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), 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 = 76

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

 Score = 40.7 bits (95), Expect = 8e-05
 Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 3/60 (5%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  L  +  E  +   F  +GP+++  ++ DK+T K RG+ F+   + ++  +A K A
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFV---YFQNHDSADKAA 58

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 7/69 (10%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L V+ L    TE  I   F + G +KR RLV         G A + Y+   D   A  +
Sbjct: 2   RLVVSNLHPSVTEDDIVELFSAIGALKRARLVR-------PGVAEVVYVRKDDALTAIDK 54

Query: 199 ADGRKLDGR 207
            + R+LDG+
Sbjct: 55  YNNRELDGQ 63

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

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 40.8 bits (95), Expect = 8e-05
 Identities = 17/49 (34%), Positives = 30/49 (61%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           K LFV  +  +T E  ++  FE YG I  + ++TD+++ K RG+ F+ +
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A2/B1, 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. 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 = 80

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

 Score = 40.4 bits (94), Expect = 8e-05
 Identities = 18/47 (38%), Positives = 28/47 (59%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           +FV  LS  TT   +K+ FE +G +    L+ DK TN+ RG+ F+ +
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48

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

 Score = 40.9 bits (95), Expect = 8e-05
 Identities = 20/79 (25%), Positives = 40/79 (50%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  L+ +  ES + + F  +G +  V+++ D  TNK +G+ F+   +  +   A    
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 200 DGRKLDGRRVLVDVERGRT 218
           +G +L  R + V  +  +T
Sbjct: 66  NGYRLGDRVLQVSFKTNKT 84

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

 Score = 44.5 bits (105), Expect = 9e-05
 Identities = 26/89 (29%), Positives = 33/89 (37%), Gaps = 11/89 (12%)

Query: 248 REQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDRE----------REREKS-LELSH 296
           R ++  RG  R+   R  + R   R R RSR+R R R           R R +S      
Sbjct: 1   RYRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYR 60

Query: 297 DRPRDRDHRDDRHHRDRDRTRDRERERDR 325
            R      RDDR      +    E ERD 
Sbjct: 61  PRGDRSYRRDDRRSGRNTKEPLTEAERDD 89

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

 Score = 40.2 bits (94), Expect = 9e-05
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  +S   T  +++  FE +G +         E +K + YAF+      +  AA +  
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVV--------ECDKVKDYAFVHMEREEEALAAIEAL 54

Query: 200 DGRKLDGRRVLVDV 213
           +G+++ GRR+ V++
Sbjct: 55  NGKEVKGRRINVEL 68

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|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 5/77 (6%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  L     + +++R F  YGP++ V +  +     P G+AF+E+   RD + A +  
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 56

Query: 200 DGRKLDGRRVLVDVERG 216
           DG+ + G RV V++  G
Sbjct: 57  DGKVICGSRVRVELSTG 73

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that 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. 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. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, 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 = 77

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 18/68 (26%), Positives = 36/68 (52%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS E T++ +   F ++      R++ D ++ + RGY F+ +   +D + A  + 
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 200 DGRKLDGR 207
           +G+ L  R
Sbjct: 62  NGKWLGSR 69

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

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 147 YETTESKIKREFESYGPIKRVRL-VTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD 205
            E  +  +++ F  +G  K V + +   ET K +GYAF+E+    + K A K  +G KLD
Sbjct: 17  LEKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLD 76

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 10/61 (16%)

Query: 145 LSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL 204
           +S E     + R FE YG ++ + +       KP  Y F+ Y    D  AAY   +G++L
Sbjct: 15  VSREE----LLRVFEKYGTVEDLVMP----PGKP--YCFVSYSSIEDAAAAYDALNGKEL 64

Query: 205 D 205
           +
Sbjct: 65  E 65

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 43.7 bits (103), Expect = 2e-04
 Identities = 25/182 (13%), Positives = 65/182 (35%), Gaps = 16/182 (8%)

Query: 238 GEEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDRD--RERSRERGRDREREREKSLELS 295
            E   +    +EQ       +  +P+        ++  +E+   + +++E+E++      
Sbjct: 100 NESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRD 159

Query: 296 HDRPRDRDHRDDRHHRDRDRTRDR-ERERDRG-RERDRDRTRDRDRGRDRGRDHERDREK 353
            +  + R+    +    +   +    ++++    E+ R   R+  +G+    D   +REK
Sbjct: 160 REEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREK 219

Query: 354 DRDKERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERDYDPTD 413
           + D  +DR+ T            + +  +     R S      S  ++         P  
Sbjct: 220 EEDDGKDRETTTSPM-------EEDESRQSSEISRRS-----SSSLKKPDPSPSMASPET 267

Query: 414 QE 415
           +E
Sbjct: 268 RE 269

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 31/181 (17%), Positives = 77/181 (42%), Gaps = 9/181 (4%)

Query: 239 EEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRE-RSRERGRDREREREKSLELSHD 297
           E V +   G  + P+     + EP+    +  ++++E    E+ + +E+ +E        
Sbjct: 75  EAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKE-------- 126

Query: 298 RPRDRDHRDDRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGRDRGRDHERDREKDRDK 357
            P+DR  +++   +   + +++E+E+     RDR+  + R+R R + R  +  ++K  +K
Sbjct: 127 EPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNK 186

Query: 358 ERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERDYDPTDQEDD 417
           +++     ++ +     V     +   + +R+ + D    +       E D      E  
Sbjct: 187 KKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEIS 246

Query: 418 R 418
           R
Sbjct: 247 R 247

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

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

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 16/50 (32%), Positives = 28/50 (56%)

Query: 137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
            K +FV  L    TE+ +++ F  +G +  V ++ D E  +PRG+ FI +
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITF 51

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           D Y ++FV +LS + T+ ++   F  +G I  V L+  K  N    +AFI++   +    
Sbjct: 2   DKY-SIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAAR 58

Query: 195 AYKQADGRKLDGRRVLV 211
           A +  +   L  + + V
Sbjct: 59  AVESENHSMLKNKTMHV 75

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

 Score = 39.4 bits (93), Expect = 2e-04
 Identities = 16/56 (28%), Positives = 29/56 (51%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           L+V  L  + TE+ +   F   GP+  +R+  D  T +  GYA++ + +  D + A
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERA 57

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|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKR--------VRLVTDKETNKPRGYAFIEYMHTRD 191
           +FV+ L   TTE  +   F S G IK         + L  DK+T +P+G A + Y     
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 192 MKAAYKQADGRKLDGRRVLV 211
             AA +  + +   G  + V
Sbjct: 61  ASAAIEWFNNKDFMGNTIKV 80

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the 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 nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 6/51 (11%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           P K LF+  L  ETT+  ++  F  +   K VRLV        RG AF+E+
Sbjct: 1   PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEF 45

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

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +TLFV  L     E  +   F   GP+ +V +  DKE  KP+ + F+ + H+  +  A  
Sbjct: 2   RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIA 60

Query: 198 QADGRKLDGRRVLV 211
             +G +L GR + V
Sbjct: 61  LLNGIRLYGRPIKV 74

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

 Score = 43.0 bits (101), Expect = 3e-04
 Identities = 24/72 (33%), Positives = 43/72 (59%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L +  TE ++++ FE +G I+ V+L  D ET + +G+ FI++    + K A +  
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 200 DGRKLDGRRVLV 211
           +G +L GR + V
Sbjct: 249 NGFELAGRPIKV 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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
           ++ LF+  LS+ETTE  ++  +E +G +    ++ D  + + RG+ F+ +    ++ AA 
Sbjct: 2   FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61

Query: 197 ----KQADGRKLDGRRVL 210
                  DGR ++ +R +
Sbjct: 62  AARPHTIDGRVVEPKRAV 79

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

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L     + +++ EF  +G I   +++TD E  + +G+ F+ +    +   A  + 
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 200 DGRKLDGRRVLV 211
           +GR + G+ + V
Sbjct: 63  NGRIIGGKPLYV 74

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 6/60 (10%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             + V  L + TTE +++  FE +G + R+ L   +        A +E++   D + A+K
Sbjct: 1   TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTI------ALVEFLEPSDARKAFK 54

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

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 16/91 (17%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVR---LVTDKETNKPRGYAFIEYMHT-RDMK 193
           +T+FV  L   T +  +K+ F+ +GPI+ VR   +   ++    +  A  +  H  +D  
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 194 AAY---KQ---------ADGRKLDGRRVLVD 212
            AY   K+          +G + +G  + VD
Sbjct: 61  NAYVVFKEEESAEKALKLNGTEFEGHHIRVD 91

This subfamily corresponds to the RRM1 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 = 91

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

 Score = 42.2 bits (99), Expect = 4e-04
 Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 3/83 (3%)

Query: 130 PNVSGDP--YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM 187
             ++        +FV  LS +T E+ + + F  +G ++ V+++ D  TN+ +GY F+   
Sbjct: 260 AQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMT 319

Query: 188 HTRDMKAAYKQADGRKLDGRRVL 210
           +  +   A    +G  L G RVL
Sbjct: 320 NYDEAAMAILSLNGYTL-GNRVL 341

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS++TT+  +K  F  +G +    +  D  T + RG+ F+ +     ++    Q 
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 200 DGRKLDGRRVLVDVER 215
           +  KLDGR  ++D +R
Sbjct: 61  E-HKLDGR--VIDPKR 73

This subfamily corresponds to the RRM1 in 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 family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 18/56 (32%), Positives = 32/56 (57%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           +FV  L +E  E  + R F   G I+ VR+V D +TN  +G+A++++     ++ A
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKA 57

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  L  + TE + K  F  YG +  V L      NK +G+ FI      + + A  + 
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRTNAEKAKAEL 57

Query: 200 DGRKLDGRRVLV 211
           DG    GR++ V
Sbjct: 58  DGIMRKGRQLRV 69

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|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 42.7 bits (101), Expect = 4e-04
 Identities = 24/99 (24%), Positives = 43/99 (43%), Gaps = 8/99 (8%)

Query: 271 DRDRERSRERGRDREREREKSLELSHDRPRDRDHRDDRHHRDRDRTRDRERERDRGRERD 330
           +   ER ++R + R+  R        DR   RD RD+R  R+    R+  R   R  ++ 
Sbjct: 597 EAKPERQQDRRKPRQNNRR-------DRNERRDTRDNRTRREGRENREENRRNRRQAQQQ 649

Query: 331 RDRTRDRDRGRDRGRDHERDREKDRDKERDRDRTRERER 369
              TR+  +     +   +D ++ +   R+R R R  E+
Sbjct: 650 TAETRESQQAEVTEKARTQDEQQ-QAPRRERQRRRNDEK 687

Length = 1068

>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 = 38.7 bits (90), Expect = 4e-04
 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 139 TLFVARLSYETTESKIKREFES-YGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           ++FV  LS E  ES +   F+S +   K  +++TD  T   RGY F+ +    D + A  
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 198 QADGRKLDGR 207
           +  G    GR
Sbjct: 63  EMQGVYCGGR 72

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

 Score = 42.5 bits (100), Expect = 4e-04
 Identities = 38/179 (21%), Positives = 66/179 (36%), Gaps = 26/179 (14%)

Query: 109 RLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVR 168
           R +K AE+ AE  +K++              L+V  L    T+ K++  F   G I   +
Sbjct: 257 RAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAK 316

Query: 169 LVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG-------------RRVLVDVER 215
           ++ D E    RG+ F+ + +  +   A  +  GR L G             RR  +  + 
Sbjct: 317 VMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQF 375

Query: 216 GRTVPNWR----PRRLGGGLGTTRVGGEEVNQRYSGREQE--------PSRGPSRSAEP 262
            +  P  R       +GG +G     G+   Q+++G+              GP     P
Sbjct: 376 MQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRP 434

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

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 20/76 (26%), Positives = 37/76 (48%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L V  L    T+ +++  F S G ++  +L+ DK      GY F+ Y++ +D + A    
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 200 DGRKLDGRRVLVDVER 215
           +G +L  + + V   R
Sbjct: 64  NGLRLQSKTIKVSYAR 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|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 20/72 (27%), Positives = 33/72 (45%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L +A L    T+ + +     +G ++R  LV  + T   +GY F+EYM       A    
Sbjct: 2   LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61

Query: 200 DGRKLDGRRVLV 211
            G++L  R + V
Sbjct: 62  LGKQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, 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-1 contains 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 PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

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

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            +FV  +  +TTE +++  F  +G +K V+++TD+     +GY F+ +    D +     
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAM 62

Query: 199 AD----GRKLD 205
            +    G+KL+
Sbjct: 63  GNLNFRGKKLN 73

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

 Score = 38.3 bits (89), Expect = 5e-04
 Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 8/73 (10%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  +  +T++ +++  FE+YG +    ++        R +AF+          A ++ 
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEEL 54

Query: 200 DGRKLDGRRVLVD 212
           +GR+L GR+++V+
Sbjct: 55  NGRELHGRKLVVE 67

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

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 38.5 bits (89), Expect = 5e-04
 Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 10/80 (12%)

Query: 138 KTLFVARLSYETTESKIKREFESYGP--IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           K L+V  L  ET+E  IK+ F  + P  ++RV+        K R YAF+ +    D   A
Sbjct: 2   KILYVRNLMIETSEDTIKKTFGQFNPGCVERVK--------KIRDYAFVHFTSREDAVHA 53

Query: 196 YKQADGRKLDGRRVLVDVER 215
               +G +L+G  + V + +
Sbjct: 54  MNNLNGTELEGSCIEVTLAK 73

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +F+  LS++TT   ++  F  +G IK   ++ D  T + RG+ F+ +     +     Q 
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 200 ----DGRKLD 205
               DG+K+D
Sbjct: 61  PHELDGKKID 70

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

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 20/67 (29%), Positives = 36/67 (53%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V+ L    T+ ++++ F  YG I   R++ D+ T   RG  FI +    + + A K  
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 200 DGRKLDG 206
           +G+K +G
Sbjct: 63  NGQKPEG 69

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

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 11/37 (29%), Positives = 25/37 (67%)

Query: 150 TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           TE  ++ +F+ +G I+ V +V DK T + +G+ ++++
Sbjct: 13  TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49

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|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 = 38.8 bits (90), Expect = 5e-04
 Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 8/81 (9%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIK--------RVRLVTDKETNKPRGYAFIEYMHTR 190
           T+FV  L  + T   +   F+  G IK         + L TD+ET K +G A + +    
Sbjct: 4   TIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 63

Query: 191 DMKAAYKQADGRKLDGRRVLV 211
             KAA    DG++  G  + V
Sbjct: 64  SAKAAIDWFDGKEFSGNPIKV 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|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 38.2 bits (89), Expect = 6e-04
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T++V  L  +  E +++  F  YGPI  + L   K   +P GYAFIE+   RD + A + 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRG 57

Query: 199 ADGRKLDGRRVLVDV 213
            DG   DG+R+ V++
Sbjct: 58  RDGYDFDGQRLRVEL 72

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 38.3 bits (89), Expect = 6e-04
 Identities = 20/72 (27%), Positives = 31/72 (43%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L V  L    T  + +    +YG I+R  LV  + T   +GY F+EYM       A  + 
Sbjct: 2   LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61

Query: 200 DGRKLDGRRVLV 211
            G++L    +  
Sbjct: 62  LGKQLGESTLFA 73

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct 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. Raver-2 contains 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. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 38.3 bits (90), Expect = 6e-04
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +F+  L        +   F ++G I   ++ TD E    +GY F+ +        A ++ 
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 200 DGRKLDGRRVLV 211
           +G  L+ ++V V
Sbjct: 64  NGMLLNDKKVFV 75

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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L   T+ ++++REF+ +G I+R+      + +  R YA+IEY      +AA +  
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRI------DYDPGRNYAYIEYESIEAAQAAKEAL 54

Query: 200 DGRKL--DGRRVLVDV 213
            G  L   GRR+ VD 
Sbjct: 55  RGFPLGGPGRRLRVDF 70

This subfamily corresponds to the RRM3 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 is a novel 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 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 = 72

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 38.1 bits (89), Expect = 7e-04
 Identities = 12/47 (25%), Positives = 25/47 (53%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           LFV  L ++ TE ++K  F+ +G +  VR+ +     +   + F+ +
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVF 52

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 37.9 bits (89), Expect = 7e-04
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
           LFV  LS   TES ++  F  +G +  V ++  K+    RG+A+I+
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYID 47

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|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T+ V  L  +TTE+KI++ F+  G I+ V++V  +        A IE+  T D   A   
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGL----VAVIEFE-TEDEALAALT 56

Query: 199 ADGRKLDGRRVLVDV 213
            D ++L G  + V  
Sbjct: 57  KDHKRLGGNEISVSR 71

This subfamily corresponds to the RRM1 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 = 71

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

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 10/73 (13%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM-KAAYKQ 198
           LFV  L   TT  +++  FE YG +    +V +        Y F+ +M   +  + A K 
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFV-HMEEEEDAEDAIKA 52

Query: 199 ADGRKLDGRRVLV 211
            +G +  G+R+ V
Sbjct: 53  LNGYEFMGKRINV 65

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

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

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L V+ L +  ++  IK  F  +G +K+  +  D+ + +  G A + +    D   A KQ
Sbjct: 2   KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVFERRADALKAMKQ 60

Query: 199 ADGRKLDGR 207
            +G  LDGR
Sbjct: 61  YNGVPLDGR 69

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  L  + TE + K  F  +G +   +L+ D +T + RG+ F+ +  +         A
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF-DSESAVERVFSA 60

Query: 200 DGRKLDGRRVLV 211
              +L G++V V
Sbjct: 61  GMLELGGKQVEV 72

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 6/63 (9%)

Query: 150 TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV 209
           TE  + R F  YGP+  V  V D++    RG A + +      +AA  +  GRKL GR++
Sbjct: 20  TEQYLTRHFSRYGPVVHV--VIDRQ----RGQALVFFDKVEAAQAAVNEMKGRKLGGRKL 73

Query: 210 LVD 212
            VD
Sbjct: 74  QVD 76

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

>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL+V     ET    +  EFE YG + R  +   + T + R +AF+EY   RD + AY++
Sbjct: 1   TLYVTGFGAETRARDLAYEFERYGRLVRCDIPPPR-TFQSRPFAFVEYESHRDAEDAYEE 59

Query: 199 ADGRKLDGRRVLVDVERGR 217
             GR+       + V+  +
Sbjct: 60  MHGRRFPDTGDTLHVQWAK 78

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 17/49 (34%), Positives = 31/49 (63%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           K +FV  +  +T E  ++  FE YG I+ + ++TD+ + K RG+AF+ +
Sbjct: 1   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 20/61 (32%), Positives = 32/61 (52%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV ++  +  E ++   FE  GPI  +RL+ D  + + RGYAFI +      + A K  
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63

Query: 200 D 200
           D
Sbjct: 64  D 64

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds 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. It 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, and 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; it binds RNA through its RRM domains. . Length = 79

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 12/78 (15%)

Query: 138 KTLFVARLSYET----TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMK 193
           +TL+V  +   +     E  ++R F  +G I+ +R++  K      G AF+ Y + R   
Sbjct: 2   RTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSK------GIAFVRYKY-RASA 54

Query: 194 AAYKQA-DGRKLDGRRVL 210
              K+A   + LDG  VL
Sbjct: 55  EFAKEAMADQSLDGGEVL 72

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

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 14/48 (29%), Positives = 29/48 (60%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM 187
           +F+  LS++TT+  ++  F  +G +K   ++ D  T + RG+ F+ +M
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 50

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 16/61 (26%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  + ++T E+ +++ F  YG +K V++V D+     +GY F+ +    D +   ++A
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQEA 63

Query: 200 D 200
           +
Sbjct: 64  N 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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +F+  L  +  E  + + F  +G +  V+++ D  TNK +G+ F+   +  +   A    
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 200 DGRKLDGRRVL 210
           +G +L G ++L
Sbjct: 64  NGYRL-GDKIL 73

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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 16/49 (32%), Positives = 31/49 (63%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           K +FV  +  +T E  ++  FE YG I+ + ++ D+++ K RG+AF+ +
Sbjct: 1   KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49

This subgroup corresponds to the RRM2 of hnRNP A3, 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 = 80

>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 = 37.7 bits (87), Expect = 0.001
 Identities = 18/78 (23%), Positives = 41/78 (52%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  L  E  +  + + F  +G +   ++  DK+TN  + + F+ Y +    +AA +  
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 200 DGRKLDGRRVLVDVERGR 217
           +G ++  +R+ V ++R +
Sbjct: 70  NGFQIGMKRLKVQLKRSK 87

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

 Score = 39.9 bits (93), Expect = 0.002
 Identities = 20/72 (27%), Positives = 32/72 (44%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +++  L     E +IK   ES+G +K   L+ D  T   +GYAF EY        A    
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 200 DGRKLDGRRVLV 211
           +G+     ++ V
Sbjct: 358 NGKDTGDNKLHV 369

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|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 38.7 bits (90), Expect = 0.002
 Identities = 30/94 (31%), Positives = 42/94 (44%)

Query: 284 REREREKSLELSHDRPRDRDHRDDRHHRDRDRTRDRERERDRGRERDRDRTRDRDRGRDR 343
           R R R         R R RD R+ R  R R R RDR R           R+R   R R R
Sbjct: 3   RSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSR 62

Query: 344 GRDHERDREKDRDKERDRDRTRERERDRDYEVGD 377
            R   R R++ R++++D    ++RER +  +  D
Sbjct: 63  SRSPSRRRDRKRERDKDAREPKKRERQKLIKEED 96

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>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 = 36.8 bits (85), Expect = 0.002
 Identities = 17/74 (22%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +F+  L++ETT+  ++  F  +G +    ++ D  T + RG+ F+ +   + +    K+ 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 200 ---DGRKLDGRRVL 210
              DG+ +D +R +
Sbjct: 61  HILDGKIIDPKRAI 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 = 76

>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma Protein (EWS)

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 8/81 (9%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIK--------RVRLVTDKETNKPRGYAFIEYMHTR 190
           T++V  L+   T  ++   F+  G +K         V + TDKET KP+G A + Y    
Sbjct: 2   TIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPP 61

Query: 191 DMKAAYKQADGRKLDGRRVLV 211
             KAA +  DG+   G ++ V
Sbjct: 62  SAKAAVEWFDGKDFQGSKLKV 82

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, 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 multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains 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. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

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

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 6/60 (10%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL+V +L   TT+  +    E +GPI+ + ++       PRG A+I  +H +D   A ++
Sbjct: 6   TLWVGQLDKRTTQQDVTSLLEEFGPIESINMI------PPRGCAYIVMVHRQDAYRALQK 59

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

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 19/58 (32%), Positives = 30/58 (51%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +FV ++  +  E ++   FE  GPI  +RL+ D  T   RGYAF+ +      + A K
Sbjct: 4   IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVK 61

This subgroup corresponds to the RRM1 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, 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 = 79

>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 8/84 (9%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM------- 192
           + +  LS  TT  +I+  F  +G I+   L  D  T +  G   + +             
Sbjct: 1   ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60

Query: 193 -KAAYKQADGRKLDGRRVLVDVER 215
            KAA    +GR++ G+RV V+++R
Sbjct: 61  AKAAVDGLNGRRIGGKRVRVELDR 84

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 40.0 bits (93), Expect = 0.002
 Identities = 46/210 (21%), Positives = 73/210 (34%), Gaps = 19/210 (9%)

Query: 129 DPNVSGDP-----YKTLFVARLSYETTESKIKREFESYGP--IKRVRLVTDKETNKPRGY 181
           +P    D       K L+V  L   TTE  I++ F  + P  ++RV+        K R Y
Sbjct: 220 EPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVK--------KIRDY 271

Query: 182 AFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNW-RPRRLGGGLGTTRVGGEE 240
           AF+ +    D   A  + +G++L+G  + V + +     ++ R  R  GG G  R    +
Sbjct: 272 AFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQ 331

Query: 241 VNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRERSRERGRDREREREKSLELSHDRPR 300
              +                 P      H  R     R RGR     R            
Sbjct: 332 SLGQVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIRGRGRGGAPSRAAGGRGYPPYGY 391

Query: 301 DRDHRDD--RHHRDRDRTRDRERERDRGRE 328
           +  +  D   +H  R +  D+    D G E
Sbjct: 392 E-AYYGDYYGYHDYRGKYEDKYYGYDPGME 420

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|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 8/77 (10%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +++ RLSY+  E  ++R F+ YG I  V L          GY F+E+   RD   A  + 
Sbjct: 2   VYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAVYEL 53

Query: 200 DGRKLDGRRVLVDVERG 216
           +G+ L G RV+V+  RG
Sbjct: 54  NGKDLCGERVIVEHARG 70

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV ++  +  E ++   FES G I  +RL+ D +  K RGYAF+ Y    + K A ++ 
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRAVREL 62

Query: 200 DGRKLDGRRVL 210
           +  ++   R+L
Sbjct: 63  NNYEIRPGRLL 73

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 39.9 bits (93), Expect = 0.003
 Identities = 30/132 (22%), Positives = 39/132 (29%), Gaps = 45/132 (34%)

Query: 349 RDREKDRDKERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRIDSKHERDRHGERD 408
           RD E DR++E+ R R R+R  +R              R R            RDR   RD
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERP-------------RRR-----------SRDRSRFRD 36

Query: 409 YDPTDQEDDRGWYDHHENYEHHRGYGDHDRYNQYHDDDNDRYDQMEEDDYRYD-RATSES 467
                                HR   +          D  RYD       RY     S  
Sbjct: 37  --------------------RHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRD 76

Query: 468 RDKERTRDLDRE 479
           R + R+R +   
Sbjct: 77  RPRRRSRSVRSI 88

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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL V  L    +   + + F +YG IK +R     ET   R + FIE+   R  +AA K 
Sbjct: 3   TLVVFNLDPSVSNDDLHQIFGAYGEIKEIR-----ETPNKRHHKFIEFYDVRSAEAALKA 57

Query: 199 ADGRKLDGRRVLVD 212
            +  ++ G+R+ ++
Sbjct: 58  LNRSEIAGKRIKLE 71

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 10/80 (12%)

Query: 138 KTLFVARLSYETTESKIKREFESYGP--IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           K L+V  L   TTE  I++EF S  P  ++RV+        K R YAF+ + +  D   A
Sbjct: 9   KILYVRNLMLSTTEETIEKEFNSIKPGAVERVK--------KIRDYAFVHFSNREDAVDA 60

Query: 196 YKQADGRKLDGRRVLVDVER 215
               +G+ +DG  + V + +
Sbjct: 61  MNALNGKVIDGSPIEVTLAK 80

This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, 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. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 83

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           D  K LFV ++     E  ++  FE +G I  + ++ DK T   +G AF+ Y        
Sbjct: 4   DAIK-LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALK 62

Query: 195 A 195
           A
Sbjct: 63  A 63

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, 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 contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, 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 additiona 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 = 87

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 18/56 (32%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           LFV  L+ + TE +++  F  YG ++ + ++ D E  + RG AF++Y  +++M  A
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKY-SSKEMAQA 55

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 3/61 (4%)

Query: 154 IKREFESYGPIKRVRLVTDKETNKP---RGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL 210
           +K E   YG +  V +   +         G  F+E+    D + A     GRK DGR V+
Sbjct: 28  VKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTVV 87

Query: 211 V 211
            
Sbjct: 88  A 88

This subfamily corresponds to the RRM3 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 = 89

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +F+ +L  +  E ++    E  G I  +R++ D   N  RGYAF+ + + ++ K A KQ 
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNN-RGYAFVTFSNKQEAKNAIKQL 62

Query: 200 DGRKLDGRRVL 210
           +  ++   R+L
Sbjct: 63  NNYEIRNGRLL 73

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, 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. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 150 TESKIKREFESYG-PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG 206
            E+ IKR F S G  +  V+++ +K T  P GY F+E+      +    + +G+ + G
Sbjct: 12  DENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKPIPG 69

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	480
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	100.0
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.81
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.75
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.73
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.72
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.7
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.66
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.63
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.61
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.61
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.59
KOG0122	270	consensus Translation initiation factor 3, subunit	99.58
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.58
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.57
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.57
PLN03120	260	nucleic acid binding protein; Provisional	99.53
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.52
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.52
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.51
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.51
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.51
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.48
PLN03213	759	repressor of silencing 3; Provisional	99.48
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.47
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.47
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.47
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.45
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.44
PLN03121	243	nucleic acid binding protein; Provisional	99.44
smart00362	72	RRM_2 RNA recognition motif.	99.43
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.43
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.41
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.4
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.4
smart00360	71	RRM RNA recognition motif.	99.39
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.39
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.37
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.37
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.37
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.36
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.35
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.35
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.35
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.34
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.3
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.29
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.29
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.27
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.27
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	99.26
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.24
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.23
smart00361	70	RRM_1 RNA recognition motif.	99.22
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.22
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.22
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.21
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.21
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.19
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	99.17
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.13
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.11
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.09
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.05
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.01
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.0
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.98
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.97
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.92
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.91
PF12220	94	U1snRNP70_N: U1 small nuclear ribonucleoprotein of	98.9
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.88
KOG0226	290	consensus RNA-binding proteins [General function p	98.86
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.86
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.84
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.83
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.83
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.82
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.81
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.81
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.8
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.77
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.76
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.76
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.75
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.74
KOG0151	877	consensus Predicted splicing regulator, contains R	98.66
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.63
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	98.57
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.55
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.54
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.54
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.25
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.2
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.19
KOG4210	285	consensus Nuclear localization sequence binding pr	98.14
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.11
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.09
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.08
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.08
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.06
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.96
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.93
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.91
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.81
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.81
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.69
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.65
KOG2314	698	consensus Translation initiation factor 3, subunit	97.63
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.6
KOG3152	278	consensus TBP-binding protein, activator of basal	97.58
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.49
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.36
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.35
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.33
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.29
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.24
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	97.19
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.13
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.09
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.07
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.03
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.01
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.94
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.92
KOG2135	526	consensus Proteins containing the RNA recognition	96.7
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.53
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.47
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.46
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.42
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.25
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.03
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	95.9
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.71
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.62
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.35
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	95.28
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.02
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.97
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.62
KOG4483	528	consensus Uncharacterized conserved protein [Funct	94.53
KOG4660	549	consensus Protein Mei2, essential for commitment t	94.39
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.91
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.83
KOG4210	285	consensus Nuclear localization sequence binding pr	93.8
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.75
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	93.05
KOG2318	650	consensus Uncharacterized conserved protein [Funct	93.03
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.58
KOG2888	453	consensus Putative RNA binding protein [General fu	90.39
KOG0226	290	consensus RNA-binding proteins [General function p	90.23
KOG2888	453	consensus Putative RNA binding protein [General fu	86.49
COG5638	622	Uncharacterized conserved protein [Function unknow	84.93
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	80.16
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	80.09

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=100.00  E-value=8.5e-38  Score=289.70  Aligned_cols=194  Identities=64%  Similarity=1.038  Sum_probs=180.8

Q ss_pred             CCCChhhhccCCCCCCCCCCCC----CCCCCCCCCCChhhhhhccCCCCCCCCCCCCCCCCChHHHHHHHHHHHHHhhhH
Q 011668           40 TGLTANLLKLFEPRAPLEYKPP----PEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAE  115 (480)
Q Consensus        40 ~~~pp~~~~lf~p~pp~~~~pp----~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~k~~~~~~  115 (480)
                      ..|||+|++||+|.||++|+||    |....+++++||++|+..|..+.+   +|+....++..+..++....++++...
T Consensus         3 ~~lp~nllaLF~pRpPl~y~pP~d~~p~kr~~~~~tGvA~~~~~~~~~~d---~p~~~p~~t~~e~~er~~~~k~e~~~~   79 (335)
T KOG0113|consen    3 QFLPPNLLALFAPRPPLPYLPPTDKLPHKRKTNPYTGVAQYLSTFEDPKD---APPKFPVETPEEPLERGRREKTEKIPH   79 (335)
T ss_pred             ccCCccHHHhcCCCCCcccCCccccChhhccCCCcccHHHHHHhhcCccc---CCCcCcccchhhHHHhhhhhhhhhhHH
Confidence            4578899999999999999998    667778899999999999988766   455566778888888888888888888


Q ss_pred             HHHHHHhhcCCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHH
Q 011668          116 KAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA  195 (480)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A  195 (480)
                      .+...+..|+|..++++.++|.+||||+-|++.++|..|+..|+.||.|+.|.||.+..||+++|||||+|+++.++..|
T Consensus        80 ~~~~~l~~wdP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~A  159 (335)
T KOG0113|consen   80 KLERRLKLWDPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAA  159 (335)
T ss_pred             HHHHHHHhcCCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHcCCceeCCeEEEEeeecCCCCCCCCCCCCCCCCCCccC
Q 011668          196 YKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRV  236 (480)
Q Consensus       196 ~~~l~g~~i~gr~l~V~~a~~~~~~~~~~~~~ggg~gg~~~  236 (480)
                      ++..+|..|+|+.|.|++..+.+++.|.+++.|||+||...
T Consensus       160 YK~adG~~Idgrri~VDvERgRTvkgW~PRRLGGGLGg~r~  200 (335)
T KOG0113|consen  160 YKDADGIKIDGRRILVDVERGRTVKGWLPRRLGGGLGGRRY  200 (335)
T ss_pred             HHhccCceecCcEEEEEecccccccccccccccCCcCCccc
Confidence            99999999999999999999999999999999999998774

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

Probab=99.81  E-value=4.3e-19  Score=155.96  Aligned_cols=84  Identities=26%  Similarity=0.599  Sum_probs=80.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+||++.+|+++|+++|++||.|..|.|+.+..|++++|||||+|.+.++|+.||..||+..|+|+.|+|+|+.
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 011668          216 GRTV  219 (480)
Q Consensus       216 ~~~~  219 (480)
                      .+..
T Consensus       113 ~~~~  116 (144)
T PLN03134        113 DRPS  116 (144)
T ss_pred             cCCC
Confidence            6554

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.75  E-value=3.2e-17  Score=142.15  Aligned_cols=78  Identities=31%  Similarity=0.681  Sum_probs=72.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++||||||+..+++.+|+.+|..||.|..|+|..+     +.|||||+|++..+|+.|+..|+|..|+|..|.|+++..
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            578999999999999999999999999999999875     459999999999999999999999999999999999987


Q ss_pred             CCC
Q 011668          217 RTV  219 (480)
Q Consensus       217 ~~~  219 (480)
                      ...
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            654

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.73  E-value=2e-17  Score=157.27  Aligned_cols=117  Identities=28%  Similarity=0.436  Sum_probs=99.1

Q ss_pred             HHHHHhhhHHHHHHHhhcCCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEE
Q 011668          107 KLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY  186 (480)
Q Consensus       107 ~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F  186 (480)
                      .+..+..+...+..|..++..+.+.+.+ |.++|||+.|++.||.++|.-||+.||.|..|.|+.+..||.+..||||+|
T Consensus       210 e~~~e~ea~~~A~iLEmvGDlpdAd~~P-PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEF  288 (479)
T KOG0415|consen  210 EVLAEKEAKAQAVILEMVGDLPDADVKP-PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEF  288 (479)
T ss_pred             HHHHHHHHHhhHhHHHHhcCCcccccCC-CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeee
Confidence            3344555555666666666666555544 778999999999999999999999999999999999999999999999999


Q ss_pred             echhhHHHHHHHcCCceeCCeEEEEeeecCCCCCCCCC
Q 011668          187 MHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRP  224 (480)
Q Consensus       187 ~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~~~~~~~~  224 (480)
                      ++.++|++|+-.|+++.|+.+.|+|.|++....-.|++
T Consensus       289 en~escE~AyFKMdNvLIDDrRIHVDFSQSVsk~k~r~  326 (479)
T KOG0415|consen  289 ENKESCEQAYFKMDNVLIDDRRIHVDFSQSVSKVKYRQ  326 (479)
T ss_pred             cchhhHHHHHhhhcceeeccceEEeehhhhhhhhhccc
Confidence            99999999999999999999999999998755544543

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.72  E-value=1.5e-16  Score=141.20  Aligned_cols=82  Identities=34%  Similarity=0.602  Sum_probs=78.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|-|-||.+.|+.++|..+|++||.|.+|.|+.|+.|..++|||||-|....+|+.||.+|+|.+|+|+.|.|++|.
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      --
T Consensus        92 yg   93 (256)
T KOG4207|consen   92 YG   93 (256)
T ss_pred             cC
Confidence            53

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.70  E-value=3.4e-17  Score=134.62  Aligned_cols=81  Identities=32%  Similarity=0.564  Sum_probs=77.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .++|||||||++.++|++|.++|++||+|..|.|-.|+.+..+.|||||+|.+.++|+.||..++|+.|+.++|.|+|..
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      +
T Consensus       115 G  115 (153)
T KOG0121|consen  115 G  115 (153)
T ss_pred             c
Confidence            4

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.66  E-value=3.9e-16  Score=156.41  Aligned_cols=83  Identities=23%  Similarity=0.420  Sum_probs=77.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC--eEEEEee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG--RRVLVDV  213 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g--r~l~V~~  213 (480)
                      ..++|||+|||+.+|+++|+++|++||+|+.|.|+.+..|++++|||||+|.+.++|++||..||++.|.+  +.|.|.|
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            35689999999999999999999999999999999999999999999999999999999999999999876  6899999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +....
T Consensus       272 a~~~~  276 (346)
T TIGR01659       272 AEEHG  276 (346)
T ss_pred             CCccc
Confidence            87643

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.63  E-value=1.6e-15  Score=153.93  Aligned_cols=83  Identities=24%  Similarity=0.427  Sum_probs=78.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+.+|||+|||+.+++++|.++|++||.|..|.|+.+..|+.++|||||+|.+.++|..||..|||..|+|+.|+|.|+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            44579999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      .+.
T Consensus       348 ~~~  350 (352)
T TIGR01661       348 NKA  350 (352)
T ss_pred             CCC
Confidence            643

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.61  E-value=2.7e-15  Score=114.95  Aligned_cols=70  Identities=29%  Similarity=0.697  Sum_probs=67.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       140 l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      |||+|||+.+|+++|.++|++||.|..+.|+.+ .++..++||||+|.+.++|+.|+..|+|..|+|+.|+
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            899999999999999999999999999999887 5688999999999999999999999999999999985

(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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.61  E-value=2.4e-15  Score=150.79  Aligned_cols=83  Identities=27%  Similarity=0.452  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ....++|||+|||+++|+++|+++|+.||.|+.|+|+.+..|+.++|||||+|.+.++|..||..|||..|.++.|+|.|
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            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      +.+
T Consensus       184 a~p  186 (346)
T TIGR01659       184 ARP  186 (346)
T ss_pred             ccc
Confidence            864

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.59  E-value=3.8e-15  Score=151.30  Aligned_cols=82  Identities=29%  Similarity=0.491  Sum_probs=78.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+++++|.++|+.||+|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.|+.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      +.
T Consensus        82 ~~   83 (352)
T TIGR01661        82 PS   83 (352)
T ss_pred             cc
Confidence            54

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

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.58  E-value=5.8e-15  Score=134.61  Aligned_cols=83  Identities=30%  Similarity=0.466  Sum_probs=79.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      +..++|-|.||+.++++.+|.++|.+||.|..|.|..|+.||.++|||||.|.+.++|.+||..|||+-++.-.|.|+|+
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            46689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 011668          215 RGR  217 (480)
Q Consensus       215 ~~~  217 (480)
                      ++.
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            864

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.58  E-value=2.8e-16  Score=136.84  Aligned_cols=85  Identities=33%  Similarity=0.532  Sum_probs=79.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+.-|||||||+..||.+|..+|++||+|+.|.|+.|+.||+++||||+.|+++.+...|+..|||..|.|+.|+|++..
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             CCCCC
Q 011668          216 GRTVP  220 (480)
Q Consensus       216 ~~~~~  220 (480)
                      ....+
T Consensus       114 ~Yk~p  118 (219)
T KOG0126|consen  114 NYKKP  118 (219)
T ss_pred             cccCC
Confidence            55444

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.57  E-value=3.7e-15  Score=135.48  Aligned_cols=80  Identities=28%  Similarity=0.583  Sum_probs=74.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++||||||+|.+..+.|+.+|++||+|+++.|+.|+.||+++|||||+|.+.++|..|++.. +-.|+|+...|++|.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccccccccchhh
Confidence            3468999999999999999999999999999999999999999999999999999999999854 467999999999876


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      -
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            4

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.57  E-value=1.4e-14  Score=126.65  Aligned_cols=80  Identities=30%  Similarity=0.529  Sum_probs=72.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||||||..|.+.+|+.||-+||.|..|.|..-   ..+.+||||+|++..+|+.||..-+|..++|..|.|+|+.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4679999999999999999999999999999988543   3356799999999999999999999999999999999988


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      +-.
T Consensus        82 ggr   84 (241)
T KOG0105|consen   82 GGR   84 (241)
T ss_pred             CCC
Confidence            643

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.53  E-value=3.7e-14  Score=133.48  Aligned_cols=77  Identities=21%  Similarity=0.315  Sum_probs=71.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+||++.+|+++|++||+.||.|..|.|+.+..   .+|||||+|.+.++|+.||. |||..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            46999999999999999999999999999999998753   46899999999999999996 999999999999999864


Q ss_pred             C
Q 011668          217 R  217 (480)
Q Consensus       217 ~  217 (480)
                      .
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            3

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

Probab=99.52  E-value=4.5e-14  Score=149.07  Aligned_cols=88  Identities=23%  Similarity=0.360  Sum_probs=81.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+||++.+++++|..+|+.||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCCCC
Q 011668          216 GRTVPNWR  223 (480)
Q Consensus       216 ~~~~~~~~  223 (480)
                      ..+...+.
T Consensus       283 ~pP~~~~~  290 (612)
T TIGR01645       283 TPPDALLQ  290 (612)
T ss_pred             CCccccCC
Confidence            75554443

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.

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

Probab=99.52  E-value=3.9e-14  Score=149.59  Aligned_cols=80  Identities=33%  Similarity=0.608  Sum_probs=76.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+||++.+++++|..+|.+||.|..|.|+.++.|++++|||||+|.+.++|..||..|||..|+|+.|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999998643

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.51  E-value=5.9e-14  Score=107.84  Aligned_cols=70  Identities=33%  Similarity=0.765  Sum_probs=65.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       140 l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      |||+|||+.+++++|.++|+.||.|..|.+..++. +.++++|||+|.+.++|..|+..++|..|+|+.|.
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            79999999999999999999999999999999877 89999999999999999999999999999999884

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 ....

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.51  E-value=2.9e-14  Score=118.41  Aligned_cols=83  Identities=33%  Similarity=0.475  Sum_probs=79.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ....|||+++...+|+++|...|..||+|+.|.|..|..||..+|||+|+|++.++|++||..|||..|.|..|.|+|+.
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      .+.
T Consensus       151 v~g  153 (170)
T KOG0130|consen  151 VKG  153 (170)
T ss_pred             ecC
Confidence            543

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.51  E-value=4.8e-14  Score=133.56  Aligned_cols=82  Identities=21%  Similarity=0.482  Sum_probs=76.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      .+..+.|+|.|||+.+.+.+|..+|++||.|.+|.|+.+.  ..+||||||+|++.++|++|-.+|||..|.|++|.|..
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            4456789999999999999999999999999999999875  55899999999999999999999999999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      |..+
T Consensus       171 ATar  174 (376)
T KOG0125|consen  171 ATAR  174 (376)
T ss_pred             cchh
Confidence            8875

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.48  E-value=4.8e-14  Score=123.23  Aligned_cols=82  Identities=28%  Similarity=0.409  Sum_probs=78.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      .+...|||||||+..++++.|.++|-++|.|+.|.|+.+..|....|||||+|.++++|+.||+.||...|.|++|+|..
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            34667999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ec
Q 011668          214 ER  215 (480)
Q Consensus       214 a~  215 (480)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            76

>PLN03213 repressor of silencing 3; Provisional

Probab=99.48  E-value=1.1e-13  Score=136.98  Aligned_cols=77  Identities=17%  Similarity=0.367  Sum_probs=71.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEech--hhHHHHHHHcCCceeCCeEEEEee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT--RDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~--~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ...+||||||++.|++++|..+|..||.|..|.|+  ..||  +|||||+|.+.  .++.+||..|||..|.|+.|+|+.
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            45789999999999999999999999999999999  4567  89999999987  689999999999999999999999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      |++
T Consensus        85 AKP   87 (759)
T PLN03213         85 AKE   87 (759)
T ss_pred             ccH
Confidence            875

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.47  E-value=9.3e-14  Score=128.37  Aligned_cols=83  Identities=24%  Similarity=0.488  Sum_probs=79.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ...-|||+.|.+.|+.+.|++.|.+||+|.+++|+.|..|++++||+||.|.+.++|+.||..|||.+|+++.|+..||.
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            34569999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      .++
T Consensus       141 RKp  143 (321)
T KOG0148|consen  141 RKP  143 (321)
T ss_pred             cCc
Confidence            665

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.47  E-value=1e-13  Score=127.71  Aligned_cols=87  Identities=21%  Similarity=0.414  Sum_probs=82.3

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ..++..|+|||-.||.++.+.+|..+|-.||.|++.+|..|..|+.+++|+||.|.+..++.+||..|||..|+-+.|+|
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKV  359 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV  359 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhh
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCC
Q 011668          212 DVERGRT  218 (480)
Q Consensus       212 ~~a~~~~  218 (480)
                      .+.+++.
T Consensus       360 QLKRPkd  366 (371)
T KOG0146|consen  360 QLKRPKD  366 (371)
T ss_pred             hhcCccc
Confidence            9987754

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.47  E-value=2.2e-13  Score=145.28  Aligned_cols=82  Identities=26%  Similarity=0.423  Sum_probs=78.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+|+++|.++|+.||.|..|.|+.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 011668          215 RG  216 (480)
Q Consensus       215 ~~  216 (480)
                      ..
T Consensus       373 ~~  374 (509)
T TIGR01642       373 CV  374 (509)
T ss_pred             cc
Confidence            64

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.45  E-value=5.6e-14  Score=125.93  Aligned_cols=84  Identities=30%  Similarity=0.536  Sum_probs=80.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..+|||||+|...+++.-|...|-.||.|+.|.|+.|..+++.+|||||+|...++|.+||..||+.+|.|+.|+|++|.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            34799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 011668          216 GRTV  219 (480)
Q Consensus       216 ~~~~  219 (480)
                      +...
T Consensus        89 P~ki   92 (298)
T KOG0111|consen   89 PEKI   92 (298)
T ss_pred             Cccc
Confidence            7544

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.44  E-value=3.3e-13  Score=141.96  Aligned_cols=80  Identities=30%  Similarity=0.625  Sum_probs=77.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++|..||..|||..|.|+.|.|.|+..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999763

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.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.44  E-value=5e-13  Score=123.85  Aligned_cols=76  Identities=20%  Similarity=0.225  Sum_probs=69.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..+|||+||++.+|+++|++||+.||+|..|.|+.+.   ...+||||+|.+.++|+.||. |+|..|.++.|.|.....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            4799999999999999999999999999999999884   455899999999999999996 999999999999987553

>smart00362 RRM_2 RNA recognition motif

Probab=99.43  E-value=8.1e-13  Score=100.65  Aligned_cols=72  Identities=38%  Similarity=0.702  Sum_probs=67.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      +|||+|||..+++++|..+|.+||.|..+.++.+.  +.+.|+|||+|.+.++|..|+..|+|..|.|+.|.|.
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            59999999999999999999999999999998776  6788999999999999999999999999999999874

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.43  E-value=7.1e-13  Score=122.61  Aligned_cols=78  Identities=23%  Similarity=0.481  Sum_probs=72.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      .+..++||||||+..+|+++|+..|+.||.|.+|+|..+      +||+||.|.+.|+|..||..|||..|.|..|+|.|
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsW  234 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSW  234 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEec
Confidence            445789999999999999999999999999999999876      58999999999999999999999999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      .+..
T Consensus       235 GKe~  238 (321)
T KOG0148|consen  235 GKEG  238 (321)
T ss_pred             cccC
Confidence            7754

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.41  E-value=7.3e-13  Score=139.78  Aligned_cols=80  Identities=28%  Similarity=0.440  Sum_probs=73.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC-CeEEEEee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD-GRRVLVDV  213 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~-gr~l~V~~  213 (480)
                      ...++|||+|||+++++++|.++|++||.|..|+|+.+ .+|.++|||||+|.+.++|+.||..||+..|. |+.|.|.+
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            34589999999999999999999999999999999999 78999999999999999999999999999985 78877776


Q ss_pred             ec
Q 011668          214 ER  215 (480)
Q Consensus       214 a~  215 (480)
                      +.
T Consensus       135 S~  136 (578)
T TIGR01648       135 SV  136 (578)
T ss_pred             cc
Confidence            54

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

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

Probab=99.40  E-value=7.3e-13  Score=142.90  Aligned_cols=78  Identities=24%  Similarity=0.520  Sum_probs=75.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      +|||+|||+.+|+++|.++|++||.|..|.|+.+..|++++|||||+|.+.++|..||..||+..|.|+.|.|.|+..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            799999999999999999999999999999999999999999999999999999999999999999999999999763

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.40  E-value=8.5e-13  Score=138.86  Aligned_cols=80  Identities=23%  Similarity=0.486  Sum_probs=76.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|.+||. |+|..|.|+.|.|.++.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            46799999999999999999999999999999999999999999999999999999999997 99999999999999865


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      .
T Consensus       167 ~  167 (457)
T TIGR01622       167 A  167 (457)
T ss_pred             h
Confidence            4

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.

>smart00360 RRM RNA recognition motif

Probab=99.39  E-value=1.6e-12  Score=98.65  Aligned_cols=71  Identities=38%  Similarity=0.708  Sum_probs=67.2

Q ss_pred             EcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          142 VARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       142 V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      |+|||..+++++|..+|..||.|..+.|..+..++.++|||||+|.+.++|..|+..|++..|.|+.|.|.
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            68999999999999999999999999999888788999999999999999999999999999999999874

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.39  E-value=2.3e-12  Score=102.35  Aligned_cols=78  Identities=28%  Similarity=0.482  Sum_probs=71.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+..|||.|||+.+|.+++.++|.+||.|..|.|-..+.   .+|-|||.|++..+|..|+..|+|..++++.|.|-+-.
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            456899999999999999999999999999999976544   57999999999999999999999999999999998855


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      +
T Consensus        94 ~   94 (124)
T KOG0114|consen   94 P   94 (124)
T ss_pred             H
Confidence            3

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

Probab=99.37  E-value=1.5e-12  Score=140.42  Aligned_cols=82  Identities=23%  Similarity=0.473  Sum_probs=77.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ...++|||+||++.+|+++|+++|+.||.|+.|+|+.+ .+|.++|||||+|.+.++|.+||..|||..|+|+.|.|.++
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            35678999999999999999999999999999999998 57999999999999999999999999999999999999998


Q ss_pred             cCC
Q 011668          215 RGR  217 (480)
Q Consensus       215 ~~~  217 (480)
                      ..+
T Consensus       362 ~~k  364 (562)
T TIGR01628       362 QRK  364 (562)
T ss_pred             cCc
Confidence            753

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=2.4e-12  Score=126.66  Aligned_cols=82  Identities=24%  Similarity=0.402  Sum_probs=76.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee-CCeEEEEee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL-DGRRVLVDV  213 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i-~gr~l~V~~  213 (480)
                      .-.+-||||.||.++.|++|.-||++.|+|.++.|+.++.+|.++|||||+|.+.++|+.||..||+++| .|+.|.|.+
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            4568899999999999999999999999999999999999999999999999999999999999999998 588888887


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      +..
T Consensus       161 Sva  163 (506)
T KOG0117|consen  161 SVA  163 (506)
T ss_pred             eee
Confidence            654

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.37  E-value=1e-12  Score=133.62  Aligned_cols=81  Identities=31%  Similarity=0.656  Sum_probs=78.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      +.|||||||+.+++++|..+|+..|.|..++++.|+.||+++|||||+|.+.+.|..|+..|||..|.|+.|+|.|+...
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            78999999999999999999999999999999999999999999999999999999999999999999999999998764


Q ss_pred             C
Q 011668          218 T  218 (480)
Q Consensus       218 ~  218 (480)
                      .
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            3

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.36  E-value=3.3e-12  Score=134.84  Aligned_cols=77  Identities=27%  Similarity=0.525  Sum_probs=70.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC--CCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESY--GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~--G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..++|||+||++.+++++|+++|++|  |.|+.|.++.        +||||+|.+.++|++||..|||..|+|+.|.|.|
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45789999999999999999999999  9999998763        5999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 011668          214 ERGRTVP  220 (480)
Q Consensus       214 a~~~~~~  220 (480)
                      +.+....
T Consensus       304 Akp~~~~  310 (578)
T TIGR01648       304 AKPVDKK  310 (578)
T ss_pred             ccCCCcc
Confidence            9875543

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.

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.35  E-value=2.9e-12  Score=124.11  Aligned_cols=79  Identities=41%  Similarity=0.787  Sum_probs=76.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..+|||+|||+.+|+++|..+|..||.|..|.|+.+..++.++|||||+|.+.++|..|+..|+|..|.|+.|.|.++.
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            5899999999999999999999999999999999998899999999999999999999999999999999999999975

>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=99.35  E-value=5.8e-12  Score=96.39  Aligned_cols=74  Identities=36%  Similarity=0.717  Sum_probs=68.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      +|||+|||+.+++++|..+|..||.|..+.+..+..+ .+.|+|||+|.+.++|..|+..+++..|.|+.|.|.+
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            4899999999999999999999999999999887654 6789999999999999999999999999999999874

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).

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.35  E-value=2.5e-12  Score=118.18  Aligned_cols=82  Identities=28%  Similarity=0.496  Sum_probs=78.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..+.|+|--||.++|+++|+.+|...|+|++|+++.|+.+|.+.||+||.|..+++|++||..|||..|..+.|+|.||.
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyAR  119 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYAR  119 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEecc
Confidence            44679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      +.
T Consensus       120 PS  121 (360)
T KOG0145|consen  120 PS  121 (360)
T ss_pred             CC
Confidence            75

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.34  E-value=4.5e-12  Score=116.51  Aligned_cols=81  Identities=25%  Similarity=0.418  Sum_probs=77.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ...|||-||.+++.|..|+++|..||.|..|+|+.|..|++++|||||.+.+.++|..||..|||+.|+++.|.|.|...
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999764


Q ss_pred             C
Q 011668          217 R  217 (480)
Q Consensus       217 ~  217 (480)
                      +
T Consensus       358 k  358 (360)
T KOG0145|consen  358 K  358 (360)
T ss_pred             C
Confidence            3

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.30  E-value=7e-12  Score=126.03  Aligned_cols=82  Identities=26%  Similarity=0.528  Sum_probs=76.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +-..|+|.||||.|...+|..+|+.||.|..|.|+.... |+.+|||||+|....+|..||..|||..|+|+.|-|+||.
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            467899999999999999999999999999999998776 5666999999999999999999999999999999999998


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      .+.
T Consensus       195 ~Kd  197 (678)
T KOG0127|consen  195 DKD  197 (678)
T ss_pred             ccc
Confidence            654

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.29  E-value=7.3e-12  Score=125.92  Aligned_cols=81  Identities=35%  Similarity=0.581  Sum_probs=75.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHc-----CC-ceeCCeEEE
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA-----DG-RKLDGRRVL  210 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l-----~g-~~i~gr~l~  210 (480)
                      ..||||.|||+++|+++|.++|++||+|.++.|+.++.|+.++|.|||.|.++.+|..||.+.     .| +.|+|+.|.
T Consensus       292 ~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lk  371 (678)
T KOG0127|consen  292 GKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLK  371 (678)
T ss_pred             cceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEe
Confidence            479999999999999999999999999999999999999999999999999999999999976     33 679999999


Q ss_pred             EeeecCC
Q 011668          211 VDVERGR  217 (480)
Q Consensus       211 V~~a~~~  217 (480)
                      |..|.++
T Consensus       372 v~~Av~R  378 (678)
T KOG0127|consen  372 VTLAVTR  378 (678)
T ss_pred             eeeccch
Confidence            9998764

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

Probab=99.29  E-value=1.2e-11  Score=130.75  Aligned_cols=79  Identities=24%  Similarity=0.369  Sum_probs=72.7

Q ss_pred             CCCCEEEEcCCCC-CCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          135 DPYKTLFVARLSY-ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       135 ~~~~~l~V~nL~~-~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      .++++|||+||++ .+|+++|.++|+.||.|..|+|+.++     +|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            4678999999998 69999999999999999999998753     58999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      ++...
T Consensus       348 s~~~~  352 (481)
T TIGR01649       348 SKQQN  352 (481)
T ss_pred             ccccc
Confidence            87643

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).

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.27  E-value=7.7e-12  Score=119.91  Aligned_cols=77  Identities=34%  Similarity=0.646  Sum_probs=74.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      -|.||||.|.+.+.|+.|+..|..||.|++|.+.||+.|++.+|||||+|+-++.|..|++.|||..|+|+.|+|..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999985

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

Probab=99.27  E-value=1.8e-11  Score=129.36  Aligned_cols=76  Identities=16%  Similarity=0.325  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHH--cCCceeCCeEEEEee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ--ADGRKLDGRRVLVDV  213 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~--l~g~~i~gr~l~V~~  213 (480)
                      |+++|||+|||+.+++++|.++|++||.|..|.|+.+      ++||||+|.+.++|..||..  +++..|.|+.|.|.|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            5689999999999999999999999999999999853      57999999999999999986  478999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      +...
T Consensus        75 s~~~   78 (481)
T TIGR01649        75 STSQ   78 (481)
T ss_pred             cCCc
Confidence            8754

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).

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=99.26  E-value=7.5e-12  Score=121.11  Aligned_cols=79  Identities=14%  Similarity=0.241  Sum_probs=64.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCC---CCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKE---TNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~---t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ..|.|.||.+.+|.++|+.||..+|+|..+.|+.+..   .....-.|||.|.+...+..|..+.|.++|+-..|+|-|.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            4899999999999999999999999999998865432   2334568999999999999999977766777777777665


Q ss_pred             cC
Q 011668          215 RG  216 (480)
Q Consensus       215 ~~  216 (480)
                      ..
T Consensus        88 ~~   89 (479)
T KOG4676|consen   88 DE   89 (479)
T ss_pred             CC
Confidence            43

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.24  E-value=1.2e-11  Score=115.64  Aligned_cols=72  Identities=25%  Similarity=0.516  Sum_probs=68.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      .+|||||||..+++.+|+.+|++||+|.+|.|++|        ||||..++...++.||..|||..|+|..|.|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            36999999999999999999999999999999865        9999999999999999999999999999999998876

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.23  E-value=1.4e-11  Score=124.57  Aligned_cols=81  Identities=33%  Similarity=0.663  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      |...||||||.+++++++|..+|+.||.|..|.++.+..||.++|||||+|.+.+.|..|+..|||..|.|+.|+|.+..
T Consensus       277 p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  277 PMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             chhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            44449999999999999999999999999999999999999999999999999999999999999999999999998755


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      .
T Consensus       357 ~  357 (549)
T KOG0147|consen  357 E  357 (549)
T ss_pred             e
Confidence            4

>smart00361 RRM_1 RNA recognition motif

Probab=99.22  E-value=4e-11  Score=92.09  Aligned_cols=62  Identities=27%  Similarity=0.573  Sum_probs=55.4

Q ss_pred             HHHHHHHhh----cCCCeeEEE-ecccCCC--CCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          151 ESKIKREFE----SYGPIKRVR-LVTDKET--NKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       151 e~~L~~~F~----~~G~i~~v~-i~~d~~t--~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      +++|.++|.    +||.|..|. |+.++.+  +.++|||||+|.+.++|..|+..|||..|+|+.|.|.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            567888888    999999995 6666666  8999999999999999999999999999999999863

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.22  E-value=2.7e-11  Score=118.81  Aligned_cols=82  Identities=27%  Similarity=0.542  Sum_probs=74.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCce-eCC--eEEEEe
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRK-LDG--RRVLVD  212 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~-i~g--r~l~V~  212 (480)
                      ...+||||-||..++|.+|+.+|++||.|.+|.|+.|+.|+.++|||||.|.+.++|.+|+.+|++.. |-|  ..|.|.
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            44579999999999999999999999999999999999999999999999999999999999998865 444  578888


Q ss_pred             eecCC
Q 011668          213 VERGR  217 (480)
Q Consensus       213 ~a~~~  217 (480)
                      +|.+.
T Consensus       113 ~Ad~E  117 (510)
T KOG0144|consen  113 YADGE  117 (510)
T ss_pred             ccchh
Confidence            87753

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.22  E-value=2.2e-11  Score=119.90  Aligned_cols=74  Identities=32%  Similarity=0.587  Sum_probs=70.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..+.|||.||+.+||++.|+++|++||.|..|+.+.|        ||||.|.+.++|.+||+.|||+.|+|..|.|.+|+
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAK  329 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAK  329 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecC
Confidence            4678999999999999999999999999999988865        99999999999999999999999999999999998


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      +.
T Consensus       330 P~  331 (506)
T KOG0117|consen  330 PV  331 (506)
T ss_pred             Ch
Confidence            73

>PF13893 RRM_5: RNA recognition motif

Probab=99.21  E-value=6e-11  Score=86.85  Aligned_cols=56  Identities=30%  Similarity=0.710  Sum_probs=50.8

Q ss_pred             HHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          154 IKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       154 L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      |..+|++||+|..|.+..+.     .++|||+|.+.++|..|+..|||..|+|+.|+|.||
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            67899999999999997643     589999999999999999999999999999999986

(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 ....

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.21  E-value=1.1e-10  Score=114.46  Aligned_cols=89  Identities=22%  Similarity=0.451  Sum_probs=82.2

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEE
Q 011668          130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV  209 (480)
Q Consensus       130 ~~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l  209 (480)
                      ....+.....|||.+||-++-..+|...|..||.|...++..|+.|+.+++|+||.|++..+|..||..|||..|+.+.|
T Consensus       417 ~q~eGpeGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~Krl  496 (510)
T KOG0144|consen  417 GQVEGPEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRL  496 (510)
T ss_pred             ccccCCCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccc
Confidence            34456667889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeecCCC
Q 011668          210 LVDVERGRT  218 (480)
Q Consensus       210 ~V~~a~~~~  218 (480)
                      +|.+...+.
T Consensus       497 kVQlk~~~~  505 (510)
T KOG0144|consen  497 KVQLKRDRN  505 (510)
T ss_pred             eEEeeeccC
Confidence            999987543

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.19  E-value=1.9e-11  Score=107.15  Aligned_cols=85  Identities=26%  Similarity=0.425  Sum_probs=77.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeE-EEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKR-VRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~-v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      .+.+..|||+||.+.+.+..|..+|+.||.|.. -+|+.+..||.++|||||.|.+.+.+.+||..|||..++.++|.|.
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~  172 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVS  172 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEE
Confidence            344578999999999999999999999998755 4788899999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      ++..+.
T Consensus       173 ya~k~~  178 (203)
T KOG0131|consen  173 YAFKKD  178 (203)
T ss_pred             EEEecC
Confidence            997543

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=99.17  E-value=1.2e-12  Score=126.49  Aligned_cols=64  Identities=16%  Similarity=0.161  Sum_probs=54.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD  205 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~  205 (480)
                      ..||+|++|+..+...+|.++|..+|+|.+..|..    +....+|.|+|........|+. ++|..+.
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             Hhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            36799999999999999999999999998887754    4445689999999999999998 6777665

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.13  E-value=1.3e-10  Score=104.22  Aligned_cols=82  Identities=23%  Similarity=0.337  Sum_probs=75.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC-CCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESY-GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~-G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ....+||..||..+.+.+|..+|.+| |.|..+.+..++.||.++|||||+|++.+.|..|.+.||++.|.++.|.|.+-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            45679999999999999999999998 78888888899999999999999999999999999999999999999999986


Q ss_pred             cCC
Q 011668          215 RGR  217 (480)
Q Consensus       215 ~~~  217 (480)
                      .+.
T Consensus       128 ppe  130 (214)
T KOG4208|consen  128 PPE  130 (214)
T ss_pred             Cch
Confidence            543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.11  E-value=2.1e-10  Score=112.52  Aligned_cols=78  Identities=22%  Similarity=0.493  Sum_probs=72.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHh-hcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          138 KTLFVARLSYETTESKIKREF-ESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F-~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..+||+|||+++.|++|+.+| ++.|+|++|.|+.|.. |+++|+|.|+|+++|.+++|++.||.+.+.|+.|+|.-...
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~-GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDES-GKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccC-CCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            459999999999999999999 5689999999999864 99999999999999999999999999999999999986544

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.09  E-value=1.6e-10  Score=108.29  Aligned_cols=76  Identities=28%  Similarity=0.552  Sum_probs=71.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++||||||.+.++.++|+..|++||.|++|.|+.+        |+||.|.-.++|..||..|+|.+|.|+.++|+++
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            36788999999999999999999999999999999864        9999999999999999999999999999999998


Q ss_pred             cCCC
Q 011668          215 RGRT  218 (480)
Q Consensus       215 ~~~~  218 (480)
                      ..+.
T Consensus       148 tsrl  151 (346)
T KOG0109|consen  148 TSRL  151 (346)
T ss_pred             cccc
Confidence            8754

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.05  E-value=5.1e-10  Score=112.95  Aligned_cols=83  Identities=22%  Similarity=0.403  Sum_probs=77.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ...+|||.+|...|...+|+.||++||+|+..+|+++..+...++|+||++.+.++|.+||..|+.+.|.|+.|.|+-++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            35789999999999999999999999999999999998888889999999999999999999999999999999999887


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ..+
T Consensus       484 NEp  486 (940)
T KOG4661|consen  484 NEP  486 (940)
T ss_pred             cCc
Confidence            544

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.01  E-value=3e-09  Score=111.44  Aligned_cols=79  Identities=25%  Similarity=0.460  Sum_probs=72.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ..++|||||+|+..|++.+|..+|+.||+|.+|.++.      ++|||||+.....+|.+||.+|+++.|.++.|+|.|+
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            3468999999999999999999999999999998865      4689999999999999999999999999999999999


Q ss_pred             cCCCC
Q 011668          215 RGRTV  219 (480)
Q Consensus       215 ~~~~~  219 (480)
                      .+..+
T Consensus       493 ~g~G~  497 (894)
T KOG0132|consen  493 VGKGP  497 (894)
T ss_pred             ccCCc
Confidence            87643

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.00  E-value=2.5e-09  Score=108.41  Aligned_cols=82  Identities=22%  Similarity=0.391  Sum_probs=69.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..+|||.|||++++..+|.++|..||.|+...|..-...++..+||||+|.+.++++.||. .+-..|+++.|.|+....
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~-Asp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIE-ASPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhh-cCccccCCeeEEEEeccc
Confidence            3459999999999999999999999999988775433224444999999999999999999 468889999999998776


Q ss_pred             CCC
Q 011668          217 RTV  219 (480)
Q Consensus       217 ~~~  219 (480)
                      ...
T Consensus       367 ~~~  369 (419)
T KOG0116|consen  367 GFR  369 (419)
T ss_pred             ccc
Confidence            443

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.98  E-value=1.3e-09  Score=99.46  Aligned_cols=80  Identities=25%  Similarity=0.452  Sum_probs=72.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHH----HhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          136 PYKTLFVARLSYETTESKIKR----EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~----~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      |..||||-||+..+..++|..    +|++||.|..|....   |.+.+|-|||.|.+.+.|..|+..|+|..|.|+.++|
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            445999999999999988776    999999999887764   5789999999999999999999999999999999999


Q ss_pred             eeecCCC
Q 011668          212 DVERGRT  218 (480)
Q Consensus       212 ~~a~~~~  218 (480)
                      +||....
T Consensus        85 qyA~s~s   91 (221)
T KOG4206|consen   85 QYAKSDS   91 (221)
T ss_pred             ecccCcc
Confidence            9998753

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=98.97  E-value=1.8e-09  Score=115.20  Aligned_cols=82  Identities=24%  Similarity=0.434  Sum_probs=68.8

Q ss_pred             CCCCEEEEcCCCCCC----------CHHHHHHHhhcCCCeeEEEecccC---CCCCccceEEEEEechhhHHHHHHHcCC
Q 011668          135 DPYKTLFVARLSYET----------TESKIKREFESYGPIKRVRLVTDK---ETNKPRGYAFIEYMHTRDMKAAYKQADG  201 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~----------te~~L~~~F~~~G~i~~v~i~~d~---~t~~~~g~afV~F~~~~~a~~A~~~l~g  201 (480)
                      .++.+|+|.||...-          ..++|.++|++||.|+.|.|+.+.   .++...|||||+|.+.++|.+||..|||
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnG  486 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNG  486 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCC
Confidence            467889999996421          235789999999999999998652   3455679999999999999999999999


Q ss_pred             ceeCCeEEEEeeecC
Q 011668          202 RKLDGRRVLVDVERG  216 (480)
Q Consensus       202 ~~i~gr~l~V~~a~~  216 (480)
                      ..|+|+.|.|.|...
T Consensus       487 r~~~gr~v~~~~~~~  501 (509)
T TIGR01642       487 RKFNDRVVVAAFYGE  501 (509)
T ss_pred             CEECCeEEEEEEeCH
Confidence            999999999999653

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.92  E-value=2.4e-09  Score=108.28  Aligned_cols=76  Identities=21%  Similarity=0.508  Sum_probs=71.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      .|||.||++.++...|.++|+.||+|.+|+|..+.. | ++|| ||+|.++++|.+||..|||..+.|+.|.|.....+
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~  153 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERK  153 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccch
Confidence            399999999999999999999999999999999875 4 9999 99999999999999999999999999999876653

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.91  E-value=1e-09  Score=107.32  Aligned_cols=82  Identities=29%  Similarity=0.534  Sum_probs=75.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++||||+|+|.++++.|..+|.+||+|..|.|+.++.|+.++||+||+|.+.+.+.++|. ...+.|+|+.|.+.-|.
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 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            45789999999999999999999999999999999999999999999999999999999987 55678999999888877


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ++.
T Consensus        84 ~r~   86 (311)
T KOG4205|consen   84 SRE   86 (311)
T ss_pred             Ccc
Confidence            654

>PF12220 U1snRNP70_N: U1 small nuclear ribonucleoprotein of 70kDa MW N terminal; InterPro: IPR022023 This domain is found in eukaryotes

Probab=98.90  E-value=7.2e-09  Score=83.97  Aligned_cols=88  Identities=55%  Similarity=0.899  Sum_probs=74.8

Q ss_pred             CCCChhhhccCCCCCCCCCCCCC----CCCCCCCCCChhhhhhccCCCCCCCCCCCCCCCCChHHHHHHHHHHHHHhhhH
Q 011668           40 TGLTANLLKLFEPRAPLEYKPPP----EKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAE  115 (480)
Q Consensus        40 ~~~pp~~~~lf~p~pp~~~~pp~----~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~k~~~~~~  115 (480)
                      ..|||+|++||+|.||++|++|+    ....+++++||++|+..|..+..   .++...+++..+........+.+..+.
T Consensus         3 ~~lPp~ll~LF~PRPPL~y~pP~d~~p~~r~t~~itGvs~~l~~~~~~~~---~~~~~~~et~~e~~~r~~~ek~~~~~~   79 (94)
T PF12220_consen    3 SKLPPNLLALFAPRPPLPYLPPIDYPPEKRKTPPITGVSQYLSEFEDYKD---EPPPEPTETKEERRERKRKEKKEKNEE   79 (94)
T ss_pred             CcCCHHHHHHcCCCCCCCCCCccccCcccccCCCCCcHHHHHHHHhcccc---CCCCCCccCHHHHHHHHHHHHHHHHHH
Confidence            57999999999999999999984    34556669999999999987765   233566899999999999999999999


Q ss_pred             HHHHHHhhcCCCCCC
Q 011668          116 KAAEELKKYDPHNDP  130 (480)
Q Consensus       116 ~~~~~~~~~~~~~~~  130 (480)
                      .+...+..|+|..++
T Consensus        80 ~l~~~l~~w~P~~DP   94 (94)
T PF12220_consen   80 KLEEELKEWDPHEDP   94 (94)
T ss_pred             HHHHHHHhcCCCCCC
Confidence            999999999988653

This domain is about 90 amino acids in length. This domain is found associated with PF00076 from PFAM. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition.

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.88  E-value=2.7e-09  Score=104.87  Aligned_cols=75  Identities=19%  Similarity=0.397  Sum_probs=68.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ...|+|||.|||+++||+.|++-|..||.|.++.|+.   .|+++|  .|.|.++++|+.|+..|+|..|+|+.|.|.|.
T Consensus       534 rKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  534 RKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            3568899999999999999999999999999999864   377776  89999999999999999999999999999873

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.86  E-value=5.3e-09  Score=96.45  Aligned_cols=79  Identities=20%  Similarity=0.487  Sum_probs=73.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      -..||+|.|...++.+.|...|.+|-.....+++.++.||+++||+||.|.+..++..|+..|||..++.+.|++.-+.
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhh
Confidence            3579999999999999999999999998899999999999999999999999999999999999999999999876543

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.86  E-value=6.6e-09  Score=100.04  Aligned_cols=80  Identities=25%  Similarity=0.422  Sum_probs=75.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .+.|||..+.++.++++|+.+|+.||+|+.|.+...+.++..+||+||+|.+..+...||..||-..|+|..|+|--+..
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999986554

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.84  E-value=6.2e-09  Score=101.84  Aligned_cols=83  Identities=28%  Similarity=0.487  Sum_probs=77.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+.+||||+|+..+++++|+++|.+||.|..+.|+.|..+..++||+||+|.+.+.+.+++. ..-+.|+|+.|.|..|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            46789999999999999999999999999999999999999999999999999999999988 67889999999999998


Q ss_pred             CCCC
Q 011668          216 GRTV  219 (480)
Q Consensus       216 ~~~~  219 (480)
                      ++..
T Consensus       175 pk~~  178 (311)
T KOG4205|consen  175 PKEV  178 (311)
T ss_pred             chhh
Confidence            8644

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.83  E-value=1.7e-08  Score=97.00  Aligned_cols=75  Identities=25%  Similarity=0.485  Sum_probs=66.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHH-cCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ-ADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~-l~g~~i~gr~l~V~~a  214 (480)
                      ..++|||+||...+++.+|..+|.+||+|..|.++..      +++|||+|.+.++|+.|... +|...|+|..|.|.|.
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            4578999999999999999999999999999998754      35999999999999988764 6777899999999998


Q ss_pred             cC
Q 011668          215 RG  216 (480)
Q Consensus       215 ~~  216 (480)
                      .+
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            76

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.83  E-value=2.4e-09  Score=111.47  Aligned_cols=81  Identities=23%  Similarity=0.574  Sum_probs=74.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ++.|+|.|||+.++-.+|+.||..||.|..|.|+.-...+..+|||||+|.++.+|..|+..|..+.|.|+.|+++||..
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKS  692 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhcc
Confidence            57899999999999999999999999999999987655566789999999999999999999999999999999999875


Q ss_pred             C
Q 011668          217 R  217 (480)
Q Consensus       217 ~  217 (480)
                      .
T Consensus       693 d  693 (725)
T KOG0110|consen  693 D  693 (725)
T ss_pred             c
Confidence            4

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.82  E-value=8.4e-09  Score=97.33  Aligned_cols=81  Identities=31%  Similarity=0.553  Sum_probs=77.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ....|||+|+.+.+|.++|..+|+.||.|..|.|+++..++.++||+||+|.+.+.++.||. |||..|.|..|.|.+..
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            45789999999999999999999999999999999999999999999999999999999999 99999999999999987


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      ..
T Consensus       179 ~~  180 (231)
T KOG4209|consen  179 TN  180 (231)
T ss_pred             ee
Confidence            65

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.81  E-value=8.3e-09  Score=107.50  Aligned_cols=77  Identities=25%  Similarity=0.519  Sum_probs=69.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCC---CCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKET---NKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t---~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +|||.||++.+|.+.|..+|...|.|..|.|...+..   -.+.|||||+|.+.++|..|+..|+|+.|+|+.|.|.++.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            3999999999999999999999999999988655431   2345999999999999999999999999999999999987

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.81  E-value=1.7e-08  Score=97.00  Aligned_cols=80  Identities=23%  Similarity=0.369  Sum_probs=72.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCee--------EEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCe
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIK--------RVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR  207 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~--------~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr  207 (480)
                      ..+.|||.|||..+|.+++.++|++||.|.        .|+|..+.. |+.+|-|+|.|...+++..||..|++..|.|+
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            456699999999999999999999999875        367777765 99999999999999999999999999999999


Q ss_pred             EEEEeeecC
Q 011668          208 RVLVDVERG  216 (480)
Q Consensus       208 ~l~V~~a~~  216 (480)
                      .|+|+.|+-
T Consensus       212 ~~rVerAkf  220 (382)
T KOG1548|consen  212 KLRVERAKF  220 (382)
T ss_pred             EEEEehhhh
Confidence            999998863

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.80  E-value=2.2e-09  Score=96.75  Aligned_cols=78  Identities=17%  Similarity=0.345  Sum_probs=71.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..||||+||...|+++-|.++|-+.|.|..|.|+.+.. ++.+ ||||.|.++..+.-|+++|||..|.+..|.|.+-.+
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            46899999999999999999999999999999988775 5566 999999999999999999999999999999988544

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.77  E-value=1.4e-08  Score=102.67  Aligned_cols=74  Identities=23%  Similarity=0.446  Sum_probs=70.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      ..||||   +.+|+..|.++|+.+|.|.+|.|+.+. |  +.|||||.|.++.+|++||..||...|.|+.|.|.|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            369999   899999999999999999999999998 6  9999999999999999999999999999999999998754

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.76  E-value=9.1e-09  Score=94.78  Aligned_cols=71  Identities=32%  Similarity=0.704  Sum_probs=65.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..||||+|++.+.+.+|..||..||.|..|.|..        ||+||+|.+..+|..||..||+..|+|-.|.|+|+..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            3699999999999999999999999999887753        6999999999999999999999999999999999875

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.76  E-value=1.4e-08  Score=94.18  Aligned_cols=81  Identities=21%  Similarity=0.486  Sum_probs=72.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCce-eCC--eEEEEe
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRK-LDG--RRVLVD  212 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~-i~g--r~l~V~  212 (480)
                      ..++||||-|...-.|++++.+|..||.|.+|.++.... |.++|+|||.|.+..+|..||..|+|.. +-|  ..|+|.
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            457899999999999999999999999999999998875 8999999999999999999999999965 433  569999


Q ss_pred             eecCC
Q 011668          213 VERGR  217 (480)
Q Consensus       213 ~a~~~  217 (480)
                      |+...
T Consensus        97 ~ADTd  101 (371)
T KOG0146|consen   97 FADTD  101 (371)
T ss_pred             eccch
Confidence            98753

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.75  E-value=6.7e-08  Score=87.58  Aligned_cols=83  Identities=22%  Similarity=0.324  Sum_probs=67.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEec-ccCCCCCccceEEEEEechhhHHHHHHHcCCceeC---CeEEEE
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLV-TDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD---GRRVLV  211 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~-~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~---gr~l~V  211 (480)
                      ..+||||.+||.++..-+|..+|..|--.+.+.|. ..+...-.+.+|||+|.+...|.+|+..|||+.|+   +..|+|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            46899999999999999999999988544444442 22222234579999999999999999999999986   788999


Q ss_pred             eeecCCC
Q 011668          212 DVERGRT  218 (480)
Q Consensus       212 ~~a~~~~  218 (480)
                      ++|+..+
T Consensus       113 ElAKSNt  119 (284)
T KOG1457|consen  113 ELAKSNT  119 (284)
T ss_pred             eehhcCc
Confidence            9998644

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.74  E-value=3.3e-08  Score=93.09  Aligned_cols=80  Identities=25%  Similarity=0.446  Sum_probs=73.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..+|+|.||++.|++++|+++|..||.++.+.|-+++. |.+.|.|-|.|...++|..||+.+||+.|+|..|+|.+...
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 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRA-GRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCC-CCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            36899999999999999999999999999888888874 99999999999999999999999999999999999988665


Q ss_pred             C
Q 011668          217 R  217 (480)
Q Consensus       217 ~  217 (480)
                      .
T Consensus       162 ~  162 (243)
T KOG0533|consen  162 P  162 (243)
T ss_pred             c
Confidence            3

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.66  E-value=4.1e-08  Score=101.98  Aligned_cols=82  Identities=20%  Similarity=0.383  Sum_probs=72.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCC---CCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKE---TNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~---t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      .+++|||+||++.++++.|...|..||.|..|+|++...   ......+|||.|.+..+|++|+..|+|..|.+..|++-
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            356799999999999999999999999999999987642   23445789999999999999999999999999999999


Q ss_pred             eecCC
Q 011668          213 VERGR  217 (480)
Q Consensus       213 ~a~~~  217 (480)
                      |+++.
T Consensus       253 Wgk~V  257 (877)
T KOG0151|consen  253 WGKAV  257 (877)
T ss_pred             ccccc
Confidence            98653

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.63  E-value=4.6e-08  Score=100.54  Aligned_cols=94  Identities=28%  Similarity=0.429  Sum_probs=83.9

Q ss_pred             hcCCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCc
Q 011668          123 KYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGR  202 (480)
Q Consensus       123 ~~~~~~~~~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~  202 (480)
                      .+.+.............|||+|||..+++.++.+++..||.+..+.++.+..+|.++||||.+|.+..-...|+..|||+
T Consensus       275 ~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm  354 (500)
T KOG0120|consen  275 KVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGM  354 (500)
T ss_pred             ccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchh
Confidence            34444444455556788999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCeEEEEeeecC
Q 011668          203 KLDGRRVLVDVERG  216 (480)
Q Consensus       203 ~i~gr~l~V~~a~~  216 (480)
                      .+++..|+|+.|-.
T Consensus       355 ~lgd~~lvvq~A~~  368 (500)
T KOG0120|consen  355 QLGDKKLVVQRAIV  368 (500)
T ss_pred             hhcCceeEeehhhc
Confidence            99999999998764

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=98.57  E-value=1.1e-07  Score=97.12  Aligned_cols=80  Identities=15%  Similarity=0.290  Sum_probs=67.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhh-cCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee---CCeE
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFE-SYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL---DGRR  208 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~-~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i---~gr~  208 (480)
                      ...++++|||.||---+|.-+|+.++. .+|.|..++|  |    +.+.+|||.|.+.++|.+.+.+|||+.+   +.+.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--D----kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--D----KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--H----HhhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            455678999999999999999999998 5777777733  2    3467999999999999999999999886   7889


Q ss_pred             EEEeeecCCC
Q 011668          209 VLVDVERGRT  218 (480)
Q Consensus       209 l~V~~a~~~~  218 (480)
                      |.|.|.....
T Consensus       514 L~adf~~~de  523 (718)
T KOG2416|consen  514 LIADFVRADE  523 (718)
T ss_pred             eEeeecchhH
Confidence            9999987643

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.55  E-value=1.3e-07  Score=91.89  Aligned_cols=83  Identities=30%  Similarity=0.403  Sum_probs=76.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCee--------EEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCe
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIK--------RVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR  207 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~--------~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr  207 (480)
                      ...+|||.+|+..+++..|.++|.+||.|.        .|+|.++++|+.+++-|.|+|.+...|++||..+++..|.+.
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            446899999999999999999999999884        467888999999999999999999999999999999999999


Q ss_pred             EEEEeeecCCC
Q 011668          208 RVLVDVERGRT  218 (480)
Q Consensus       208 ~l~V~~a~~~~  218 (480)
                      .|+|.+|...+
T Consensus       145 ~ikvs~a~~r~  155 (351)
T KOG1995|consen  145 TIKVSLAERRT  155 (351)
T ss_pred             Cchhhhhhhcc
Confidence            99999887655

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.54  E-value=3.9e-07  Score=73.77  Aligned_cols=78  Identities=18%  Similarity=0.297  Sum_probs=69.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhc--CCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC----CeEEEE
Q 011668          138 KTLFVARLSYETTESKIKREFES--YGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD----GRRVLV  211 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~--~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~----gr~l~V  211 (480)
                      +||.|.|||...|.++|.+++..  .|..-.+.|+.|..++.+.|||||-|.+++.|......++|..+.    .+.+.|
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            68999999999999999999865  367788899999999999999999999999999999999999875    567788


Q ss_pred             eeec
Q 011668          212 DVER  215 (480)
Q Consensus       212 ~~a~  215 (480)
                      .||.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            8875

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.54  E-value=6e-08  Score=98.85  Aligned_cols=75  Identities=28%  Similarity=0.487  Sum_probs=66.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          131 NVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       131 ~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      .....+..+|+|-|||..|++++|..+|+.||+|..|...     ....|.+||+|.+.-+|+.|++.|++..|.|+.|+
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3344567899999999999999999999999999997653     44568999999999999999999999999999998

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.25  E-value=3.3e-06  Score=85.08  Aligned_cols=80  Identities=23%  Similarity=0.375  Sum_probs=68.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ....|-+.+|||.+|+++|.+||+.|+ |..+.+++  .+|++.|-|||+|.++++++.||+ .+-..|..+.|.|--+.
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAG   84 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccC
Confidence            445788999999999999999999995 77766654  469999999999999999999999 68888999999998776


Q ss_pred             CCCC
Q 011668          216 GRTV  219 (480)
Q Consensus       216 ~~~~  219 (480)
                      ....
T Consensus        85 ~~e~   88 (510)
T KOG4211|consen   85 GAEA   88 (510)
T ss_pred             Cccc
Confidence            5443

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.20  E-value=2.9e-06  Score=81.66  Aligned_cols=75  Identities=16%  Similarity=0.341  Sum_probs=67.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCC--CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          138 KTLFVARLSYETTESKIKREFESYG--PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G--~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..+|||||-|++|+++|.+.+...|  .|.++++..+..+|.++|||+|...+..++++.++.|-...|.|..-+|.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            4699999999999999999998877  67788889999999999999999999999999999999999999865554

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.19  E-value=9.9e-06  Score=77.76  Aligned_cols=91  Identities=19%  Similarity=0.311  Sum_probs=69.0

Q ss_pred             CCCCCCCCCCCCEEEEcCCCCCCCHHH------HHHHhhcCCCeeEEEecccC-CCCCccce--EEEEEechhhHHHHHH
Q 011668          127 HNDPNVSGDPYKTLFVARLSYETTESK------IKREFESYGPIKRVRLVTDK-ETNKPRGY--AFIEYMHTRDMKAAYK  197 (480)
Q Consensus       127 ~~~~~~~~~~~~~l~V~nL~~~~te~~------L~~~F~~~G~i~~v~i~~d~-~t~~~~g~--afV~F~~~~~a~~A~~  197 (480)
                      +...++...+.+-|||-+|++.+..++      -.++|.+||.|..|.|-... ......+.  .||+|.+.++|..||.
T Consensus       104 khlsniRVvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa  183 (480)
T COG5175         104 KHLSNIRVVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIA  183 (480)
T ss_pred             cccccceeeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHH
Confidence            344455556667899999999887766      24789999999887664322 11111232  3999999999999999


Q ss_pred             HcCCceeCCeEEEEeeecCC
Q 011668          198 QADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       198 ~l~g~~i~gr~l~V~~a~~~  217 (480)
                      .++|..++|+.|++.|...+
T Consensus       184 ~vDgs~~DGr~lkatYGTTK  203 (480)
T COG5175         184 EVDGSLLDGRVLKATYGTTK  203 (480)
T ss_pred             HhccccccCceEeeecCchH
Confidence            99999999999999987654

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.14  E-value=2.1e-06  Score=83.87  Aligned_cols=82  Identities=30%  Similarity=0.586  Sum_probs=74.4

Q ss_pred             CCCEEE-EcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLF-VARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~-V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      +..++| |+||+..++.++|..+|..+|.|..+.++.+..++.++|||||.|.....+..|+.. ....|.+..|.|.+.
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            445555 999999999999999999999999999999999999999999999999999999886 788899999999988


Q ss_pred             cCCC
Q 011668          215 RGRT  218 (480)
Q Consensus       215 ~~~~  218 (480)
                      ....
T Consensus       262 ~~~~  265 (285)
T KOG4210|consen  262 EPRP  265 (285)
T ss_pred             CCCc
Confidence            7654

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.11  E-value=1.4e-06  Score=88.90  Aligned_cols=79  Identities=22%  Similarity=0.495  Sum_probs=74.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..|||+--|+..++.-+|.+||+.+|+|..|.|+.|..++.++|.|||+|.+.+.+..||. |.|..+.|.+|.|.....
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sEa  257 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSEA  257 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccHH
Confidence            5789999999999999999999999999999999999999999999999999999999996 999999999999998654

>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=98.09  E-value=1.2e-05  Score=62.21  Aligned_cols=68  Identities=19%  Similarity=0.338  Sum_probs=48.0

Q ss_pred             CEEEEcCCCCCCCHHH----HHHHhhcCC-CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          138 KTLFVARLSYETTESK----IKREFESYG-PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~----L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..|||.|||.+.....    |..++..|| .|..|.          .+-|+|.|.+++.|..|+..|+|..+-|..|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            4699999999888654    567777886 665551          2689999999999999999999999999999999


Q ss_pred             eec
Q 011668          213 VER  215 (480)
Q Consensus       213 ~a~  215 (480)
                      |..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            974

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.08  E-value=2.4e-05  Score=75.69  Aligned_cols=101  Identities=20%  Similarity=0.429  Sum_probs=76.5

Q ss_pred             hhhHHHHHHHhhcCCCCCCCCCCCCCCEEEEcCCCC----CCC-------HHHHHHHhhcCCCeeEEEecccCCCCCccc
Q 011668          112 KGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSY----ETT-------ESKIKREFESYGPIKRVRLVTDKETNKPRG  180 (480)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~----~~t-------e~~L~~~F~~~G~i~~v~i~~d~~t~~~~g  180 (480)
                      +...++...+..|.|........-..+||+|.||=.    ..+       .++|.+-..+||.|..|.|.-    ..+.|
T Consensus       240 kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdG  315 (382)
T KOG1548|consen  240 KKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDG  315 (382)
T ss_pred             HHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCc
Confidence            334455555666766664444445668899999732    223       255667789999999997753    45779


Q ss_pred             eEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          181 YAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       181 ~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .+.|.|.+.++|..||+.|+|..|+|+.|...+..+
T Consensus       316 vvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  316 VVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             eeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence            999999999999999999999999999999988654

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.08  E-value=8.7e-06  Score=74.08  Aligned_cols=65  Identities=22%  Similarity=0.342  Sum_probs=53.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      .+.||||.||.++|||++|+.+|+.|-...-++|-..   | ...+|||+|++.+.|..||..|.|..|
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~---~-g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR---G-GMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC---C-CcceEeecHHHHHHHHHHHHHhhccee
Confidence            4678999999999999999999999976655655321   2 235899999999999999999988765

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.06  E-value=2.2e-05  Score=77.42  Aligned_cols=78  Identities=24%  Similarity=0.424  Sum_probs=70.1

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          137 YKTLFVARLSY-ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       137 ~~~l~V~nL~~-~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .++|.|.||.. .+|.+-|..+|+-||.|..|+|+.++.     -.|+|.|.+...|..|+..|+|..|.|+.|+|.+++
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            57899999975 489999999999999999999998753     479999999999999999999999999999999988


Q ss_pred             CCCC
Q 011668          216 GRTV  219 (480)
Q Consensus       216 ~~~~  219 (480)
                      -..+
T Consensus       372 H~~v  375 (492)
T KOG1190|consen  372 HTNV  375 (492)
T ss_pred             Cccc
Confidence            6544

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=97.96  E-value=2.4e-05  Score=71.79  Aligned_cols=77  Identities=23%  Similarity=0.487  Sum_probs=67.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC-CeEEEEe
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD-GRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~-gr~l~V~  212 (480)
                      ..|..+||+.|||..++.+.|..+|.+|.....|.++...     .+.|||+|.+...+..|...|.|..|- ...+.|.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~  217 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQIT  217 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEec
Confidence            4577899999999999999999999999999999987643     479999999999999999999998886 7788887


Q ss_pred             eec
Q 011668          213 VER  215 (480)
Q Consensus       213 ~a~  215 (480)
                      ++.
T Consensus       218 ~a~  220 (221)
T KOG4206|consen  218 FAK  220 (221)
T ss_pred             ccC
Confidence            764

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.93  E-value=5.1e-06  Score=76.75  Aligned_cols=67  Identities=34%  Similarity=0.559  Sum_probs=60.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      .+.|+|.||+..+.+.+|..+|.++|.+....+        ..+++||+|.+.++|..||..|+|..|.++.|.|
T Consensus        99 ~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   99 HFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             cceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            467999999999999999999999999855443        2469999999999999999999999999999999

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.91  E-value=1.7e-05  Score=65.62  Aligned_cols=70  Identities=19%  Similarity=0.346  Sum_probs=44.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCC-----ceeCCeEEEEe
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADG-----RKLDGRRVLVD  212 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g-----~~i~gr~l~V~  212 (480)
                      +.|+|.||+..++.++|+++|+.||.|..|.+....      ..|||-|.+.+.|+.|+..+.-     ..|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            579999999999999999999999999999886542      3799999999999999886543     35666666665


Q ss_pred             e
Q 011668          213 V  213 (480)
Q Consensus       213 ~  213 (480)
                      +
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            4

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.81  E-value=5.7e-05  Score=76.90  Aligned_cols=69  Identities=23%  Similarity=0.326  Sum_probs=62.9

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHhh-cCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHH
Q 011668          130 PNVSGDPYKTLFVARLSYETTESKIKREFE-SYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ  198 (480)
Q Consensus       130 ~~~~~~~~~~l~V~nL~~~~te~~L~~~F~-~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~  198 (480)
                      .+..-+|.+|||||+||--++.++|..||. -||.|..+.|=+|++-+-++|-|-|+|.+..+..+||.+
T Consensus       363 ~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  363 HNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            344567889999999999999999999998 799999999999988889999999999999999999974

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.81  E-value=5.3e-05  Score=76.60  Aligned_cols=79  Identities=18%  Similarity=0.250  Sum_probs=65.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeE-EEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKR-VRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~-v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      .+..+|-+.+||+.||+++|.+||+..-.|.. |.|+.+.. +.+.|-|||.|++.+.|+.||. -|...|+.+-|.|..
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~r-gR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~  178 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQR-GRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFR  178 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCC-CCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeeh
Confidence            34568999999999999999999998755544 55666654 7788999999999999999998 466788999998876


Q ss_pred             ec
Q 011668          214 ER  215 (480)
Q Consensus       214 a~  215 (480)
                      +.
T Consensus       179 Ss  180 (510)
T KOG4211|consen  179 SS  180 (510)
T ss_pred             hH
Confidence            44

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.69  E-value=3.5e-05  Score=76.51  Aligned_cols=81  Identities=19%  Similarity=0.286  Sum_probs=62.6

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEeccc---CCC--CCc--------cceEEEEEechhhHHHHHHH
Q 011668          132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTD---KET--NKP--------RGYAFIEYMHTRDMKAAYKQ  198 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d---~~t--~~~--------~g~afV~F~~~~~a~~A~~~  198 (480)
                      ...-+.+||.+.|||.+-.-+.|.+||+.||.|+.|.|+..   +..  +.+        +-+|||+|...+.|.+|.++
T Consensus       226 ~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            33458899999999999999999999999999999999765   221  222        45799999999999999998


Q ss_pred             cCCceeCCeEEEEe
Q 011668          199 ADGRKLDGRRVLVD  212 (480)
Q Consensus       199 l~g~~i~gr~l~V~  212 (480)
                      |+.....-..|+|.
T Consensus       306 ~~~e~~wr~glkvk  319 (484)
T KOG1855|consen  306 LNPEQNWRMGLKVK  319 (484)
T ss_pred             hchhhhhhhcchhh
Confidence            86544333333333

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=97.65  E-value=0.00043  Score=61.48  Aligned_cols=63  Identities=22%  Similarity=0.334  Sum_probs=56.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG  206 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g  206 (480)
                      ...|.|.+||+..+|++|+.++.+.|.|+...+..|       |++.|+|...++++.||..|....+..
T Consensus       115 e~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  115 EYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             ceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccccC
Confidence            356999999999999999999999999999988776       589999999999999999998877643

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.63  E-value=0.00015  Score=74.28  Aligned_cols=76  Identities=26%  Similarity=0.440  Sum_probs=62.4

Q ss_pred             CCEEEEcCCCCCCCH------HHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC-CeEE
Q 011668          137 YKTLFVARLSYETTE------SKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD-GRRV  209 (480)
Q Consensus       137 ~~~l~V~nL~~~~te------~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~-gr~l  209 (480)
                      -..|+|.|+|.--..      .-|..+|+++|+|+.+.++.+..+| .+||.|++|.+..+|+.|++.|||+.|+ .+.+
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            357999999864221      3467889999999999999888755 8999999999999999999999999986 4566


Q ss_pred             EEee
Q 011668          210 LVDV  213 (480)
Q Consensus       210 ~V~~  213 (480)
                      .|..
T Consensus       137 ~v~~  140 (698)
T KOG2314|consen  137 FVRL  140 (698)
T ss_pred             Eeeh
Confidence            6654

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.60  E-value=3.4e-05  Score=72.04  Aligned_cols=73  Identities=21%  Similarity=0.444  Sum_probs=58.2

Q ss_pred             HHHHHHhh-cCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCCCCCCCCCCCCC
Q 011668          152 SKIKREFE-SYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLG  228 (480)
Q Consensus       152 ~~L~~~F~-~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~~~~~~~~~~~g  228 (480)
                      ++|...|+ +||+|..+.|..+.. -...|-+||.|...++|++|+..|||.+|.|++|.+++..   +..|..+.++
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p---vT~~rea~C~  156 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP---VTDFREAICG  156 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC---cCchhhhhhc
Confidence            34445555 899999998776643 5678999999999999999999999999999999999874   4555544443

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.58  E-value=5.4e-05  Score=70.49  Aligned_cols=72  Identities=13%  Similarity=0.327  Sum_probs=61.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCC--------CCccce----EEEEEechhhHHHHHHHcCCcee
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKET--------NKPRGY----AFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t--------~~~~g~----afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      +.+|||+|||+.+...-|++||+.||.|-.|.|.....+        |.+..+    |.|+|.+...|..+...|||..|
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPI  153 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCcc
Confidence            458999999999999999999999999999988655443        333332    56999999999999999999999


Q ss_pred             CCeE
Q 011668          205 DGRR  208 (480)
Q Consensus       205 ~gr~  208 (480)
                      +|+.
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            9875

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.49  E-value=0.0002  Score=70.87  Aligned_cols=78  Identities=17%  Similarity=0.193  Sum_probs=64.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCe-EEEEee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR-RVLVDV  213 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr-~l~V~~  213 (480)
                      +|+.+|++.|||+.+++++|..+|..-|-.+......    ++.+.+|++.|.+.++|..|+..|+++.+++. .|+|.|
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            5778999999999999999999999887554433322    33445999999999999999999999998765 899999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      ++.
T Consensus       488 Sks  490 (492)
T KOG1190|consen  488 SKS  490 (492)
T ss_pred             ecc
Confidence            874

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.36  E-value=0.00053  Score=71.96  Aligned_cols=75  Identities=20%  Similarity=0.418  Sum_probs=64.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCee-EEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIK-RVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~-~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ++|-|.|+|+.++-++|.+||.-|-.+- +|.|-.+ ..|.+.|-|.|.|++.++|..|..-|++..|..+.|.|.+
T Consensus       868 ~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  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            4788999999999999999999996543 3434333 4589999999999999999999999999999999998865

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.35  E-value=0.00045  Score=49.61  Aligned_cols=52  Identities=15%  Similarity=0.368  Sum_probs=42.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHH
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY  196 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~  196 (480)
                      +.|-|.|.++... +.|..+|..||+|..+.+..      ...+.||.|.+..+|+.||
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            4688999997765 45666999999999988862      2348999999999999985

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.33  E-value=0.0014  Score=56.85  Aligned_cols=74  Identities=24%  Similarity=0.431  Sum_probs=53.6

Q ss_pred             CCCCCEEEEcCCC------CCCCH---HHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee
Q 011668          134 GDPYKTLFVARLS------YETTE---SKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       134 ~~~~~~l~V~nL~------~~~te---~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      ++|-.||.|.=+.      ..+.+   .+|.+.|..||+|.-|+++.+        .-+|+|.+...|.+|+. |+|..|
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEE
Confidence            3455677776655      12332   367788999999988888753        56899999999999999 999999


Q ss_pred             CCeEEEEeeecC
Q 011668          205 DGRRVLVDVERG  216 (480)
Q Consensus       205 ~gr~l~V~~a~~  216 (480)
                      +|+.|+|.+..+
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            999999998654

; PDB: 1UFW_A 2DNR_A.

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.29  E-value=0.0012  Score=64.74  Aligned_cols=81  Identities=23%  Similarity=0.307  Sum_probs=71.2

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          134 GDPYKTLFVARLSYE-TTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~-~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..+.+.+.|-+|... ++-+.|-.+|..||.|..|+++..+     .|-|+|++.+..+++.||..||+..|-|..|.|.
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~  358 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVC  358 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEe
Confidence            456789999999875 5667899999999999999998754     3789999999999999999999999999999999


Q ss_pred             eecCCCC
Q 011668          213 VERGRTV  219 (480)
Q Consensus       213 ~a~~~~~  219 (480)
                      +++...+
T Consensus       359 ~SkQ~~v  365 (494)
T KOG1456|consen  359 VSKQNFV  365 (494)
T ss_pred             ecccccc
Confidence            9887544

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=97.24  E-value=0.0008  Score=69.80  Aligned_cols=63  Identities=22%  Similarity=0.426  Sum_probs=51.3

Q ss_pred             HHHHHhhcCCCeeEEEecccCC---CCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          153 KIKREFESYGPIKRVRLVTDKE---TNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       153 ~L~~~F~~~G~i~~v~i~~d~~---t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +|+..+++||.|..|.|+..-.   ..-..|-.||+|.+.++|+.|++.|+|..|.++.|++.|-.
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            3455577899999999987622   22235778999999999999999999999999999988743

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=97.19  E-value=0.00042  Score=72.69  Aligned_cols=70  Identities=19%  Similarity=0.321  Sum_probs=62.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      +.-+|||+||...+..+-+..++..||.|..|..+.         |||+.|..+..+..|+..|+-..++|..|.+...
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            445899999999999999999999999998887653         9999999999999999999999999999888764

>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=97.13  E-value=0.0022  Score=52.43  Aligned_cols=76  Identities=18%  Similarity=0.197  Sum_probs=51.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccC-------CCCCccceEEEEEechhhHHHHHHHcCCceeCCeE-E
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDK-------ETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRR-V  209 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~-------~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~-l  209 (480)
                      ..|.|-+.|+. ....|..+|++||+|.+..-+...       ..........|+|.+..+|.+||. -||..|.|.. |
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEE
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEE
Confidence            46888899987 556799999999999877411100       001123588999999999999999 7999998864 4


Q ss_pred             EEeeec
Q 011668          210 LVDVER  215 (480)
Q Consensus       210 ~V~~a~  215 (480)
                      -|.++.
T Consensus        85 GV~~~~   90 (100)
T PF05172_consen   85 GVKPCD   90 (100)
T ss_dssp             EEEE-H
T ss_pred             EEEEcH
Confidence            466653

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.

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.09  E-value=0.002  Score=63.18  Aligned_cols=77  Identities=16%  Similarity=0.226  Sum_probs=62.7

Q ss_pred             CCCEEEEcCCC--CCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC--CeEEEE
Q 011668          136 PYKTLFVARLS--YETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD--GRRVLV  211 (480)
Q Consensus       136 ~~~~l~V~nL~--~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~--gr~l~V  211 (480)
                      +.+.|.++=|.  +.+|.+-|..|...+|.|..|.|...  +|   --|.|||++.+.|++|...|||..|.  -..|+|
T Consensus       119 pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKI  193 (494)
T KOG1456|consen  119 PNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKI  193 (494)
T ss_pred             CCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeEEE
Confidence            45666665554  56899999999999999999988653  22   46999999999999999999999874  467999


Q ss_pred             eeecCC
Q 011668          212 DVERGR  217 (480)
Q Consensus       212 ~~a~~~  217 (480)
                      +||++.
T Consensus       194 eyAkP~  199 (494)
T KOG1456|consen  194 EYAKPT  199 (494)
T ss_pred             EecCcc
Confidence            999875

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.07  E-value=0.00076  Score=72.92  Aligned_cols=78  Identities=29%  Similarity=0.489  Sum_probs=67.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC--eEEE
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG--RRVL  210 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g--r~l~  210 (480)
                      ...+++.|||++|.+++....|..+|..||.|..|.+-.      ...||||.|++...++.|+..|-|..|++  +.|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h------gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH------GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc------CCcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            345678899999999999999999999999998877632      23599999999999999999999999986  5699


Q ss_pred             EeeecC
Q 011668          211 VDVERG  216 (480)
Q Consensus       211 V~~a~~  216 (480)
                      |.|+..
T Consensus       525 vdla~~  530 (975)
T KOG0112|consen  525 VDLASP  530 (975)
T ss_pred             cccccC
Confidence            999775

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.03  E-value=0.0017  Score=66.41  Aligned_cols=63  Identities=24%  Similarity=0.536  Sum_probs=47.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCC--C-CCccc---eEEEEEechhhHHHHHHHc
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKE--T-NKPRG---YAFIEYMHTRDMKAAYKQA  199 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~--t-~~~~g---~afV~F~~~~~a~~A~~~l  199 (480)
                      -.+.||||+||+.++|++|...|..||.|. |.++....  . -.++|   |+|+.|+++..+..-|.++
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            357899999999999999999999999874 55552111  1 12356   9999999998887666543

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.01  E-value=0.00064  Score=66.72  Aligned_cols=78  Identities=22%  Similarity=0.310  Sum_probs=67.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCC-CeeE--EEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          137 YKTLFVARLSYETTESKIKREFESYG-PIKR--VRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G-~i~~--v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ...|-+.+||+..+.++|..||..|- .|..  |.++.+.. |.+.|-|||+|.+.+.|.+|....+++.+..+.|.|--
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~q-GrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQ-GRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCC-CCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            45689999999999999999999886 3433  78887765 89999999999999999999999998888899998876


Q ss_pred             ec
Q 011668          214 ER  215 (480)
Q Consensus       214 a~  215 (480)
                      +.
T Consensus       359 ~S  360 (508)
T KOG1365|consen  359 CS  360 (508)
T ss_pred             cc
Confidence            54

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.94  E-value=0.0021  Score=61.09  Aligned_cols=64  Identities=22%  Similarity=0.278  Sum_probs=50.9

Q ss_pred             HHHHHHhhcCCCeeEEEecccCCCCCc-cceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          152 SKIKREFESYGPIKRVRLVTDKETNKP-RGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       152 ~~L~~~F~~~G~i~~v~i~~d~~t~~~-~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .++.+.+++||.|..|.|...+..... .--.||+|...++|.+|+..|||..|+|+.+...|-.
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            467778899999999887665432222 2347999999999999999999999999999877643

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.92  E-value=0.0006  Score=73.37  Aligned_cols=79  Identities=20%  Similarity=0.257  Sum_probs=72.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ...|||.|+|+..|.++|..+|.++|.++.+.++..+. |+++|.|||.|.++.++..++..+++..+....+.|.++.+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~-gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRA-GKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhc-cccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            35699999999999999999999999999999888765 99999999999999999999998998888888888888665

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.70  E-value=0.0023  Score=64.67  Aligned_cols=74  Identities=15%  Similarity=0.256  Sum_probs=60.0

Q ss_pred             CCEEEEcCCCCCC-CHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          137 YKTLFVARLSYET-TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       137 ~~~l~V~nL~~~~-te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+.|-|.-+++.. +-++|...|.+||+|..|.|-..      .-.|.|+|.+..+|-.|.. .++..|+++.|+|.|-.
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEec
Confidence            3455566666665 45789999999999999988554      2479999999999988877 79999999999999987


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      ..
T Consensus       445 ps  446 (526)
T KOG2135|consen  445 PS  446 (526)
T ss_pred             CC
Confidence            63

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.53  E-value=0.00079  Score=72.81  Aligned_cols=80  Identities=23%  Similarity=0.363  Sum_probs=68.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+.|||+|||...+++.+|+..|..+|.|..|.|-.-+. +.-..|+||.|.+...+..|+..|.+..|....+++-+..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            467999999999999999999999999999998865533 4445699999999999999999999998877777777764


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      +
T Consensus       450 ~  450 (975)
T KOG0112|consen  450 P  450 (975)
T ss_pred             c
Confidence            3

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.47  E-value=0.013  Score=45.56  Aligned_cols=55  Identities=20%  Similarity=0.315  Sum_probs=42.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADG  201 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g  201 (480)
                      ...||+ +|..+...+|.++|+.||.|. |.++.+       .-|||.+...+.|..|+..+.-
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhcc
Confidence            456677 999999999999999999984 555554       3799999999999999987753

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.46  E-value=0.00024  Score=76.37  Aligned_cols=68  Identities=26%  Similarity=0.436  Sum_probs=59.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD  205 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~  205 (480)
                      +++||.||++.+.+++|...|..+|.|..+.|.....++..+|+|||+|...+.+.+||....++.++
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            57999999999999999999999998888877766677999999999999999999999865555444

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.42  E-value=0.0037  Score=58.54  Aligned_cols=78  Identities=22%  Similarity=0.398  Sum_probs=62.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCC----ceeCCeEEEEee
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADG----RKLDGRRVLVDV  213 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g----~~i~gr~l~V~~  213 (480)
                      ..|||.||...++.+.|...|+.||.|....++.|-. ++..+-++|+|...-.+.+|+..++-    ..+.+..+-|.-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r-~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDR-GKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccc-ccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            6799999999999999999999999998776666643 77888999999999999999887632    234555665554


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      ...
T Consensus       111 ~eq  113 (275)
T KOG0115|consen  111 MEQ  113 (275)
T ss_pred             hhc
Confidence            443

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.25  E-value=0.0033  Score=61.31  Aligned_cols=86  Identities=17%  Similarity=0.282  Sum_probs=65.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH---HHhhcCCCeeEEEecccCC--CC-CccceEEEEEechhhHHHHHHHcCCceeCCe
Q 011668          134 GDPYKTLFVARLSYETTESKIK---REFESYGPIKRVRLVTDKE--TN-KPRGYAFIEYMHTRDMKAAYKQADGRKLDGR  207 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~---~~F~~~G~i~~v~i~~d~~--t~-~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr  207 (480)
                      .....-+||-+|+..+..+.+.   ++|.+||.|..|.+..+..  .+ ....-+||+|...++|..||..++|..++|+
T Consensus        74 vVqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~  153 (327)
T KOG2068|consen   74 VVQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGR  153 (327)
T ss_pred             hhhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhh
Confidence            3344568999999887655543   6789999999888876552  11 1122379999999999999999999999999


Q ss_pred             EEEEeeecCCCC
Q 011668          208 RVLVDVERGRTV  219 (480)
Q Consensus       208 ~l~V~~a~~~~~  219 (480)
                      .|++.+...+..
T Consensus       154 ~lka~~gttkyc  165 (327)
T KOG2068|consen  154 ALKASLGTTKYC  165 (327)
T ss_pred             hhHHhhCCCcch
Confidence            988888766543

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.03  E-value=0.005  Score=61.33  Aligned_cols=72  Identities=25%  Similarity=0.401  Sum_probs=57.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcC--CCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCc-eeCCeEEEEeee
Q 011668          138 KTLFVARLSYETTESKIKREFESY--GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGR-KLDGRRVLVDVE  214 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~--G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~-~i~gr~l~V~~a  214 (480)
                      ..|||+||.+.++..+|..+|...  |--..+ |+.       .||+||.+.+...|.+|++.|+|. .+.|+.+.|.++
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~f-l~k-------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQF-LVK-------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcce-eee-------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccch
Confidence            369999999999999999999754  111111 221       379999999999999999999996 489999999987


Q ss_pred             cCC
Q 011668          215 RGR  217 (480)
Q Consensus       215 ~~~  217 (480)
                      .++
T Consensus        74 v~k   76 (584)
T KOG2193|consen   74 VPK   76 (584)
T ss_pred             hhH
Confidence            654

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=95.90  E-value=0.0065  Score=64.10  Aligned_cols=79  Identities=19%  Similarity=0.145  Sum_probs=65.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeE-EEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKR-VRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~-v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+..|||..||..+++..+..+|...-.|+. |.|..- -++...+.|||+|..++++..|+..-+.+.++.+.|.|.-.
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            3578999999999999999999998877877 555443 35778899999999999998888877777788899999754


Q ss_pred             c
Q 011668          215 R  215 (480)
Q Consensus       215 ~  215 (480)
                      .
T Consensus       512 ~  512 (944)
T KOG4307|consen  512 A  512 (944)
T ss_pred             h
Confidence            3

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.71  E-value=0.048  Score=46.79  Aligned_cols=76  Identities=17%  Similarity=0.256  Sum_probs=57.4

Q ss_pred             CCCCCCCEEEEcCCCCCCC----HHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCe
Q 011668          132 VSGDPYKTLFVARLSYETT----ESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR  207 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~~t----e~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr  207 (480)
                      ...+|-.||.|.=|..++.    ...|...++.||+|.+|.++.       +--|.|.|.+..+|-.|+.++.. ..-|.
T Consensus        81 ~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s-~~pgt  152 (166)
T PF15023_consen   81 TKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS-RAPGT  152 (166)
T ss_pred             CCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC-CCCCc
Confidence            3455778899986665553    234566678999999998753       23799999999999999998875 56777


Q ss_pred             EEEEeeec
Q 011668          208 RVLVDVER  215 (480)
Q Consensus       208 ~l~V~~a~  215 (480)
                      .+.+.|-.
T Consensus       153 m~qCsWqq  160 (166)
T PF15023_consen  153 MFQCSWQQ  160 (166)
T ss_pred             eEEeeccc
Confidence            78887754

>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=95.62  E-value=0.025  Score=51.48  Aligned_cols=82  Identities=12%  Similarity=0.111  Sum_probs=51.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhc-CCCe---eEEE--ecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC----
Q 011668          137 YKTLFVARLSYETTESKIKREFES-YGPI---KRVR--LVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG----  206 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~-~G~i---~~v~--i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g----  206 (480)
                      ...|.|.+||+++|++++.+.+.. ++..   ..+.  +...........-|||.|.+.+++...+..++|+.|.+    
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            458999999999999999987776 6655   3333  11111111123568999999999999999999977632    


Q ss_pred             -eEEEEeeecCCC
Q 011668          207 -RRVLVDVERGRT  218 (480)
Q Consensus       207 -r~l~V~~a~~~~  218 (480)
                       ....|++|.-..
T Consensus        87 ~~~~~VE~Apyqk   99 (176)
T PF03467_consen   87 EYPAVVEFAPYQK   99 (176)
T ss_dssp             EEEEEEEE-SS--
T ss_pred             CcceeEEEcchhc
Confidence             346677775433

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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.35  E-value=0.074  Score=39.25  Aligned_cols=54  Identities=15%  Similarity=0.230  Sum_probs=44.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcC---CCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHc
Q 011668          138 KTLFVARLSYETTESKIKREFESY---GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA  199 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~---G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l  199 (480)
                      ..|+|.||. +++.++|+.+|..|   .....|.++-|.       -|=|.|.+.+.|..||.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            479999997 47778899999988   135578888774       5889999999999999765

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=95.28  E-value=0.044  Score=54.22  Aligned_cols=74  Identities=19%  Similarity=0.288  Sum_probs=56.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcC----CCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          138 KTLFVARLSYETTESKIKREFESY----GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~----G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      -.|-+.+||+++++.++.+||..-    |.+..|.++..+ .|+..|-|||.|..+++|..||.. |...|+-+.|.|--
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFR  239 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFR  239 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHH
Confidence            456778999999999999999632    234456555544 388899999999999999999984 55556666665543

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.02  E-value=0.03  Score=57.83  Aligned_cols=71  Identities=13%  Similarity=0.265  Sum_probs=55.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhc--CCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCC--ceeCCeEEEE
Q 011668          136 PYKTLFVARLSYETTESKIKREFES--YGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADG--RKLDGRRVLV  211 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~--~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g--~~i~gr~l~V  211 (480)
                      ..|.|+|.-||..+-.++|+.||..  |-.+++|.+..+-       -=||+|++..+|+.|+..|.-  .+|.|+.|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            3577899999999999999999965  7888899886542       359999999999999876643  3466666554


Q ss_pred             ee
Q 011668          212 DV  213 (480)
Q Consensus       212 ~~  213 (480)
                      .+
T Consensus       247 RI  248 (684)
T KOG2591|consen  247 RI  248 (684)
T ss_pred             hh
Confidence            43

>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=94.97  E-value=0.2  Score=41.67  Aligned_cols=69  Identities=14%  Similarity=0.230  Sum_probs=50.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCC-CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYG-PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG  206 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g  206 (480)
                      .+..+.+...|+.++-+.|..+.+.+- .|..++|+.+..  .++-.++|.|.+.+.|......+||..|+.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            344555555666666667766666654 677888887643  245578999999999999999999998753

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=94.62  E-value=0.057  Score=58.54  Aligned_cols=74  Identities=14%  Similarity=0.205  Sum_probs=63.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCce--eCCeEEEEeeec
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRK--LDGRRVLVDVER  215 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~--i~gr~l~V~~a~  215 (480)
                      .+.++.|.+-..+-..|..+|..||.|..++.+.+-      ..|.|+|...+.|..|+.+|+|..  +.|.+.+|.+|+
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak  372 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecc
Confidence            356777888888889999999999999999887764      389999999999999999999987  468889999987


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      ..
T Consensus       373 ~~  374 (1007)
T KOG4574|consen  373 TL  374 (1007)
T ss_pred             cc
Confidence            54

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.53  E-value=0.78  Score=45.92  Aligned_cols=56  Identities=16%  Similarity=0.163  Sum_probs=46.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCC-eeEEEecccCCCCCccceEEEEEechhhHHHHHHH
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGP-IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ  198 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~-i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~  198 (480)
                      -..+|-|-|+|.....++|...|+.|+. -..|.|+-+.       +||..|.+...|..||..
T Consensus       390 lpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  390 LPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTL  446 (528)
T ss_pred             ccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhc
Confidence            4578999999999999999999999973 4567777653       899999999999999883

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=94.39  E-value=0.054  Score=56.20  Aligned_cols=80  Identities=23%  Similarity=0.310  Sum_probs=62.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhc-CCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee---C-CeEEE
Q 011668          136 PYKTLFVARLSYETTESKIKREFES-YGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL---D-GRRVL  210 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~-~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i---~-gr~l~  210 (480)
                      +-+++.|.|++...|...|...-++ .|.-..+.++.|-.+..+.|||||-|.+.+++..+.+++||+.+   + .+.+.
T Consensus       387 ~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~  466 (549)
T KOG4660|consen  387 PRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIAS  466 (549)
T ss_pred             chhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeee
Confidence            4567888898888777776666543 57767788888888888899999999999999999999999864   3 45566


Q ss_pred             Eeeec
Q 011668          211 VDVER  215 (480)
Q Consensus       211 V~~a~  215 (480)
                      |.||.
T Consensus       467 itYAr  471 (549)
T KOG4660|consen  467 ITYAR  471 (549)
T ss_pred             eehhh
Confidence            66654

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=93.91  E-value=0.31  Score=37.47  Aligned_cols=59  Identities=19%  Similarity=0.329  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHHhhcCC-----CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          147 YETTESKIKREFESYG-----PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       147 ~~~te~~L~~~F~~~G-----~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ..++..+|..+|...+     .|-.|.|..        .|+||+-.. +.|..++..|++..+.|+.|.|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3578888888887764     455677754        389998865 4788999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.83  E-value=0.2  Score=48.21  Aligned_cols=67  Identities=16%  Similarity=0.172  Sum_probs=50.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEE-EEeee
Q 011668          140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV-LVDVE  214 (480)
Q Consensus       140 l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l-~V~~a  214 (480)
                      |-|-++++. .-..|..+|++||+|+.....      ..-.+-+|.|.+..+|.+||. -||..|+|-.+ -|.-+
T Consensus       200 VTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpC  267 (350)
T KOG4285|consen  200 VTVFGFPPG-QVSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPC  267 (350)
T ss_pred             EEEeccCcc-chhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeec
Confidence            555567765 346788999999999776543      223588999999999999999 69999988653 34443

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=93.80  E-value=0.067  Score=52.51  Aligned_cols=83  Identities=20%  Similarity=0.215  Sum_probs=68.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..+++||+++.+.+.+.++..+|..+|.+..+.+........+++|++|.|...+.+..||.......+.+..+...+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            46789999999999999999999999988888777766678889999999999999999999544457777777666655


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ...
T Consensus       167 ~~~  169 (285)
T KOG4210|consen  167 RRG  169 (285)
T ss_pred             ccc
Confidence            433

>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=93.75  E-value=0.23  Score=45.42  Aligned_cols=62  Identities=13%  Similarity=0.227  Sum_probs=45.6

Q ss_pred             CHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcC--CceeCCeEEEEeeecCC
Q 011668          150 TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD--GRKLDGRRVLVDVERGR  217 (480)
Q Consensus       150 te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~--g~~i~gr~l~V~~a~~~  217 (480)
                      ....|..+|..|+.+..+.++..      -+=..|.|.+.+.|..|...|+  +..|.|..|+|.|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            45789999999998888776542      2457899999999999999999  99999999999998643

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.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=93.05  E-value=0.29  Score=49.77  Aligned_cols=68  Identities=19%  Similarity=0.312  Sum_probs=57.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCC-CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYG-PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG  206 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g  206 (480)
                      .+.|+|-.+|..+|--+|..|+..|- .|..|.|+.+...  +.-.++|.|.+.++|...+..+||..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            77899999999999999999987764 7889999986432  23357899999999999999999998754

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.03  E-value=0.53  Score=49.32  Aligned_cols=80  Identities=23%  Similarity=0.383  Sum_probs=61.3

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhcC----CCeeEEEecccC----------CCCC---------------------
Q 011668          134 GDPYKTLFVARLSYE-TTESKIKREFESY----GPIKRVRLVTDK----------ETNK---------------------  177 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~-~te~~L~~~F~~~----G~i~~v~i~~d~----------~t~~---------------------  177 (480)
                      +.+++.|-|.||.|. +...+|..+|+.|    |.|.+|.|..-.          .+|.                     
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            557889999999997 6778999999877    588888764321          1122                     


Q ss_pred             ---------------c-cceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          178 ---------------P-RGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       178 ---------------~-~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                                     . .-||.|+|.+.+.|.+.+..++|..|..-.+.+.+
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DL  302 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDL  302 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeee
Confidence                           0 13789999999999999999999999766555554

>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=91.58  E-value=0.94  Score=33.96  Aligned_cols=55  Identities=18%  Similarity=0.413  Sum_probs=42.9

Q ss_pred             CCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          148 ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       148 ~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      .++-++|+..|..|+-.   .|..+.     .|| ||.|.+..+|+.|+...+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~---~I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD---RIRDDR-----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc---eEEecC-----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            46778999999999732   233333     134 89999999999999999999988887765

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2888 consensus Putative RNA binding protein [General function prediction only]

Probab=90.39  E-value=0.28  Score=47.76  Aligned_cols=10  Identities=20%  Similarity=0.441  Sum_probs=5.1

Q ss_pred             HHHHHHhhcC
Q 011668          152 SKIKREFESY  161 (480)
Q Consensus       152 ~~L~~~F~~~  161 (480)
                      .+|...|+.|
T Consensus       172 ~dLw~WyEpy  181 (453)
T KOG2888|consen  172 ADLWDWYEPY  181 (453)
T ss_pred             hHHHHHhhhh
Confidence            4455555554

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=90.23  E-value=0.16  Score=47.75  Aligned_cols=73  Identities=16%  Similarity=0.235  Sum_probs=52.2

Q ss_pred             CEEEEcCCCCCCCHHH-H--HHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          138 KTLFVARLSYETTESK-I--KREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~-L--~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ..+|++|+-..+..+- |  ...|+.+-.+...+++.+.. +...+++|+.|........+...-++..|+-..|++
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p-~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~  172 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRP-QPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRL  172 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCC-CccCcccccCcchhhhhhhhccccccccccCcceee
Confidence            4577777776666554 3  67777777777677776654 667899999999888777777767777777666444

>KOG2888 consensus Putative RNA binding protein [General function prediction only]

Probab=86.49  E-value=0.5  Score=46.04  Aligned_cols=10  Identities=10%  Similarity=0.115  Sum_probs=6.1

Q ss_pred             CHHHHHHHhh
Q 011668          150 TESKIKREFE  159 (480)
Q Consensus       150 te~~L~~~F~  159 (480)
                      .-+-|..||.
T Consensus       128 AyCLLYklft  137 (453)
T KOG2888|consen  128 AYCLLYKLFT  137 (453)
T ss_pred             HHHHHHHHHH
Confidence            4456777764

>COG5638 Uncharacterized conserved protein [Function unknown]

Probab=84.93  E-value=3.2  Score=41.78  Aligned_cols=36  Identities=25%  Similarity=0.632  Sum_probs=28.4

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhcC----CCeeEEEe
Q 011668          134 GDPYKTLFVARLSYE-TTESKIKREFESY----GPIKRVRL  169 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~-~te~~L~~~F~~~----G~i~~v~i  169 (480)
                      +.+++.|-|-||.|. +...+|..+|+.|    |.|..|.|
T Consensus       143 G~~tkrLAvVnmDWd~v~a~DLf~~fsSf~P~ggkl~kV~i  183 (622)
T COG5638         143 GNPTKRLAVVNMDWDRVDAKDLFKIFSSFLPYGGKLSKVKI  183 (622)
T ss_pred             CCcccceeEeecccccchHHHHHHHHHhhCCCCCccceeEe
Confidence            668889999999996 6778898888876    56666654

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=80.16  E-value=0.096  Score=52.53  Aligned_cols=75  Identities=15%  Similarity=0.275  Sum_probs=62.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEec-ccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLV-TDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~-~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+.|.|.|||+...|+.|..++.+||.|..|..+ .+..    ....-|+|...+.+..||..|+|..|....++|.|-.
T Consensus        80 srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e----tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen   80 SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE----TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH----HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            3568999999999999999999999999988763 2222    2345578999999999999999999999999998743

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=80.09  E-value=21  Score=39.27  Aligned_cols=61  Identities=10%  Similarity=0.071  Sum_probs=45.4

Q ss_pred             CCCCHHHHHHHhhcCCCe-----eEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          147 YETTESKIKREFESYGPI-----KRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       147 ~~~te~~L~~~F~~~G~i-----~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..++...|..++..-+.|     -.|.|..        .|.||+... ..+...+..|++..|.|+.|.|+.+..
T Consensus       497 ~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~--------~~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (629)
T PRK11634        497 DGVEVRHIVGAIANEGDISSRYIGNIKLFA--------SHSTIELPK-GMPGEVLQHFTRTRILNKPMNMQLLGD  562 (629)
T ss_pred             cCCCHHHHHHHHHhhcCCChhhCCcEEEeC--------CceEEEcCh-hhHHHHHHHhccccccCCceEEEECCC
Confidence            357778888887765544     3444532        489999864 457888888999999999999998753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	480
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		6e-45
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		6e-45
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-11
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		4e-11
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		5e-11
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		5e-11
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-10
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-09
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		4e-09
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		6e-09
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		3e-08
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-07
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		6e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		8e-07
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-06
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		1e-06
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		1e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		1e-06
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		2e-06
2cqi_A	103	Solution Structure Of The Rna Binding Domain Of Nuc		2e-06
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		2e-06
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-06
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-06
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		2e-06
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-06
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		3e-06
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		3e-06
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		3e-06
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		3e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		4e-06
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		4e-06
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		4e-06
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-06
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		5e-06
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		5e-06
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-06
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		5e-06
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		5e-06
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		5e-06
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		6e-06
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		6e-06
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		6e-06
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		7e-06
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-05
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		1e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-05
1x4h_A	111	Solution Structure Of Rrm Domain In Rna-Binding Pro		3e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		3e-05
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		4e-05
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		4e-05
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		5e-05
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		5e-05
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		6e-05
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		6e-05
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		7e-05
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		8e-05
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		9e-05
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		1e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-04
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		2e-04
2dng_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		3e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		3e-04
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		6e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		6e-04
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		7e-04

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score =  178 bits (451), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 108/213 (50%), Positives = 129/213 (60%), Gaps = 8/213 (3%)
Query: 42  LTANLLKLFEPRAPLEYKPPPEK-----RKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
           L  NLL LF PR P+ Y PP EK         P  G+A ++  F +P D   APP  +AE
Sbjct: 5   LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61
Query: 97  TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
           T  ER  R                   +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct: 62  TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121
Query: 157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
           EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct: 122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181
Query: 217 RTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGRE 249
           RTV  WRPR                N R+SGR+
Sbjct: 182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD 214

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score =  178 bits (451), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 108/213 (50%), Positives = 129/213 (60%), Gaps = 8/213 (3%)
Query: 42  LTANLLKLFEPRAPLEYKPPPEK-----RKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
           L  NLL LF PR P+ Y PP EK         P  G+A ++  F +P D   APP  +AE
Sbjct: 5   LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRD---APPPTRAE 61
Query: 97  TPVERRARIHXXXXXXXXXXXXXXXXXYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
           T  ER  R                   +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct: 62  TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121
Query: 157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
           EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct: 122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181
Query: 217 RTVPNWRPRXXXXXXXXXXXXXXXXNQRYSGRE 249
           RTV  WRPR                N R+SGR+
Sbjct: 182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD 214

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 66.2 bits (160), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 49/78 (62%)
Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           DP   L V  LS  TTE  ++  F  YGPI  V +V D+++ + RG+AF+ + +  D K 
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 195 AYKQADGRKLDGRRVLVD 212
           A ++A+G +LDGRR+ VD
Sbjct: 73  AKERANGMELDGRRIRVD 90

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 66.2 bits (160), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 49/78 (62%)
Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           DP   L V  LS  TTE  ++  F  YGPI  V +V D+++ + RG+AF+ + +  D K 
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 195 AYKQADGRKLDGRRVLVD 212
           A ++A+G +LDGRR+ VD
Sbjct: 104 AKERANGMELDGRRIRVD 121

>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 = 65.9 bits (159), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 44/75 (58%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +++FV  + YE TE ++K  F   GP+   RLV D+ET KP+GY F EY       +A +
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 198 QADGRKLDGRRVLVD 212
             +GR+  GR + VD
Sbjct: 69  NLNGREFSGRALRVD 83

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 65.9 bits (159), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 49/78 (62%)
Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           DP   L V  LS  TTE  ++  F  YGPI  V +V D+++ + RG+AF+ + +  D K 
Sbjct: 10  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 69
Query: 195 AYKQADGRKLDGRRVLVD 212
           A ++A+G +LDGRR+ VD
Sbjct: 70  AKERANGMELDGRRIRVD 87

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/77 (41%), Positives = 48/77 (62%)
Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           DP   L V  LS  TTE  ++  F  YGPI  V +V D+++ + RG+AF+ + +  D K 
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 195 AYKQADGRKLDGRRVLV 211
           A ++A+G +LDGRR+ V
Sbjct: 73  AKERANGMELDGRRIRV 89

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/82 (36%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  LS++T E  +++ F  YG I  V +V D+ET + RG+ F+ + +  D K A    
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 200 DGRKLDGRRVLVDVERGRTVPN 221
           +G+ +DGR++ VD + G++  N
Sbjct: 75  NGKSVDGRQIRVD-QAGKSSDN 95

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 41/72 (56%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  LSY ++E  +++ F +YGP+  +    D  T KP+G+AF+ +M       AY + 
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 200 DGRKLDGRRVLV 211
           DG+   GR + V
Sbjct: 71  DGQVFQGRMLHV 82

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 33/83 (39%), Positives = 49/83 (59%), Gaps = 3/83 (3%)
Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
           PN    P KTLFV  LS +TTE  +K   ES+    R R+VTD+ET   +G+ F+++   
Sbjct: 8   PNARSQPSKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSE 64
Query: 190 RDMKAAYKQADGRKLDGRRVLVD 212
            D KAA +  +  ++DG +V +D
Sbjct: 65  EDAKAAKEAMEDGEIDGNKVTLD 87

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 48/88 (54%), Gaps = 2/88 (2%)
Query: 128 NDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM 187
           + P+V G    TL V  L+Y T+   ++R FE YG +  V +  +  T  PRG+AF+ + 
Sbjct: 6   SGPDVDG--MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 188 HTRDMKAAYKQADGRKLDGRRVLVDVER 215
             RD + A    DG +LDGR + V V R
Sbjct: 64  DRRDAQDAEAAMDGAELDGRELRVQVAR 91

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 47/86 (54%), Gaps = 2/86 (2%)
Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
           P+V G    +L V  L+Y T+   ++R FE YG +  V +  D+ T + RG+AF+ +   
Sbjct: 42  PDVEG--MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 99
Query: 190 RDMKAAYKQADGRKLDGRRVLVDVER 215
           RD + A    DG  LDGR + V + R
Sbjct: 100 RDAEDAMDAMDGAVLDGRELRVQMAR 125

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 52.0 bits (123), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 41/78 (52%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL+V  LS+ TTE +I   F   G IK++ +  DK      G+ F+EY    D + A + 
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 199 ADGRKLDGRRVLVDVERG 216
            +G +LD R +  D + G
Sbjct: 101 INGTRLDDRIIRTDWDAG 118

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 51.6 bits (122), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 31/81 (38%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRD 191
           V  D    LF+  L+ ET E  +K  F  +GPI  V L+ D+ T+K RG+AFI + +  D
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPAD 60
Query: 192 MKAAYKQADGRKLDGRRVLVD 212
            K A K  +G+ L G+ + V+
Sbjct: 61  AKNAAKDMNGKSLHGKAIKVE 81

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/68 (35%), Positives = 40/68 (58%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L +  TE  ++  FE +G I+ ++L+ D ET + +GY FI +  +   K A +Q 
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 200 DGRKLDGR 207
           +G +L GR
Sbjct: 89  NGFELAGR 96

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 43/77 (55%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           +L V  L+Y T+   ++R FE YG +  V +  D+ T + RG+AF+ +   RD + A   
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 199 ADGRKLDGRRVLVDVER 215
            DG  LDGR + V + R
Sbjct: 132 MDGAVLDGRELRVQMAR 148

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/87 (34%), Positives = 46/87 (52%), Gaps = 4/87 (4%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           KTL ++ LSY  TE  ++  FE    IK    V   +  K +GYAFIE+    D K A  
Sbjct: 16  KTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEALN 71
Query: 198 QADGRKLDGRRVLVDVERGRTVPNWRP 224
             + R+++GR + ++++  R  PN  P
Sbjct: 72  SCNKREIEGRAIRLELQGPRGSPNSGP 98

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L+V  L    TE  +K+ F+  GPI  ++++ DK  NK   YAF+EY  + D   A +
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQ 59
Query: 198 QADGRKLDGRRVLVD 212
             +G++++   V ++
Sbjct: 60  TLNGKQIENNIVKIN 74

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 40/74 (54%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  +  E TE  I  +F  YG IK + L  D+ T   +GY  +EY   ++ +AA + 
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 199 ADGRKLDGRRVLVD 212
            +G+ L G+ + VD
Sbjct: 85  LNGQDLMGQPISVD 98

>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of Nucleolysin Tiar Length = 103

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/79 (37%), Positives = 45/79 (56%), Gaps = 3/79 (3%)
Query: 134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMK 193
           G P +TL+V  LS + TE  I + F   GP K  +++T+  +N P  Y F+E+   RD  
Sbjct: 13  GQP-RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAA 69
Query: 194 AAYKQADGRKLDGRRVLVD 212
           AA    +GRK+ G+ V V+
Sbjct: 70  AALAAMNGRKILGKEVKVN 88

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 40/74 (54%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  +  E TE  I  +F  YG IK + L  D+ T   +GY  +EY   ++ +AA + 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 199 ADGRKLDGRRVLVD 212
            +G+ L G+ + VD
Sbjct: 84  LNGQDLMGQPISVD 97

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/88 (30%), Positives = 40/88 (45%)
Query: 124 YDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAF 183
           Y P     V  D    LF+  L     + ++K    S+GP+K   LV D  T   +GYAF
Sbjct: 101 YVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 160
Query: 184 IEYMHTRDMKAAYKQADGRKLDGRRVLV 211
            EY+       A    +G +L  +++LV
Sbjct: 161 CEYVDINVTDQAIAGLNGMQLGDKKLLV 188

>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 = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 39/72 (54%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  + YE  E  I++ F  +GPIK + +  D  T K +G+AF+EY      + A +Q 
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 200 DGRKLDGRRVLV 211
           +   L GR + V
Sbjct: 91  NSVMLGGRNIKV 102

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 40/74 (54%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  +  E  E +I+ +F  YG IK + L  D+ T   +GYA +EY   +   AA + 
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 199 ADGRKLDGRRVLVD 212
            +G ++ G+ + VD
Sbjct: 88  LNGAEIMGQTIQVD 101

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 39/72 (54%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  + YE  E  I++ F  +GPIK + +  D  T K +G+AF+EY      + A +Q 
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 200 DGRKLDGRRVLV 211
           +   L GR + V
Sbjct: 76  NSVMLGGRNIKV 87

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 40/74 (54%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  +  E TE  I  +F  YG IK + L  D+ T   +GY  +EY   ++ +AA + 
Sbjct: 11  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 70
Query: 199 ADGRKLDGRRVLVD 212
            +G+ L G+ + VD
Sbjct: 71  LNGQDLMGQPISVD 84

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 40/74 (54%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  +  E TE  I  +F  YG IK + L  D+ T   +GY  +EY   ++ +AA + 
Sbjct: 9   ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 199 ADGRKLDGRRVLVD 212
            +G+ L G+ + VD
Sbjct: 69  LNGQDLMGQPISVD 82

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 40/74 (54%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  +  E  E +I+ +F  YG IK + L  D+ T   +GYA +EY   +   AA + 
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 199 ADGRKLDGRRVLVD 212
            +G ++ G+ + VD
Sbjct: 134 LNGAEIMGQTIQVD 147

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 40/74 (54%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  +  E TE  I  +F  YG IK + L  D+ T   +GY  +EY   ++ +AA + 
Sbjct: 9   ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 199 ADGRKLDGRRVLVD 212
            +G+ L G+ + VD
Sbjct: 69  LNGQDLMGQPISVD 82

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + ++V  L Y  T  ++K  F  +G +  V+L+ D+ET KP+G+ F+E M    +  A  
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIA 60
Query: 198 QADGRKLDGRRVLV 211
           + D     GR + V
Sbjct: 61  KLDNTDFMGRTIRV 74

>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 = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 38/72 (52%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  + YE  E  I++ F  +GPIK +    D  T K +G+AF+EY      + A +Q 
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 200 DGRKLDGRRVLV 211
           +   L GR + V
Sbjct: 75  NSVXLGGRNIKV 86

>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 = 49.3 bits (116), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 38/70 (54%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS E T   IK  F  +G I   R+V D  T K +GY F+ + +  D + A +Q 
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 200 DGRKLDGRRV 209
            G+ L GR++
Sbjct: 78  GGQWLGGRQI 87

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  LS+ETT+  ++  FE +G +    ++ D  T + RG+ F+ Y    ++ AA   A
Sbjct: 14  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 72
Query: 200 DGRKLDGRRV 209
              K+DGR V
Sbjct: 73  RPHKVDGRVV 82

>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 = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  LS+ETT+  ++  FE +G +    ++ D  T + RG+ F+ Y    ++ AA   A
Sbjct: 15  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 73
Query: 200 DGRKLDGRRV 209
              K+DGR V
Sbjct: 74  RPHKVDGRVV 83

>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 = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  LS+ETT+  ++  FE +G +    ++ D  T + RG+ F+ Y    ++ AA   A
Sbjct: 17  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 75
Query: 200 DGRKLDGRRV 209
              K+DGR V
Sbjct: 76  RPHKVDGRVV 85

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  LS+ETT+  ++  FE +G +    ++ D  T + RG+ F+ Y    ++ AA   A
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 74
Query: 200 DGRKLDGRRV 209
              K+DGR V
Sbjct: 75  RPHKVDGRVV 84

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  LS+ETT+  ++  FE +G +    ++ D  T + RG+ F+ Y    ++ AA   A
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 74
Query: 200 DGRKLDGRRV 209
              K+DGR V
Sbjct: 75  RPHKVDGRVV 84

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 36/72 (50%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  L     + ++K    S+GP+K   LV D  T   +GYAF EY+       A    
Sbjct: 99  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 200 DGRKLDGRRVLV 211
           +G +L  +++LV
Sbjct: 159 NGMQLGDKKLLV 170

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  LS+ETT+  ++  FE +G +    ++ D  T + RG+ F+ Y    ++ AA   A
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 67
Query: 200 DGRKLDGRRV 209
              K+DGR V
Sbjct: 68  RPHKVDGRVV 77

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 26/73 (35%), Positives = 40/73 (54%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  +  E TE  I  +F  YG IK + L  D+ T   +GY  +EY   ++ +AA +  
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 200 DGRKLDGRRVLVD 212
           +G+ L G+ + VD
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 36/72 (50%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  L     + ++K    S+GP+K   LV D  T   +GYAF EY+       A    
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 200 DGRKLDGRRVLV 211
           +G +L  +++LV
Sbjct: 157 NGMQLGDKKLLV 168

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/86 (29%), Positives = 44/86 (51%)
Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
           P    N   D  + L V  +     E ++++ FE YGPI+ V++V D+ET + RGY F++
Sbjct: 31  PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90
Query: 186 YMHTRDMKAAYKQADGRKLDGRRVLV 211
           +      + A    +G  +  +R+ V
Sbjct: 91  FQSGSSAQQAIAGLNGFNILNKRLKV 116

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 5/77 (6%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  L     +++++R F  YGP++ V +  +     P G+AF+E+   RD   A ++ 
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130
Query: 200 DGRKLDGRRVLVDVERG 216
           DGR L G RV V++  G
Sbjct: 131 DGRTLCGCRVRVELSNG 147

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
           +  +FV  L Y TT++ +++ FE +G I+   ++TD++T K RGY F+        + A 
Sbjct: 17  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76
Query: 197 KQADGRKLDGRRVLVDV 213
           K  +   +DGR+  V++
Sbjct: 77  KDPN-PIIDGRKANVNL 92

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  L     +++++R F  YGP++ V +  +     P G+AF+E+   RD   A +  
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRDL 130
Query: 200 DGRKLDGRRVLVDVERG 216
           DGR L G RV V++  G
Sbjct: 131 DGRTLCGCRVRVELSNG 147

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/70 (35%), Positives = 36/70 (51%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS E T   IK  F  +G I   R+V D  T K +GY F+ + +  D + A    
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 200 DGRKLDGRRV 209
            G+ L GR++
Sbjct: 78  GGQWLGGRQI 87

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 40/72 (55%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L +  TE  ++  FE +G I  + L+ D +T + +GY FI +  +   + A +Q 
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 200 DGRKLDGRRVLV 211
           +G +L GR + V
Sbjct: 68  NGFELAGRPMRV 79

>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28 Length = 111

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/86 (32%), Positives = 49/86 (56%), Gaps = 6/86 (6%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM----HTRDMK 193
           KT+F+  LS+++ E  +    + +G +K VR+V   +T   +G AF ++M      + + 
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 194 AAYKQAD--GRKLDGRRVLVDVERGR 217
           AA  +A+  G KLDGR++ VD+   R
Sbjct: 76  AASLEAEGGGLKLDGRQLKVDLAVTR 101

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/95 (30%), Positives = 45/95 (47%), Gaps = 2/95 (2%)
Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
           PN   D   T+ V  LS +T E+ ++  F  +G I R+ L  DK T + +G+AFI +   
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 190 RDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRP 224
            D   A     G   D   ++++VE  +   N  P
Sbjct: 68  EDAARAIAGVSGFGYD--HLILNVEWAKPSTNSGP 100

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 7/90 (7%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKP-----RGYAFIEYMHTRDMKA 194
           LF+  L++ TTE  +K  F   G IK   +   K+ NK       G+ F+EY      + 
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTI--SKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 195 AYKQADGRKLDGRRVLVDVERGRTVPNWRP 224
           A KQ  G  +DG ++ V +    T P   P
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERATKPASGP 95

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
           ++ LF+  LS+ETTE  ++  +E +G +    ++ D  + + RG+ F+ +    ++ AA 
Sbjct: 27  FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Query: 197 K----QADGRKLDGRRVLVDVERG 216
                  DGR ++ +R +   E G
Sbjct: 87  AARPHSIDGRVVEPKRAVAREESG 110

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           ++++V  + Y +T   ++  F S G I R+ ++ DK +  P+GYA+IE+     + AA  
Sbjct: 37  RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 198 QADGRKLDGRRVLV 211
             D     GR + V
Sbjct: 97  M-DETVFRGRTIKV 109

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/71 (28%), Positives = 40/71 (56%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T++V+ L +  T + + R F  YG + +V ++ DK+T K +G AFI ++     +   + 
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 199 ADGRKLDGRRV 209
            + ++L GR +
Sbjct: 78  INNKQLFGRVI 88

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL+V  LS+ TTE +I   F   G IK++ +  DK      G+ F+EY    D + A + 
Sbjct: 20  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYSRADAENAMRY 78
Query: 199 ADGRKLDGRRVLVDVERG 216
            +G +LD R +  D + G
Sbjct: 79  INGTRLDDRIIRTDWDAG 96

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 19/72 (26%), Positives = 40/72 (55%)
Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P + +++  + Y+ TE +I     + GP+  ++++ D +T + +GYAFIE+       +A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 196 YKQADGRKLDGR 207
            +  +G +L  R
Sbjct: 61  VRNLNGYQLGSR 72

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 19/72 (26%), Positives = 40/72 (55%)
Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P + +++  + Y+ TE +I     + GP+  ++++ D +T + +GYAFIE+       +A
Sbjct: 2   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 196 YKQADGRKLDGR 207
            +  +G +L  R
Sbjct: 62  VRNLNGYQLGSR 73

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 36/72 (50%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  L     + ++K    S+GP+K   LV D  T   +GYAF EY+       A    
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 200 DGRKLDGRRVLV 211
           +G +L  +++LV
Sbjct: 64  NGMQLGDKKLLV 75

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  L     + +++R F  YGP++ V +  +     P G+AF+E+   RD + A +  
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 200 DGRKLDGRRVLVDVERG 216
           DG+ + G RV V++  G
Sbjct: 58  DGKVICGSRVRVELSTG 74

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/72 (26%), Positives = 40/72 (55%)
Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P + +++  + Y+ TE +I     + GP+  ++++ D +T + +GYAFIE+       +A
Sbjct: 3   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 196 YKQADGRKLDGR 207
            +  +G +L  R
Sbjct: 63  VRNLNGYQLGSR 74

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 41/78 (52%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L+V  L+ E  +  +   F  +G I  +++  D ET K RG+AF+E+    D  AA  
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 198 QADGRKLDGRRVLVDVER 215
             +  +L GR + V++ +
Sbjct: 68  NMNESELFGRTIRVNLAK 85

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 40/76 (52%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L+V  L+ E  +  +   F  +G I  +++  D ET K RG+AF+E+    D  AA  
Sbjct: 64  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 198 QADGRKLDGRRVLVDV 213
             +  +L GR + V++
Sbjct: 124 NMNESELFGRTIRVNL 139

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 41/78 (52%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L+V  L+ E  +  +   F  +G I  +++  D ET K RG+AF+E+    D  AA  
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 198 QADGRKLDGRRVLVDVER 215
             +  +L GR + V++ +
Sbjct: 66  NMNESELFGRTIRVNLAK 83

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 41/78 (52%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L+V  L+ E  +  +   F  +G I  +++  D ET K RG+AF+E+    D  AA  
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 198 QADGRKLDGRRVLVDVER 215
             +  +L GR + V++ +
Sbjct: 73  NMNESELFGRTIRVNLAK 90

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/56 (37%), Positives = 32/56 (57%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMK 193
           K +FV  LS +T E KI+  F  +G ++ + L  D +TNK RG+ FI +     +K
Sbjct: 2   KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 57

>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4h Length = 103

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           +P  T +V  L + T +  I   F+    I+ VRLV DK+T+K +G+ ++E+     +K 
Sbjct: 13  EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71
Query: 195 AYKQADGRKLDGRRVLVDVERGR 217
           A    DG  L  R + VD+  GR
Sbjct: 72  ALTY-DGALLGDRSLRVDIAEGR 93

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 40/76 (52%)
Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L+V  L+ E  +  +   F  +G I  +++  D ET K RG+AF+E+    D  AA  
Sbjct: 3   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 198 QADGRKLDGRRVLVDV 213
             +  +L GR + V++
Sbjct: 63  NMNESELFGRTIRVNL 78

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/47 (38%), Positives = 27/47 (57%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           +FV  LS  TT   +K  FE +G +    L+ DK TN+ RG+ F+ +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ- 198
           +F+  L+++TTE  ++  F  YG +  ++++ D  T + RG+ F+ +     +    K  
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 199 --ADGRKLDGRRVL 210
              DG+ +D +R +
Sbjct: 66  HILDGKVIDPKRAI 79

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 20/54 (37%), Positives = 31/54 (57%)
Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMK 193
           +FV  LS +T E KI+  F  +G ++ + L  D +TNK RG+ FI +     +K
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 55

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	480
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-30
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-28
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-25
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-24
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-23
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-22
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-22
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-21
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-21
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-21
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-21
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-21
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	7e-21
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-20
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-20
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-20
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-20
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-20
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-20
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-13
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-20
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-20
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-19
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-19
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-19
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-19
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-18
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-18
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-18
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-18
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-18
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-18
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-18
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-18
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-18
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-17
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-17
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-17
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-17
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-17
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-17
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-17
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-17
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-12
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-15
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	9e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-16
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-16
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-13
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-16
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-10
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-15
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	9e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-15
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-15
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-14
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-15
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-15
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-14
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-14
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-14
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-14
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-14
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-14
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-14
2div_A	99	TRNA selenocysteine associated protein; structural	2e-14
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-14
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-14
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-14
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	6e-14
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	6e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	7e-14
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	8e-14
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-13
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-13
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-13
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-13
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-13
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-13
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-13
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	9e-13
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-12
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-12
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-12
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-12
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-12
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	9e-12
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	9e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-11
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	9e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-08
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-10
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-10
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-10
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	6e-10
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	6e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	7e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	8e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-07
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	6e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	7e-07
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	8e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	5e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	3e-05
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	4e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	8e-04

>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 =  113 bits (285), Expect = 1e-30
 Identities = 30/99 (30%), Positives = 48/99 (48%), Gaps = 4/99 (4%)

Query: 128 NDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM 187
           +  +      KTL ++ LSY  TE  ++  FE    IK    V   +  K +GYAFIE+ 
Sbjct: 6   SGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFA 61

Query: 188 HTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
              D K A    + R+++GR + ++++  R  PN  P  
Sbjct: 62  SFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100

>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 =  106 bits (267), Expect = 3e-28
 Identities = 33/101 (32%), Positives = 51/101 (50%), Gaps = 3/101 (2%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
             + PN    P KTLFV  LS +TTE  +K  F       R R+VTD+ET   +G+ F++
Sbjct: 4   GSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVD 60

Query: 186 YMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
           +    D KAA +  +  ++DG +V +D  + +      P  
Sbjct: 61  FNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101

>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 = 97.7 bits (244), Expect = 7e-25
 Identities = 32/97 (32%), Positives = 45/97 (46%)

Query: 129 DPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH 188
                 D   TL V  L+Y T+   ++R FE YG +  V +  +  T  PRG+AF+ +  
Sbjct: 5   SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64

Query: 189 TRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPR 225
            RD + A    DG +LDGR + V V R        P 
Sbjct: 65  RRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPS 101

>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 = 95.3 bits (238), Expect = 3e-24
 Identities = 32/85 (37%), Positives = 50/85 (58%)

Query: 128 NDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM 187
           +    + DP   L V  LS  TTE  ++  F  YGPI  V +V D+++ + RG+AF+ + 
Sbjct: 6   SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 65

Query: 188 HTRDMKAAYKQADGRKLDGRRVLVD 212
           +  D K A ++A+G +LDGRR+ V 
Sbjct: 66  NVDDAKEAKERANGMELDGRRIRVS 90

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 92.4 bits (230), Expect = 4e-23
 Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 6/90 (6%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYG--PIKRVRLVTDKETNKPRGYAFIEYMHTR 190
                 T+ +  ++  T    I      Y    +  +RL+ DK+T + RG+AF++     
Sbjct: 5   HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64

Query: 191 DMKAAYKQADGR----KLDGRRVLVDVERG 216
           D     +         K+DG+ + VD  + 
Sbjct: 65  DASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>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 = 92.1 bits (229), Expect = 1e-22
 Identities = 34/105 (32%), Positives = 57/105 (54%)

Query: 113 GAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTD 172
            +    +++ +   H     + DP   L V  LS  TTE  ++  F  YGPI  V +V D
Sbjct: 22  ASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD 81

Query: 173 KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           +++ + RG+AF+ + +  D K A ++A+G +LDGRR+ VD    +
Sbjct: 82  QQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 91.4 bits (227), Expect = 3e-22
 Identities = 24/89 (26%), Positives = 40/89 (44%)

Query: 124 YDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAF 183
                    S    + L+V  L+ E  +  +   F  +G I  +++  D ET K RG+AF
Sbjct: 50  SGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAF 109

Query: 184 IEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
           +E+    D  AA    +  +L GR + V+
Sbjct: 110 VEFELAEDAAAAIDNMNESELFGRTIRVN 138

>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 = 87.7 bits (218), Expect = 2e-21
 Identities = 20/75 (26%), Positives = 40/75 (53%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
            T++V+ L +  T + + R F  YG + +V ++ DK+T K +G AFI ++     +   +
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 198 QADGRKLDGRRVLVD 212
             + ++L GR +   
Sbjct: 77  AINNKQLFGRVIKAS 91

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 87.8 bits (218), Expect = 3e-21
 Identities = 21/98 (21%), Positives = 36/98 (36%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P K +  ARL+    E+ +K     YG ++ V ++    T K  G A + +  TR  K  
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64

Query: 196 YKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGT 233
            K      + G  +   ++            +  G  T
Sbjct: 65  VKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYT 102

>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 = 86.5 bits (215), Expect = 6e-21
 Identities = 31/96 (32%), Positives = 45/96 (46%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
              +++FV  + YE TE ++K  F   GP+   RLV D+ET KP+GY F EY       +
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 195 AYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGG 230
           A +  +GR+  GR + VD                G 
Sbjct: 66  AMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGA 101

>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 = 87.9 bits (218), Expect = 6e-21
 Identities = 27/117 (23%), Positives = 55/117 (47%)

Query: 114 AEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDK 173
            ++  ++ +++ P    N   D  + L V  +     E ++++ FE YGPI+ V++V D+
Sbjct: 19  LQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR 78

Query: 174 ETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGG 230
           ET + RGY F+++      + A    +G  +  +R+ V +             +G G
Sbjct: 79  ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDG 135

>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 = 86.5 bits (215), Expect = 7e-21
 Identities = 24/92 (26%), Positives = 43/92 (46%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
              + L+V  L+ E  +  +   F  +G I  +++  D ET K RG+AF+E+    D  A
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69

Query: 195 AYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
           A    +  +L GR + V++ +   +    P  
Sbjct: 70  AIDNMNESELFGRTIRVNLAKPMRIKESGPSS 101

>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 = 85.7 bits (213), Expect = 7e-21
 Identities = 23/75 (30%), Positives = 39/75 (52%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L+V  L+ E  +  +   F  +G I  +++  D ET K RG+AF+E+    D  AA  
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 198 QADGRKLDGRRVLVD 212
             +  +L GR + V+
Sbjct: 68  NMNESELFGRTIRVN 82

>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 = 86.1 bits (214), Expect = 7e-21
 Identities = 19/91 (20%), Positives = 42/91 (46%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P + +++  + Y+ TE +I     + GP+  ++++ D +T + +GYAFIE+       +A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 196 YKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
            +  +G +L  R +         +       
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISGVSLEH 91

>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 = 85.8 bits (213), Expect = 1e-20
 Identities = 29/92 (31%), Positives = 47/92 (51%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
                LFV  LS++T E  +++ F  YG I  V +V D+ET + RG+ F+ + +  D K 
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69

Query: 195 AYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
           A    +G+ +DGR++ VD     +     P  
Sbjct: 70  AMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101

>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 = 85.3 bits (212), Expect = 1e-20
 Identities = 26/80 (32%), Positives = 42/80 (52%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             LFV  LSY ++E  +++ F +YGP+  +    D  T KP+G+AF+ +M       AY 
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 198 QADGRKLDGRRVLVDVERGR 217
           + DG+   GR + V     +
Sbjct: 69  EVDGQVFQGRMLHVLPSTIK 88

>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 = 84.6 bits (210), Expect = 3e-20
 Identities = 27/91 (29%), Positives = 42/91 (46%)

Query: 128 NDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM 187
           + PN   D   T+ V  LS +T E+ ++  F  +G I R+ L  DK T + +G+AFI + 
Sbjct: 6   SGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFH 65

Query: 188 HTRDMKAAYKQADGRKLDGRRVLVDVERGRT 218
              D   A     G   D   + V+  +  T
Sbjct: 66  RREDAARAIAGVSGFGYDHLILNVEWAKPST 96

>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 = 84.1 bits (209), Expect = 3e-20
 Identities = 25/91 (27%), Positives = 42/91 (46%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
                L+V  L +  TE  ++  FE +G I  + L+ D +T + +GY FI +  +   + 
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 195 AYKQADGRKLDGRRVLVDVERGRTVPNWRPR 225
           A +Q +G +L GR + V     R      P 
Sbjct: 63  ALEQLNGFELAGRPMRVGHVTERLDGGSGPS 93

>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 = 84.2 bits (209), Expect = 4e-20
 Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 5/88 (5%)

Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
            +      +TL    LS+  TE ++K  FE    I+ V      +  K +G A+IE+   
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSE 63

Query: 190 RDMKAAYKQADGRKLDGRRVLVDVERGR 217
            D +   ++  G ++DGR V +     +
Sbjct: 64  ADAEKNLEEKQGAEIDGRSVSLYYTGEK 91

>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 = 87.0 bits (216), Expect = 5e-20
 Identities = 28/102 (27%), Positives = 43/102 (42%)

Query: 111 EKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLV 170
            +     +E    Y P     V  D    LF+  L     + ++K    S+GP+K   LV
Sbjct: 88  YQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV 147

Query: 171 TDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
            D  T   +GYAF EY+       A    +G +L  +++LV 
Sbjct: 148 KDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 189

>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 = 66.6 bits (163), Expect = 6e-13
 Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 6/84 (7%)

Query: 134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRL-----VTDKETNKPRGYAFIEYMH 188
           G   + L+V  + +  TE  +   F +   +  +       V   + N+ + +AF+E+  
Sbjct: 1   GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 189 TRDMKAAYKQADGRKLDGRRVLVD 212
             +   A    DG    G+ + + 
Sbjct: 61  VDETTQAM-AFDGIIFQGQSLKIR 83

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 83.8 bits (208), Expect = 6e-20
 Identities = 28/86 (32%), Positives = 42/86 (48%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
                LFV  +  E TE  I  +F  YG IK + L  D+ T   +GY  +EY   ++ +A
Sbjct: 21  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80

Query: 195 AYKQADGRKLDGRRVLVDVERGRTVP 220
           A +  +G+ L G+ + VD    R  P
Sbjct: 81  AMEGLNGQDLMGQPISVDWCFVRGPP 106

>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 = 83.9 bits (208), Expect = 7e-20
 Identities = 30/115 (26%), Positives = 52/115 (45%), Gaps = 10/115 (8%)

Query: 117 AAEELKKYDPHNDPNVSGDPYK-----TLFVARLSYETTESKIKREFESYGPIKRVRLVT 171
           A    ++    +D  +   P +      LFV  +  E  E +I+ +F  YG IK + L  
Sbjct: 1   AIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 60

Query: 172 DKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
           D+ T   +GYA +EY   +   AA +  +G ++ G+ + VD    +      P+R
Sbjct: 61  DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK-----GPKR 110

>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 = 82.7 bits (205), Expect = 1e-19
 Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 3/101 (2%)

Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
           P    +   T++V  L  + +E  +   F   GP+    +  D+ T + +GY F+E++  
Sbjct: 8   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67

Query: 190 RDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGG 230
            D   A K  D  KL G+ + V+        N        G
Sbjct: 68  EDADYAIKIMDMIKLYGKPIRVNKASAH---NKNLSGPSSG 105

>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 = 82.8 bits (205), Expect = 2e-19
 Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 6/89 (6%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
              KT+F+  LS+++ E  +    + +G +K VR+V   +T   +G AF ++M     + 
Sbjct: 13  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72

Query: 195 AYKQAD------GRKLDGRRVLVDVERGR 217
               A       G KLDGR++ VD+   R
Sbjct: 73  CLAAASLEAEGGGLKLDGRQLKVDLAVTR 101

>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 = 80.7 bits (200), Expect = 5e-19
 Identities = 19/80 (23%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDK-ETNKPRGYAFIEYMHTRDMKAAYK 197
            + + RL+   T+  I   F +YG IK + +  ++   +  +GYA++E+ +  + + A K
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 198 QADGRKLDGRRVLVDVERGR 217
             DG ++DG+ +        
Sbjct: 66  HMDGGQIDGQEITATAVLAP 85

>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 = 80.8 bits (200), Expect = 8e-19
 Identities = 29/106 (27%), Positives = 47/106 (44%)

Query: 113 GAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTD 172
           G              N+          L+V  L +  TE  ++  FE +G I+ ++L+ D
Sbjct: 2   GHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD 61

Query: 173 KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRT 218
            ET + +GY FI +  +   K A +Q +G +L GR + V     RT
Sbjct: 62  SETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 80.0 bits (198), Expect = 1e-18
 Identities = 20/85 (23%), Positives = 43/85 (50%), Gaps = 1/85 (1%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           +      LF++ L +  T+ +++   +++G +K +RLVT++   KP+G A++EY +    
Sbjct: 13  TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQA 71

Query: 193 KAAYKQADGRKLDGRRVLVDVERGR 217
             A  + DG  +    + V +    
Sbjct: 72  SQAVMKMDGMTIKENIIKVAISNSG 96

>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 = 79.6 bits (197), Expect = 1e-18
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           +  +T+FV  L     E  +   F   GP+ +V +  D+E  KP+ + F+ + H   +  
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSY 72

Query: 195 AYKQADGRKLDGRRVLVD 212
           A    +G +L GR + V 
Sbjct: 73  AIALLNGIRLYGRPINVS 90

>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 = 80.4 bits (199), Expect = 1e-18
 Identities = 24/105 (22%), Positives = 45/105 (42%)

Query: 113 GAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTD 172
           G+  ++ E  +  P       G+P K L++  LS   TE  +   F  +   K   +   
Sbjct: 1   GSSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFR 60

Query: 173 KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
             T + RG AFI + +      A    +G KL G+ ++++  + +
Sbjct: 61  MMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK 105

>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 = 80.1 bits (198), Expect = 2e-18
 Identities = 33/95 (34%), Positives = 51/95 (53%), Gaps = 1/95 (1%)

Query: 132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRD 191
           V  D    LF+  L+ ET E  +K  F  +GPI  V L+ D+ T+K RG+AFI + +  D
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPAD 60

Query: 192 MKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
            K A K  +G+ L G+ + V+  +  +  +   RR
Sbjct: 61  AKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRR 95

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 79.4 bits (196), Expect = 2e-18
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 9/89 (10%)

Query: 132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRD 191
           V+G P     +        +  +   F   G +  +    D+ T K +G+ F+E     D
Sbjct: 11  VNGAPV----IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMND 66

Query: 192 MKAAYKQADGRKLDGRRVLV-----DVER 215
            K   K   G++LD +  L      DVER
Sbjct: 67  AKKIIKSFHGKRLDLKHRLFLYTMKDVER 95

>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 = 77.5 bits (192), Expect = 5e-18
 Identities = 17/78 (21%), Positives = 34/78 (43%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LFV  L+    +  ++  F+ +       ++ D +T   RGY F+ +    D + A    
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 200 DGRKLDGRRVLVDVERGR 217
            G+ L+GR + ++     
Sbjct: 64  QGQDLNGRPLRINWAAKL 81

>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 = 77.6 bits (192), Expect = 6e-18
 Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           ++++V  + Y  T  +++  F   G + RV ++ DK +  P+G+A+IE+     ++ +  
Sbjct: 7   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-L 65

Query: 198 QADGRKLDGRRVLVDVERGR 217
             D     GR++ V  +R  
Sbjct: 66  ALDESLFRGRQIKVIPKRTN 85

>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 = 77.6 bits (192), Expect = 6e-18
 Identities = 16/72 (22%), Positives = 31/72 (43%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L++  L   TT+  + +  + YG I   + + DK TNK +GY F+++      + A    
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 200 DGRKLDGRRVLV 211
               +  +    
Sbjct: 68  KASGVQAQMAKQ 79

>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 = 78.5 bits (194), Expect = 7e-18
 Identities = 18/105 (17%), Positives = 52/105 (49%), Gaps = 1/105 (0%)

Query: 113 GAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTD 172
           G+  ++ +    +P ++ +      +T+F  +L+       ++  F + G ++ VR+++D
Sbjct: 1   GSSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD 60

Query: 173 KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           + + + +G A++E+   + +  A     G++L G  ++V   +  
Sbjct: 61  RNSRRSKGIAYVEFCEIQSVPLAIGL-TGQRLLGVPIIVQASQAE 104

>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 = 76.8 bits (190), Expect = 1e-17
 Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 1/89 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + ++V  L Y  T  ++K  F  +G +  V+L+ D+ET KP+G+ F+E M    +  A  
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIA 60

Query: 198 QADGRKLDGRRVLVDVERGRTVPNWRPRR 226
           + D     GR + V     +         
Sbjct: 61  KLDNTDFMGRTIRVTEANPKKSLEHHHHH 89

>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 = 77.4 bits (191), Expect = 1e-17
 Identities = 26/92 (28%), Positives = 43/92 (46%), Gaps = 1/92 (1%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
                  + + +  +FV  LS E T   IK  F  +G I   R+V D  T K +GY F+ 
Sbjct: 5   SSGQKKDTSNHFH-VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63

Query: 186 YMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           + +  D + A +Q  G+ L GR++  +    +
Sbjct: 64  FFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95

>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 = 77.0 bits (190), Expect = 2e-17
 Identities = 26/94 (27%), Positives = 39/94 (41%), Gaps = 8/94 (8%)

Query: 127 HNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIK--------RVRLVTDKETNKP 178
           H+  + S     T+FV  L    T   +   F+  G IK         + L TD+ET K 
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 179 RGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
           +G A + +      KAA    DG++  G  + V 
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 96

>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 = 78.7 bits (194), Expect = 2e-17
 Identities = 28/132 (21%), Positives = 54/132 (40%), Gaps = 5/132 (3%)

Query: 100 ERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYK-----TLFVARLSYETTESKI 154
            +  +      +    +A    ++    +D  +   P +      LFV  +  E  E +I
Sbjct: 30  AKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEI 89

Query: 155 KREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE 214
           + +F  YG IK + L  D+ T   +GYA +EY   +   AA +  +G ++ G+ + VD  
Sbjct: 90  QEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC 149

Query: 215 RGRTVPNWRPRR 226
             +     +   
Sbjct: 150 FVKGPKRVKKSE 161

>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-17
 Identities = 38/146 (26%), Positives = 55/146 (37%), Gaps = 9/146 (6%)

Query: 81  AEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTL 140
            E  D   A  V K                        E    +  H D     +   +L
Sbjct: 18  TEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV----EGMTSL 73

Query: 141 FVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD 200
            V  L+Y T+   ++R FE YG +  V +  D+ T + RG+AF+ +   RD + A    D
Sbjct: 74  KVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD 133

Query: 201 GRKLDGRRVLVDVERGRTVPNWRPRR 226
           G  LDGR + V + R       RP  
Sbjct: 134 GAVLDGRELRVQMARYG-----RPPD 154

>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 = 78.3 bits (193), Expect = 2e-17
 Identities = 30/102 (29%), Positives = 45/102 (44%)

Query: 129 DPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH 188
           +         TL+V  LS+ TTE +I   F   G IK++ +  DK      G+ F+EY  
Sbjct: 31  EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS 90

Query: 189 TRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGG 230
             D + A +  +G +LD R +  D + G        R   GG
Sbjct: 91  RADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGG 132

>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 = 76.1 bits (188), Expect = 3e-17
 Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 3/90 (3%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKP---RGYAFIEYMHTRDMKAA 195
            LF+  L++ TTE  +K  F   G IK   +   K         G+ F+EY      + A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 196 YKQADGRKLDGRRVLVDVERGRTVPNWRPR 225
            KQ  G  +DG ++ V +    T P   P 
Sbjct: 67  LKQLQGHTVDGHKLEVRISERATKPASGPS 96

>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 = 77.1 bits (190), Expect = 3e-17
 Identities = 25/107 (23%), Positives = 44/107 (41%), Gaps = 1/107 (0%)

Query: 111 EKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLV 170
                  A       P +         ++++V  + Y +T   ++  F S G I R+ ++
Sbjct: 10  HSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69

Query: 171 TDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
            DK +  P+GYA+IE+     + AA    D     GR + V  +R  
Sbjct: 70  CDKFSGHPKGYAYIEFAERNSVDAA-VAMDETVFRGRTIKVLPKRTN 115

>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 = 75.7 bits (187), Expect = 3e-17
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
            G  +  +FV  LS E T + I   F  +G I   R+V D  T K +GY F+ + +  D 
Sbjct: 3   LGSHFH-VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61

Query: 193 KAAYKQADGRKLDGRRVLVD 212
           + A +Q  G+ L GR++  +
Sbjct: 62  ENAIQQMGGQWLGGRQIRTN 81

>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 = 80.4 bits (199), Expect = 4e-17
 Identities = 26/101 (25%), Positives = 39/101 (38%), Gaps = 2/101 (1%)

Query: 114 AEKAAEELKKYDPHNDP-NVSGDPYKT-LFVARLSYETTESKIKREFESYGPIKRVRLVT 171
           AE A     +        +V   P    L VA L    T+ + +     +G ++R  LV 
Sbjct: 70  AEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129

Query: 172 DKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
            + T + +GY F EYM       A     G+ L  R + V 
Sbjct: 130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVH 170

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 64.6 bits (158), Expect = 9e-12
 Identities = 21/112 (18%), Positives = 37/112 (33%), Gaps = 13/112 (11%)

Query: 114 AEKAAEELKKYDPHN-----------DPNVSGDPYKTLFVARLSYETTES-KIKREFESY 161
           A +A  +L                      +    + L V RL     +   + R   + 
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAV 209

Query: 162 GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV 213
                 +L    +  + +G+A +EY      + A +QADG  L G  + V  
Sbjct: 210 HSPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260

>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 = 53.8 bits (130), Expect = 4e-08
 Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 9/93 (9%)

Query: 119 EELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKP 178
           EE++K   H +        + + +  L  + T  ++      Y        +     +K 
Sbjct: 6   EEIRKRLEHTERQFRN--RRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKY 56

Query: 179 RGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV 211
           +G AF+  ++    +AA       +L  R + V
Sbjct: 57  KGTAFVTLLNGEQAEAAINAFHQSRLRERELSV 89

>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 = 75.8 bits (187), Expect = 4e-17
 Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKE-TNKPRGYAFIEYMHTRD 191
                  + V  + ++  + +I+  F ++G +K VRL      T   RG+ F++++  +D
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70

Query: 192 MKAAYKQ-ADGRKLDGRRVLVD 212
            K A+        L GRR++++
Sbjct: 71  AKKAFNALCHSTHLYGRRLVLE 92

>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 = 77.7 bits (192), Expect = 4e-17
 Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
           PH+   +       LF+  L     + ++K    S+GP+K   LV D  T   +GYAF E
Sbjct: 85  PHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142

Query: 186 YMHTRDMKAAYKQADGRKLDGRRVLVD 212
           Y+       A    +G +L  +++LV 
Sbjct: 143 YVDINVTDQAIAGLNGMQLGDKKLLVQ 169

>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 = 63.4 bits (155), Expect = 4e-12
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRL-----VTDKETNKPRGYAFIEYMHTRDM 192
           + L+V  + +  TE  +   F +   +  +       V   + N+ + +AF+E+    + 
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 193 KAAYKQADGRKLDGRRVLV 211
             A    DG    G+ + +
Sbjct: 65  TQAMA-FDGIIFQGQSLKI 82

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 78.1 bits (193), Expect = 8e-17
 Identities = 24/88 (27%), Positives = 40/88 (45%)

Query: 125 DPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
                   +      ++V  + YE  E  I++ F  +GPIK + +  D  T K +G+AF+
Sbjct: 16  GSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75

Query: 185 EYMHTRDMKAAYKQADGRKLDGRRVLVD 212
           EY      + A +Q +   L GR + V 
Sbjct: 76  EYEVPEAAQLALEQMNSVMLGGRNIKVG 103

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 73.1 bits (180), Expect = 4e-15
 Identities = 25/90 (27%), Positives = 41/90 (45%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
             +  ++VA +  + ++  IK  FE++G IK   L  D  T K +GY FIEY   +  + 
Sbjct: 123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD 182

Query: 195 AYKQADGRKLDGRRVLVDVERGRTVPNWRP 224
           A    +   L G+ + V       +P   P
Sbjct: 183 AVSSMNLFDLGGQYLRVGKAVTPPMPLLTP 212

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 75.9 bits (187), Expect = 9e-17
 Identities = 31/102 (30%), Positives = 48/102 (47%), Gaps = 5/102 (4%)

Query: 125 DPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
             +  P    +   +L V  L+Y T+   ++R FE YG +  V +  D+ T + RG+AF+
Sbjct: 35  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94

Query: 185 EYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
            +   RD + A    DG  LDGR + V + R       RP  
Sbjct: 95  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG-----RPPD 131

>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 = 75.1 bits (185), Expect = 1e-16
 Identities = 30/111 (27%), Positives = 48/111 (43%)

Query: 116 KAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKET 175
           +   +  + D              LFV  +  E TE  I  +F  YG IK + L  D+ T
Sbjct: 1   REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60

Query: 176 NKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
              +GY  +EY   ++ +AA +  +G+ L G+ + VD    R  P  + R 
Sbjct: 61  GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRG 111

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 73.9 bits (182), Expect = 3e-16
 Identities = 19/100 (19%), Positives = 45/100 (45%), Gaps = 1/100 (1%)

Query: 117 AAEELK-KYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKET 175
           A+  L           + G     LF+  L  E T++ +   F  +G +   ++  DK+T
Sbjct: 19  ASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQT 78

Query: 176 NKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER 215
           +  + + F+ + +    + A K  +G ++  +R+ V +++
Sbjct: 79  SLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>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 = 73.0 bits (180), Expect = 3e-16
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P   L+V  L   T+ + + REF+ +G I+ +  V          +A+I+Y      +AA
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAA 69

Query: 196 YKQADGRKLDGRRVLVDVERGRTVP 220
             +  G  L G    + V+  ++ P
Sbjct: 70  CAKMRGFPLGGPDRRLRVDFAKSGP 94

>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 = 74.9 bits (185), Expect = 4e-16
 Identities = 21/73 (28%), Positives = 37/73 (50%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L V  L  + T+ ++   F + GPI   R++ D +T    GYAF+++    D + A K 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 199 ADGRKLDGRRVLV 211
            +G  +  +R+ V
Sbjct: 65  LNGITVRNKRLKV 77

>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 = 66.4 bits (163), Expect = 4e-13
 Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 8/102 (7%)

Query: 114 AEKAAEELKKYDPHN--------DPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIK 165
           +++A + L      N         P         L+V  L    T+ ++   F  YG I 
Sbjct: 58  SQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIV 117

Query: 166 RVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR 207
           +  ++ DK T +PRG AF+ Y    + + A    +    +G 
Sbjct: 118 QKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG 159

>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 = 73.1 bits (180), Expect = 4e-16
 Identities = 19/98 (19%), Positives = 47/98 (47%), Gaps = 2/98 (2%)

Query: 128 NDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM 187
           +  + S    K L V+ + +   +  +++ F  +G I  V ++ ++     +G+ F+ + 
Sbjct: 6   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFE 63

Query: 188 HTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPR 225
           ++ D   A ++  G  ++GR++ V+    R + N  P 
Sbjct: 64  NSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPS 101

>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 = 73.1 bits (180), Expect = 5e-16
 Identities = 21/118 (17%), Positives = 49/118 (41%), Gaps = 3/118 (2%)

Query: 113 GAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTD 172
           G+  ++   ++          G     LF+  L  E  +  + + F  +G +   ++  D
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60

Query: 173 KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGG 230
           K+TN  + + F+ Y +    +AA +  +G ++  +R+ V ++R +            G
Sbjct: 61  KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND---SKSGPSSG 115

>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 = 76.6 bits (189), Expect = 1e-15
 Identities = 20/105 (19%), Positives = 40/105 (38%)

Query: 111 EKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLV 170
             GA  A  +  K    N+  VS     TL++       T+  I+   +    +     +
Sbjct: 91  YDGALAAITKTHKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRL 150

Query: 171 TDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER 215
                N  R +A+I+     D +   ++ +G K++G  ++  V  
Sbjct: 151 PSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN 195

>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 = 63.1 bits (154), Expect = 3e-11
 Identities = 18/115 (15%), Positives = 40/115 (34%), Gaps = 9/115 (7%)

Query: 111 EKGAEKAAEELKKYDPHNDPNVSGDPYK------TLFVARLSYETTESKIKREFESYGPI 164
              +++  +E            + +         T+ V  L     ++K+ + F+  GPI
Sbjct: 9   RPDSKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPI 68

Query: 165 KRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTV 219
             V +    + N    +A IE+       AA  +   + +    ++V      T+
Sbjct: 69  IHVDVADSLKKNF--RFARIEFARYDGALAAITK-THKVVGQNEIIVSHLTECTL 120

>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 = 61.2 bits (149), Expect = 1e-10
 Identities = 20/116 (17%), Positives = 42/116 (36%), Gaps = 18/116 (15%)

Query: 114 AEKAAEEL---------------KKYDPHNDPNVSGDPYKTLFVARLSYETT-ESKIKRE 157
           A    E+L                  +     + +    + + +  LS E   E+ ++  
Sbjct: 172 ARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRES 231

Query: 158 FESYGPIKRVRLVTD-KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
           FE +G I+++ +    KE +     AF+ + +    + A  Q +   L  R + V 
Sbjct: 232 FEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA-LQMNRSLLGNREISVS 286

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 71.5 bits (176), Expect = 1e-15
 Identities = 30/103 (29%), Positives = 49/103 (47%), Gaps = 7/103 (6%)

Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
             +  +P  T +V  L + T +  I   F+    I+ VRLV DK+T+K +G+ ++E+   
Sbjct: 8   KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEV 66

Query: 190 RDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLG 232
             +K A    DG  L  R + VD+  GR     +  + G   G
Sbjct: 67  DSLKEALT-YDGALLGDRSLRVDIAEGR-----KQDKSGPSSG 103

>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 = 71.5 bits (176), Expect = 1e-15
 Identities = 15/83 (18%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
                LF+  L+   + +++K           +  V D  T   R + ++++    D++ 
Sbjct: 15  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDLEK 73

Query: 195 AYKQADGRKLDGRRVLVDVERGR 217
           A  +  G K+ G  + ++  +GR
Sbjct: 74  AL-ELTGLKVFGNEIKLEKPKGR 95

>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 = 73.4 bits (181), Expect = 1e-15
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L V  L    T+ + +  F S G I+  +LV DK T +  GY F+ Y+  +D + A   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 199 ADGRKLDGRRVLV 211
            +G +L  + + V
Sbjct: 64  LNGLRLQTKTIKV 76

>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 = 62.6 bits (153), Expect = 9e-12
 Identities = 27/105 (25%), Positives = 44/105 (41%), Gaps = 8/105 (7%)

Query: 111 EKGAEKAAEELKKYDPHN--------DPNVSGDPYKTLFVARLSYETTESKIKREFESYG 162
            K AEKA   L                P+ +      L+V+ L    T+ ++++ F  YG
Sbjct: 54  PKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYG 113

Query: 163 PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR 207
            I   R++ D+ T   RG  FI +    + + A K  +G+K  G 
Sbjct: 114 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA 158

>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 = 2e-15
 Identities = 14/89 (15%), Positives = 31/89 (34%), Gaps = 5/89 (5%)

Query: 140 LFVARLSYETTESKIKREFESYGP--IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           L++  L++ TT+  +     S G   I  ++   ++   + +G+A +        K    
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 198 QADGRKLDGRRVLVDVERGRTVPNWRPRR 226
               R+L G+  +V               
Sbjct: 64  LLPKRELHGQNPVVTPSNKL---EHHHHH 89

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 70.8 bits (174), Expect = 2e-15
 Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 5/86 (5%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           ++V  L     + +++R F  YGP++ V +  +     P G+AF+E+   RD + A +  
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 200 DGRKLDGRRVLVDVERGRTVPNWRPR 225
           DG+ + G RV V++  G    +   R
Sbjct: 58  DGKVICGSRVRVELSTGMPRRSRFDR 83

>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 = 71.2 bits (175), Expect = 2e-15
 Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 5/98 (5%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
               +  +FV  L Y TT++ +++ FE +G I+   ++TD++T K RGY F+        
Sbjct: 13  KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72

Query: 193 KAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGG 230
           + A K      +DGR+  V+          +PR L  G
Sbjct: 73  ERACK-DPNPIIDGRKANVN----LAYLGAKPRSLQTG 105

>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 = 70.8 bits (174), Expect = 3e-15
 Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 1/91 (1%)

Query: 123 KYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYA 182
            +D         +    L V+ L +  +++ I+  F  +G +K+  +  D  + +  G A
Sbjct: 15  LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTA 73

Query: 183 FIEYMHTRDMKAAYKQADGRKLDGRRVLVDV 213
            + +    D   A KQ +G  LDGR + + +
Sbjct: 74  DVHFERKADALKAMKQYNGVPLDGRPMNIQL 104

>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 = 73.9 bits (182), Expect = 3e-15
 Identities = 21/81 (25%), Positives = 39/81 (48%)

Query: 129 DPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH 188
           +P+    P  +L+V  L  + TE+ +  +F   GPI  +R+  D  T +  GYA++ +  
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 189 TRDMKAAYKQADGRKLDGRRV 209
             D + A    +   + G+ V
Sbjct: 67  PADAERALDTMNFDVIKGKPV 87

>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 = 56.5 bits (137), Expect = 2e-09
 Identities = 22/109 (20%), Positives = 43/109 (39%), Gaps = 12/109 (11%)

Query: 114 AEKAAEELKKYD----------PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGP 163
           AE+A + +                 DP++       +F+  L        +   F ++G 
Sbjct: 70  AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129

Query: 164 IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
           I   ++V D   N  +GY F+ +      + A ++ +G  L+ R+V V 
Sbjct: 130 ILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG 176

>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 = 70.4 bits (173), Expect = 3e-15
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +TL+V  LS + TE  I + F   GP K  +++T+  +N    Y F+E+   RD  AA  
Sbjct: 16  RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALA 73

Query: 198 QADGRKLDGRRVLVD 212
             +GRK+ G+ V V+
Sbjct: 74  AMNGRKILGKEVKVN 88

>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 = 5e-15
 Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 2/91 (2%)

Query: 127 HNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           H            LF+  L+   + +++K           +  V D  T   R + ++++
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDF 61

Query: 187 MHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
               D++ A +   G K+ G  + ++  +GR
Sbjct: 62  ESAEDLEKALEL-TGLKVFGNEIKLEKPKGR 91

>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 = 68.8 bits (169), Expect = 7e-14
 Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 5/87 (5%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
           P    +      +TL    LS+  TE ++K  FE    I+ V      +  K +G A+IE
Sbjct: 88  PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIE 142

Query: 186 YMHTRDMKAAYKQADGRKLDGRRVLVD 212
           +    D +   ++  G ++DGR V + 
Sbjct: 143 FKSEADAEKNLEEKQGAEIDGRSVSLY 169

>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 = 73.2 bits (179), Expect = 7e-15
 Identities = 24/159 (15%), Positives = 54/159 (33%), Gaps = 7/159 (4%)

Query: 111 EKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGP--IKRVR 168
           +       +++ K    N           L++  L++ TT+  +     S G   I  ++
Sbjct: 42  DTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIK 101

Query: 169 LVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNW-----R 223
              ++   + +G+A +        K        R+L G+  +V     + +  +     +
Sbjct: 102 FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 161

Query: 224 PRRLGGGLGTTRVGGEEVNQRYSGREQEPSRGPSRSAEP 262
             + G   G  + G    + R +  +    RG    A P
Sbjct: 162 TTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVP 200

>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 = 71.0 bits (175), Expect = 8e-15
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L+V  L    TE  +K+ F+  GPI  ++++ DK  NK   YAF+EY  + D   A +
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59

Query: 198 QADGRKLDGRRVLVD 212
             +G++++   V ++
Sbjct: 60  TLNGKQIENNIVKIN 74

>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 = 67.9 bits (167), Expect = 1e-13
 Identities = 23/110 (20%), Positives = 41/110 (37%), Gaps = 10/110 (9%)

Query: 114 AEKAAEELKKYDPHN----------DPNVSGDPYKTLFVARLSYETTESKIKREFESYGP 163
           A  A + L      N              S D    LFV  L+    +  ++  F+ +  
Sbjct: 54  ANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPS 113

Query: 164 IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV 213
                ++ D +T   RGY F+ +    D + A     G+ L+GR + ++ 
Sbjct: 114 YLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW 163

>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 = 68.8 bits (169), Expect = 1e-14
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
              K L+V  L   T+E  I++EF +  P    R+       K R YAF+ + +  D   
Sbjct: 13  SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVE 66

Query: 195 AYKQADGRKLDGRRVLVD 212
           A K  +G+ LDG  + V 
Sbjct: 67  AMKALNGKVLDGSPIEVT 84

>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 = 68.8 bits (169), Expect = 1e-14
 Identities = 22/89 (24%), Positives = 34/89 (38%), Gaps = 6/89 (6%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
               LFV  L  + TE ++++ FE YG    V +  DK      G+ FI        + A
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIA 67

Query: 196 YKQADGRKLDGRRVLVDVERGRTVPNWRP 224
             + D   L G+++ V            P
Sbjct: 68  KVELDNMPLRGKQLRVRFACHSASLTSGP 96

>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 = 74.9 bits (183), Expect = 1e-14
 Identities = 162/423 (38%), Positives = 216/423 (51%), Gaps = 8/423 (1%)

Query: 42  LTANLLKLFEPRAPLEYKPP-----PEKRKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAE 96
           L  NLL LF PR P+ Y PP      EK    P  G+A ++  F +P D    PP  +AE
Sbjct: 5   LPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDA---PPPTRAE 61

Query: 97  TPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
           T  ER  R  + ++E+  ++   ELK +DPHNDPN  GD +KTLFVAR++Y+TTESK++R
Sbjct: 62  TREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRR 121

Query: 157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG 216
           EFE YGPIKR+ +V  K + KPRGYAFIEY H RDM +AYK ADG+K+DGRRVLVDVERG
Sbjct: 122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181

Query: 217 RTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDRDRER 276
           RTV  WRPRRLGGGLG TR GG +VN R+SGR+            P    DR  DR+RER
Sbjct: 182 RTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERER 241

Query: 277 SRERGRDREREREKSLELSHDRPRDRDHRDDRHHRDRDRTRDRERERDRGRERDRDRTRD 336
                   +    +       R R R    +   R R+R++D++R+R R   R R+R R 
Sbjct: 242 RERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARR 301

Query: 337 RDRGRDRGRDHERDREKDRDKERDRDRTRERERDRDYEVGDPDRDRGYSRDRDSDYDRID 396
               ++  R    D  +  +                     P+              R +
Sbjct: 302 ERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSE 361

Query: 397 SKHERDRHGERDYDPTDQEDDRGWYDHHENYEHHRGYGDHDRYNQYHDDDNDRYDQMEED 456
            +  RDR  +RD D   +  +RG     +      G  D+      +D  +   +    D
Sbjct: 362 RERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGD 421

Query: 457 DYR 459
            Y 
Sbjct: 422 GYL 424

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 68.4 bits (168), Expect = 1e-14
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 2/89 (2%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
                  +FV  L ++ T   +K +F   G +    +  +    K +G   +++      
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVA 61

Query: 193 KAAYKQADGRKLDGRRVLVDVERGRTVPN 221
           + A +  +G KL GR + V ++R  + P+
Sbjct: 62  ERACRMMNGMKLSGREIDVRIDRNASGPS 90

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 70.3 bits (172), Expect = 1e-14
 Identities = 14/97 (14%), Positives = 40/97 (41%), Gaps = 2/97 (2%)

Query: 131 NVSGDPYKTLFVARLSYETTESKIKREFESYGP--IKRVRLVTDKETNKPRGYAFIEYMH 188
           +   +    ++V   S+ TT+ ++ +   S G   +  ++   ++   + +GYA +    
Sbjct: 49  SGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVAS 108

Query: 189 TRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPR 225
              +    +   G+ L+G +V V     + +  +  +
Sbjct: 109 ENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQ 145

>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 = 68.0 bits (167), Expect = 1e-14
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 8/92 (8%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           SG     L V  +S   T  +++ +FE YGP+    +V        + YAF+      D 
Sbjct: 6   SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDA 57

Query: 193 KAAYKQADGRKLDGRRVLVDVERGRTVPNWRP 224
             A +  D  +  G+R+ V +   R      P
Sbjct: 58  VEAIRGLDNTEFQGKRMHVQLSTSRLRTASGP 89

>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 = 69.5 bits (170), Expect = 2e-14
 Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 7/131 (5%)

Query: 89  APPVEKAETPVERRARIHKLRLEKGAEKAAEELKKYDPHNDP--NVSGDPYKTLFVARLS 146
           A   EK          +        A K     +    H+      S      ++V  L 
Sbjct: 23  AATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLG 82

Query: 147 YETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG 206
               +++++R F  YGP++ V +  +     P G+AF+E+   RD   A ++ DGR L G
Sbjct: 83  NNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCG 137

Query: 207 RRVLVDVERGR 217
            RV V++  G 
Sbjct: 138 CRVRVELSNGE 148

>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 = 68.1 bits (167), Expect = 2e-14
 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 3/89 (3%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+ ++     E  +K  FE +G I  + ++ D+ T   +G AF+ Y        A    
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75

Query: 200 DGRKL---DGRRVLVDVERGRTVPNWRPR 225
             +K      R + V      +     P 
Sbjct: 76  HEQKTLPGMNRPIQVKPADSESRGGSGPS 104

>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 = 67.7 bits (166), Expect = 2e-14
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 1/80 (1%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYG-PIKRVRLVTDKETNKPRGYAFIEYMHTRD 191
           S     +L++  L     E+ I R F + G  +  V+++ ++ T  P GY F+E+     
Sbjct: 5   SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64

Query: 192 MKAAYKQADGRKLDGRRVLV 211
            +    + +G+ L G     
Sbjct: 65  AEKCLHKINGKPLPGATPAK 84

>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 = 68.1 bits (167), Expect = 3e-14
 Identities = 28/105 (26%), Positives = 47/105 (44%), Gaps = 6/105 (5%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           +G    T+FVA L Y+    K+K  F   G + R  ++ DK+  K RG   + +  + + 
Sbjct: 11  AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEA 69

Query: 193 KAAYKQADGRKLDGRRVLVDV-----ERGRTVPNWRPRRLGGGLG 232
             A    +G+ L  R + V +      +G   P  RP++ G   G
Sbjct: 70  VQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 67.8 bits (166), Expect = 3e-14
 Identities = 27/108 (25%), Positives = 40/108 (37%), Gaps = 10/108 (9%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIK--------RVRLVTDKETNKPRGYAFIEYMHT 189
            T+FV  L    T   +   F+  G IK         + L TD+ET K +G A + +   
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 190 RDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVG 237
              KAA    DG++  G  + V     R   ++      G  G     
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRR--ADFNRGGGNGRGGLEHHH 113

>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 = 67.7 bits (166), Expect = 3e-14
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 10/92 (10%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
              K LFV  L+   TE  +++ F  +G ++RV+        K + YAFI +        
Sbjct: 9   AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVK 60

Query: 195 AYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
           A ++ +G+ L+G    +++   +     R  R
Sbjct: 61  AMEEMNGKDLEGEN--IEIVFAKPPDQKRKER 90

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 66.5 bits (163), Expect = 5e-14
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 8/80 (10%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             LF+  L  E TE +I+  FE YG +    ++        + Y F+        + A +
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIR 60

Query: 198 QADGRKLDGRRVLVDVERGR 217
                KL G  + V+  + +
Sbjct: 61  NLHHYKLHGVNINVEASKNK 80

>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 = 66.5 bits (163), Expect = 6e-14
 Identities = 18/89 (20%), Positives = 34/89 (38%), Gaps = 7/89 (7%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             L++  LS   T   +++ F          L    +     GYAF++Y        A +
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62

Query: 198 QADGR-KLDGRRVLVDVERGRTVPNWRPR 225
              G+ +L G+ + VD    + + +  P 
Sbjct: 63  TLSGKVELHGKIMEVDYSVSKKLRSSGPS 91

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 65.9 bits (161), Expect = 6e-14
 Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 142 VARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADG 201
           V     E  ++ I + F  +G I        +E  K +GY F+EY        A K ADG
Sbjct: 12  VGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNADG 69

Query: 202 RKLDGRRVL 210
            KLD +   
Sbjct: 70  YKLDKQHTF 78

>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 = 66.1 bits (162), Expect = 7e-14
 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 14/95 (14%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             +FV  +S   T  +++  FE  G +    +V        + YAF+      D KAA  
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIA 61

Query: 198 QADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLG 232
           Q +G+++ G+R+ V++           ++ G   G
Sbjct: 62  QLNGKEVKGKRINVELSTK------GQKKSGPSSG 90

>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 = 66.5 bits (163), Expect = 8e-14
 Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 3/100 (3%)

Query: 128 NDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDK-ETNKPRGYAFIEY 186
           +   +   P  T F+  L Y+ TE  IK  F     I  VRL  +     + +G+ + E+
Sbjct: 6   SGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64

Query: 187 MHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
                + +A    +   L  +R+ VDV       +  P  
Sbjct: 65  EDLDSLLSALS-LNEESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 66.3 bits (162), Expect = 1e-13
 Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 8/96 (8%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKR--------VRLVTDKETNKPRGYAFIEYMHTR 190
            ++V  L+   T   +   F+  G +K         + +  DKET KP+G A + Y    
Sbjct: 17  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76

Query: 191 DMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
             KAA +  DG+   G ++ V + R +   N  P  
Sbjct: 77  TAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112

>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 = 67.9 bits (167), Expect = 1e-13
 Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 1/83 (1%)

Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
           P    D    +FV  +  +    + +  F  +G I   +L+ DK+T + RG+ F+ Y   
Sbjct: 80  PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA 139

Query: 190 RDMKAAYKQADGRKLDGRRVLVD 212
             +    +         R++ + 
Sbjct: 140 DAVDRVCQN-KFIDFKDRKIEIK 161

>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 = 67.2 bits (165), Expect = 2e-13
 Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             +F+  L+++TTE  ++  F  YG +  ++++ D  T + RG+ F+ +     +     
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV-- 61

Query: 198 QADGRKLDGRRV 209
                 LDG+ +
Sbjct: 62  VKTQHILDGKVI 73

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 66.2 bits (162), Expect = 2e-13
 Identities = 21/115 (18%), Positives = 44/115 (38%), Gaps = 1/115 (0%)

Query: 111 EKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLV 170
           + G +    +   +D         +    L V+ L +  +++ I+  F  +G +K+  + 
Sbjct: 9   QMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVD 68

Query: 171 TDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPR 225
            D  + +  G A + +    D   A KQ  G  LDGR + + +   +        
Sbjct: 69  YD-RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 122

>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 = 2e-13
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 7/85 (8%)

Query: 126 PHNDPNVSGDPYKT-LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
             +    S  P  T  ++  + +  TE+ +   F+++G I   +   +K      G  FI
Sbjct: 15  AVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFI 68

Query: 185 EYMHTRDMKAAYKQADGRKLDGRRV 209
           +Y                   GR +
Sbjct: 69  KYDTHEQAAVCIVALANFPFQGRNL 93

>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 = 68.1 bits (167), Expect = 2e-13
 Identities = 31/103 (30%), Positives = 49/103 (47%), Gaps = 7/103 (6%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + LF+  LS+ETT+  ++  FE +G +    ++ D  T + RG+ F+ Y    ++ AA  
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73

Query: 198 QADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTR--VGG 238
                K+DGR V       R V     +R G  L   +  VGG
Sbjct: 74  A-RPHKVDGRVVEPK----RAVSREDSQRPGAHLTVKKIFVGG 111

>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 = 66.2 bits (162), Expect = 7e-13
 Identities = 23/103 (22%), Positives = 43/103 (41%), Gaps = 6/103 (5%)

Query: 128 NDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM 187
           +    +    K +FV  +  +T E  ++  FE YG I+ + ++TD+ + K RG+AF+ + 
Sbjct: 95  SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154

Query: 188 HTRDMKAAYKQADGRKLDGRRVLVDV-----ERGRTVPNWRPR 225
               +     Q     ++G    V       E      + R R
Sbjct: 155 DHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMASASSSQRGR 196

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 65.5 bits (160), Expect = 2e-13
 Identities = 22/80 (27%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 141 FVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD 200
            V     E  ++ I + F  +G I        +E  K +GY F+EY        A K AD
Sbjct: 25  QVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNAD 82

Query: 201 GRKLDGRRVLV-----DVER 215
           G KLD +         D ++
Sbjct: 83  GYKLDKQHTFRVNLFTDFDK 102

>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 = 65.3 bits (160), Expect = 2e-13
 Identities = 24/96 (25%), Positives = 39/96 (40%), Gaps = 3/96 (3%)

Query: 123 KYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKET-NKPRGY 181
            +  H+   +   P  T F+  L Y+ TE  IK  F     I  VRL  +     + +G+
Sbjct: 5   HHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 63

Query: 182 AFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
            + E+     + +A    +   L  RR+ VDV    
Sbjct: 64  GYAEFEDLDSLLSALS-LNEESLGNRRIRVDVADQA 98

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 64.4 bits (158), Expect = 2e-13
 Identities = 16/70 (22%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +F+  LS++TT+  ++  F  +G +K   ++ D  T + RG+ F+ +M    +       
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 61

Query: 200 DGRKLDGRRV 209
              +LD + +
Sbjct: 62  SRHELDSKTI 71

>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 = 65.4 bits (160), Expect = 3e-13
 Identities = 23/98 (23%), Positives = 45/98 (45%), Gaps = 1/98 (1%)

Query: 112 KGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVT 171
                  E+  +  P        + ++ LF+  LS+ETTE  ++  +E +G +    ++ 
Sbjct: 2   SSGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMR 61

Query: 172 DKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV 209
           D  + + RG+ F+ +    ++ AA   A    +DGR V
Sbjct: 62  DPASKRSRGFGFVTFSSMAEVDAA-MAARPHSIDGRVV 98

>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 = 64.1 bits (157), Expect = 3e-13
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS +T E KI+  F  +G ++ + L  D +TNK RG+ FI +     +K   ++ 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 200 DGRKLDGRRV 209
               +   + 
Sbjct: 61  KYHNVGLSKC 70

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 65.0 bits (159), Expect = 3e-13
 Identities = 18/109 (16%), Positives = 47/109 (43%), Gaps = 4/109 (3%)

Query: 109 RLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVR 168
                   ++  + +    N  N      K L V+ + +   +  +++ F  +G I  V 
Sbjct: 3   SSHHHHHHSSGLVPRGSHMNTEN--KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE 60

Query: 169 LVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           ++ ++     +G+ F+ + ++ D   A ++  G  ++GR++ V+    R
Sbjct: 61  IIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>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 = 64.2 bits (157), Expect = 3e-13
 Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 14/86 (16%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
              D  +      TL+V  L    TE+ ++  F  +G I+ + +V  +        AFI+
Sbjct: 6   SGEDKTI-----TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQ 54

Query: 186 YMHTRDM--KAAYKQADGRKLDGRRV 209
           +  TR     AA K  +   ++GRR+
Sbjct: 55  FA-TRQAAEVAAEKSFNKLIVNGRRL 79

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 63.6 bits (156), Expect = 3e-13
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS  TT   +K  FE +G +    L+ DK TN+ RG+ F+ +     ++   +  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60

Query: 200 DGRKLDGRRVLVD 212
              +++ + V   
Sbjct: 61  HFHEINNKMVECK 73

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 65.0 bits (159), Expect = 3e-13
 Identities = 17/109 (15%), Positives = 38/109 (34%), Gaps = 8/109 (7%)

Query: 109 RLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVR 168
                   ++  + +    +           LFV     +  ES++   F  +GP+K V+
Sbjct: 3   SSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK 62

Query: 169 LVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           +          G+AF+E+        A ++  G+    + + V   +  
Sbjct: 63  I--------LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP 103

>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 = 64.7 bits (158), Expect = 4e-13
 Identities = 18/97 (18%), Positives = 41/97 (42%), Gaps = 6/97 (6%)

Query: 113 GAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTD 172
           G+  ++   K+    +  N S     T++   ++   T+  +++ F  +G I  +R+  +
Sbjct: 1   GSSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

Query: 173 KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV 209
           K      GY+F+ +        A    +G  ++G  V
Sbjct: 61  K------GYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91

>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 = 64.1 bits (157), Expect = 4e-13
 Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           SG     +FV  + +   E++++  F+ +G +  V ++ D E  +PRG+ FI +   + +
Sbjct: 6   SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSV 65

Query: 193 KAAYKQADGRKLDGRRVLVD 212
             A        + G++V V 
Sbjct: 66  DQAVNM-HFHDIMGKKVEVK 84

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 64.7 bits (158), Expect = 4e-13
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           +  + L++  L Y+ T  ++   F  YGPI+++R+     T + RG A++ Y    D K 
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKN 62

Query: 195 AYKQADGRKLDGRRVLVD 212
           A     G  +  R ++V 
Sbjct: 63  AVDHLSGFNVSNRYLVVL 80

>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 = 64.6 bits (158), Expect = 4e-13
 Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 3/94 (3%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           +G+    ++V  L  +     I+  F  YG I+ + L   K       +AF+E+   RD 
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDA 74

Query: 193 KAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRR 226
           + A    DG   DG R+ V+  R        P  
Sbjct: 75  EDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSS 108

>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 = 63.8 bits (156), Expect = 5e-13
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRV-RLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
            +F+  L  E  E  +   F ++G I +  +++ D +T   +GYAFI +       AA +
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 198 QADGRKLDGRRVLVD 212
             +G+ L  R + V 
Sbjct: 67  AMNGQYLCNRPITVS 81

>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 = 63.7 bits (155), Expect = 9e-13
 Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 139 TLFVARLSYETTESKIKREFESYGP-IKRVRLVTD-KETNKPRGYAFIEYMHTRDMKAAY 196
            LF+  +       +I  E       +  V +     +  K RG+AF+EY   R    A 
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 197 K--QADGRKLDGRRVLVD 212
           +       +L G ++ VD
Sbjct: 70  RKLMPGRIQLWGHQIAVD 87

>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 = 62.2 bits (152), Expect = 2e-12
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 128 NDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM 187
           +    +      L V  L ++TTE  +K  F ++G +  V++  D +T   +G+ F+ + 
Sbjct: 6   SGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65

Query: 188 HTRDMKAAYKQADGRKLDGRRV 209
                      +    +DGR  
Sbjct: 66  EYETQVKV--MSQRHMIDGRWC 85

>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 = 61.8 bits (151), Expect = 2e-12
 Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 129 DPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH 188
           + + + +    +FV  LS++T++  +K  F  +G +    +  D  T + RG+ FI +  
Sbjct: 3   NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62

Query: 189 TRDMKAAYKQADGRKLDGRRV 209
              ++    Q +  +LDGR +
Sbjct: 63  AASVEKVLDQKE-HRLDGRVI 82

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 125 DPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
                 N   D    LFV  L + TT+  ++  F  YG +    ++ DK TN+ RG+ F+
Sbjct: 4   GSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63

Query: 185 EYMHTRDMKAAYKQADGRKLDGRRV 209
           ++     +      +    LDGR +
Sbjct: 64  KFKDPNCVGTV-LASRPHTLDGRNI 87

>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 = 62.3 bits (152), Expect = 3e-12
 Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 3/91 (3%)

Query: 122 KKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGY 181
               P      S    K +F+  LS++TT+  ++  F  +G +K   ++ D  T + RG+
Sbjct: 12  SGLVPRGSHMGS-SGCK-MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGF 69

Query: 182 AFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
            F+ +M    +          +LD + +   
Sbjct: 70  GFVTFMDQAGVDKV-LAQSRHELDSKTIDPK 99

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 62.3 bits (151), Expect = 3e-12
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 14/118 (11%)

Query: 113 GAEKAAEELKKYDPHNDPNVSGDPYKTLFVAR--LSYETTESKIKREFESYGPIKRVRLV 170
           G+  A   L +   H          ++L VA   L    + +++    E  G +  + + 
Sbjct: 4   GSSGAKHTLLR---HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP 60

Query: 171 TDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL---DGRRVLVDVERGRTVPNWRPR 225
            +K       Y+F  Y  T + K AY   +G+++    G+++ + +     V    P 
Sbjct: 61  PNK------PYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWSGPS 112

>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 = 61.6 bits (150), Expect = 4e-12
 Identities = 17/87 (19%), Positives = 32/87 (36%), Gaps = 1/87 (1%)

Query: 126 PHNDPNVSGDPYK-TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
             +  + SG P    + V  + +  +  +I   F  Y  I     +   E   P G A +
Sbjct: 3   SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 185 EYMHTRDMKAAYKQADGRKLDGRRVLV 211
            +    +  AA    + R +  R+V +
Sbjct: 63  AFESRDEATAAVIDLNDRPIGSRKVKL 89

>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 = 60.7 bits (148), Expect = 9e-12
 Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 4/91 (4%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA-- 195
            T+FV  +     E++I+  F  YG +K V+++TD+ T   +GY F+ + +  D++    
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68

Query: 196 -YKQADGRKLDGRRVLVDVERGRTVPNWRPR 225
                 G+KL     +            RP 
Sbjct: 69  SQINFHGKKLKLGPAIRKQNLSTYHVQPRPL 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 = 61.8 bits (150), Expect = 9e-12
 Identities = 25/134 (18%), Positives = 52/134 (38%), Gaps = 12/134 (8%)

Query: 89  APPVEKAETPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYE 148
               ++  +    R  + K R+ +   +     + Y+P       G+P   ++V  L+  
Sbjct: 4   GSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEP-------GEPNCRIYVKNLAKH 56

Query: 149 TTESKIKREFESYGPI-----KRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRK 203
             E  +K  F  Y        + +  +   +  + +G AFI   + +    A K+A+G  
Sbjct: 57  VQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYV 116

Query: 204 LDGRRVLVDVERGR 217
           L G+ ++V   R  
Sbjct: 117 LFGKPMVVQFARSA 130

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 62.6 bits (153), Expect = 1e-11
 Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKP--RGYAFIEYMHTRDMKAAY 196
            +FV ++    +E  ++  FE YG +  + ++ D+  N P  +G  F+ +   +    A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 197 KQADGRKLDGRRVLV 211
                 K+       
Sbjct: 65  NALHNMKVLPGMHHP 79

>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 = 53.4 bits (129), Expect = 1e-08
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 13/88 (14%)

Query: 111 EKGAEKAAEEL------------KKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREF 158
            K A +A   L             +  P +    +    + LF+  +S + TE+ I+  F
Sbjct: 57  RKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMF 116

Query: 159 ESYGPIKRVRLVTDKETNKPRGYAFIEY 186
            S+G I+  R++        RG AF+ +
Sbjct: 117 SSFGQIEECRILRGP-DGLSRGCAFVTF 143

>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 = 60.0 bits (146), Expect = 1e-11
 Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 1/88 (1%)

Query: 126 PHNDPNVSGDPYKT-LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
             +    SG P  T + V  + +  +  +I   F  Y  I     +   E   P G A +
Sbjct: 3   SGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 185 EYMHTRDMKAAYKQADGRKLDGRRVLVD 212
            +    +  AA    + R +  R+V + 
Sbjct: 63  AFESRDEATAAVIDLNDRPIGSRKVKLV 90

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 61.8 bits (150), Expect = 2e-11
 Identities = 20/105 (19%), Positives = 40/105 (38%), Gaps = 1/105 (0%)

Query: 109 RLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVR 168
                      +   +D         +    L V+ L +  +++ I+  F  +G +K+  
Sbjct: 60  YSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA 119

Query: 169 LVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV 213
           +  D  + +  G A + +    D   A KQ  G  LDGR + + +
Sbjct: 120 VDYD-RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 163

>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 = 60.0 bits (146), Expect = 2e-11
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 5/92 (5%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             +F+  L        +   F ++G I   ++V D   N  +GY F+ +      + A +
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIE 63

Query: 198 QADGRKLDGRRVLVDVERGRTVPNWRPRRLGG 229
           + +G  L+ R+V V   + R     R   LG 
Sbjct: 64  KMNGMLLNDRKVFVGRFKSRKE---REAELGA 92

>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 = 59.7 bits (145), Expect = 2e-11
 Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 14/95 (14%)

Query: 139 TLFVARLSYE-TTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
            +F+  L+     +S ++  F  YG +    +         +GYAF++Y + R  +AA  
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80

Query: 198 QADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLG 232
             +GR L G+ + +++         +P R G   G
Sbjct: 81  GENGRVLAGQTLDINMAGEP-----KPDRSGPSSG 110

>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 = 59.6 bits (145), Expect = 3e-11
 Identities = 13/107 (12%), Positives = 33/107 (30%), Gaps = 1/107 (0%)

Query: 113 GAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTD 172
           G+  ++                     L+++ L     E +++   + +G +   R++ D
Sbjct: 1   GSSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD 60

Query: 173 KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTV 219
             +   RG  F     T   +A     +G+ +     +         
Sbjct: 61  -SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLC 106

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 16/94 (17%), Positives = 39/94 (41%), Gaps = 9/94 (9%)

Query: 136 PYKTLFVARLSYET-TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           P   LF+  L  +  ++  + R F  YG I ++ +           + FI++ + + ++ 
Sbjct: 9   PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRD 60

Query: 195 AYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLG 228
           A +        G++++++V      P +     G
Sbjct: 61  AIECESQEMNFGKKLILEVSSSNARPQFDHGDHG 94

>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 = 57.6 bits (140), Expect = 9e-11
 Identities = 14/91 (15%), Positives = 39/91 (42%), Gaps = 5/91 (5%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L+V  L     + ++++ F  +G I   +++ +    + +G+ F+ +    +   A  + 
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 200 DGRKLDGRRVLVDVERGRTVPNWRPRRLGGG 230
           +GR +  + + V + + +     R      G
Sbjct: 76  NGRIVATKPLYVALAQRKEE---RQSGPSSG 103

>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 = 57.5 bits (139), Expect = 1e-10
 Identities = 11/90 (12%), Positives = 27/90 (30%), Gaps = 8/90 (8%)

Query: 125 DPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
              +  +        + V  L     E+ +    E +G I  V +         +  A +
Sbjct: 3   SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALV 56

Query: 185 EYMHTRDMKAA--YKQADGRKLDGRRVLVD 212
           E+ +    K    +       + G++   +
Sbjct: 57  EFENIDSAKECVTFAADVPVYIAGQQAFFN 86

>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 = 60.4 bits (146), Expect = 1e-10
 Identities = 26/127 (20%), Positives = 52/127 (40%), Gaps = 8/127 (6%)

Query: 130 PNVSGDPYKTLFVARLSYET-TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH 188
           P ++G     L V+ L+ E  T   +   F  YG ++RV+++ +K     +  A ++   
Sbjct: 27  PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMAD 81

Query: 189 TRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGR 248
               + A    +G KL G+ + + + + + V    PR      G T+  G     R+   
Sbjct: 82  GNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQL--PREGQEDQGLTKDYGNSPLHRFKKP 139

Query: 249 EQEPSRG 255
             +  + 
Sbjct: 140 GSKNFQN 146

>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 = 5e-08
 Identities = 23/128 (17%), Positives = 39/128 (30%), Gaps = 5/128 (3%)

Query: 83  PGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFV 142
            G P+     +     + R  +  +   +          KK    N  N+   P  TL +
Sbjct: 98  HGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP-PSATLHL 156

Query: 143 ARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGR 202
           + +    +E  +K  F S G + +      K   K R  A I+     +   A       
Sbjct: 157 SNIPPSVSEEDLKVLFSSNGGVVKGF----KFFQKDRKMALIQMGSVEEAVQALIDLHNH 212

Query: 203 KLDGRRVL 210
            L     L
Sbjct: 213 DLGENHHL 220

>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 = 57.2 bits (139), Expect = 1e-10
 Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 7/84 (8%)

Query: 133 SGDPYKTLFVARLSYETTESKIKRE----FESYGPIKRVRLVTDKETNKPRGYAFIEYMH 188
              P  T+++  L+ +  + ++K+     F  +G I  + +     + K RG AF+ +  
Sbjct: 4   ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKE 60

Query: 189 TRDMKAAYKQADGRKLDGRRVLVD 212
                 A +   G     + + + 
Sbjct: 61  VSSATNALRSMQGFPFYDKPMRIQ 84

>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 = 59.7 bits (144), Expect = 2e-10
 Identities = 11/116 (9%), Positives = 24/116 (20%)

Query: 97  TPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKR 156
            P +           K   ++             N    P   L       E TE     
Sbjct: 83  MPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFE 142

Query: 157 EFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
             +  G  +   +      ++      +E+    D        +  ++        
Sbjct: 143 ICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 198

>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 = 58.2 bits (140), Expect = 6e-10
 Identities = 24/127 (18%), Positives = 44/127 (34%), Gaps = 6/127 (4%)

Query: 134 GDPYKTLFVARLSYE-TTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           G     L V  L        ++   F  YG +++V+ +  K      G A +E      +
Sbjct: 1   GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAV 55

Query: 193 KAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGREQEP 252
             A    +   + G+++ V V +   +   +   L  G  + +   E  N R+S  EQ  
Sbjct: 56  DRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAA 115

Query: 253 SRGPSRS 259
                  
Sbjct: 116 KNRIQHP 122

>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 = 57.1 bits (138), Expect = 2e-10
 Identities = 12/75 (16%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             +    L   T  ++I+  F  +G + RV L       +    A +E++   + + A++
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFR 64

Query: 198 QADGRKLDGRRVLVD 212
                K     + ++
Sbjct: 65  HLAYSKFHHVPLYLE 79

>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 = 56.2 bits (136), Expect = 2e-10
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           SG    T+ +    +  TE  +        P   +R+V +       GY F+++ +  ++
Sbjct: 6   SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKP-VAIRIVRNAH-GNKTGYIFVDFSNEEEV 63

Query: 193 KAAYKQADGRKLDGRRVLV 211
           K A  + +   + GR + V
Sbjct: 64  KQA-LKCNREYMGGRYIEV 81

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 57.2 bits (138), Expect = 2e-10
 Identities = 15/109 (13%), Positives = 41/109 (37%), Gaps = 8/109 (7%)

Query: 108 LRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKRE----FESYGP 163
           ++    A+   + +   D  + P    +P + + +  ++ E  + K++        S G 
Sbjct: 1   MKETAAAKFERQHMDSPDLGSTPP-HTEPSQVVLITNINPEVPKEKLQALLYALASSQGD 59

Query: 164 IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
           I  + +     ++   G A+I +      +A  +   G    G  +++ 
Sbjct: 60  ILDIVV---DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT 105

>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 = 56.2 bits (136), Expect = 3e-10
 Identities = 14/100 (14%), Positives = 39/100 (39%), Gaps = 12/100 (12%)

Query: 122 KKYDPHNDPNVSGDPYKT---LFVARLSYET-TESKIKREFESYGPIKRVRLVTDKETNK 177
             +  H+   +          LF+  L  +  ++  + R F  YG I ++ +        
Sbjct: 4   SHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------- 56

Query: 178 PRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
              + FI++ + + ++ A +        G++++++V    
Sbjct: 57  -NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN 95

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 56.0 bits (135), Expect = 3e-10
 Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 5/93 (5%)

Query: 125 DPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
            P + P         ++V  L  +   S +KR     G +  +RL        PR  AF+
Sbjct: 7   GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFL 61

Query: 185 EYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
            Y  +   + A     G +L    + V + R +
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 55.9 bits (135), Expect = 4e-10
 Identities = 9/75 (12%), Positives = 22/75 (29%), Gaps = 3/75 (4%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L +  +        +      YG ++    V             + Y      + A  
Sbjct: 16  RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALD 72

Query: 198 QADGRKLDGRRVLVD 212
           + +G +L+   + V 
Sbjct: 73  KLNGFQLENFTLKVA 87

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 55.4 bits (134), Expect = 4e-10
 Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +++FV+        +++   F ++GP+  V  V DK+      +A +E       +A   
Sbjct: 9   RSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS 63

Query: 198 QADGRKLDGRRVLVDVERGRTVPNWRPRRLGG 229
           Q     L G R+ V     +   +   +   G
Sbjct: 64  Q-SQHSLGGHRLRVRPREQKEFQSPASKSPKG 94

>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 = 55.9 bits (135), Expect = 5e-10
 Identities = 11/86 (12%), Positives = 30/86 (34%), Gaps = 1/86 (1%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
             +             +  + +  T+  + +  E     +    V      +  G A ++
Sbjct: 4   GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQ 63

Query: 186 YMHTRDMKAAYKQADGRKLDGRRVLV 211
           + +  D + + ++   +KL+GR   V
Sbjct: 64  FKNEDDARKS-ERLHRKKLNGREAFV 88

>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 = 56.0 bits (135), Expect = 5e-10
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 139 TLFVARLSYETTESKIKRE---FESYGPIKRVRLVTDKETNK---PRGYAFIEYMHTRDM 192
            +FV  LS    + ++ +    F  +G I +V +           P   A++ Y+ + D 
Sbjct: 17  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76

Query: 193 KAAYKQADGRKLDGRRVLVD 212
             A +  +   +DGR +   
Sbjct: 77  LRAIQCVNNVVVDGRTLKAS 96

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 55.5 bits (134), Expect = 6e-10
 Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 13/90 (14%)

Query: 125 DPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
           DPH  P         + +  L     E+ +    + +GPI  V ++        +  A +
Sbjct: 14  DPHKTP-----ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALV 62

Query: 185 EYMHTRDMKAA--YKQADGRKLDGRRVLVD 212
           E+        A  Y   +   + G    V+
Sbjct: 63  EFEDVLGACNAVNYAADNQIYIAGHPAFVN 92

>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 = 54.6 bits (132), Expect = 1e-09
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
             +     G   + LFV  L+ + +E  + R F+ +G I    ++        +G AF++
Sbjct: 4   GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVK 62

Query: 186 YMHTRDMKAAYKQADGRKL 204
           +    + +AA     G + 
Sbjct: 63  FSSHTEAQAAIHALHGSQT 81

>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 = 56.4 bits (136), Expect = 2e-09
 Identities = 24/121 (19%), Positives = 48/121 (39%), Gaps = 8/121 (6%)

Query: 138 KTLFVARLSYET-TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
             L V+ L+ E  T   +   F  YG ++RV+++ +K     +  A ++       + A 
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAM 58

Query: 197 KQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRYSGREQEPSRGP 256
              +G KL G+ + + + + + V    PR      G T+  G     R+     +  +  
Sbjct: 59  SHLNGHKLHGKPIRITLSKHQNVQL--PREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI 116

Query: 257 S 257
            
Sbjct: 117 F 117

>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 = 53.4 bits (128), Expect = 2e-08
 Identities = 21/117 (17%), Positives = 33/117 (28%), Gaps = 4/117 (3%)

Query: 94  KAETPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESK 153
           K +     R       L K    +     K     +      P  TL ++ +    +E  
Sbjct: 77  KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEED 136

Query: 154 IKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL 210
           +K  F S G + +      K   K R  A I+     +   A        L     L
Sbjct: 137 LKVLFSSNGGVVKGF----KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL 189

>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 = 54.0 bits (130), Expect = 2e-09
 Identities = 15/95 (15%), Positives = 32/95 (33%), Gaps = 3/95 (3%)

Query: 123 KYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYA 182
                  P         + V  + +   E+ ++  F     +  V L+ D    +  G  
Sbjct: 2   SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHV-GRNNGNG 59

Query: 183 FIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
            ++++  +D   A K+ +   +  R V V     R
Sbjct: 60  LVKFLSPQDTFEALKR-NRMLMIQRYVEVSPATER 93

>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 = 57.0 bits (138), Expect = 3e-09
 Identities = 24/92 (26%), Positives = 36/92 (39%), Gaps = 8/92 (8%)

Query: 120 ELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPR 179
           ++K +    +   +      LFV  L  + TE   KR FE YG    V +  D      R
Sbjct: 7   DIKSFLKPGEKTYTQR--CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------R 58

Query: 180 GYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV 211
           G+ FI        + A  + DG  L  R + +
Sbjct: 59  GFGFIRLESRTLAEIAKAELDGTILKSRPLRI 90

>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 = 53.5 bits (129), Expect = 3e-08
 Identities = 32/190 (16%), Positives = 62/190 (32%), Gaps = 26/190 (13%)

Query: 114 AEKAAEELKKYDPHNDP-NVS-GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVT 171
           AE A  EL      + P  +        L V  LS   +   +++ F  +GP+++  +V 
Sbjct: 71  AEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV 130

Query: 172 DKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGL 231
           D +  +  G  F+E+      + A +     +      L+       +     +      
Sbjct: 131 D-DRGRATGKGFVEFAAKPPARKALE-----RCGDGAFLLTTTPRPVIVEPMEQF----- 179

Query: 232 GTTRVGGEEVNQRYSGREQEPSRGPSRSAEPRIREDRHGDR-----------DRERSRER 280
                G  E   + + +  +    P R A+P   E  +  R             +  R  
Sbjct: 180 -DDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKALDEMEKQQREQVDRNI 238

Query: 281 GRDRER-ERE 289
              +E+ E E
Sbjct: 239 REAKEKLEAE 248

>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 = 53.4 bits (129), Expect = 3e-09
 Identities = 17/98 (17%), Positives = 39/98 (39%), Gaps = 9/98 (9%)

Query: 128 NDPNVSGDPYK-TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEY 186
           +           TL+V     + T + ++  F  +G I  +        + PR  AF+ Y
Sbjct: 5   SSGERRAPRKGNTLYVY--GEDMTPTLLRGAFSPFGNIIDLS------MDPPRNCAFVTY 56

Query: 187 MHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRP 224
                   A  + +G +++  ++ V++ R + + +  P
Sbjct: 57  EKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSGP 94

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 52.6 bits (126), Expect = 6e-09
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           SG P + + + +L  + TE ++      +G +  + +       K +  AFIE       
Sbjct: 12  SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM------LKGKNQAFIEMNTEEAA 65

Query: 193 KAA--YKQADGRKLDGRRVLVD 212
                Y  +    L G+ + + 
Sbjct: 66  NTMVNYYTSVTPVLRGQPIYIQ 87

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 15/81 (18%), Positives = 30/81 (37%), Gaps = 8/81 (9%)

Query: 134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMK 193
           G P + L + +L  E TE+++      +G +  + +       K +  AF+E        
Sbjct: 12  GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLELATEEAAI 65

Query: 194 AA--YKQADGRKLDGRRVLVD 212
               Y  A    L  + + + 
Sbjct: 66  TMVNYYSAVTPHLRNQPIYIQ 86

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 15/89 (16%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
              D   +G P + + + +L  + TE ++      +G +  + ++      K +  AFIE
Sbjct: 20  HMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIE 73

Query: 186 YMHTRDMKAA--YKQADGRKLDGRRVLVD 212
                       Y  +    L G+ + + 
Sbjct: 74  MNTEEAANTMVNYYTSVTPVLRGQPIYIQ 102

>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 = 51.8 bits (124), Expect = 2e-08
 Identities = 14/100 (14%), Positives = 35/100 (35%), Gaps = 1/100 (1%)

Query: 113 GAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTD 172
           G+  ++ +       +      +    +++  L +E     +   F+    ++    +  
Sbjct: 1   GSSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAY 60

Query: 173 KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
               K  G  F+E+ +  D KAA      + +  R + V 
Sbjct: 61  GPNGKATGEGFVEFRNEADYKAA-LCRHKQYMGNRFIQVH 99

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 11/74 (14%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +++++     + T   IK   E  G +  +++         +G  F+ +      K   +
Sbjct: 12  RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE 70

Query: 198 QADGRKLDGRRVLV 211
              G+K     +L+
Sbjct: 71  T-PGQKYKETDLLI 83

>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 = 50.5 bits (121), Expect = 3e-08
 Identities = 8/79 (10%), Positives = 27/79 (34%), Gaps = 1/79 (1%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
                  + +  L +  ++ +I + F     +     +      +  G AF+++      
Sbjct: 11  DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70

Query: 193 KAAYKQADGRKLDGRRVLV 211
           + A  +    ++  R + +
Sbjct: 71  EKA-LKKHKERIGHRYIEI 88

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 54.1 bits (129), Expect = 3e-08
 Identities = 16/92 (17%), Positives = 35/92 (38%), Gaps = 13/92 (14%)

Query: 125 DPHNDPNVSGDPYKTLFVARLSYETTESKIKRE----FESYGPIKRVRLVTDKETNKPRG 180
            P   PN       T+++  L+ +  + ++K+     F  +G I  + +     + K RG
Sbjct: 3   VPETRPN------HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRG 53

Query: 181 YAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
            AF+ +        A +   G     + + + 
Sbjct: 54  QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 85

>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 = 53.0 bits (126), Expect = 6e-08
 Identities = 30/194 (15%), Positives = 54/194 (27%), Gaps = 6/194 (3%)

Query: 18  ARTKAQNRANV-LQLKLIGQSHPTGLTANLLKLFEPRAPLEYKPPPEKRKCPPLTGMAQF 76
           A+T +   A +        +        +       +A       P              
Sbjct: 87  AKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPP 146

Query: 77  VSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEELKKYDPHNDPNVSGDP 136
           ++        +   P       +     +   ++  GA    + +    P   P     P
Sbjct: 147 MTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPP 206

Query: 137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
              LF+  L  ET E  +   F  +   K VRLV  +        AF+E+ +     AA 
Sbjct: 207 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAAR 261

Query: 197 KQADGRKLDGRRVL 210
               G K+     +
Sbjct: 262 DALQGFKITQNNAM 275

>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 = 48.9 bits (117), Expect = 7e-08
 Identities = 8/74 (10%), Positives = 26/74 (35%), Gaps = 7/74 (9%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             + V  L  ++   ++    + Y        +     ++ +  AF+  ++    + A +
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 198 QADGRKLDGRRVLV 211
                   G+ ++V
Sbjct: 59  MFHQYSFRGKDLIV 72

>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 = 49.3 bits (118), Expect = 7e-08
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 3/84 (3%)

Query: 128 NDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYM 187
           +  +        + +  L Y  TE+ I   F    P+ RV +    +  +  G A +E+ 
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPD-GRVTGEADVEFA 63

Query: 188 HTRDMKAAYKQADGRKLDGRRVLV 211
              D  AA  + D   +  R V +
Sbjct: 64  THEDAVAAMAK-DKANMQHRYVEL 86

>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 = 48.8 bits (117), Expect = 8e-08
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 7/73 (9%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV R + + TE +++  F  YG +  V +         R +AF+ +   +  ++   + 
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCGE- 61

Query: 200 DGRKLDGRRVLVD 212
               + G  V + 
Sbjct: 62  -DLIIKGISVHIS 73

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 49.2 bits (117), Expect = 1e-07
 Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETN--KPRGYAFIEYMHTRDMKAA 195
           + +FV  L  +  E +I   F  +GP+        +  +   P+GYAF+ +     ++A 
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 139 TLFVARLSYETTESKIKREF-ESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +LFV  L+ +  +  +   F + Y   +  ++V D+ T   +GY F+++    + K A  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69

Query: 198 QADGRKLDGRR 208
           +  G    G +
Sbjct: 70  ECQGAVGLGSK 80

>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 = 47.2 bits (112), Expect = 6e-07
 Identities = 17/116 (14%), Positives = 36/116 (31%), Gaps = 6/116 (5%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESY---GPIKRVRLVTDKETNKPRGYA 182
                   G     + +  L +  +   ++           +  V  +  +E  +  G A
Sbjct: 6   SGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEA 64

Query: 183 FIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGG 238
           F+E     D+K A  + D   +  R + V       + +W  +  G    +    G
Sbjct: 65  FVELESEDDVKLA-LKKDRESMGHRYIEVFKSHRTEM-DWVLKHSGPNSASGPSSG 118

>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 = 48.7 bits (115), Expect = 7e-07
 Identities = 19/143 (13%), Positives = 39/143 (27%), Gaps = 8/143 (5%)

Query: 69  PLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGAEKAAEELKKYDPHN 128
           PL  M +F        D                         E   +      K      
Sbjct: 47  PLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEIS------EDKTKIRRSPSKPLPEVT 100

Query: 129 DPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH 188
           D   +    +++++     + T   IK   E  G +  +++         +G  F+ +  
Sbjct: 101 DEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDS 159

Query: 189 TRDMKAAYKQADGRKLDGRRVLV 211
               K   +   G+K     +L+
Sbjct: 160 IESAKKFVE-TPGQKYKETDLLI 181

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 46.1 bits (109), Expect = 8e-07
 Identities = 17/95 (17%), Positives = 40/95 (42%), Gaps = 8/95 (8%)

Query: 131 NVSGDPYKTLFVARLSYETTESKIKRE----FESYGPIKRVRLVTDKETNKPRGYAFIEY 186
             SG+    + V+ + Y  +  ++++     F  +G +K V L    +       A ++ 
Sbjct: 4   GSSGNGA-DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQ---LKAVVQM 59

Query: 187 MHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPN 221
            + +D   A       K+  +++LV +  G + P+
Sbjct: 60  ENLQDAIGAVNSLHRYKIGSKKILVSLATGASGPS 94

>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 = 45.7 bits (109), Expect = 9e-07
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 7/73 (9%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV R + + T  ++++ F  YG +  V +         R +AF+ +   +  ++     
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSL--CG 66

Query: 200 DGRKLDGRRVLVD 212
           +   + G  V + 
Sbjct: 67  EDLIIKGISVHIS 79

>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 = 46.4 bits (110), Expect = 1e-06
 Identities = 11/83 (13%), Positives = 27/83 (32%), Gaps = 1/83 (1%)

Query: 129 DPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH 188
             +        + +  L +  T+ +I + F     +     +      K  G AF+++  
Sbjct: 34  SNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFAS 93

Query: 189 TRDMKAAYKQADGRKLDGRRVLV 211
               + A       ++  R + V
Sbjct: 94  QELAEKA-LGKHKERIGHRYIEV 115

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 15/92 (16%), Positives = 33/92 (35%), Gaps = 6/92 (6%)

Query: 124 YDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPI----KRVRLVTDKETNKPR 179
                   +S +    + +  L +  T  ++   F  + PI    + +  VT  +  +P 
Sbjct: 10  TSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD-GRPT 68

Query: 180 GYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV 211
           G AF+ +      + A  +     L  R + +
Sbjct: 69  GDAFVLFACEEYAQNA-LRKHKDLLGKRYIEL 99

>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 = 44.7 bits (106), Expect = 2e-06
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRL-----VTDKETNKPRGYAFIEYMHTRDM 192
           + L+V  + +  TE  +   F +   +  +       V   + N+ + +AF+E+    + 
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66

Query: 193 KAAYKQADGRKLDGRRVLV 211
             A    DG    G+ + +
Sbjct: 67  TQA-MAFDGIIFQGQSLKI 84

>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 = 45.6 bits (108), Expect = 3e-06
 Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 3/93 (3%)

Query: 117 AAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETN 176
             +++ +    ++  V       + +  L Y+ TE+ I   F    P+ RV +    +  
Sbjct: 26  GGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPD-G 83

Query: 177 KPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV 209
           +  G A +E+    +  AA    D   +  R +
Sbjct: 84  RVTGEADVEFATHEEAVAA-MSKDRANMQHRYI 115

>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 = 44.1 bits (104), Expect = 5e-06
 Identities = 12/65 (18%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 148 ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR 207
           E  E       E YG ++ +  V D   +   G  ++++    D + A    + R  +G+
Sbjct: 38  EFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96

Query: 208 RVLVD 212
            +  +
Sbjct: 97  PIHAE 101

>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 = 43.3 bits (102), Expect = 1e-05
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 5/82 (6%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESY---GPIKRVRLVTDKETNKPRGYAFIEYMHT 189
             D    +    L +  T   +   F           +  + +++  K RG A IE    
Sbjct: 7   EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESE 65

Query: 190 RDMKAAYKQADGRKLDGRRVLV 211
           +D++ A  +     +  R V V
Sbjct: 66  QDVQKA-LEKHRMYMGQRYVEV 86

>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 = 43.8 bits (103), Expect = 1e-05
 Identities = 15/89 (16%), Positives = 29/89 (32%), Gaps = 5/89 (5%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESY---GPIKRVRLVTDKETNKPRGYA 182
                   G     + +  L +  +   ++              V  +  +E  +  G A
Sbjct: 33  GSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEA 91

Query: 183 FIEYMHTRDMKAAYKQADGRKLDGRRVLV 211
           F+E     D+K A K+ D   +  R + V
Sbjct: 92  FVELGSEDDVKMALKK-DRESMGHRYIEV 119

>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 = 43.6 bits (102), Expect = 3e-05
 Identities = 12/79 (15%), Positives = 29/79 (36%), Gaps = 4/79 (5%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           + V  L Y  T   + + F  +G + ++   T       +  A ++Y      + A    
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSL 104

Query: 200 DGRKLDGRRVLVDVERGRT 218
           DG+ +      + ++  + 
Sbjct: 105 DGQNIYNACCTLRIDFSKL 123

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 42.7 bits (100), Expect = 3e-05
 Identities = 13/99 (13%), Positives = 29/99 (29%), Gaps = 7/99 (7%)

Query: 122 KKYDPHNDPNVSGDPYKTLF--VARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPR 179
           K+     + +      K L   +    Y  T   +       G ++R+         +  
Sbjct: 8   KRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIV-----IFKRNG 62

Query: 180 GYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRT 218
             A +E+      + A    +G  +      + +E  R 
Sbjct: 63  IQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 101

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 42.7 bits (100), Expect = 3e-05
 Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 4/75 (5%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           + V  L Y  T   + + F  +G + ++   T       +  A ++Y      + A    
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSL 86

Query: 200 DGRKLDGRRVLVDVE 214
           DG+ +      + ++
Sbjct: 87  DGQNIYNACCTLRID 101

>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 = 40.6 bits (95), Expect = 1e-04
 Identities = 13/79 (16%), Positives = 25/79 (31%), Gaps = 7/79 (8%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            + V+ L    +   +K      G +    +  D       G   +E++   DM  A ++
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 69

Query: 199 ADGRKLDGRRVLVDVERGR 217
            D  K           R +
Sbjct: 70  LDNTKFRSHEGETAYIRVK 88

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 21/104 (20%), Positives = 41/104 (39%), Gaps = 9/104 (8%)

Query: 113 GAEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYE-TTESKIKREFESYGPIKRVRLVT 171
           G+  ++ +  +  P    +   +  + + ++ L +   ++S + +  E YG IK   L  
Sbjct: 1   GSSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL-- 58

Query: 172 DKETNKPRGYAFIEYMHTRDMKAA--YKQADGRKLDGRRVLVDV 213
                + +  AFIE     D  A   +         GR V VD+
Sbjct: 59  ----MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL 98

>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 Length = 105

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 147 YETTESKIKREFESYGPIKRVRL--VTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL 204
           YE     ++ E   YG +K + +    D       G  F+E+    D + A +   GRK 
Sbjct: 25  YEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF 84

Query: 205 DGRRVLV 211
             R V+ 
Sbjct: 85  ANRVVVT 91

>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 Length = 114

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 10/65 (15%), Positives = 23/65 (35%), Gaps = 7/65 (10%)

Query: 154 IKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV---L 210
           +  E   +G +  + +    + N  +G  +++        AA     GR   G+ +    
Sbjct: 34  VIEECNKHGGVIHIYV----DKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAY 89

Query: 211 VDVER 215
           V +  
Sbjct: 90  VPLPT 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	480
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	100.0
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.84
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.81
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.81
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.81
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.8
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.8
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.8
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.8
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.8
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.8
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.8
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.79
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.79
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.79
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.79
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.79
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.79
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.78
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.78
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.78
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.78
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.78
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.78
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.78
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.78
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.77
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.77
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.77
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.77
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.77
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.77
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.77
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.77
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.76
2div_A	99	TRNA selenocysteine associated protein; structural	99.76
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.76
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.76
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.76
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.76
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.76
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.76
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.76
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.76
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.76
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.76
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.75
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.75
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.75
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.75
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.75
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.75
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.75
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.75
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.75
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.75
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.75
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.75
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.75
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.74
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.74
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.74
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.74
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.74
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.74
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.74
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.74
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.74
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.73
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.73
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.73
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.73
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.73
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.73
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.73
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.73
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.73
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.73
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.73
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.73
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.73
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.73
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.73
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.73
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.72
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.72
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.72
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.72
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.72
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.72
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.72
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.72
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.71
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.71
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.55
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.71
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.71
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.71
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.7
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.7
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.7
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.7
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.7
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.7
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.7
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.7
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.7
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.69
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.69
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.69
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.69
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.69
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.69
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.69
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.69
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.69
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.69
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.69
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.69
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.69
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.68
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.68
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.68
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.68
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.68
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.68
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.68
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.68
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.67
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.67
1x5p_A	97	Negative elongation factor E; structure genomics,	99.67
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.67
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.66
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.66
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.66
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.65
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.65
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.65
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.64
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.64
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.63
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.63
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.63
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.62
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.62
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.61
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.61
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.61
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.6
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.6
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.6
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.6
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.6
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.6
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.6
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.59
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.58
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.58
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.58
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.58
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.57
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.56
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.56
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.55
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.54
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.53
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.53
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.52
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.52
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.52
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.51
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.51
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.51
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.51
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.5
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.49
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.47
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.46
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.46
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.46
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.45
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.44
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.43
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.43
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.42
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.41
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.39
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.39
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.38
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.38
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.38
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.37
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.33
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.18
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.17
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.16
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.98
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.79
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.42
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.92
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.56
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.42
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.32
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.2
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.09
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.83
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.22
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.27
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	94.52
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	93.76
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	87.21

>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=100.00  E-value=1.8e-40  Score=342.87  Aligned_cols=201  Identities=59%  Similarity=1.039  Sum_probs=165.6

Q ss_pred             CCCChhhhccCCCCCCCCCCCCCCC-----CCCCCCCChhhhhhccCCCCCCCCCCCCCCCCChHHHHHHHHHHHHHhhh
Q 011668           40 TGLTANLLKLFEPRAPLEYKPPPEK-----RKCPPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKGA  114 (480)
Q Consensus        40 ~~~pp~~~~lf~p~pp~~~~pp~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~k~~~~~  114 (480)
                      ..|||+|+.||+|.||++++||+..     ..+++++++++|+..|..+...   ++...++++.+........+++...
T Consensus         3 ~~lPp~L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~---~~~~~~e~~~~~~~~~~~~k~~~~~   79 (437)
T 3pgw_S            3 QFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDA---PPPTRAETREERMERKRREKIERRQ   79 (437)
T ss_pred             CcCCccHHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccc---cccccccCHHHHHHHHHHHHHHHHH
Confidence            3589999999999999999877543     2467788999998888765432   3333456666666555666666666


Q ss_pred             HHHHHHHhhcCCCCCCCCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHH
Q 011668          115 EKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA  194 (480)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~  194 (480)
                      ..+...+..|.+...+.....+.++|||+|||+.||+++|..||++||.|+.|.|+.+..|+.++|||||+|.+.++|.+
T Consensus        80 ~~~~~~~~~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~  159 (437)
T 3pgw_S           80 QEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS  159 (437)
T ss_pred             HHHHHhhhhcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHH
Confidence            67777788888888888888889999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHcCCceeCCeEEEEeeecCCCCCCCCCCCCCCCCCCccCCCccccc
Q 011668          195 AYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQ  243 (480)
Q Consensus       195 A~~~l~g~~i~gr~l~V~~a~~~~~~~~~~~~~ggg~gg~~~g~~~~~~  243 (480)
                      ||..|||+.|+|+.|.|.|+.+.....|.+..+|||+|++++++...+.
T Consensus       160 Ai~~lng~~i~gr~i~V~~a~~~~~~~~~~~~~ggG~gg~~~gg~~~~~  208 (437)
T 3pgw_S          160 AYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNI  208 (437)
T ss_pred             HHHHcCCCEECCEEEEEEEeCCCCCCCCCCCCcCCCCCCCCCCCCcccc
Confidence            9999999999999999999999998888887777666665555444433

>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=99.84  E-value=9.7e-21  Score=155.14  Aligned_cols=81  Identities=25%  Similarity=0.481  Sum_probs=78.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+|+++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|.+||..|||..|+|+.|.|.||+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            4

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=2.8e-19  Score=150.77  Aligned_cols=89  Identities=28%  Similarity=0.565  Sum_probs=81.7

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ....+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|++ .|.|+.|.|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            3345678999999999999999999999999999999999999999999999999999999999999998 899999999


Q ss_pred             eeecCCCCCC
Q 011668          212 DVERGRTVPN  221 (480)
Q Consensus       212 ~~a~~~~~~~  221 (480)
                      .|+.....+.
T Consensus        91 ~~a~~~~~~~  100 (116)
T 2cqd_A           91 NLAYLGAKPR  100 (116)
T ss_dssp             EESTTTCCCC
T ss_pred             EEcccCCCcc
Confidence            9998654443

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.81  E-value=9e-20  Score=152.31  Aligned_cols=82  Identities=23%  Similarity=0.307  Sum_probs=78.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .|.++|||+||++.+++++|.++|++||.|..|.|+.++.|+.++|||||+|.+.++|.+||..|||..|+|+.|.|.++
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            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 011668          215 RG  216 (480)
Q Consensus       215 ~~  216 (480)
                      ..
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            64

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.81  E-value=1.4e-19  Score=157.55  Aligned_cols=87  Identities=26%  Similarity=0.511  Sum_probs=81.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|..+|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|+|+.|.|.|
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            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 011668          214 ERGRTVP  220 (480)
Q Consensus       214 a~~~~~~  220 (480)
                      +......
T Consensus       119 a~~~~~~  125 (139)
T 1u6f_A          119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9875443

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=2.2e-19  Score=147.97  Aligned_cols=86  Identities=36%  Similarity=0.592  Sum_probs=81.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+++++|.++|++||.|..|.|+.+..|+.++|||||+|.+.++|.+||..|||..|+|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      |+....
T Consensus        89 ~a~~~~   94 (103)
T 2dnm_A           89 VARYGR   94 (103)
T ss_dssp             ECSSCC
T ss_pred             ECCcCC
Confidence            998644

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=2.3e-19  Score=145.53  Aligned_cols=85  Identities=28%  Similarity=0.508  Sum_probs=80.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
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            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 011668          215 RGRTV  219 (480)
Q Consensus       215 ~~~~~  219 (480)
                      ..+..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            86543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3e-19  Score=147.21  Aligned_cols=89  Identities=29%  Similarity=0.430  Sum_probs=82.7

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          131 NVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       131 ~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      .....+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|+|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (103)
T 2cq0_A            9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   88 (103)
T ss_dssp             CCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            34456789999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EeeecCCCC
Q 011668          211 VDVERGRTV  219 (480)
Q Consensus       211 V~~a~~~~~  219 (480)
                      |.|+.+...
T Consensus        89 v~~a~~~~~   97 (103)
T 2cq0_A           89 VEWAKPSTN   97 (103)
T ss_dssp             EEESSCCCC
T ss_pred             EEECCCCCC
Confidence            999986543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.80  E-value=7.5e-20  Score=147.42  Aligned_cols=82  Identities=23%  Similarity=0.446  Sum_probs=76.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCC-CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHc-CCceeCCeEEEEeee
Q 011668          137 YKTLFVARLSYETTESKIKREFESYG-PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA-DGRKLDGRRVLVDVE  214 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l-~g~~i~gr~l~V~~a  214 (480)
                      +++|||+|||+.+|+++|.++|++|| .|..|.|+.++.|+.++|||||+|.+.++|.+||..| ++..|+|+.|.|.||
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 8999999999999999999999999999999999977 456799999999999


Q ss_pred             cCCC
Q 011668          215 RGRT  218 (480)
Q Consensus       215 ~~~~  218 (480)
                      .++.
T Consensus        81 ~~~~   84 (91)
T 2lxi_A           81 DPKP   84 (91)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=4.7e-19  Score=144.94  Aligned_cols=85  Identities=22%  Similarity=0.486  Sum_probs=80.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||. ||+..|+|+.|.|.+
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            4467899999999999999999999999999999999999999999999999999999999999 999999999999999


Q ss_pred             ecCCCC
Q 011668          214 ERGRTV  219 (480)
Q Consensus       214 a~~~~~  219 (480)
                      +.+...
T Consensus        86 a~~~~~   91 (99)
T 2dgs_A           86 AEPRDS   91 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCCcc
Confidence            986554

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.1e-19  Score=146.80  Aligned_cols=88  Identities=26%  Similarity=0.476  Sum_probs=82.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 011668          214 ERGRTVPN  221 (480)
Q Consensus       214 a~~~~~~~  221 (480)
                      +.+.....
T Consensus        89 a~~~~~~~   96 (102)
T 2cqb_A           89 AKPMRIKE   96 (102)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCCCC
Confidence            98765443

>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=99.80  E-value=5.4e-19  Score=144.51  Aligned_cols=85  Identities=31%  Similarity=0.581  Sum_probs=80.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|..||..|||..|.|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            46789999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 011668          215 RGRTV  219 (480)
Q Consensus       215 ~~~~~  219 (480)
                      .....
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            87554

>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=99.80  E-value=1.8e-19  Score=154.23  Aligned_cols=86  Identities=33%  Similarity=0.475  Sum_probs=81.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|+|+.|.|.|+
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            45689999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 011668          215 RGRTVP  220 (480)
Q Consensus       215 ~~~~~~  220 (480)
                      .....+
T Consensus       100 ~~~~~~  105 (126)
T 3ex7_B          100 FVRGPP  105 (126)
T ss_dssp             EESSSC
T ss_pred             cCCCCC
Confidence            876543

>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=99.80  E-value=3.6e-19  Score=158.22  Aligned_cols=84  Identities=32%  Similarity=0.498  Sum_probs=80.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.|+.++|||||+|.+.++|++||..||+..|+|+.|.|.|+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 011668          215 RGRT  218 (480)
Q Consensus       215 ~~~~  218 (480)
                      .+..
T Consensus       117 ~~~~  120 (156)
T 1h2v_Z          117 AGFK  120 (156)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8644

>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=99.80  E-value=4.7e-19  Score=146.51  Aligned_cols=89  Identities=24%  Similarity=0.365  Sum_probs=82.5

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          131 NVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       131 ~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      .....+.++|||+|||+.+|+++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|..||..|||..|+|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (105)
T 1x5u_A            9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   88 (105)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            33455778999999999999999999999999999999999998999999999999999999999999999999999999


Q ss_pred             EeeecCCCC
Q 011668          211 VDVERGRTV  219 (480)
Q Consensus       211 V~~a~~~~~  219 (480)
                      |.++.....
T Consensus        89 v~~a~~~~~   97 (105)
T 1x5u_A           89 VNKASAHNK   97 (105)
T ss_dssp             EEETTTTSC
T ss_pred             EEECCCCCc
Confidence            999986543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.79  E-value=1.1e-19  Score=147.35  Aligned_cols=81  Identities=23%  Similarity=0.468  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCC--eeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCc----eeCCeEE
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGP--IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGR----KLDGRRV  209 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~--i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~----~i~gr~l  209 (480)
                      .-.||||+|||+.+|+++|.++|++||.  |..|.|+.|+.||.++|||||+|.+.++|..||..|||.    .|+|+.|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            4579999999999999999999999994  679999999999999999999999999999999999997    5999999


Q ss_pred             EEeeecC
Q 011668          210 LVDVERG  216 (480)
Q Consensus       210 ~V~~a~~  216 (480)
                      .|+||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999974

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.5e-19  Score=144.70  Aligned_cols=85  Identities=24%  Similarity=0.420  Sum_probs=80.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEE-EecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRV-RLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v-~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      .+.++|||+|||+.+++++|..+|++||.|..| .|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            367899999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 011668          214 ERGRTV  219 (480)
Q Consensus       214 a~~~~~  219 (480)
                      +.+...
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            986543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.79  E-value=1.6e-18  Score=145.87  Aligned_cols=87  Identities=30%  Similarity=0.497  Sum_probs=81.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 011668          213 VERGRTV  219 (480)
Q Consensus       213 ~a~~~~~  219 (480)
                      |+.....
T Consensus        91 ~a~~~~~   97 (115)
T 2dgo_A           91 WATRKPP   97 (115)
T ss_dssp             ESSCCCC
T ss_pred             EccCCCC
Confidence            9986543

>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=99.79  E-value=4.3e-19  Score=141.38  Aligned_cols=82  Identities=30%  Similarity=0.526  Sum_probs=77.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            56799999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>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=99.79  E-value=5.6e-19  Score=148.65  Aligned_cols=86  Identities=22%  Similarity=0.426  Sum_probs=80.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|.++|+.||.|..|.|+.+..++.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            34668999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 011668          214 ERGRTV  219 (480)
Q Consensus       214 a~~~~~  219 (480)
                      +.+...
T Consensus       102 a~~~~~  107 (115)
T 2cpz_A          102 KRSKND  107 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCc
Confidence            986543

>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=99.79  E-value=7.3e-19  Score=148.26  Aligned_cols=83  Identities=36%  Similarity=0.606  Sum_probs=78.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.+. ++.++|||||+|.+.++|++||..|||..|+|+.|.|.|+
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            466899999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 011668          215 RGRT  218 (480)
Q Consensus       215 ~~~~  218 (480)
                      ....
T Consensus        84 ~~~~   87 (116)
T 2fy1_A           84 KKPS   87 (116)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            8644

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.4e-19  Score=144.88  Aligned_cols=86  Identities=33%  Similarity=0.608  Sum_probs=81.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            44678999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 011668          214 ERGRTV  219 (480)
Q Consensus       214 a~~~~~  219 (480)
                      +.....
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            986553

>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=99.78  E-value=7.3e-19  Score=142.96  Aligned_cols=83  Identities=23%  Similarity=0.501  Sum_probs=79.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      |.++|||+|||+.+++++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      +..
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            643

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=8.9e-19  Score=141.74  Aligned_cols=84  Identities=24%  Similarity=0.473  Sum_probs=79.1

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ....+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            33456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeec
Q 011668          212 DVER  215 (480)
Q Consensus       212 ~~a~  215 (480)
                      .||+
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9974

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=7.3e-19  Score=142.46  Aligned_cols=86  Identities=37%  Similarity=0.592  Sum_probs=80.6

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          131 NVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       131 ~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      .....+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|+|+.|.
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34455778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeecC
Q 011668          211 VDVERG  216 (480)
Q Consensus       211 V~~a~~  216 (480)
                      |.|+..
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999863

>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=99.78  E-value=1.3e-18  Score=145.24  Aligned_cols=87  Identities=30%  Similarity=0.525  Sum_probs=81.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcC------CceeCC
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD------GRKLDG  206 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~------g~~i~g  206 (480)
                      ...+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|..||..||      |..|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            34567899999999999999999999999999999999999999999999999999999999999999      999999


Q ss_pred             eEEEEeeecCCCC
Q 011668          207 RRVLVDVERGRTV  219 (480)
Q Consensus       207 r~l~V~~a~~~~~  219 (480)
                      +.|.|.|+.+...
T Consensus        91 ~~l~v~~a~~~~~  103 (111)
T 1x4h_A           91 RQLKVDLAVTRDE  103 (111)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCcc
Confidence            9999999986543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=5.9e-19  Score=144.02  Aligned_cols=86  Identities=29%  Similarity=0.509  Sum_probs=79.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCC---CCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKE---TNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~---t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      .+.++|||+|||+.+++++|.++|++||.|..|.|+.+..   |+.++|||||+|.+.++|..||..|||..|+|+.|.|
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            3668999999999999999999999999999999998876   6689999999999999999999999999999999999


Q ss_pred             eeecCCCCC
Q 011668          212 DVERGRTVP  220 (480)
Q Consensus       212 ~~a~~~~~~  220 (480)
                      .++.....+
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999875543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=1.1e-18  Score=144.75  Aligned_cols=87  Identities=22%  Similarity=0.531  Sum_probs=81.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEeccc-CCCCCccceEEEEEechhhHHHHHHHc-CCceeCCeEEE
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTD-KETNKPRGYAFIEYMHTRDMKAAYKQA-DGRKLDGRRVL  210 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d-~~t~~~~g~afV~F~~~~~a~~A~~~l-~g~~i~gr~l~  210 (480)
                      ...+.++|||+|||+.+++++|..+|++||.|..|.|+.+ ..++.++|||||+|.+.++|.+||..| ||..|.|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3456789999999999999999999999999999999998 788999999999999999999999999 99999999999


Q ss_pred             EeeecCCCC
Q 011668          211 VDVERGRTV  219 (480)
Q Consensus       211 V~~a~~~~~  219 (480)
                      |.|+.....
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999986543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=1.1e-18  Score=143.85  Aligned_cols=85  Identities=33%  Similarity=0.594  Sum_probs=79.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+++++|.++|++|| |..|.|+.+..|+.++|||||+|.+.++|..|| .|||..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            345678999999999999999999999997 999999999999999999999999999999999 799999999999999


Q ss_pred             eecCCCC
Q 011668          213 VERGRTV  219 (480)
Q Consensus       213 ~a~~~~~  219 (480)
                      ++.+...
T Consensus        89 ~a~~~~~   95 (103)
T 2dng_A           89 IAEGRKQ   95 (103)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            9986543

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.78  E-value=7.3e-19  Score=138.76  Aligned_cols=81  Identities=21%  Similarity=0.431  Sum_probs=77.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      +.+|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|.|+.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999988999999999999999999999999999999999999999976


Q ss_pred             C
Q 011668          217 R  217 (480)
Q Consensus       217 ~  217 (480)
                      +
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.78  E-value=6.5e-19  Score=139.68  Aligned_cols=81  Identities=28%  Similarity=0.515  Sum_probs=77.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            46789999999999999999999999999999999999889999999999999999999999999999999999999997


Q ss_pred             c
Q 011668          215 R  215 (480)
Q Consensus       215 ~  215 (480)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.78  E-value=1.4e-18  Score=143.43  Aligned_cols=84  Identities=26%  Similarity=0.451  Sum_probs=78.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCC-CCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKET-NKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t-~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..+.++|||+|||+.+++++|.++|+.|| |..|.|+.+..+ +.++|||||+|.+.++|.+|| .|||..|+|+.|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            44678999999999999999999999999 999999999887 999999999999999999999 899999999999999


Q ss_pred             eecCCCC
Q 011668          213 VERGRTV  219 (480)
Q Consensus       213 ~a~~~~~  219 (480)
                      ++.....
T Consensus        90 ~a~~~~~   96 (104)
T 1wi8_A           90 VADQAQD   96 (104)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9986543

>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=99.78  E-value=9.2e-19  Score=144.99  Aligned_cols=87  Identities=21%  Similarity=0.343  Sum_probs=80.9

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee---CCeE
Q 011668          132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL---DGRR  208 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i---~gr~  208 (480)
                      ....+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|   .|+.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            3445678999999999999999999999999999999999999999999999999999999999999999987   8999


Q ss_pred             EEEeeecCCC
Q 011668          209 VLVDVERGRT  218 (480)
Q Consensus       209 l~V~~a~~~~  218 (480)
                      |.|.++....
T Consensus        88 l~v~~a~~~~   97 (106)
T 2dgp_A           88 IQVKPADSES   97 (106)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEECCccc
Confidence            9999998644

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1e-18  Score=144.00  Aligned_cols=86  Identities=14%  Similarity=0.429  Sum_probs=79.8

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ....+.++|||+|||+.+|+++|.++|++||.|..|.|+.+  ++.++|||||+|.+.++|..||..|||..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            34457789999999999999999999999999999999988  7999999999999999999999999999999999999


Q ss_pred             eeecCCCC
Q 011668          212 DVERGRTV  219 (480)
Q Consensus       212 ~~a~~~~~  219 (480)
                      .|+.....
T Consensus        88 ~~a~~~~~   95 (103)
T 2d9p_A           88 ALAQRKEE   95 (103)
T ss_dssp             EECSSCCC
T ss_pred             EEeccccc
Confidence            99987554

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.7e-18  Score=141.83  Aligned_cols=84  Identities=24%  Similarity=0.470  Sum_probs=79.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.+. ++.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            4467899999999999999999999999999999999988 899999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +.+..
T Consensus        93 a~~~~   97 (100)
T 2do4_A           93 SNSGP   97 (100)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98644

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=6.7e-19  Score=145.83  Aligned_cols=84  Identities=32%  Similarity=0.463  Sum_probs=79.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+++++|..+|++||.|..|.|+.+..++.++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 011668          215 RGRT  218 (480)
Q Consensus       215 ~~~~  218 (480)
                      .+..
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            8654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.77  E-value=8.7e-19  Score=143.35  Aligned_cols=84  Identities=30%  Similarity=0.398  Sum_probs=79.2

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeE--------EEecccCCCCCccceEEEEEechhhHHHHHHHcCCce
Q 011668          132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKR--------VRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRK  203 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~--------v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~  203 (480)
                      ....+.++|||+|||+.+++++|.++|++||.|..        |.|+.++.+|.++|||||+|.+.++|..||..|||..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34557789999999999999999999999999999        9999999999999999999999999999999999999


Q ss_pred             eCCeEEEEeeec
Q 011668          204 LDGRRVLVDVER  215 (480)
Q Consensus       204 i~gr~l~V~~a~  215 (480)
                      |.|+.|.|.+|+
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999974

>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=99.77  E-value=4.1e-18  Score=140.35  Aligned_cols=89  Identities=20%  Similarity=0.467  Sum_probs=80.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.+..  .++|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   88 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345678999999999999999999999999999999998864  388999999999999999999999999999999999


Q ss_pred             eecCCCCCCCC
Q 011668          213 VERGRTVPNWR  223 (480)
Q Consensus       213 ~a~~~~~~~~~  223 (480)
                      ++.+.....+.
T Consensus        89 ~a~~~~~~~~~   99 (103)
T 2cq3_A           89 NATARVMTNSG   99 (103)
T ss_dssp             ECCSSCCCCCS
T ss_pred             EcccCCCCCCC
Confidence            99887655443

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.7e-18  Score=145.20  Aligned_cols=86  Identities=27%  Similarity=0.441  Sum_probs=80.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCee--------EEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIK--------RVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~--------~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      ...+.++|||+|||+.+|+++|.++|++||.|.        .|.|+.++.++.++|||||+|.+.++|..||..|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999999        699999988999999999999999999999999999999


Q ss_pred             CCeEEEEeeecCCC
Q 011668          205 DGRRVLVDVERGRT  218 (480)
Q Consensus       205 ~gr~l~V~~a~~~~  218 (480)
                      .|+.|.|.++....
T Consensus        91 ~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           91 QGSKLKVSLARKKP  104 (113)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCCEEEEEECCCCC
Confidence            99999999998654

>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=99.77  E-value=2e-19  Score=144.62  Aligned_cols=82  Identities=17%  Similarity=0.336  Sum_probs=72.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCC--CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          138 KTLFVARLSYETTESKIKREFESYG--PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G--~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+|||+|||+.+|+++|.++|++||  .|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|+|+.|.|.++.
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            4799999999999999999999999  99999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 011668          216 GRTV  219 (480)
Q Consensus       216 ~~~~  219 (480)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

>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=99.77  E-value=1.6e-18  Score=144.62  Aligned_cols=85  Identities=29%  Similarity=0.436  Sum_probs=80.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.|+.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +.+..
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            98644

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2e-18  Score=142.74  Aligned_cols=87  Identities=25%  Similarity=0.467  Sum_probs=80.9

Q ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          132 VSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ....+.++|||+|||+.+++++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|.+||.. |+..|+|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            3455778999999999999999999999999999999999999999999999999999999999998 999999999999


Q ss_pred             eeecCCCC
Q 011668          212 DVERGRTV  219 (480)
Q Consensus       212 ~~a~~~~~  219 (480)
                      .++.++..
T Consensus        90 ~~a~~~~~   97 (105)
T 2dh8_A           90 KPCTPRGM   97 (105)
T ss_dssp             CCSCCSSC
T ss_pred             EEccCCCC
Confidence            99986543

>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=99.77  E-value=2.1e-18  Score=142.60  Aligned_cols=86  Identities=20%  Similarity=0.381  Sum_probs=79.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC---eEE
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG---RRV  209 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g---r~l  209 (480)
                      ...+.++|||+|||+.+++++|..+|++||.|..|.|+.+. ++.++|||||+|.+.++|..||..|||..|.|   +.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34567899999999999999999999999999999999987 79999999999999999999999999999998   999


Q ss_pred             EEeeecCCCC
Q 011668          210 LVDVERGRTV  219 (480)
Q Consensus       210 ~V~~a~~~~~  219 (480)
                      .|.|+.....
T Consensus        90 ~V~~a~~~~~   99 (105)
T 2dnh_A           90 VVKFADTDKE   99 (105)
T ss_dssp             EEEESCSSCC
T ss_pred             EEEECccCcc
Confidence            9999986543

>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=99.76  E-value=1.2e-18  Score=144.91  Aligned_cols=85  Identities=31%  Similarity=0.535  Sum_probs=80.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+++++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34467899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             eecCC
Q 011668          213 VERGR  217 (480)
Q Consensus       213 ~a~~~  217 (480)
                      ++.++
T Consensus       102 ~a~~k  106 (108)
T 2jrs_A          102 HVTER  106 (108)
T ss_dssp             CSCSS
T ss_pred             EcccC
Confidence            98764

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=1.3e-18  Score=142.28  Aligned_cols=84  Identities=20%  Similarity=0.389  Sum_probs=79.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCee-EEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeE----
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIK-RVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRR----  208 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~-~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~----  208 (480)
                      ..+.++|||+|||+.+++++|.++|++||.|. .|.|+.++.++.++|||||+|.+.++|+.||..|||..|.|+.    
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            34678999999999999999999999999999 9999999999999999999999999999999999999999999    


Q ss_pred             EEEeeecCC
Q 011668          209 VLVDVERGR  217 (480)
Q Consensus       209 l~V~~a~~~  217 (480)
                      |+|.|+...
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998753

>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=99.76  E-value=5.8e-18  Score=140.98  Aligned_cols=83  Identities=27%  Similarity=0.456  Sum_probs=75.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.+   +.++|||||+|.+.++|..||..||+..|+|+.|.|.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3456789999999999999999999999999999999654   5688999999999999999999999999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      |+....
T Consensus        95 ~a~~~~  100 (109)
T 1x4a_A           95 FPRSGR  100 (109)
T ss_dssp             CCCCCC
T ss_pred             EcccCC
Confidence            998644

>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=99.76  E-value=2.8e-18  Score=142.33  Aligned_cols=81  Identities=23%  Similarity=0.423  Sum_probs=77.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.+. ++.++|||||+|.+.++|.+||..|||..|+|+.|.|.|
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            3467899999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             ec
Q 011668          214 ER  215 (480)
Q Consensus       214 a~  215 (480)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.76  E-value=2.5e-18  Score=145.28  Aligned_cols=82  Identities=21%  Similarity=0.435  Sum_probs=77.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|+|.|
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            34678999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ec
Q 011668          214 ER  215 (480)
Q Consensus       214 a~  215 (480)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=1.9e-18  Score=142.58  Aligned_cols=84  Identities=23%  Similarity=0.418  Sum_probs=79.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhc-CCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCce-eCCeEEEE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFES-YGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRK-LDGRRVLV  211 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~-~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~-i~gr~l~V  211 (480)
                      ..+.++|||+|||+.+|+++|.++|++ ||.|..|.|+.+. ++.++|||||+|.+.++|..||..|||.. |+|+.|.|
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            346789999999999999999999999 9999999999998 89999999999999999999999999999 99999999


Q ss_pred             eeecCCC
Q 011668          212 DVERGRT  218 (480)
Q Consensus       212 ~~a~~~~  218 (480)
                      .++....
T Consensus        85 ~~a~~~~   91 (104)
T 2dhg_A           85 SVAIPKA   91 (104)
T ss_dssp             CBCCCCC
T ss_pred             EEccCCC
Confidence            9997644

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=2e-18  Score=144.38  Aligned_cols=90  Identities=19%  Similarity=0.326  Sum_probs=80.4

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHH---HHhhcCCCeeEEEecccCCCC---CccceEEEEEechhhHHHHHHHcCCcee
Q 011668          131 NVSGDPYKTLFVARLSYETTESKIK---REFESYGPIKRVRLVTDKETN---KPRGYAFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       131 ~~~~~~~~~l~V~nL~~~~te~~L~---~~F~~~G~i~~v~i~~d~~t~---~~~g~afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      .....+.++|||+|||+.+++++|.   ++|++||.|..|.|+.+..++   .++|||||+|.+.++|.+||..|||..|
T Consensus         9 ~~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   88 (111)
T 2cpi_A            9 SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   88 (111)
T ss_dssp             CCCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             cccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEE
Confidence            3444567899999999999999999   999999999999999887654   4569999999999999999999999999


Q ss_pred             CCeEEEEeeecCCCCC
Q 011668          205 DGRRVLVDVERGRTVP  220 (480)
Q Consensus       205 ~gr~l~V~~a~~~~~~  220 (480)
                      +|+.|.|.|+.++...
T Consensus        89 ~gr~l~V~~a~~k~~~  104 (111)
T 2cpi_A           89 DGRTLKASLGTTKYCS  104 (111)
T ss_dssp             TTEEEEEESCCCCSCS
T ss_pred             CCEEEEEEeccccccc
Confidence            9999999999876643

>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=99.76  E-value=3.2e-18  Score=136.37  Aligned_cols=80  Identities=23%  Similarity=0.471  Sum_probs=75.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||. +++..|+|+.|.|.+
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            4467899999999999999999999999999999999999999999999999999999999997 688899999999987


Q ss_pred             e
Q 011668          214 E  214 (480)
Q Consensus       214 a  214 (480)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=1e-17  Score=140.51  Aligned_cols=84  Identities=26%  Similarity=0.388  Sum_probs=78.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+++++|.++|++||.|..|.|+.+. ++.++|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34567899999999999999999999999999999999987 59999999999999999999999999999999999999


Q ss_pred             eecCC
Q 011668          213 VERGR  217 (480)
Q Consensus       213 ~a~~~  217 (480)
                      |+...
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            98753

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.76  E-value=4e-19  Score=145.76  Aligned_cols=81  Identities=20%  Similarity=0.331  Sum_probs=77.7

Q ss_pred             CCCEEEEcCCCC------CCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC-eE
Q 011668          136 PYKTLFVARLSY------ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG-RR  208 (480)
Q Consensus       136 ~~~~l~V~nL~~------~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g-r~  208 (480)
                      ..++|||+|||+      .+++++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|.+||..|||..|.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            357999999999      99999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             EEEeeecC
Q 011668          209 VLVDVERG  216 (480)
Q Consensus       209 l~V~~a~~  216 (480)
                      |.|.++.+
T Consensus        85 l~V~~a~~   92 (100)
T 3ns6_A           85 LFLYTMKD   92 (100)
T ss_dssp             CEEEESHH
T ss_pred             EEEEECch
Confidence            99999875

>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=99.76  E-value=8.4e-18  Score=138.46  Aligned_cols=84  Identities=31%  Similarity=0.511  Sum_probs=77.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+++++|..+|++||.|..|.|+.+..  .++|||||+|.+.++|..||..|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            345678999999999999999999999999999999998854  368999999999999999999999999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      |+.+..
T Consensus        89 ~a~~~~   94 (103)
T 2cqi_A           89 WATTPS   94 (103)
T ss_dssp             ECCCTT
T ss_pred             ECCCCc
Confidence            998644

>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=99.76  E-value=1.5e-18  Score=149.13  Aligned_cols=88  Identities=38%  Similarity=0.605  Sum_probs=81.9

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          131 NVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       131 ~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      .....+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|+|+.|.
T Consensus        40 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~  119 (129)
T 2kxn_B           40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR  119 (129)
T ss_dssp             SSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34456778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeecCCC
Q 011668          211 VDVERGRT  218 (480)
Q Consensus       211 V~~a~~~~  218 (480)
                      |.|+..+.
T Consensus       120 V~~a~~~~  127 (129)
T 2kxn_B          120 VDFSITKR  127 (129)
T ss_dssp             ESCCSSSS
T ss_pred             EEEecCCC
Confidence            99997643

>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=99.76  E-value=2.2e-18  Score=145.07  Aligned_cols=80  Identities=23%  Similarity=0.478  Sum_probs=74.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.|.++..
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            4689999999999999999999999999999999885  45799999999999999999999999999999999999875


Q ss_pred             CC
Q 011668          217 RT  218 (480)
Q Consensus       217 ~~  218 (480)
                      ..
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=9.6e-18  Score=138.18  Aligned_cols=79  Identities=24%  Similarity=0.474  Sum_probs=72.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+        ++||||+|.+.++|.+||..|||..|.|+.|.|.|
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3467899999999999999999999999999999986        35999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 011668          214 ERGRTVP  220 (480)
Q Consensus       214 a~~~~~~  220 (480)
                      +......
T Consensus        80 a~~~~~~   86 (103)
T 2dgu_A           80 AKPPDQK   86 (103)
T ss_dssp             CCCCCCC
T ss_pred             cCCCccc
Confidence            9875543

>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=99.75  E-value=6.4e-18  Score=137.44  Aligned_cols=81  Identities=17%  Similarity=0.302  Sum_probs=75.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHH----HHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          136 PYKTLFVARLSYETTESKIK----REFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~----~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ..++|||+|||+.+++++|.    ++|++||.|..|.|+.+..+   +|||||+|.+.++|..||..|||..|+|+.|.|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            45799999999999999999    99999999999999998765   789999999999999999999999999999999


Q ss_pred             eeecCCCC
Q 011668          212 DVERGRTV  219 (480)
Q Consensus       212 ~~a~~~~~  219 (480)
                      .++.+...
T Consensus        85 ~~a~~~~~   92 (96)
T 2dgx_A           85 SLATGASG   92 (96)
T ss_dssp             EECCCSSC
T ss_pred             EEcCCCCC
Confidence            99976543

>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=99.75  E-value=2e-18  Score=144.96  Aligned_cols=80  Identities=20%  Similarity=0.491  Sum_probs=76.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+|||+.+++++|.++|+.||.|..|.|+.+..++.++|||||+|.+.++|.+|| .|||..|+|+.|.|.++..
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            479999999999999999999999999999999999999999999999999999999999 8999999999999999875


Q ss_pred             C
Q 011668          217 R  217 (480)
Q Consensus       217 ~  217 (480)
                      .
T Consensus       104 ~  104 (114)
T 2cq4_A          104 E  104 (114)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.75  E-value=3.6e-18  Score=136.23  Aligned_cols=81  Identities=23%  Similarity=0.502  Sum_probs=76.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCC-ccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNK-PRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~-~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ..++|||+|||+.+|+++|.++|++||.|..|.|+.+..++. ++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            457999999999999999999999999999999999887766 8999999999999999999999999999999999999


Q ss_pred             cC
Q 011668          215 RG  216 (480)
Q Consensus       215 ~~  216 (480)
                      .+
T Consensus        83 ~~   84 (88)
T 4a8x_A           83 LA   84 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.3e-18  Score=140.52  Aligned_cols=82  Identities=15%  Similarity=0.297  Sum_probs=73.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcC--CceeCCeEEEE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD--GRKLDGRRVLV  211 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~--g~~i~gr~l~V  211 (480)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|..||..|+  +..|.|+.|.|
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            346789999999999999999999999999999999864      6899999999999999999886  47899999999


Q ss_pred             eeecCCCCCC
Q 011668          212 DVERGRTVPN  221 (480)
Q Consensus       212 ~~a~~~~~~~  221 (480)
                      .|+..+....
T Consensus        87 ~~A~~~~~~~   96 (105)
T 1sjq_A           87 QFSNHKELKT   96 (105)
T ss_dssp             CCCSSSSCCC
T ss_pred             EEcCCCCCCc
Confidence            9998765543

>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=99.75  E-value=4.8e-18  Score=135.86  Aligned_cols=79  Identities=24%  Similarity=0.570  Sum_probs=76.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+|||+.+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|.+|| .|||..|+|+.|.|.++.+
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            369999999999999999999999999999999999989999999999999999999999 8999999999999999875

>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=99.75  E-value=1.2e-17  Score=137.61  Aligned_cols=85  Identities=20%  Similarity=0.391  Sum_probs=78.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+++++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|..||.  ++..|+|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999998  4789999999999


Q ss_pred             eecCCCC
Q 011668          213 VERGRTV  219 (480)
Q Consensus       213 ~a~~~~~  219 (480)
                      |+..+..
T Consensus        89 ~a~~~~~   95 (103)
T 2cqg_A           89 LPNSKQS   95 (103)
T ss_dssp             CCCTTCC
T ss_pred             ecCCCCc
Confidence            9987544

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.1e-18  Score=145.31  Aligned_cols=83  Identities=25%  Similarity=0.533  Sum_probs=78.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+|+++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|..||.. ++..|+|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            347999999999999999999999999999999999999999999999999999999999996 9999999999999998


Q ss_pred             CCCC
Q 011668          216 GRTV  219 (480)
Q Consensus       216 ~~~~  219 (480)
                      ++..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            6543

>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=99.75  E-value=2.4e-18  Score=140.32  Aligned_cols=83  Identities=18%  Similarity=0.249  Sum_probs=78.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ....++|||+|||+.+++++|+.+|++||.|..+.++.+..++.++|||||+|.+.++|.+||..|||..|+|+.|.|.+
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            44568999999999999999999999999999888888888999999999999999999999999999999999999999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      +..
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            874

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.75  E-value=4.6e-18  Score=141.71  Aligned_cols=84  Identities=24%  Similarity=0.485  Sum_probs=75.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|..+|+.||.|..|.|+.+..||.++|||||+|.+.++|..||..+ +..|+|+.|.|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            446789999999999999999999999999999999999999999999999999999999999976 5999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +.++.
T Consensus       101 a~~~~  105 (109)
T 2rs2_A          101 AFPRR  105 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            97643

>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=99.75  E-value=4e-18  Score=138.15  Aligned_cols=81  Identities=26%  Similarity=0.475  Sum_probs=76.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.+.. +.++|||||+|.+.++|.+||..|||..|+|+.|.|.|
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            34668999999999999999999999999999999999876 89999999999999999999999999999999999999


Q ss_pred             ec
Q 011668          214 ER  215 (480)
Q Consensus       214 a~  215 (480)
                      +.
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            86

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.75  E-value=3.7e-18  Score=151.56  Aligned_cols=82  Identities=17%  Similarity=0.347  Sum_probs=77.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCC--CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYG--PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G--~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..++|||+|||+++|+++|.++|+.||  .|..|.|+.++.||.++|||||+|.+.++|..||..|||..|+|+.|.|.+
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            457999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      +...
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8753

>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=99.75  E-value=1.8e-17  Score=137.76  Aligned_cols=77  Identities=19%  Similarity=0.307  Sum_probs=71.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC-----eEE
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG-----RRV  209 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g-----r~l  209 (480)
                      ...++|||+|||+.+|+++|+++|++||.|..|.|+.+       |||||+|.+.++|++||..|||..|.|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            35689999999999999999999999999999999875       899999999999999999999999999     999


Q ss_pred             EEeeecCCC
Q 011668          210 LVDVERGRT  218 (480)
Q Consensus       210 ~V~~a~~~~  218 (480)
                      .|.++.++.
T Consensus        86 ~V~~a~~~~   94 (108)
T 1x4c_A           86 RVKVDGPRS   94 (108)
T ss_dssp             EEEESSCCS
T ss_pred             EEEeCCCCC
Confidence            999998643

>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=99.74  E-value=5.5e-18  Score=152.04  Aligned_cols=85  Identities=29%  Similarity=0.436  Sum_probs=79.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.||.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            34568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +....
T Consensus       149 a~~~~  153 (165)
T 1rk8_A          149 CFVKG  153 (165)
T ss_dssp             SEECC
T ss_pred             ecCCC
Confidence            98644

>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=99.74  E-value=1.9e-17  Score=135.77  Aligned_cols=83  Identities=14%  Similarity=0.268  Sum_probs=74.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHc--CCceeCCeEEE
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA--DGRKLDGRRVL  210 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l--~g~~i~gr~l~  210 (480)
                      ...|.++|||+|||+.+|+++|.++|++||.|..|.|+.+      +|||||+|.+.++|..||..|  ++..|.|+.|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3457899999999999999999999999999999998764      689999999999999999976  57889999999


Q ss_pred             EeeecCCCCCC
Q 011668          211 VDVERGRTVPN  221 (480)
Q Consensus       211 V~~a~~~~~~~  221 (480)
                      |.|+.......
T Consensus        85 V~~a~~~~~~~   95 (101)
T 2cq1_A           85 IQYSNHKELKT   95 (101)
T ss_dssp             EEECSCSSCCC
T ss_pred             EEEcCcccCcC
Confidence            99998766544

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.5e-17  Score=133.62  Aligned_cols=82  Identities=20%  Similarity=0.372  Sum_probs=76.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ....++|||+|||+.+++++|.++|+.| .|..|.|+.+ .+|.++|||||+|.+.++|..||. |||..|+|+.|.|.+
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            3456899999999999999999999999 9999999998 789999999999999999999999 999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +....
T Consensus        84 a~~~~   88 (91)
T 2dgw_A           84 EKSGP   88 (91)
T ss_dssp             ESSCC
T ss_pred             CCcCC
Confidence            98653

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.74  E-value=2.7e-18  Score=148.01  Aligned_cols=84  Identities=23%  Similarity=0.430  Sum_probs=78.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeE--EEecccCCCCCccceEEEEEechhhHHHHHHHcCCc----eeCCe
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKR--VRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGR----KLDGR  207 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~--v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~----~i~gr  207 (480)
                      ..+.++|||+|||+.+|+++|.++|++||.|..  |.|+.++.||.++|||||+|.+. +|..||..|||.    .|+|+
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            356789999999999999999999999999976  99999999999999999999999 999999999999    99999


Q ss_pred             EEEEeeecCCC
Q 011668          208 RVLVDVERGRT  218 (480)
Q Consensus       208 ~l~V~~a~~~~  218 (480)
                      .|.|.|+.+..
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999998643

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=9.1e-18  Score=139.88  Aligned_cols=86  Identities=19%  Similarity=0.467  Sum_probs=78.2

Q ss_pred             CCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          131 NVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       131 ~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      .....+.++|||+|||+.+++++|..+|++||.|..|.|+.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3344567899999999999999999999999999999999885  45899999999999999999999999999999999


Q ss_pred             EeeecCCC
Q 011668          211 VDVERGRT  218 (480)
Q Consensus       211 V~~a~~~~  218 (480)
                      |.++.++.
T Consensus       101 V~~a~~~~  108 (109)
T 2err_A          101 VNNATARV  108 (109)
T ss_dssp             EEECCCSC
T ss_pred             EEECCCCc
Confidence            99998653

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2.7e-18  Score=141.49  Aligned_cols=79  Identities=14%  Similarity=0.270  Sum_probs=75.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+|+++|.++|++||.|..|.|+.+.. +.++|||||+|.+.++|..||. ++|..|+|+.|.|.++.
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            457999999999999999999999999999999999987 9999999999999999999999 99999999999999876


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.74  E-value=7.8e-18  Score=135.56  Aligned_cols=82  Identities=21%  Similarity=0.399  Sum_probs=76.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+++++|+.+|++||.|..|.|+.+  ++.++|||||+|.+.++|..||..|||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            46789999999999999999999999999999999874  7889999999999999999999999999999999999999


Q ss_pred             cCCC
Q 011668          215 RGRT  218 (480)
Q Consensus       215 ~~~~  218 (480)
                      .+..
T Consensus        84 ~~~~   87 (92)
T 2dgv_A           84 RNAS   87 (92)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            8644

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.74  E-value=2e-17  Score=141.10  Aligned_cols=85  Identities=22%  Similarity=0.383  Sum_probs=79.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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 899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 011668          214 ERGRTV  219 (480)
Q Consensus       214 a~~~~~  219 (480)
                      |.....
T Consensus       111 a~~~~~  116 (124)
T 2kt5_A          111 VASQID  116 (124)
T ss_dssp             ECCTTC
T ss_pred             eCCCCC
Confidence            987543

>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=99.74  E-value=2e-18  Score=141.60  Aligned_cols=82  Identities=28%  Similarity=0.483  Sum_probs=74.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccC-CCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDK-ETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~-~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..+.++|||+|||+.+++++|..+|+.|| |..|.|+.+. .+|.++|||||+|.+.++|..|| .|||..|+|+.|.|.
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            44678999999999999999999999999 9999999998 68999999999999999999999 899999999999999


Q ss_pred             eecCC
Q 011668          213 VERGR  217 (480)
Q Consensus       213 ~a~~~  217 (480)
                      ++.+.
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            98754

>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=99.73  E-value=2.5e-18  Score=139.33  Aligned_cols=80  Identities=18%  Similarity=0.235  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+|+++|.++|++||.|..+.++.+..++.++|||||+|.+.++|.+||..|||..|+|+.|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            46899999999999999999999999999989898888899999999999999999999999999999999999999875

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.73  E-value=7.9e-18  Score=143.91  Aligned_cols=81  Identities=15%  Similarity=0.294  Sum_probs=73.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEE
Q 011668          134 GDPYKTLFVARLSYETTESKIK----REFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV  209 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~----~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l  209 (480)
                      ..|.++|||+|||+.+++++|+    ++|++||.|..|.|..   ++.++|||||+|.+.++|..||..|||..|.|+.|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            4567899999999999998865    7999999999988854   58899999999999999999999999999999999


Q ss_pred             EEeeecCC
Q 011668          210 LVDVERGR  217 (480)
Q Consensus       210 ~V~~a~~~  217 (480)
                      .|.|+...
T Consensus       103 ~V~~a~~~  110 (127)
T 2a3j_A          103 VITFSETP  110 (127)
T ss_dssp             EEEECCCC
T ss_pred             EEEEccCc
Confidence            99999754

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.8e-17  Score=135.96  Aligned_cols=82  Identities=30%  Similarity=0.543  Sum_probs=74.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|+++|++||.|   .|+.+ .++.++|||||+|.+.++|.+||..|||..|.|+.|.|.|
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            4467899999999999999999999999987   56665 5789999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 011668          214 ERGRTV  219 (480)
Q Consensus       214 a~~~~~  219 (480)
                      +.+...
T Consensus        88 a~~~~~   93 (101)
T 2fc9_A           88 QGPRGS   93 (101)
T ss_dssp             CSSCCC
T ss_pred             cCCCCC
Confidence            986543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.73  E-value=8.6e-18  Score=139.04  Aligned_cols=82  Identities=26%  Similarity=0.372  Sum_probs=75.3

Q ss_pred             CCCCCCEEEEcCCCCCC------CHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC
Q 011668          133 SGDPYKTLFVARLSYET------TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG  206 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~------te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g  206 (480)
                      .....++|||+|||+.+      |+++|..+|++||.|..|.|+  ..+|.++|||||+|.+.++|..||..|||..|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            34457899999999999      789999999999999999998  4679999999999999999999999999999999


Q ss_pred             e-EEEEeeecC
Q 011668          207 R-RVLVDVERG  216 (480)
Q Consensus       207 r-~l~V~~a~~  216 (480)
                      + .|.|.++..
T Consensus        89 ~~~l~V~~a~~   99 (105)
T 2nlw_A           89 QHTFRVNLFTD   99 (105)
T ss_dssp             TCEEEEECSCC
T ss_pred             CceEEEEEcch
Confidence            8 999999864

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.3e-18  Score=138.08  Aligned_cols=81  Identities=20%  Similarity=0.327  Sum_probs=76.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+++++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|+.|+|.++
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            46789999999999999999999999999999999999999999999999999999999999999999999999988775


Q ss_pred             c
Q 011668          215 R  215 (480)
Q Consensus       215 ~  215 (480)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.73  E-value=2.3e-18  Score=144.78  Aligned_cols=83  Identities=16%  Similarity=0.282  Sum_probs=77.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCe-eEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPI-KRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i-~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..+.++|||+|||+.+|+++|.++|+.||.| ..|.|+.+. ++.++|||||+|.+.++|.+||.. |+..|+|+.|.|.
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            4467899999999999999999999999999 899999998 899999999999999999999996 9999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      ++....
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            987643

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=136.74  Aligned_cols=86  Identities=37%  Similarity=0.643  Sum_probs=77.0

Q ss_pred             CCCCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEE
Q 011668          130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV  209 (480)
Q Consensus       130 ~~~~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l  209 (480)
                      +.....+.++|||+|||+.+|+++|.++|+.|+   .|.|+.+..++.++|||||+|.+.++|..||..|||..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   84 (102)
T 2fc8_A            8 PNARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKV   84 (102)
T ss_dssp             TSSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            344456788999999999999999999999874   57778888889999999999999999999999999999999999


Q ss_pred             EEeeecCCC
Q 011668          210 LVDVERGRT  218 (480)
Q Consensus       210 ~V~~a~~~~  218 (480)
                      .|.|+.++.
T Consensus        85 ~V~~a~~~~   93 (102)
T 2fc8_A           85 TLDWAKPKG   93 (102)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEecCCC
Confidence            999998644

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.73  E-value=1.2e-17  Score=142.44  Aligned_cols=79  Identities=29%  Similarity=0.594  Sum_probs=75.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      ++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..|| .|||..|+|+.|.|.|+...
T Consensus        37 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             TEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCC
Confidence            69999999999999999999999999999999999889999999999999999999999 79999999999999998753

>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=99.73  E-value=7.1e-18  Score=138.80  Aligned_cols=83  Identities=22%  Similarity=0.269  Sum_probs=75.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+|+++|+++|+.||. +.|.|+.++ ++.++|||||+|.+.++|++||. ||+..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            3446689999999999999999999999994 599999998 89999999999999999999995 89999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      ++....
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            987543

>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=99.73  E-value=2.3e-17  Score=146.71  Aligned_cols=85  Identities=33%  Similarity=0.576  Sum_probs=80.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34578999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +.+..
T Consensus       147 a~~~~  151 (158)
T 2kn4_A          147 ARYGR  151 (158)
T ss_dssp             ECCSS
T ss_pred             CCCCC
Confidence            98643

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.73  E-value=3.4e-18  Score=132.23  Aligned_cols=75  Identities=25%  Similarity=0.447  Sum_probs=72.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      +|||+|||+.+++++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|++|+. |||..|+|+.|.|.+|
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            49999999999999999999999999999999999899999999999999999999998 9999999999999875

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.7e-17  Score=137.98  Aligned_cols=85  Identities=21%  Similarity=0.273  Sum_probs=78.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCC-eeEEEec-ccCCCCCccceEEEEEechhhHHHHHHHcC--CceeCCeEEE
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGP-IKRVRLV-TDKETNKPRGYAFIEYMHTRDMKAAYKQAD--GRKLDGRRVL  210 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~-i~~v~i~-~d~~t~~~~g~afV~F~~~~~a~~A~~~l~--g~~i~gr~l~  210 (480)
                      .+.++|||+|||+.+|+++|.++|++||. |..|.|+ .+..++.++|||||+|.+.++|..||..||  +..|+|+.|.
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            35689999999999999999999999998 9999998 888889999999999999999999999996  5899999999


Q ss_pred             EeeecCCCC
Q 011668          211 VDVERGRTV  219 (480)
Q Consensus       211 V~~a~~~~~  219 (480)
                      |.|+.+...
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987554

>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=99.73  E-value=4.8e-18  Score=140.10  Aligned_cols=83  Identities=36%  Similarity=0.689  Sum_probs=78.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            34789999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ...
T Consensus        87 ~~~   89 (104)
T 1p1t_A           87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            643

>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=99.73  E-value=4.5e-18  Score=160.73  Aligned_cols=81  Identities=17%  Similarity=0.339  Sum_probs=76.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCC--CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYG--PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G--~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..++|||+||++.||+++|+++|++||  .|+.|.|+.++.|+.++|||||+|.+.++|.+||..|||+.|+|+.|+|.+
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            456899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.73  E-value=1.1e-17  Score=131.37  Aligned_cols=74  Identities=12%  Similarity=0.185  Sum_probs=69.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+.-|||+||++.+|+++|+++|.+||+|..+.|+.      ++|||||+|.+.++|.+|+..|||..|.|+.|.|++|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            356799999999999999999999999999999865      58999999999999999999999999999999999984

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.73  E-value=1.7e-17  Score=134.83  Aligned_cols=79  Identities=15%  Similarity=0.275  Sum_probs=71.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCce--eCCeEEEE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRK--LDGRRVLV  211 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~--i~gr~l~V  211 (480)
                      ..|+++|||+|||+.+|+++|.++|++||.|..|.|+.      .+|||||+|.+.++|..||..|++..  |.|+.|.|
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 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            34788999999999999999999999999999999975      36899999999999999999999875  88999999


Q ss_pred             eeecCCC
Q 011668          212 DVERGRT  218 (480)
Q Consensus       212 ~~a~~~~  218 (480)
                      +|++.+.
T Consensus        92 ~~S~~k~   98 (100)
T 3r27_A           92 NYSTSQK   98 (100)
T ss_dssp             EECSCSC
T ss_pred             Eeccccc
Confidence            9998653

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.72  E-value=2.2e-17  Score=143.54  Aligned_cols=81  Identities=28%  Similarity=0.506  Sum_probs=76.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|+|+.|.|.|
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            34678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             e
Q 011668          214 E  214 (480)
Q Consensus       214 a  214 (480)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            6

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.4e-17  Score=132.26  Aligned_cols=78  Identities=23%  Similarity=0.459  Sum_probs=72.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|..+|++||.|..|.|+        +|||||+|.+.++|..||..|||..|+|+.|.|.|
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            3467899999999999999999999999999999997        47999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 011668          214 ERGRTV  219 (480)
Q Consensus       214 a~~~~~  219 (480)
                      +.....
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            986543

>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=99.72  E-value=2.2e-17  Score=136.27  Aligned_cols=84  Identities=14%  Similarity=0.197  Sum_probs=76.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeE-EEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKR-VRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~-v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..+.++|||+|||+.+|+++|.++|++||.|.. |.|+.+ .++.++|||||+|.+.++|.+||.. |+..|+|+.|.|.
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            345689999999999999999999999999987 888888 7899999999999999999999996 9999999999999


Q ss_pred             eecCCCC
Q 011668          213 VERGRTV  219 (480)
Q Consensus       213 ~a~~~~~  219 (480)
                      ++.....
T Consensus        90 ~~~~~~~   96 (104)
T 1wg5_A           90 KSSRAEV   96 (104)
T ss_dssp             EECTTTS
T ss_pred             ECCHHHH
Confidence            9876543

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=4e-18  Score=143.31  Aligned_cols=86  Identities=24%  Similarity=0.373  Sum_probs=74.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.+..+..++.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            34678999999999999999999999999984333322223688999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 011668          214 ERGRTV  219 (480)
Q Consensus       214 a~~~~~  219 (480)
                      +.....
T Consensus       102 a~~~~~  107 (115)
T 2cpx_A          102 GKNKKQ  107 (115)
T ss_dssp             CCCCSC
T ss_pred             ccCCCC
Confidence            986543

>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=99.72  E-value=1.6e-17  Score=136.22  Aligned_cols=80  Identities=18%  Similarity=0.202  Sum_probs=72.1

Q ss_pred             CCCCCCCEEEEcCCCC-CCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCC--ceeCCeE
Q 011668          132 VSGDPYKTLFVARLSY-ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADG--RKLDGRR  208 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~-~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g--~~i~gr~  208 (480)
                      ....|.++|||+|||+ .+|+++|.++|++||.|..|.|+.+      +|||||+|.+.++|..||..||+  ..|.|+.
T Consensus        10 ~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~   83 (102)
T 1x4d_A           10 GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKP   83 (102)
T ss_dssp             CCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcE
Confidence            3455789999999999 9999999999999999999999864      47999999999999999999886  4599999


Q ss_pred             EEEeeecCC
Q 011668          209 VLVDVERGR  217 (480)
Q Consensus       209 l~V~~a~~~  217 (480)
                      |.|.|+...
T Consensus        84 l~V~~a~~~   92 (102)
T 1x4d_A           84 VRVHLSQKY   92 (102)
T ss_dssp             CEEEEECCC
T ss_pred             EEEEECCCC
Confidence            999999853

>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=99.72  E-value=2.2e-17  Score=138.91  Aligned_cols=83  Identities=14%  Similarity=0.304  Sum_probs=74.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCC--ceeCCeEEE
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADG--RKLDGRRVL  210 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g--~~i~gr~l~  210 (480)
                      ...|.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+||..|++  ..|.|+.|.
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            3457889999999999999999999999999999999864      68999999999999999998874  689999999


Q ss_pred             EeeecCCCCCC
Q 011668          211 VDVERGRTVPN  221 (480)
Q Consensus       211 V~~a~~~~~~~  221 (480)
                      |.|+..+....
T Consensus       101 V~~a~~k~~~~  111 (119)
T 2ad9_A          101 IQFSNHKELKT  111 (119)
T ss_dssp             EEECSSSSCCC
T ss_pred             EEEccCCCCCc
Confidence            99998765543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.72  E-value=5.5e-18  Score=146.82  Aligned_cols=87  Identities=32%  Similarity=0.558  Sum_probs=81.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|+.||..|||..|+|+.|.|.
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  122 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  122 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34467899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 011668          213 VERGRTV  219 (480)
Q Consensus       213 ~a~~~~~  219 (480)
                      |+.....
T Consensus       123 ~a~~~~~  129 (135)
T 2lea_A          123 MARYGRP  129 (135)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9986443

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=6.7e-17  Score=130.20  Aligned_cols=78  Identities=28%  Similarity=0.538  Sum_probs=71.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+++++|..+|++||.|..|.|+.        +||||+|.+.++|.+||..|||..|.|+.|.|.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            345678999999999999999999999999999999974        499999999999999999999999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      |+.+..
T Consensus        78 ~a~~~~   83 (92)
T 2dgt_A           78 LSTSRL   83 (92)
T ss_dssp             ESSCCC
T ss_pred             EccCCC
Confidence            998654

>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=99.71  E-value=2.8e-18  Score=137.68  Aligned_cols=81  Identities=27%  Similarity=0.574  Sum_probs=74.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      ++|||+|||+.+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.+ |..|+..|||..|+|+.|.|.+|...
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            58999999999999999999999999999999999999999999999999999 99999999999999999999999875


Q ss_pred             CC
Q 011668          218 TV  219 (480)
Q Consensus       218 ~~  219 (480)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            44

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=5.8e-18  Score=131.50  Aligned_cols=76  Identities=24%  Similarity=0.524  Sum_probs=73.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ++|||+|||+.+++++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|+ ..|+|+.|.|.+|
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            479999999999999999999999999999999999899999999999999999999999999 9999999999987

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.55  E-value=5.4e-19  Score=149.03  Aligned_cols=83  Identities=30%  Similarity=0.423  Sum_probs=78.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeE--------EEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCe
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKR--------VRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR  207 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~--------v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr  207 (480)
                      +.++|||+|||+.+++++|..+|++||.|..        |.|+.++.++.++|||||+|.+.++|..||..|||..|.|+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   85 (116)
Confidence            5679999999999999999999999999998        89999988999999999999999999999999999999999


Q ss_pred             EEEEeeecCCC
Q 011668          208 RVLVDVERGRT  218 (480)
Q Consensus       208 ~l~V~~a~~~~  218 (480)
                      .|.|.++....
T Consensus        86 ~l~V~~a~~~~   96 (116)
T 2lcw_A           86 PIKVSFATRRA   96 (116)
Confidence            99999998654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.71  E-value=2.6e-17  Score=137.20  Aligned_cols=77  Identities=10%  Similarity=0.084  Sum_probs=71.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCC-CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYG-PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ..++|||+|||+.+++++|+++|++|| .|..|.|+.    ..++|||||+|.+.++|+.||..|||..|+|+.|.|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            457999999999999999999999999 999998864    347899999999999999999999999999999999998


Q ss_pred             cC
Q 011668          215 RG  216 (480)
Q Consensus       215 ~~  216 (480)
                      ..
T Consensus       103 ~~  104 (111)
T 2jvr_A          103 DN  104 (111)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>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=99.71  E-value=5.2e-17  Score=132.16  Aligned_cols=79  Identities=28%  Similarity=0.507  Sum_probs=72.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC--CeEEEE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD--GRRVLV  211 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~--gr~l~V  211 (480)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.+      +|||||+|.+.++|++||..|||..|.  |+.|.|
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            456789999999999999999999999999999999753      689999999999999999999999999  999999


Q ss_pred             eeecCCC
Q 011668          212 DVERGRT  218 (480)
Q Consensus       212 ~~a~~~~  218 (480)
                      .|+.+..
T Consensus        88 ~~a~~~~   94 (97)
T 1why_A           88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998643

>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=99.71  E-value=6.2e-17  Score=134.74  Aligned_cols=78  Identities=17%  Similarity=0.399  Sum_probs=72.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+++++|..+|++||.|..|.|+.+      +|||||+|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   97 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   97 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecC
Confidence            5689999999999999999999999999999999875      6899999999999999999999999999999999998


Q ss_pred             CCCC
Q 011668          216 GRTV  219 (480)
Q Consensus       216 ~~~~  219 (480)
                      ....
T Consensus        98 ~~~~  101 (109)
T 1x4g_A           98 ESPD  101 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.6e-16  Score=129.79  Aligned_cols=77  Identities=31%  Similarity=0.556  Sum_probs=71.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcC--CCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESY--GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~--G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ..+.++|||+|||+.+|+++|..+|++|  |.|..|.++        +|||||+|.+.++|..||..|||..|+|+.|.|
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            3467899999999999999999999999  999999875        479999999999999999999999999999999


Q ss_pred             eeecCCC
Q 011668          212 DVERGRT  218 (480)
Q Consensus       212 ~~a~~~~  218 (480)
                      .|+.+..
T Consensus        84 ~~a~~~~   90 (99)
T 2cpd_A           84 TLAKPVD   90 (99)
T ss_dssp             ECCCCCC
T ss_pred             EECCCCC
Confidence            9998654

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=3.9e-17  Score=136.99  Aligned_cols=82  Identities=16%  Similarity=0.346  Sum_probs=76.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee--------C
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL--------D  205 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i--------~  205 (480)
                      ..+.++|||+|||+.+|+++|..+|+.||.|..|.|+.+. ++.++|||||+|.+.++|..||..|||..|        .
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            3466899999999999999999999999999999999998 899999999999999999999999999999        5


Q ss_pred             CeEEEEeeecC
Q 011668          206 GRRVLVDVERG  216 (480)
Q Consensus       206 gr~l~V~~a~~  216 (480)
                      ++.|.|.|+.+
T Consensus       101 ~~~l~v~~a~p  111 (114)
T 1x5o_A          101 TEPLLCKFSGP  111 (114)
T ss_dssp             SSCBEEEECCC
T ss_pred             CCceeEEccCC
Confidence            78899999874

>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=99.70  E-value=6.6e-17  Score=133.28  Aligned_cols=80  Identities=15%  Similarity=0.240  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCC--ceeCCeEEEE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADG--RKLDGRRVLV  211 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g--~~i~gr~l~V  211 (480)
                      ..|.++|||+|||+.+++++|.++|++||.|..|.|+.+      +|||||+|.+.++|..||..|++  ..|.|+.|.|
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            347789999999999999999999999999999998753      68999999999999999998865  4599999999


Q ss_pred             eeecCCCC
Q 011668          212 DVERGRTV  219 (480)
Q Consensus       212 ~~a~~~~~  219 (480)
                      .|+..+..
T Consensus        86 ~~a~~~~~   93 (104)
T 1wex_A           86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEccCccc
Confidence            99986543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.70  E-value=2e-17  Score=134.49  Aligned_cols=79  Identities=19%  Similarity=0.449  Sum_probs=71.3

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          134 GDPYKTLFVARLSY-ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~-~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..+.++|||+|||+ .+++++|..+|++||.|..|.|.        +|||||+|.+.++|..||..|||..|.|+.|.|.
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            34678999999999 99999999999999999999984        5899999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 011668          213 VERGRTVP  220 (480)
Q Consensus       213 ~a~~~~~~  220 (480)
                      |+.....+
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99865543

>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=99.70  E-value=6.2e-18  Score=146.75  Aligned_cols=81  Identities=19%  Similarity=0.240  Sum_probs=74.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ...++|||+|||+.+|+++|+++|++|| |+.|.|+.++. +.++|||||+|.+.++|++|| .||+..|+|+.|.|.++
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            3567899999999999999999999999 77999999986 999999999999999999999 69999999999999998


Q ss_pred             cCCC
Q 011668          215 RGRT  218 (480)
Q Consensus       215 ~~~~  218 (480)
                      ....
T Consensus       121 ~~~~  124 (139)
T 2hgn_A          121 STTG  124 (139)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7644

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.70  E-value=3.3e-17  Score=138.53  Aligned_cols=81  Identities=17%  Similarity=0.224  Sum_probs=75.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCC---eeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGP---IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~---i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ...++|||+|||+.+|+++|.++|+.||.   |..|.|+.+.. |.++|||||+|.+.++|.+||. ||+..|+|+.|.|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            45689999999999999999999999998   89999999887 9999999999999999999999 9999999999999


Q ss_pred             eeecCC
Q 011668          212 DVERGR  217 (480)
Q Consensus       212 ~~a~~~  217 (480)
                      .++...
T Consensus        93 ~~a~~~   98 (118)
T 2db1_A           93 FKSHRT   98 (118)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998653

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.70  E-value=5.5e-18  Score=139.05  Aligned_cols=83  Identities=18%  Similarity=0.334  Sum_probs=75.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|..+|++||.|.. .++.+..++.++|||||+|.+.++|.+||. |||..|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            346789999999999999999999999999887 677777789999999999999999999999 999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +.++.
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            97643

>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=99.70  E-value=9e-17  Score=130.88  Aligned_cols=77  Identities=17%  Similarity=0.429  Sum_probs=70.8

Q ss_pred             CCCCCCEEEEcCCCC-CCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          133 SGDPYKTLFVARLSY-ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~-~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ...+.++|||+|||+ .+++++|..+|++||.|..|.|.        +|||||+|.+.++|..||..|||..|+|+.|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345678999999998 99999999999999999999983        689999999999999999999999999999999


Q ss_pred             eeecCC
Q 011668          212 DVERGR  217 (480)
Q Consensus       212 ~~a~~~  217 (480)
                      .++...
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            998753

>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=99.70  E-value=2.7e-17  Score=133.72  Aligned_cols=81  Identities=17%  Similarity=0.348  Sum_probs=74.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEE
Q 011668          134 GDPYKTLFVARLSYETTESKIK----REFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV  209 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~----~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l  209 (480)
                      ..+.++|||+|||+.+++++|.    .+|++||.|..|.|+.   ++.++|||||+|.+.++|..|+..|||..|+|+.|
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            3477899999999999999999    9999999999999874   47788999999999999999999999999999999


Q ss_pred             EEeeecCC
Q 011668          210 LVDVERGR  217 (480)
Q Consensus       210 ~V~~a~~~  217 (480)
                      .|.|+.+.
T Consensus        82 ~v~~a~~~   89 (97)
T 1nu4_A           82 RIQYAKTD   89 (97)
T ss_dssp             EEEECSSC
T ss_pred             EEEEccCC
Confidence            99999764

>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=99.69  E-value=9e-17  Score=131.29  Aligned_cols=79  Identities=25%  Similarity=0.373  Sum_probs=73.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|+.+|++||.|..|.|+.+      +|||||+|.+.++|.+||..|||..|.|+.|.|.|
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            456789999999999999999999999999999999753      68999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +....
T Consensus        86 a~~~~   90 (99)
T 2cpj_A           86 ACHSA   90 (99)
T ss_dssp             SSCCS
T ss_pred             cCCCC
Confidence            98644

>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=99.69  E-value=1e-17  Score=142.93  Aligned_cols=82  Identities=16%  Similarity=0.250  Sum_probs=75.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+|+++|..+|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||. |||..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            356899999999999999999999999999886666667789999999999999999999999 9999999999999998


Q ss_pred             cCC
Q 011668          215 RGR  217 (480)
Q Consensus       215 ~~~  217 (480)
                      ...
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            753

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=4.3e-17  Score=132.72  Aligned_cols=79  Identities=23%  Similarity=0.377  Sum_probs=71.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ....++|||+|||+.+++++|..+|++||.|. +.|+.    +.++|||||+|.+.++|..||..|||..|+|+.|.|.+
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            44578999999999999999999999999996 66664    46789999999999999999999999999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      +.+.
T Consensus        91 a~~~   94 (97)
T 2e5j_A           91 ARQQ   94 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9764

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.69  E-value=1.5e-17  Score=130.67  Aligned_cols=72  Identities=29%  Similarity=0.442  Sum_probs=67.6

Q ss_pred             CEEEEcCCCCCC------CHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCe-EEE
Q 011668          138 KTLFVARLSYET------TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR-RVL  210 (480)
Q Consensus       138 ~~l~V~nL~~~~------te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr-~l~  210 (480)
                      ++|||+|||+.+      |+++|..+|++||.|..|.|+  ..+|.++|||||+|.+.++|..||..|||..|+|+ .|+
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 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      779999999999999999987  46799999999999999999999999999999999 887


Q ss_pred             E
Q 011668          211 V  211 (480)
Q Consensus       211 V  211 (480)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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=99.69  E-value=6.1e-17  Score=136.05  Aligned_cols=80  Identities=25%  Similarity=0.456  Sum_probs=74.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|..+|+.||.|..|.|+.+   +.++|||||+|.+.++|..||..|||..|+|+.|.|.|
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            346789999999999999999999999999999999875   55689999999999999999999999999999999999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      +.+
T Consensus        82 a~~   84 (115)
T 3lqv_A           82 YNA   84 (115)
T ss_dssp             CCH
T ss_pred             ecC
Confidence            875

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.69  E-value=6.5e-17  Score=146.60  Aligned_cols=84  Identities=23%  Similarity=0.399  Sum_probs=79.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.+. ++.++|||||+|.+.++|.+||..|||..|+|+.|+|.|
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            3467899999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            97643

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.69  E-value=6.7e-17  Score=134.37  Aligned_cols=77  Identities=22%  Similarity=0.471  Sum_probs=71.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.|+        +|||||+|.+.++|..||..|||..|+|+.|.|.|
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            4467899999999999999999999999999999997        58999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +....
T Consensus       100 a~~~~  104 (108)
T 2jvo_A          100 SKLPA  104 (108)
T ss_dssp             CSCCC
T ss_pred             ecCCC
Confidence            97643

>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=99.69  E-value=5.6e-17  Score=130.90  Aligned_cols=77  Identities=22%  Similarity=0.354  Sum_probs=69.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCC-eeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCC-ceeCCeEEEEe
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGP-IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADG-RKLDGRRVLVD  212 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~-i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g-~~i~gr~l~V~  212 (480)
                      .+.++|||+|||+.+|+++|.++|++||. |..+.|.       ++|||||+|.+.++|..||..||| ..|+|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            46689999999999999999999999999 6655552       468999999999999999999999 99999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      |+.+..
T Consensus        79 ~a~~~~   84 (93)
T 2cqh_A           79 YSVSKK   84 (93)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            998654

>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=99.69  E-value=1.4e-16  Score=132.77  Aligned_cols=74  Identities=24%  Similarity=0.505  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCC-CCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLSYE-TTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~~~-~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      +.++|||+|||+. +++++|..+|++||.|..|.|        ++|||||+|.+.++|..||..|||..|+|+.|.|.|+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4589999999999 999999999999999999988        4689999999999999999999999999999999999


Q ss_pred             cCC
Q 011668          215 RGR  217 (480)
Q Consensus       215 ~~~  217 (480)
                      ...
T Consensus        98 ~~~  100 (110)
T 1wf1_A           98 GEP  100 (110)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>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=99.69  E-value=1.6e-17  Score=128.42  Aligned_cols=75  Identities=28%  Similarity=0.502  Sum_probs=71.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      +|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||. +++..|+|+.|.|.+|
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            59999999999999999999999999999999999999999999999999999999999 5899999999999875

>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=99.69  E-value=1.2e-16  Score=126.60  Aligned_cols=76  Identities=25%  Similarity=0.463  Sum_probs=70.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHc-CCceeCCeEEEEe
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA-DGRKLDGRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l-~g~~i~gr~l~V~  212 (480)
                      ..+.++|||+|||+.+++++|..+|++||.|..|.|+.+      +|||||+|.+.++|..||..| +|..|+|+.|.|.
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            346789999999999999999999999999999999863      689999999999999999988 9999999999999


Q ss_pred             eec
Q 011668          213 VER  215 (480)
Q Consensus       213 ~a~  215 (480)
                      |++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

>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=99.69  E-value=6.9e-17  Score=134.40  Aligned_cols=82  Identities=23%  Similarity=0.250  Sum_probs=72.5

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcC--CceeCCeEEE
Q 011668          134 GDPYKTLFVARLSYE-TTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD--GRKLDGRRVL  210 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~-~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~--g~~i~gr~l~  210 (480)
                      ..|.++|||+|||+. +|+++|.++|++||.|..|.|+.      .+|||||+|.+.++|..||..||  +..|.|+.|.
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 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            457889999999998 99999999999999999999974      36899999999999999999885  4669999999


Q ss_pred             EeeecCCCCCC
Q 011668          211 VDVERGRTVPN  221 (480)
Q Consensus       211 V~~a~~~~~~~  221 (480)
                      |.|+.......
T Consensus        96 V~~a~~~~~~~  106 (112)
T 1x4f_A           96 VDLSEKYKKLV  106 (112)
T ss_dssp             EEEECSCSSSS
T ss_pred             EEECccccccc
Confidence            99998655433

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.8e-16  Score=127.10  Aligned_cols=76  Identities=26%  Similarity=0.451  Sum_probs=70.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.|+.        +||||+|.+.++|..||..|||..|+|+.|.|.+
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 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34678999999999999999999999999999999974        4999999999999999999999999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      +...
T Consensus        78 a~~~   81 (90)
T 2dnp_A           78 STKG   81 (90)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            9764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.5e-16  Score=128.66  Aligned_cols=77  Identities=21%  Similarity=0.403  Sum_probs=69.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+|+++|..+|++||.|..|  +.+..++.   ||||+|.+.++|.+||. |||..|+|+.|.|.++.
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            45799999999999999999999999999987  55555555   99999999999999999 99999999999999887


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      .+.
T Consensus        81 ~~~   83 (94)
T 2e5g_A           81 QKE   83 (94)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            544

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=7.7e-17  Score=134.01  Aligned_cols=77  Identities=16%  Similarity=0.261  Sum_probs=72.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..+|||+|||+.+|+++|+++|+.| .|..|.|+.+.. |.++|||||+|.+.++|.+|| .||+..|+|+.|.|..+..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4689999999999999999999999 899999999976 999999999999999999999 5999999999999988764

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.68  E-value=7.7e-17  Score=132.16  Aligned_cols=75  Identities=16%  Similarity=0.270  Sum_probs=70.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+++++|..+|++||.|..|.|+      .++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            45799999999999999999999999999999997      357899999999999999999999999999999999987


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.68  E-value=5.1e-17  Score=136.67  Aligned_cols=74  Identities=19%  Similarity=0.308  Sum_probs=66.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeE-----EE
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRR-----VL  210 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~-----l~  210 (480)
                      ..++|||+|||+.+|+++|.++|++||.|..|.|+.+       |||||+|.+.++|++||..|||..|+|+.     |+
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            3578999999999999999999999999999999865       89999999999999999999999999998     66


Q ss_pred             EeeecC
Q 011668          211 VDVERG  216 (480)
Q Consensus       211 V~~a~~  216 (480)
                      |..+.+
T Consensus        88 v~~~~~   93 (115)
T 3beg_B           88 VKVDGP   93 (115)
T ss_dssp             EEECC-
T ss_pred             eccCCC
Confidence            666543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.68  E-value=7.7e-17  Score=135.01  Aligned_cols=78  Identities=21%  Similarity=0.295  Sum_probs=71.4

Q ss_pred             CEEEEcCC----CCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEec----hhh----HHHHHH--HcCCce
Q 011668          138 KTLFVARL----SYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH----TRD----MKAAYK--QADGRK  203 (480)
Q Consensus       138 ~~l~V~nL----~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~----~~~----a~~A~~--~l~g~~  203 (480)
                      +.|||+||    |+.|++.+|+.+|+.||+|..|.++.|+.||.++|||||+|.+    +++    |..||.  .|||..
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            58999999    9999999999999999999999999999999999999999996    333    788888  789999


Q ss_pred             eCCeEEEEeeec
Q 011668          204 LDGRRVLVDVER  215 (480)
Q Consensus       204 i~gr~l~V~~a~  215 (480)
                      |+|+.|+|.+..
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999865

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=5.4e-17  Score=133.10  Aligned_cols=76  Identities=30%  Similarity=0.651  Sum_probs=71.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      ++|||+|||+.+|+++|.++|++||.|..|.|+.+     ++|||||+|.+.++|..||..|||..|+|+.|.|.++...
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            48999999999999999999999999999999876     6799999999999999999999999999999999999865


Q ss_pred             C
Q 011668          218 T  218 (480)
Q Consensus       218 ~  218 (480)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.68  E-value=5.9e-17  Score=131.50  Aligned_cols=80  Identities=28%  Similarity=0.444  Sum_probs=72.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|..+|+.||.|..+     ..++.++|||||+|.+.++|..||..|||..|+|+.|.|.+
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            3467899999999999999999999999988766     34688999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +.+..
T Consensus        88 a~~~~   92 (96)
T 1fjc_A           88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             cCCCC
Confidence            97643

>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=99.68  E-value=4.3e-17  Score=140.94  Aligned_cols=80  Identities=18%  Similarity=0.205  Sum_probs=75.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCC---eeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGP---IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~---i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ...++|||+|||+.+|+++|.++|+.||.   |..|.|+.+.. |.++|||||+|.+.++|.+||. |||..|+|+.|.|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            35689999999999999999999999999   89999999987 9999999999999999999999 9999999999999


Q ss_pred             eeecC
Q 011668          212 DVERG  216 (480)
Q Consensus       212 ~~a~~  216 (480)
                      .++..
T Consensus       120 ~~a~~  124 (136)
T 2hgl_A          120 FKSHR  124 (136)
T ss_dssp             EECCH
T ss_pred             EECCh
Confidence            99864

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.67  E-value=1.4e-16  Score=148.88  Aligned_cols=83  Identities=24%  Similarity=0.438  Sum_probs=77.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..|.++|||+|||+.+|+++|.++|++||.|..|.|+.+..|+.++|||||+|.+.++|..||..||+..+.|+.|.|.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      +..
T Consensus        92 ~~~   94 (213)
T 4f02_A           92 SQR   94 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            764

>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=99.67  E-value=3e-17  Score=136.28  Aligned_cols=81  Identities=19%  Similarity=0.188  Sum_probs=76.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCC---eeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGP---IKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~---i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      ....++|||+|||+.+|+++|.++|+.||.   |..|.|+.+.. |.++|||||+|.+.++|.+||. ||+..|+|+.|.
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            346789999999999999999999999998   89999999987 9999999999999999999999 999999999999


Q ss_pred             EeeecC
Q 011668          211 VDVERG  216 (480)
Q Consensus       211 V~~a~~  216 (480)
                      |.++..
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            999875

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=5.8e-16  Score=125.98  Aligned_cols=78  Identities=21%  Similarity=0.404  Sum_probs=70.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+||  .+|+++|..+|++||.|..|.|.      .++|||||+|.+.++|.+||..|||..|+|+.|.|.|
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            446789999996  89999999999999999999984      4678999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 011668          214 ERGRTV  219 (480)
Q Consensus       214 a~~~~~  219 (480)
                      +.....
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            986543

>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=99.67  E-value=2.4e-16  Score=131.20  Aligned_cols=80  Identities=16%  Similarity=0.311  Sum_probs=71.6

Q ss_pred             CCCCCCEEEE--cCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee-----C
Q 011668          133 SGDPYKTLFV--ARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL-----D  205 (480)
Q Consensus       133 ~~~~~~~l~V--~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i-----~  205 (480)
                      ...|+++|||  |||++.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++|+..|||..|     .
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~   94 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   94 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCC
Confidence            3457889999  779999999999999999999999988642      68999999999999999999999998     7


Q ss_pred             CeEEEEeeecCCC
Q 011668          206 GRRVLVDVERGRT  218 (480)
Q Consensus       206 gr~l~V~~a~~~~  218 (480)
                      |..|.|.|+...+
T Consensus        95 g~~l~v~~a~~~p  107 (114)
T 2cq2_A           95 KITLYLNFVEKVQ  107 (114)
T ss_dssp             EEECEEEEESCCC
T ss_pred             CcEEEEEecccCc
Confidence            8999999997543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.66  E-value=1e-16  Score=131.68  Aligned_cols=79  Identities=23%  Similarity=0.517  Sum_probs=74.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+++++|..+|++||.|..|.|+.+. ++.++|||||+|.+.++|..||.  ++..|+|+.|.|.++.
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            45799999999999999999999999999999999998 89999999999999999999998  9999999999999987


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      ..
T Consensus        85 ~~   86 (102)
T 2xs2_A           85 RK   86 (102)
T ss_dssp             EC
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=99.66  E-value=2.5e-16  Score=131.60  Aligned_cols=77  Identities=16%  Similarity=0.255  Sum_probs=71.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+|+++|..+|++||.|..|.|+.      ++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
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            357899999999999999999999999999998864      46899999999999999999999999999999999997


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ...
T Consensus        83 ~~~   85 (111)
T 1whx_A           83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            643

>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=99.66  E-value=5.1e-17  Score=142.11  Aligned_cols=84  Identities=26%  Similarity=0.432  Sum_probs=73.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEE--Eeccc---CCCCCccceEEEEEechhhHHHHHHHcCCceeCCeE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRV--RLVTD---KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRR  208 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v--~i~~d---~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~  208 (480)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|  .++.+   ..++.++|||||+|.+.++|..||..|||..|.|+.
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            4577899999999999999999999999998764  11111   236889999999999999999999999999999999


Q ss_pred             EEEeeecCC
Q 011668          209 VLVDVERGR  217 (480)
Q Consensus       209 l~V~~a~~~  217 (480)
                      |.|.|+...
T Consensus       122 l~V~~a~~~  130 (143)
T 3egn_A          122 MVVQFARSA  130 (143)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999999753

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=3.5e-16  Score=126.93  Aligned_cols=79  Identities=15%  Similarity=0.219  Sum_probs=72.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEE-EecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRV-RLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v-~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ...++|||+|||+.+++++|..+|++||.|..| .|+.++.++    .|||+|.+.++|..||..|||..|+|+.|.|.+
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 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            346899999999999999999999999999999 588776544    499999999999999999999999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      +.+.
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9865

>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=99.65  E-value=3.3e-16  Score=138.02  Aligned_cols=79  Identities=32%  Similarity=0.621  Sum_probs=73.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.|+.+     ++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            446789999999999999999999999999999999876     579999999999999999999999999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      +.+.
T Consensus       145 a~~~  148 (150)
T 2i2y_A          145 SNGE  148 (150)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8753

>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=99.65  E-value=2.5e-16  Score=134.15  Aligned_cols=79  Identities=19%  Similarity=0.212  Sum_probs=72.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCee--EEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIK--RVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~--~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      .+.++|||+|||+.+|+++|+++|+.| .|+  .|.|+.++. |.++|||||+|.+.++|.+||. +++..|+|+.|.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            356789999999999999999999999 677  899999987 9999999999999999999999 57899999999999


Q ss_pred             eecC
Q 011668          213 VERG  216 (480)
Q Consensus       213 ~a~~  216 (480)
                      ++..
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1.5e-16  Score=135.18  Aligned_cols=79  Identities=18%  Similarity=0.232  Sum_probs=72.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCe----eEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPI----KRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i----~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ..++|||+|||+.+|+++|+++|++||.|    ..|.|+.+. +|.++|||||+|.+.++|.+||.. |+..|+|+.|.|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            45799999999999999999999999975    689999884 799999999999999999999995 999999999999


Q ss_pred             eeecC
Q 011668          212 DVERG  216 (480)
Q Consensus       212 ~~a~~  216 (480)
                      ..+..
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.64  E-value=5.3e-16  Score=144.50  Aligned_cols=88  Identities=27%  Similarity=0.470  Sum_probs=82.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+|+++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++|.+||..|||..|+|+.|.|.|+.
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~  203 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV  203 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEec
Confidence            45799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCCCCCC
Q 011668          216 GRTVPNWR  223 (480)
Q Consensus       216 ~~~~~~~~  223 (480)
                      ....+...
T Consensus       204 ~~~~~~~~  211 (216)
T 2qfj_A          204 TPPMPLLT  211 (216)
T ss_dssp             SCSSTTSC
T ss_pred             CCCCCCCC
Confidence            76554433

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.63  E-value=1.2e-15  Score=135.61  Aligned_cols=83  Identities=23%  Similarity=0.460  Sum_probs=78.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|.+||..|||..|+|+.|.|.
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eec
Q 011668          213 VER  215 (480)
Q Consensus       213 ~a~  215 (480)
                      ||.
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            985

>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=99.63  E-value=1.1e-15  Score=136.06  Aligned_cols=81  Identities=28%  Similarity=0.488  Sum_probs=77.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+|||+.+++++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|.|+.|.|.++.+
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            57999999999999999999999999999999999998999999999999999999999999999999999999999875


Q ss_pred             C
Q 011668          217 R  217 (480)
Q Consensus       217 ~  217 (480)
                      .
T Consensus        82 ~   82 (167)
T 1fxl_A           82 S   82 (167)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.63  E-value=8.8e-16  Score=137.09  Aligned_cols=82  Identities=27%  Similarity=0.455  Sum_probs=78.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+++++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|+|..|.|+.|.|.|+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            56899999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      +.
T Consensus        82 ~~   83 (168)
T 1b7f_A           82 PG   83 (168)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.62  E-value=1.1e-15  Score=121.98  Aligned_cols=76  Identities=12%  Similarity=0.264  Sum_probs=70.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+++++|+++|++| .|..|.|.      .++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
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            45789999999999999999999999 99999884      568999999999999999999999999999999999987


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.62  E-value=2.1e-15  Score=138.50  Aligned_cols=85  Identities=28%  Similarity=0.484  Sum_probs=80.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +.+..
T Consensus       191 a~~~~  195 (198)
T 2yh0_A          191 ASVGA  195 (198)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            97643

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=1.1e-15  Score=121.17  Aligned_cols=74  Identities=18%  Similarity=0.327  Sum_probs=66.0

Q ss_pred             CCCCE-EEEcCCCCCCCHHH----HHHHhhcC-CCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeE
Q 011668          135 DPYKT-LFVARLSYETTESK----IKREFESY-GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRR  208 (480)
Q Consensus       135 ~~~~~-l~V~nL~~~~te~~----L~~~F~~~-G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~  208 (480)
                      .|+.| |||+|||+.+++++    |.++|++| |+|..|       |+   |||||.|.+.++|..|++.|||..|.|+.
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            35666 99999999999987    66899999 599887       34   99999999999999999999999999999


Q ss_pred             EEEeeecCCC
Q 011668          209 VLVDVERGRT  218 (480)
Q Consensus       209 l~V~~a~~~~  218 (480)
                      |+|.||+...
T Consensus        76 i~v~~A~~~s   85 (96)
T 2diu_A           76 IIVSFTPKNR   85 (96)
T ss_dssp             CEEESSCCSC
T ss_pred             EEEEecCCCc
Confidence            9999998643

>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=99.61  E-value=1.8e-15  Score=121.06  Aligned_cols=74  Identities=19%  Similarity=0.353  Sum_probs=62.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCce--eCCeEEEEe
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRK--LDGRRVLVD  212 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~--i~gr~l~V~  212 (480)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.+     ++|||||+|.+.++|.+    |+|..  +.|+.|.|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            46789999999999999999999999999999999874     68999999999999883    45554  569999999


Q ss_pred             eecCC
Q 011668          213 VERGR  217 (480)
Q Consensus       213 ~a~~~  217 (480)
                      ++.++
T Consensus        80 ~a~~k   84 (89)
T 3d2w_A           80 NAEPK   84 (89)
T ss_dssp             ECC--
T ss_pred             EcCCC
Confidence            98754

>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=99.61  E-value=1.5e-15  Score=139.25  Aligned_cols=83  Identities=24%  Similarity=0.459  Sum_probs=75.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+|+++|.++|+.||.|..|.|+.+..++.++|||||+|.+.++|.+||.. +|..|+|+.|.|.|+.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            568999999999999999999999999999999999988999999999999999999999985 8999999999999998


Q ss_pred             CCCC
Q 011668          216 GRTV  219 (480)
Q Consensus       216 ~~~~  219 (480)
                      ++..
T Consensus       182 ~k~~  185 (196)
T 1l3k_A          182 SKQE  185 (196)
T ss_dssp             ----
T ss_pred             ChhH
Confidence            7553

>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=99.61  E-value=2.3e-15  Score=134.94  Aligned_cols=79  Identities=29%  Similarity=0.516  Sum_probs=76.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ..++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.||
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            4688999999999999999999999999999999999889999999999999999999999999999999999999997

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.60  E-value=4.3e-15  Score=125.95  Aligned_cols=77  Identities=16%  Similarity=0.221  Sum_probs=68.3

Q ss_pred             CCCE--EEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccce-EEEEEechhhHHHHHHHcCCceeCC--eEEE
Q 011668          136 PYKT--LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGY-AFIEYMHTRDMKAAYKQADGRKLDG--RRVL  210 (480)
Q Consensus       136 ~~~~--l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~-afV~F~~~~~a~~A~~~l~g~~i~g--r~l~  210 (480)
                      |.++  |||+||++.+|+++|.++|++||.|..|.|+..      .|| |||+|.+.++|..|+..|||..|.|  +.|.
T Consensus        22 ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~   95 (124)
T 2e5i_A           22 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLK   95 (124)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEE
T ss_pred             CCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEE
Confidence            4444  679999999999999999999999999998642      276 9999999999999999999999987  6899


Q ss_pred             EeeecCCC
Q 011668          211 VDVERGRT  218 (480)
Q Consensus       211 V~~a~~~~  218 (480)
                      |+||++..
T Consensus        96 V~~Ak~~~  103 (124)
T 2e5i_A           96 IEYARPTR  103 (124)
T ss_dssp             EECCSCSC
T ss_pred             EEEecCCc
Confidence            99998754

>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=99.60  E-value=1.8e-15  Score=133.71  Aligned_cols=78  Identities=17%  Similarity=0.276  Sum_probs=70.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC--eEEEEeee
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG--RRVLVDVE  214 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g--r~l~V~~a  214 (480)
                      ..+|||+||++.+|+++|.++|++||.|..|.|+..    .++|||||+|.+.++|+.|+..|||..|.|  +.|+|+|+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            456999999999999999999999999999998643    357899999999999999999999999965  99999999


Q ss_pred             cCCC
Q 011668          215 RGRT  218 (480)
Q Consensus       215 ~~~~  218 (480)
                      +...
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            8754

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.60  E-value=3.4e-15  Score=123.22  Aligned_cols=83  Identities=20%  Similarity=0.251  Sum_probs=73.8

Q ss_pred             CCCCCEEEEcCCCC-----CCCHHHHHHHhhcCCCeeEEEecccCCC-CCccceEEEEEechhhHHHHHHHcCCceeCCe
Q 011668          134 GDPYKTLFVARLSY-----ETTESKIKREFESYGPIKRVRLVTDKET-NKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR  207 (480)
Q Consensus       134 ~~~~~~l~V~nL~~-----~~te~~L~~~F~~~G~i~~v~i~~d~~t-~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr  207 (480)
                      ..++++|+|.||..     ..++++|.++|++||.|..|.|+.++.+ +.++|||||+|.+.++|.+|+..|||..|+|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            34788999999963     2378999999999999999999988654 68899999999999999999999999999999


Q ss_pred             EEEEeeecC
Q 011668          208 RVLVDVERG  216 (480)
Q Consensus       208 ~l~V~~a~~  216 (480)
                      .|.|.++..
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999864

>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=99.60  E-value=1.3e-15  Score=121.54  Aligned_cols=76  Identities=18%  Similarity=0.323  Sum_probs=65.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+|+++|..+|++||.|..|.|+.+     ++|||||+|.+.++|++|+..  ...+.|..|.|.++.
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            5689999999999999999999999999999999864     679999999999999754331  345699999999987


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ++.
T Consensus        77 ~~~   79 (88)
T 1wf0_A           77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.60  E-value=3.3e-15  Score=127.25  Aligned_cols=79  Identities=18%  Similarity=0.350  Sum_probs=70.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccce-EEEEEechhhHHHHHHHcCCceeCC--eEEEEe
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGY-AFIEYMHTRDMKAAYKQADGRKLDG--RRVLVD  212 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~-afV~F~~~~~a~~A~~~l~g~~i~g--r~l~V~  212 (480)
                      +.-.|||+||++.+|+++|.++|++||.|..|.|+..     .+|| |||+|.+.++|..|+..|||..|.|  ..|+|+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            3346889999999999999999999999999988753     3578 9999999999999999999999988  899999


Q ss_pred             eecCCCC
Q 011668          213 VERGRTV  219 (480)
Q Consensus       213 ~a~~~~~  219 (480)
                      |++....
T Consensus       102 ~ak~~~l  108 (130)
T 3zzy_A          102 FSKLTSL  108 (130)
T ss_dssp             ECSCSSC
T ss_pred             ecCCCce
Confidence            9987543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=3.9e-15  Score=124.89  Aligned_cols=77  Identities=25%  Similarity=0.436  Sum_probs=68.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCC---CCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKET---NKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t---~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..++|||+|||+.+|+++|.++|++||.|. +.++.+..+   |.++|||||+|.+.++|.+||..|+  .|+|+.|.|.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            568899999999999999999999999999 888888877   7999999999999999999999884  3777777776


Q ss_pred             eec
Q 011668          213 VER  215 (480)
Q Consensus       213 ~a~  215 (480)
                      .+.
T Consensus        84 ~~~   86 (114)
T 2dnl_A           84 SSP   86 (114)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            543

>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=99.60  E-value=2.6e-15  Score=137.67  Aligned_cols=83  Identities=29%  Similarity=0.583  Sum_probs=77.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||.. ++..|.|+.|.|.+
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            34678999999999999999999999999999999999999999999999999999999999985 99999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      +...
T Consensus        89 ~~~~   92 (196)
T 1l3k_A           89 AVSR   92 (196)
T ss_dssp             CCC-
T ss_pred             ccCc
Confidence            8754

>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=99.59  E-value=1.4e-15  Score=135.82  Aligned_cols=81  Identities=19%  Similarity=0.392  Sum_probs=76.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+|+++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++|.+|+. |+|..|+|+.|.|.|+.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            35689999999999999999999999999999999998899999999999999999999998 89999999999999997


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.58  E-value=5.3e-15  Score=137.29  Aligned_cols=79  Identities=18%  Similarity=0.267  Sum_probs=72.9

Q ss_pred             CCCCEEEEcCCC-CCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          135 DPYKTLFVARLS-YETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       135 ~~~~~l~V~nL~-~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      .+.++|||+||+ +.+|+++|.++|++||.|..|.|+.+     .+|||||+|.+.++|..||..|||..|.|+.|.|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            367899999999 89999999999999999999999865     369999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +....
T Consensus        77 s~~~~   81 (205)
T 3tyt_A           77 SKQPA   81 (205)
T ss_dssp             CSCSC
T ss_pred             ccCCc
Confidence            87543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.58  E-value=4e-15  Score=138.92  Aligned_cols=80  Identities=23%  Similarity=0.475  Sum_probs=74.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+|+++|.++|++||.|..|.|+.+.  +.++|||||+|.+.++|.+||..|||..|+|+.|.|.++.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            35689999999999999999999999999999999885  4579999999999999999999999999999999999987


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      ++
T Consensus       180 ~~  181 (213)
T 4f02_A          180 SR  181 (213)
T ss_dssp             CH
T ss_pred             CC
Confidence            53

>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=99.58  E-value=3.8e-15  Score=118.28  Aligned_cols=71  Identities=23%  Similarity=0.482  Sum_probs=66.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC----C-------CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESY----G-------PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~----G-------~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      +.++|||+|||+.+++++|.++|++|    |       .|..|.++.+      +|||||+|.+.++|.+|| .|||..|
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            56799999999999999999999999    8       8999998754      689999999999999999 8999999


Q ss_pred             CCeEEEEee
Q 011668          205 DGRRVLVDV  213 (480)
Q Consensus       205 ~gr~l~V~~  213 (480)
                      +|+.|.|+.
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            999999973

>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=99.57  E-value=7.3e-15  Score=131.08  Aligned_cols=81  Identities=25%  Similarity=0.441  Sum_probs=76.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC--eEEEE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG--RRVLV  211 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g--r~l~V  211 (480)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|..|+..|||..|.|  +.|.|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            3467899999999999999999999999999999999998889999999999999999999999999999988  99999


Q ss_pred             eee
Q 011668          212 DVE  214 (480)
Q Consensus       212 ~~a  214 (480)
                      .||
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.56  E-value=1.1e-14  Score=129.51  Aligned_cols=80  Identities=29%  Similarity=0.537  Sum_probs=74.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      ++|||+|||+.+|+++|.++|++||.|..|.|+.++. +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++...
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 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            4899999999999999999999999999999998875 779999999999999999999999999999999999998754


Q ss_pred             C
Q 011668          218 T  218 (480)
Q Consensus       218 ~  218 (480)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.56  E-value=6e-15  Score=137.32  Aligned_cols=80  Identities=30%  Similarity=0.540  Sum_probs=73.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+|||+.+|+++|.++|+.||.|..|.|+.+..++.++|||||+|.+.++|..||..|||..|.|+.|.|.++..
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            46999999999999999999999999999999999998999999999999999999999999999999999999988654

>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=99.55  E-value=1e-14  Score=129.77  Aligned_cols=80  Identities=26%  Similarity=0.431  Sum_probs=74.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeE--EEEe
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRR--VLVD  212 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~--l~V~  212 (480)
                      .+.++|||+|||+.+++++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++|..|+..|||..|.|+.  |.|.
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK  165 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEE
Confidence            35678999999999999999999999999999999999888999999999999999999999999999999975  8887


Q ss_pred             ee
Q 011668          213 VE  214 (480)
Q Consensus       213 ~a  214 (480)
                      ||
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.54  E-value=1.2e-14  Score=129.70  Aligned_cols=79  Identities=22%  Similarity=0.488  Sum_probs=73.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||..  +..|+|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            457999999999999999999999999999999999999999999999999999999999984  678999999999876


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      .
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
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=99.53  E-value=2.1e-14  Score=131.89  Aligned_cols=78  Identities=14%  Similarity=0.275  Sum_probs=71.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.+. ++.++|||||+|.+.++|..||..+ +..|+|+.|.|.++..
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            3699999999999999999999999999999999876 4889999999999999999999855 5699999999998764

>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=99.53  E-value=2e-14  Score=129.31  Aligned_cols=79  Identities=28%  Similarity=0.455  Sum_probs=72.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|.++|+.||.|..+     ..++.++|||||+|.+.++|.+||..|||..|+|+.|.|.|
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  170 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY  170 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEE
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEe
Confidence            3456899999999999999999999999988765     45688999999999999999999999999999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      +.++
T Consensus       171 a~~k  174 (175)
T 1fje_B          171 TGEK  174 (175)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            9764

>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=99.52  E-value=1.3e-13  Score=133.93  Aligned_cols=77  Identities=26%  Similarity=0.409  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC-CeEEEEe
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD-GRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~-gr~l~V~  212 (480)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.+.     +|||||+|.+.++|..||..|||..|+ |+.|+|.
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            4467899999999999999999999999999999998643     589999999999999999999999999 9999999


Q ss_pred             eec
Q 011668          213 VER  215 (480)
Q Consensus       213 ~a~  215 (480)
                      |++
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            986

>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=99.52  E-value=3.9e-14  Score=137.77  Aligned_cols=82  Identities=17%  Similarity=0.351  Sum_probs=75.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEE
Q 011668          134 GDPYKTLFVARLSYETTESKIK----REFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV  209 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~----~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l  209 (480)
                      ..+.++|||+|||+.+|+++|+    ++|+.||.|..|.|+.   ++.++|||||+|.+.++|..||..|||..|.|+.|
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            3467899999999999999966    8999999999999886   68899999999999999999999999999999999


Q ss_pred             EEeeecCCC
Q 011668          210 LVDVERGRT  218 (480)
Q Consensus       210 ~V~~a~~~~  218 (480)
                      .|.|+....
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999987543

>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=99.52  E-value=2.3e-14  Score=128.56  Aligned_cols=80  Identities=23%  Similarity=0.370  Sum_probs=73.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC---CeEEEE
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD---GRRVLV  211 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~---gr~l~V  211 (480)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++|.+||..|||..|.   ++.|.|
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V  171 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV  171 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEE
Confidence            356899999999999999999999999999999999886 4899999999999999999999999998776   499999


Q ss_pred             eeec
Q 011668          212 DVER  215 (480)
Q Consensus       212 ~~a~  215 (480)
                      .||.
T Consensus       172 ~~ad  175 (175)
T 3nmr_A          172 KFAD  175 (175)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9973

>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=99.51  E-value=2.3e-14  Score=128.65  Aligned_cols=82  Identities=16%  Similarity=0.355  Sum_probs=74.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCC--CccceEEEEEechhhHHHHHHHcCCceeC---CeEEE
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETN--KPRGYAFIEYMHTRDMKAAYKQADGRKLD---GRRVL  210 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~--~~~g~afV~F~~~~~a~~A~~~l~g~~i~---gr~l~  210 (480)
                      ..++|||+|||+.+|+++|.++|++||.|..|.|+.+..++  .++|||||+|.+.++|..||..|||..+.   +..|.
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            45799999999999999999999999999999999998876  89999999999999999999999998875   57788


Q ss_pred             EeeecCC
Q 011668          211 VDVERGR  217 (480)
Q Consensus       211 V~~a~~~  217 (480)
                      |.++...
T Consensus        82 ~~~~~~~   88 (175)
T 3nmr_A           82 MKPADSE   88 (175)
T ss_dssp             EEECGGG
T ss_pred             Ecccccc
Confidence            8776643

>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=99.51  E-value=2.5e-14  Score=135.06  Aligned_cols=84  Identities=21%  Similarity=0.428  Sum_probs=76.2

Q ss_pred             CCCCCCCCCCEEEEcCCCC-CCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCe
Q 011668          129 DPNVSGDPYKTLFVARLSY-ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR  207 (480)
Q Consensus       129 ~~~~~~~~~~~l~V~nL~~-~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr  207 (480)
                      .+.....+.++|||+|||+ .+++++|.++|++||.|..|.|+.+.     +|||||+|.+.++|..||..|||..|.|+
T Consensus        26 ~p~~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~  100 (229)
T 2adc_A           26 IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGK  100 (229)
T ss_dssp             CGGGGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSS
T ss_pred             CCCCCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            3344456789999999999 99999999999999999999998764     68999999999999999999999999999


Q ss_pred             EEEEeeecCC
Q 011668          208 RVLVDVERGR  217 (480)
Q Consensus       208 ~l~V~~a~~~  217 (480)
                      .|.|.++...
T Consensus       101 ~l~v~~a~~~  110 (229)
T 2adc_A          101 PIRITLSKHQ  110 (229)
T ss_dssp             BCEEECCSCC
T ss_pred             EEEEEEecCc
Confidence            9999998754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.51  E-value=1.6e-14  Score=135.96  Aligned_cols=80  Identities=25%  Similarity=0.415  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCCCC---------CHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee-
Q 011668          135 DPYKTLFVARLSYET---------TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL-  204 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~---------te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i-  204 (480)
                      .+.++|||+||++.+         ++++|..+|++||.|..|.|+.      ++|||||+|.+.++|+.|+..|+|..| 
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            357899999999998         7999999999999999999985      479999999999999999999999999 


Q ss_pred             -----------CCeEEEEeeecCCCCC
Q 011668          205 -----------DGRRVLVDVERGRTVP  220 (480)
Q Consensus       205 -----------~gr~l~V~~a~~~~~~  220 (480)
                                 .|+.|.|.||...+.+
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             ccccccccccCCCCEEEEEEccCCCCH
Confidence                       8999999999875543

>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=99.51  E-value=3.5e-14  Score=138.80  Aligned_cols=83  Identities=18%  Similarity=0.338  Sum_probs=76.3

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhcCCCeeEEEecccCC-CCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          134 GDPYKTLFVARLSYE-TTESKIKREFESYGPIKRVRLVTDKE-TNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~-~te~~L~~~F~~~G~i~~v~i~~d~~-t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      ..+.++|||+|||+. +|+++|.++|+.||.|..|.|+.+.. ||.++|||||+|.+.++|..|| .|||..|+|+.|.|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            346789999999999 99999999999999999999999876 6999999999999999999999 99999999999999


Q ss_pred             eeecCC
Q 011668          212 DVERGR  217 (480)
Q Consensus       212 ~~a~~~  217 (480)
                      .|+.++
T Consensus       286 ~~a~~k  291 (292)
T 2ghp_A          286 SLADKK  291 (292)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999864

>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=99.50  E-value=1.1e-13  Score=115.57  Aligned_cols=82  Identities=18%  Similarity=0.369  Sum_probs=70.2

Q ss_pred             CCCCCCEEEEcCCCCCCC-----------HHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCC
Q 011668          133 SGDPYKTLFVARLSYETT-----------ESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADG  201 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~t-----------e~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g  201 (480)
                      .+.++++|+|.||.....           +++|.++|++||.|..|.| .+.   .++|||||+|.+.++|..||..|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            445788999999954432           5799999999999999966 443   3789999999999999999999999


Q ss_pred             ceeCCeEEEEeeecCCC
Q 011668          202 RKLDGRRVLVDVERGRT  218 (480)
Q Consensus       202 ~~i~gr~l~V~~a~~~~  218 (480)
                      ..|+|+.|.|.|+.+..
T Consensus        87 ~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             CEECCcEEEEEEeCCCC
Confidence            99999999999987643

>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=99.49  E-value=7.9e-14  Score=115.00  Aligned_cols=82  Identities=21%  Similarity=0.326  Sum_probs=71.5

Q ss_pred             CCCCEEEEcCC--CCCCC--------HHHHHHHhhcCCCeeEEEecccCCC--CCccceEEEEEechhhHHHHHHHcCCc
Q 011668          135 DPYKTLFVARL--SYETT--------ESKIKREFESYGPIKRVRLVTDKET--NKPRGYAFIEYMHTRDMKAAYKQADGR  202 (480)
Q Consensus       135 ~~~~~l~V~nL--~~~~t--------e~~L~~~F~~~G~i~~v~i~~d~~t--~~~~g~afV~F~~~~~a~~A~~~l~g~  202 (480)
                      .|+++|+|.||  +..+.        +++|+++|++||.|..|.|+.+..+  +.++|||||+|.+.++|.+|+..|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            47889999998  33332        3689999999999999999988764  367899999999999999999999999


Q ss_pred             eeCCeEEEEeeecC
Q 011668          203 KLDGRRVLVDVERG  216 (480)
Q Consensus       203 ~i~gr~l~V~~a~~  216 (480)
                      .|+|+.|.|.|+..
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999999753

>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=99.47  E-value=2.2e-14  Score=129.15  Aligned_cols=83  Identities=18%  Similarity=0.335  Sum_probs=73.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ...+.++|||+|||+.+|+++|.++|..||.|.. .++.+..++.++|||||+|.+.++|..||. |||..|.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            3456789999999999999999999999998766 344555678899999999999999999995 99999999999999


Q ss_pred             eecCC
Q 011668          213 VERGR  217 (480)
Q Consensus       213 ~a~~~  217 (480)
                      ++...
T Consensus        87 ~~~~~   91 (175)
T 1fje_B           87 KPKGR   91 (175)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            98754

>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=99.46  E-value=1.7e-13  Score=133.28  Aligned_cols=83  Identities=25%  Similarity=0.380  Sum_probs=78.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+|+++|.++|+.||.|..|.|+.+..+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            55799999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ...
T Consensus       174 ~~~  176 (284)
T 3smz_A          174 AGQ  176 (284)
T ss_dssp             GGG
T ss_pred             CCC
Confidence            643

>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=99.46  E-value=1.4e-13  Score=134.04  Aligned_cols=84  Identities=21%  Similarity=0.229  Sum_probs=78.0

Q ss_pred             CCCCCEEEEcCCCCCC-CHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          134 GDPYKTLFVARLSYET-TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~-te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..+.++|||+|||+.+ ++++|.++|+.||.|..|.|+.+. +|.++|||||+|.+.++|..||..|||..|+|+.|.|.
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  259 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS  259 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEE
Confidence            3467899999999995 999999999999999999999887 69999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      |+.+..
T Consensus       260 ~a~~~~  265 (284)
T 3smz_A          260 FCAPGP  265 (284)
T ss_dssp             ECCSSS
T ss_pred             EecCCC
Confidence            997643

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.46  E-value=7.5e-14  Score=129.48  Aligned_cols=78  Identities=13%  Similarity=0.171  Sum_probs=70.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCe--eEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCe----E
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPI--KRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR----R  208 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i--~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr----~  208 (480)
                      .|.++|||+|||+.+|+++|+++|++||.|  ..|.|+.+.  +..+|||||+|.+.++|..||..|||..|.|.    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            467899999999999999999999999999  899998765  55679999999999999999999999999887    5


Q ss_pred             EEEeee
Q 011668          209 VLVDVE  214 (480)
Q Consensus       209 l~V~~a  214 (480)
                      |.|.||
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            777665

>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=99.45  E-value=1.8e-13  Score=115.17  Aligned_cols=81  Identities=19%  Similarity=0.356  Sum_probs=71.0

Q ss_pred             CCCEEEEcCCCC--CC---CHHHHHHHhhcCCCeeEEEecccCC----CCCccceEEEEEechhhHHHHHHHcCCceeCC
Q 011668          136 PYKTLFVARLSY--ET---TESKIKREFESYGPIKRVRLVTDKE----TNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG  206 (480)
Q Consensus       136 ~~~~l~V~nL~~--~~---te~~L~~~F~~~G~i~~v~i~~d~~----t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g  206 (480)
                      |+++|+|.||-.  .+   .+++|.++|++||.|..|.|+.+..    ++.++|||||+|.+.++|.+|+..|||..|+|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            678999999842  22   3689999999999999999998864    45678999999999999999999999999999


Q ss_pred             eEEEEeeecC
Q 011668          207 RRVLVDVERG  216 (480)
Q Consensus       207 r~l~V~~a~~  216 (480)
                      +.|.|.|+..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999753

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.44  E-value=1.1e-13  Score=127.11  Aligned_cols=77  Identities=21%  Similarity=0.418  Sum_probs=71.9

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          137 YKTLFVARLSY-ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       137 ~~~l~V~nL~~-~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .++|||+|||+ .+++++|.++|++||.|..|.|+.+.     +|||||+|.+.++|..||..|||..|.|+.|.|.++.
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            47999999999 99999999999999999999998764     6899999999999999999999999999999999987


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ...
T Consensus        78 ~~~   80 (198)
T 1qm9_A           78 HQN   80 (198)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            643

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.43  E-value=5.7e-14  Score=115.65  Aligned_cols=73  Identities=12%  Similarity=0.366  Sum_probs=64.9

Q ss_pred             EEcCCCCCCCHHHHHHHh------------hcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeE
Q 011668          141 FVARLSYETTESKIKREF------------ESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRR  208 (480)
Q Consensus       141 ~V~nL~~~~te~~L~~~F------------~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~  208 (480)
                      ++.||++.+++++|.++|            ++||.|..|.|+.+.. +.++|||||+|.+.++|.+|+..|||..|+|+.
T Consensus        19 ~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~   97 (104)
T 1jmt_A           19 SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQP   97 (104)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             ccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEE
Confidence            367788888888777666            9999999999998764 789999999999999999999999999999999


Q ss_pred             EEEeee
Q 011668          209 VLVDVE  214 (480)
Q Consensus       209 l~V~~a  214 (480)
                      |.|.|+
T Consensus        98 i~v~~s  103 (104)
T 1jmt_A           98 IHAELS  103 (104)
T ss_dssp             CCEEEC
T ss_pred             EEEEEc
Confidence            999986

>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=99.43  E-value=3.3e-13  Score=129.92  Aligned_cols=77  Identities=29%  Similarity=0.374  Sum_probs=71.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|..+|+.||.|..|.|..      ++|||||+|.+.++|..||..|||..|.|+.|.|.+
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 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            34568999999999999999999999999999999964      368999999999999999999999999999999999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      +..
T Consensus        93 a~~   95 (261)
T 3sde_A           93 ATH   95 (261)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.42  E-value=2.2e-13  Score=125.19  Aligned_cols=77  Identities=19%  Similarity=0.300  Sum_probs=71.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCC-CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC-CeEEEEe
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYG-PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD-GRRVLVD  212 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~-gr~l~V~  212 (480)
                      .+.++|||+|||+.+++++|.++|+.|| .|..|.|+.+     .+|||||+|.+.++|..||..|||..|+ |+.|.|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4678999999999999999999999999 9999999653     2689999999999999999999999999 9999999


Q ss_pred             eecC
Q 011668          213 VERG  216 (480)
Q Consensus       213 ~a~~  216 (480)
                      |+.+
T Consensus       193 ~a~~  196 (198)
T 1qm9_A          193 FSKS  196 (198)
T ss_dssp             EECC
T ss_pred             eecc
Confidence            9975

>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=99.41  E-value=4.3e-13  Score=126.50  Aligned_cols=77  Identities=19%  Similarity=0.300  Sum_probs=71.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCC-CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC-CeEEEEe
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYG-PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD-GRRVLVD  212 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~-gr~l~V~  212 (480)
                      .+.++|||+|||+.+++++|.++|++|| .|..|.|+..     .+|||||+|.+.++|.+||..|||..|+ |+.|.|.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            4578999999999999999999999999 9999999643     3689999999999999999999999999 9999999


Q ss_pred             eecC
Q 011668          213 VERG  216 (480)
Q Consensus       213 ~a~~  216 (480)
                      |+.+
T Consensus       224 ~a~~  227 (229)
T 2adc_A          224 FSKS  227 (229)
T ss_dssp             ECSS
T ss_pred             EecC
Confidence            9875

>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=99.39  E-value=5.4e-13  Score=128.40  Aligned_cols=81  Identities=23%  Similarity=0.401  Sum_probs=73.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHc-CCceeC---CeEEEE
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA-DGRKLD---GRRVLV  211 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l-~g~~i~---gr~l~V  211 (480)
                      +.++|||+|||+.+|+++|..+|+.||.|..|.|+.+ .+|.++|||||+|.+.++|.+||..| ++..+.   ++.|.|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            5679999999999999999999999999999999998 57999999999999999999999999 455555   999999


Q ss_pred             eeecCC
Q 011668          212 DVERGR  217 (480)
Q Consensus       212 ~~a~~~  217 (480)
                      .++...
T Consensus       174 ~~~~~~  179 (261)
T 3sde_A          174 EPMEQF  179 (261)
T ss_dssp             EECCCE
T ss_pred             eecccc
Confidence            998754

>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=99.39  E-value=6.6e-13  Score=129.66  Aligned_cols=81  Identities=19%  Similarity=0.306  Sum_probs=71.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCC-CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYG-PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G-~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      +.++|||+|||+.+++++|.++|+.|| .|..|.|+.+.. +.++|||||+|.+.++|..||..|||..|.|+.|.|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            578999999999999999999999999 999999998876 788999999999999999999999999999999999998


Q ss_pred             cCC
Q 011668          215 RGR  217 (480)
Q Consensus       215 ~~~  217 (480)
                      .+.
T Consensus       195 ~~~  197 (292)
T 2ghp_A          195 NPL  197 (292)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.38  E-value=9.3e-13  Score=120.65  Aligned_cols=75  Identities=21%  Similarity=0.446  Sum_probs=66.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC----C-------CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESY----G-------PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~----G-------~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      ..++|||+|||+.+|+++|.++|+.|    |       .|..+.+      +.++|||||+|.+.++|.+|| .|||..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46799999999999999999999999    4       5555555      456799999999999999999 7999999


Q ss_pred             CCeEEEEeeecCC
Q 011668          205 DGRRVLVDVERGR  217 (480)
Q Consensus       205 ~gr~l~V~~a~~~  217 (480)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999998754

>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=99.38  E-value=8.3e-13  Score=118.16  Aligned_cols=75  Identities=20%  Similarity=0.432  Sum_probs=66.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC----C-------CeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESY----G-------PIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~----G-------~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      +.++|||+|||+.+|+++|.++|++|    |       .|..+.+.      .++|||||+|.+.++|..|| .|||..|
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            45799999999999999999999999    6       67777664      34799999999999999999 7999999


Q ss_pred             CCeEEEEeeecCC
Q 011668          205 DGRRVLVDVERGR  217 (480)
Q Consensus       205 ~gr~l~V~~a~~~  217 (480)
                      .|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999987653

>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=99.38  E-value=1.1e-12  Score=129.99  Aligned_cols=81  Identities=19%  Similarity=0.346  Sum_probs=69.0

Q ss_pred             CCCCCCCCCCEEEEcC--CCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC-
Q 011668          129 DPNVSGDPYKTLFVAR--LSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD-  205 (480)
Q Consensus       129 ~~~~~~~~~~~l~V~n--L~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~-  205 (480)
                      .......|+.+|||+|  |++.+|+++|.++|++||+|..|.|+.      .+|||||+|.+.++|++||..|||..|. 
T Consensus        10 ~v~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~   83 (345)
T 3tht_A           10 GIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVD   83 (345)
T ss_dssp             TCCCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CceecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCcccc
Confidence            3455567899999999  578999999999999999999988754      4689999999999999999999999873 


Q ss_pred             --Ce--EEEEeeec
Q 011668          206 --GR--RVLVDVER  215 (480)
Q Consensus       206 --gr--~l~V~~a~  215 (480)
                        |+  .|.|.|+.
T Consensus        84 ~~g~~~~ly~~~~~   97 (345)
T 3tht_A           84 DLGQKITLYLNFVE   97 (345)
T ss_dssp             TTSCEEECEEEECS
T ss_pred             ccCCceEEEEEEee
Confidence              44  57777764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.37  E-value=3.9e-12  Score=103.63  Aligned_cols=75  Identities=17%  Similarity=0.232  Sum_probs=63.1

Q ss_pred             CCEEEEcCCC-------CCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEE
Q 011668          137 YKTLFVARLS-------YETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRV  209 (480)
Q Consensus       137 ~~~l~V~nL~-------~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l  209 (480)
                      ...|.|.-..       ..+++++|+++|++||.|..|.|+     +.++|||||+|.+.++|..||..+++  +.|+.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeE
Confidence            4566666543       458999999999999999999997     46789999999999999999997554  689999


Q ss_pred             EEeeecCCC
Q 011668          210 LVDVERGRT  218 (480)
Q Consensus       210 ~V~~a~~~~  218 (480)
                      +|.|+....
T Consensus        83 ~V~~a~~~~   91 (100)
T 2d9o_A           83 KISWLEGQP   91 (100)
T ss_dssp             EEECSSCCC
T ss_pred             EEEEccCCC
Confidence            999987654

>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=99.33  E-value=6.1e-12  Score=105.02  Aligned_cols=78  Identities=12%  Similarity=0.156  Sum_probs=66.8

Q ss_pred             CCCCEEEEcCCCCCCC----------HHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee
Q 011668          135 DPYKTLFVARLSYETT----------ESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~t----------e~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      .|+++|.|.||-....          +++|.++|++||.|..|.|+.+.    ++|||||+|.+.++|.+|+..|||..|
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            4678999999743221          35789999999999999997653    589999999999999999999999999


Q ss_pred             CCeEEEEeeecC
Q 011668          205 DGRRVLVDVERG  216 (480)
Q Consensus       205 ~gr~l~V~~a~~  216 (480)
                      +|+.|.|.|+..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999999753

>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=99.18  E-value=3.3e-10  Score=116.73  Aligned_cols=15  Identities=0%  Similarity=-0.150  Sum_probs=6.8

Q ss_pred             EEEEEechhhHHHHH
Q 011668          182 AFIEYMHTRDMKAAY  196 (480)
Q Consensus       182 afV~F~~~~~a~~A~  196 (480)
                      .|....+...|..+|
T Consensus       150 ~F~~~e~A~~Ai~~l  164 (437)
T 3pgw_S          150 EYEHERDMHSAYKHA  164 (437)
T ss_pred             eeccHHHHHHHHHHc
Confidence            344444444444444

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.17  E-value=7.9e-11  Score=98.54  Aligned_cols=78  Identities=17%  Similarity=0.162  Sum_probs=69.1

Q ss_pred             CCCCCCCEEEEcCCCCC-CCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEec-hhhHHHHHHHcC--CceeCCe
Q 011668          132 VSGDPYKTLFVARLSYE-TTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH-TRDMKAAYKQAD--GRKLDGR  207 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~-~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~-~~~a~~A~~~l~--g~~i~gr  207 (480)
                      ..-.+++.|||+||++. ++.++|+++|++||+|.+|.|+.+..      .|||.|.+ ..+|..|+..||  +..|+|.
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            44557899999999999 99999999999999999999988754      69999999 799999999994  7889999


Q ss_pred             EEEEeeec
Q 011668          208 RVLVDVER  215 (480)
Q Consensus       208 ~l~V~~a~  215 (480)
                      .++|++..
T Consensus        87 ~~~~evL~   94 (121)
T 1owx_A           87 EVTWEVLE   94 (121)
T ss_dssp             SEEEEECC
T ss_pred             EEEEEECC
Confidence            99888754

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.16  E-value=9.7e-11  Score=91.95  Aligned_cols=74  Identities=18%  Similarity=0.378  Sum_probs=63.2

Q ss_pred             CCCCCEEEEcCCCC----CC-CH---HHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeC
Q 011668          134 GDPYKTLFVARLSY----ET-TE---SKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLD  205 (480)
Q Consensus       134 ~~~~~~l~V~nL~~----~~-te---~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~  205 (480)
                      ++|..||+|.-++.    ++ .+   .+|.+.|.+||+|..++|+.+        .+||+|.+.++|.+||. |||..|+
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 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED--------KMWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS--------SEEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC--------CEEEEECChHHHHHHHh-cCCeEeC
Confidence            45677898888762    23 32   578999999999999999875        38999999999999999 9999999


Q ss_pred             CeEEEEeeecC
Q 011668          206 GRRVLVDVERG  216 (480)
Q Consensus       206 gr~l~V~~a~~  216 (480)
                      |+.|+|+++.+
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

>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=98.98  E-value=5.2e-10  Score=88.18  Aligned_cols=74  Identities=23%  Similarity=0.344  Sum_probs=63.4

Q ss_pred             CCCCCCEEEEcCCCCC------CCH---HHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCce
Q 011668          133 SGDPYKTLFVARLSYE------TTE---SKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRK  203 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~------~te---~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~  203 (480)
                      .++|..||+|..++..      ..+   .+|.+.|.+||+|..++|+.+.        +||+|.+.++|.+||. |||..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee
Confidence            4567789999988742      332   4688999999999999999863        9999999999999999 99999


Q ss_pred             eCCeEEEEeeec
Q 011668          204 LDGRRVLVDVER  215 (480)
Q Consensus       204 i~gr~l~V~~a~  215 (480)
                      |+|+.|+|.+..
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999999754

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.79  E-value=4.6e-09  Score=98.17  Aligned_cols=79  Identities=20%  Similarity=0.382  Sum_probs=65.8

Q ss_pred             CCEEEEcCCCC-----CCCHHHHHHHhhcCCCeeEEEecccC----CCCCccceEEEEEechhhHHHHHHHcCCceeCCe
Q 011668          137 YKTLFVARLSY-----ETTESKIKREFESYGPIKRVRLVTDK----ETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR  207 (480)
Q Consensus       137 ~~~l~V~nL~~-----~~te~~L~~~F~~~G~i~~v~i~~d~----~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr  207 (480)
                      ...|.+.|+-.     .-.+++|.+.|++||.|..|.|+.+.    .++.++||+||+|.+.++|.+|+..|||..|+|+
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            34566655422     23457899999999999999998543    4568999999999999999999999999999999


Q ss_pred             EEEEeeec
Q 011668          208 RVLVDVER  215 (480)
Q Consensus       208 ~l~V~~a~  215 (480)
                      .|.|.|..
T Consensus       204 ~i~~~~~~  211 (222)
T 3dxb_A          204 KVVAEVYD  211 (222)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEcC
Confidence            99999975

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.42  E-value=9.8e-07  Score=70.87  Aligned_cols=72  Identities=17%  Similarity=0.174  Sum_probs=65.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC-----CCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          136 PYKTLFVARLSYETTESKIKREFESY-----GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~-----G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      ..++|-|-|||..++...|+.|++.+     |.|+.|.+..+.      +-|+|+|.+...|.+|.-.|+|..|.|+.|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            35789999999999999999999999     999999998875      4799999999999999988999999999999


Q ss_pred             Eee
Q 011668          211 VDV  213 (480)
Q Consensus       211 V~~  213 (480)
                      |.-
T Consensus        94 ~gT   96 (117)
T 2l9w_A           94 SGT   96 (117)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            863

>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=97.92  E-value=4.1e-05  Score=61.32  Aligned_cols=75  Identities=9%  Similarity=0.098  Sum_probs=62.9

Q ss_pred             CCEEEEcCCCCCC-C----HHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          137 YKTLFVARLSYET-T----ESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       137 ~~~l~V~nL~~~~-t----e~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      .++|+|+||+..+ +    .+.|+++|..|+++..+.+...      -.=..|.|.+.++|.+|-..|++..|+|..|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            4689999998865 2    2578999999999888776543      125689999999999999999999999999999


Q ss_pred             eeecCC
Q 011668          212 DVERGR  217 (480)
Q Consensus       212 ~~a~~~  217 (480)
                      .|+.+.
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            999843

>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=97.56  E-value=0.00046  Score=54.24  Aligned_cols=78  Identities=12%  Similarity=0.191  Sum_probs=61.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCC--ccceEEEEEechhhHHHHHHHcCCceeCC-----eEEE
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNK--PRGYAFIEYMHTRDMKAAYKQADGRKLDG-----RRVL  210 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~--~~g~afV~F~~~~~a~~A~~~l~g~~i~g-----r~l~  210 (480)
                      ++|.|.+||+.+|++++.+.++.+..+....++....+..  .-.-|||.|.+.+++......++|+.|-+     ....
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            4799999999999999999999998887777665543333  23578999999999999999999988732     2345


Q ss_pred             Eeeec
Q 011668          211 VDVER  215 (480)
Q Consensus       211 V~~a~  215 (480)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66654

>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=97.42  E-value=0.00037  Score=54.87  Aligned_cols=54  Identities=20%  Similarity=0.362  Sum_probs=46.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHc
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA  199 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l  199 (480)
                      ...++| ++|+.+...+|.++|+.||.| .|.++.|       ..|||.|.+.+.|..||..+
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidD-------TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEET-------TEEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcC-------CeEEEEecCHHHHHHHHHhc
Confidence            456777 999999999999999999965 4666665       38999999999999999876

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.32  E-value=0.0032  Score=50.17  Aligned_cols=71  Identities=13%  Similarity=0.142  Sum_probs=58.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhc----C-CCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          136 PYKTLFVARLSYETTESKIKREFES----Y-GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~----~-G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      -.++|.|.|||+.+.++.|.-+|+.    . |+|..|....        +-|+|+|.+...|+..|. -..+.|.+..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~-k~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLA-QADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHT-CSCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhc-CCcceecCeEEE
Confidence            3578999999999999999999987    2 5888887743        478999999999999987 336788999998


Q ss_pred             Eeeec
Q 011668          211 VDVER  215 (480)
Q Consensus       211 V~~a~  215 (480)
                      |.-..
T Consensus        78 V~P~~   82 (104)
T 2dhx_A           78 LRPAP   82 (104)
T ss_dssp             EEECC
T ss_pred             EEcCC
Confidence            86544

>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=97.20  E-value=0.00069  Score=53.49  Aligned_cols=54  Identities=22%  Similarity=0.393  Sum_probs=45.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD  200 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~  200 (480)
                      ..++| ++|+.+...+|..+|+.||.| .|.++.|       ..|||.|.+.+.|..||..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            34666 999999999999999999944 5777765       379999999999999999764

>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=97.09  E-value=0.0017  Score=53.47  Aligned_cols=70  Identities=20%  Similarity=0.221  Sum_probs=56.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC-eEEEEeee
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG-RRVLVDVE  214 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g-r~l~V~~a  214 (480)
                      .+-|.|-++|+.. ...|..+|++||+|.......      ...+-.|.|.+..+|++||. .||..|+| -.|-|...
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            4578899999875 577899999999999887632      23589999999999999999 79999985 55666654

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.83  E-value=0.0019  Score=51.12  Aligned_cols=77  Identities=13%  Similarity=0.203  Sum_probs=55.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCc--cceEEEEEechhhHHHHHHHcCCceeCC-----eEEE
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKP--RGYAFIEYMHTRDMKAAYKQADGRKLDG-----RRVL  210 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~--~g~afV~F~~~~~a~~A~~~l~g~~i~g-----r~l~  210 (480)
                      -+|.|..||+.+|++++.+.++.+-++....++....+.+.  -.-|||.|.+.+++......++|..|-+     -...
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a~   89 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPAV   89 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeeeE
Confidence            47999999999999998888877655533333332222221  2568999999999999999999988632     2455


Q ss_pred             Eeee
Q 011668          211 VDVE  214 (480)
Q Consensus       211 V~~a  214 (480)
                      |++|
T Consensus        90 VE~A   93 (97)
T 2l08_A           90 VEFA   93 (97)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            6665

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.22  E-value=0.0051  Score=51.28  Aligned_cols=76  Identities=13%  Similarity=0.207  Sum_probs=54.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeE-EEeccc--------CCCC-----CccceEEEEEechhhHHHHHHHcCCce
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKR-VRLVTD--------KETN-----KPRGYAFIEYMHTRDMKAAYKQADGRK  203 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~-v~i~~d--------~~t~-----~~~g~afV~F~~~~~a~~A~~~l~g~~  203 (480)
                      .-|.|-+.|+..+ ..|...|++||.|.. +.+...        ..+.     ...++..|+|.+..+|.+||. .||..
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            4577888877654 568889999999876 222110        0000     123577999999999999999 79999


Q ss_pred             eCCeEEEEeeec
Q 011668          204 LDGRRVLVDVER  215 (480)
Q Consensus       204 i~gr~l~V~~a~  215 (480)
                      |+|..|-|....
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            999877777654

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.27  E-value=0.009  Score=61.02  Aligned_cols=54  Identities=17%  Similarity=0.336  Sum_probs=41.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHH
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK  197 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~  197 (480)
                      ++|||. .+..+++.+|.++|++||.|..+.+-.+.     ..||+|+|.+.+++..++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            589998 78899999999999999999999886543     2699999999999997765

>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=94.52  E-value=0.018  Score=49.76  Aligned_cols=36  Identities=14%  Similarity=0.242  Sum_probs=29.1

Q ss_pred             EEEecccCCCCCccceEEEEEechhhHHHHHHHcCCce
Q 011668          166 RVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRK  203 (480)
Q Consensus       166 ~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~  203 (480)
                      .+.|+.+.  ..++|||||+|.+.++|++||..+++..
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~   37 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDN   37 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccC
Confidence            45666664  3689999999999999999998877643

>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=93.76  E-value=0.016  Score=49.82  Aligned_cols=40  Identities=18%  Similarity=0.218  Sum_probs=36.7

Q ss_pred             CCccceEEEEEechhhHHHHHHHc-CCceeCCeEEEEeeecC
Q 011668          176 NKPRGYAFIEYMHTRDMKAAYKQA-DGRKLDGRRVLVDVERG  216 (480)
Q Consensus       176 ~~~~g~afV~F~~~~~a~~A~~~l-~g~~i~gr~l~V~~a~~  216 (480)
                      ...+|+++|+|.+.++|++|+..| ||..|+| .|.|.++..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            567899999999999999999999 9999999 999998764

>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=87.21  E-value=1.2  Score=46.15  Aligned_cols=55  Identities=20%  Similarity=0.363  Sum_probs=45.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD  200 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~  200 (480)
                      ..+++|+ +|..+...+|.++|+.||.| .|.++.+       ..|||.|.+.+.|..++..++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            3566776 88889999999999999965 6666654       379999999999999999875

---

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	480
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	9e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-11
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	7e-11
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:) 7e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	8e-11
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-10
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	9e-10
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-09
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	7e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	8e-09
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	9e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-08
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	3e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	5e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	9e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	5e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	9e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	9e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	9e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.001
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002

>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 = 67.3 bits (164), Expect = 9e-15
 Identities = 19/74 (25%), Positives = 36/74 (48%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           +L+V  L  + TE+ +  +F   GPI  +R+  D  T +  GYA++ +    D + A   
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 199 ADGRKLDGRRVLVD 212
            +   + G+ V + 
Sbjct: 62  MNFDVIKGKPVRIM 75

>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 = 63.5 bits (154), Expect = 1e-13
 Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +F+  LS++TT+  ++  F  +G +K   ++ D  T + RG+ F+ +M    +     Q 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 200 DGRKLDGRRVLVDV 213
              +LD + +   V
Sbjct: 62  SRHELDSKTIDPKV 75

>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 = 63.0 bits (153), Expect = 3e-13
 Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 134 GDPYK--TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRD 191
           G+  K   L+V  L    T+ ++   F  YG I +  ++ DK T +PRG AF+ Y    +
Sbjct: 1   GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 60

Query: 192 MKAAYKQADGRKLDGRRVLVDVER 215
            + A    +    +G    + V  
Sbjct: 61  AQEAISALNNVIPEGGSQPLSVRL 84

>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 = 62.3 bits (151), Expect = 6e-13
 Identities = 27/80 (33%), Positives = 41/80 (51%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
            TL+V  LS+ TTE +I   F   G IK++ +  DK      G+ F+EY    D + A +
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 198 QADGRKLDGRRVLVDVERGR 217
             +G +LD R +  D + G 
Sbjct: 68  YINGTRLDDRIIRTDWDAGF 87

>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 = 61.2 bits (148), Expect = 1e-12
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 1/82 (1%)

Query: 133 SGDPYKT-LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRD 191
           SG P  T + V  + +  +  +I   F  Y  I     +   E   P G A + +    +
Sbjct: 4   SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 63

Query: 192 MKAAYKQADGRKLDGRRVLVDV 213
             AA    + R +  R+V + +
Sbjct: 64  ATAAVIDLNDRPIGSRKVKLVL 85

>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 = 61.3 bits (148), Expect = 1e-12
 Identities = 32/79 (40%), Positives = 49/79 (62%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           + DP   L V  LS  TTE  ++  F  YGPI  V +V D+++ + RG+AF+ + +  D 
Sbjct: 5   NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 64

Query: 193 KAAYKQADGRKLDGRRVLV 211
           K A ++A+G +LDGRR+ V
Sbjct: 65  KEAKERANGMELDGRRIRV 83

>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 = 60.3 bits (146), Expect = 2e-12
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L V+ L +  +++ I+  F  +G +K+  +  D+ + +  G A + +    D   A KQ 
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 200 DGRKLDGRRVLVDV 213
           +G  LDGR + + +
Sbjct: 62  NGVPLDGRPMNIQL 75

>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 = 60.7 bits (147), Expect = 2e-12
 Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKE-TNKPRGYAFIEYMHTRDMKAAY 196
             + V  + ++  + +I+  F ++G +K VRL      T   RG+ F++++  +D K A+
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 197 KQ-ADGRKLDGRRVLVD 212
                   L GRR++++
Sbjct: 69  NALCHSTHLYGRRLVLE 85

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 60.0 bits (145), Expect = 3e-12
 Identities = 22/77 (28%), Positives = 38/77 (49%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L V  L  + T+ ++   F + GPI   R++ D +T    GYAF+++    D + A K 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 199 ADGRKLDGRRVLVDVER 215
            +G  +  +R+ V   R
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>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 = 59.3 bits (143), Expect = 5e-12
 Identities = 21/76 (27%), Positives = 38/76 (50%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L+V+ L    T+ ++++ F  YG I   R++ D+ T   RG  FI +    + + A K 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 199 ADGRKLDGRRVLVDVE 214
            +G+K  G    + V+
Sbjct: 68  LNGQKPSGATEPITVK 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 = 57.3 bits (138), Expect = 3e-11
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS +T E KI+  F  +G ++ + L  D +TNK RG+ FI +     +K   ++ 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 200 DGRKLDGRRVLVDV 213
               +   +  + V
Sbjct: 61  KYHNVGLSKCEIKV 74

>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 = 57.0 bits (137), Expect = 4e-11
 Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 3/84 (3%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKE---TNKPRGYAFIEYMHTRDMKAAY 196
           LF+  L++ TTE  +K  F   G IK   +   K         G+ F+EY      + A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 197 KQADGRKLDGRRVLVDVERGRTVP 220
           KQ  G  +DG ++ V +    T P
Sbjct: 61  KQLQGHTVDGHKLEVRISERATKP 84

>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 = 56.9 bits (137), Expect = 4e-11
 Identities = 23/73 (31%), Positives = 36/73 (49%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           LF+  L     + ++K    S+GP+K   LV D  T   +GYAF EY+       A    
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 200 DGRKLDGRRVLVD 212
           +G +L  +++LV 
Sbjct: 64  NGMQLGDKKLLVQ 76

>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 = 57.3 bits (138), Expect = 4e-11
 Identities = 16/96 (16%), Positives = 37/96 (38%), Gaps = 6/96 (6%)

Query: 122 KKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGY 181
           K+    +  N S     T++   ++   T+  +++ F  +G I  +R+         +GY
Sbjct: 3   KQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGY 56

Query: 182 AFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           +F+ +        A    +G  ++G  V     +  
Sbjct: 57  SFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>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 = 56.7 bits (136), Expect = 5e-11
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRV-RLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           +F+  L  E  E  +   F ++G I +  +++ D +T   +GYAFI +       AA + 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 199 ADGRKLDGRRVLVDVERGR 217
            +G+ L  R + V     +
Sbjct: 61  MNGQYLCNRPITVSYAFKK 79

>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 = 56.6 bits (136), Expect = 7e-11
 Identities = 22/88 (25%), Positives = 39/88 (44%)

Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
           P    +   T++V  L  + +E  +   F   GP+    +  D+ T + +GY F+E++  
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 190 RDMKAAYKQADGRKLDGRRVLVDVERGR 217
            D   A K  D  KL G+ + V+     
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAH 89

>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 = 57.0 bits (137), Expect = 7e-11
 Identities = 13/91 (14%), Positives = 32/91 (35%), Gaps = 4/91 (4%)

Query: 125 DPHNDPNVSGDP---YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGY 181
           +P N    +         + +     E  E       E YG ++ + +  D   +   G 
Sbjct: 12  NPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC-DNLGDHLVGN 70

Query: 182 AFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
            ++++    D + A    + R  +G+ +  +
Sbjct: 71  VYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>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 = 56.4 bits (136), Expect = 7e-11
 Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 14/99 (14%)

Query: 135 DPYKTLFVARLS-YETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMK 193
                +F+  L+     +S ++  F  YG I    +         +G+AF++Y++ R+ +
Sbjct: 13  SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNAR 64

Query: 194 AAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLG 232
           AA    DGR + G+ + +++         +  R G   G
Sbjct: 65  AAVAGEDGRMIAGQVLDINLAAEP-----KVNRSGPSSG 98

>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 = 56.2 bits (135), Expect = 8e-11
 Identities = 27/89 (30%), Positives = 41/89 (46%)

Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
           PN   D   T+ V  LS +T E+ ++  F  +G I R+ L  DK T + +G+AFI +   
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 190 RDMKAAYKQADGRKLDGRRVLVDVERGRT 218
            D   A     G   D   + V+  +  T
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWAKPST 89

>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 = 55.5 bits (133), Expect = 1e-10
 Identities = 23/77 (29%), Positives = 37/77 (48%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L V  L    T+ + +  F S G I+  +LV DK T +  GY F+ Y+  +D + A   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 199 ADGRKLDGRRVLVDVER 215
            +G +L  + + V   R
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>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 = 55.4 bits (133), Expect = 2e-10
 Identities = 23/82 (28%), Positives = 42/82 (51%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L+V  L+ E  +  +   F  +G I  +++  D ET K RG+AF+E+    D  AA  
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 198 QADGRKLDGRRVLVDVERGRTV 219
             +  +L GR + V++ +   +
Sbjct: 66  NMNESELFGRTIRVNLAKPMRI 87

>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 = 56.1 bits (134), Expect = 3e-10
 Identities = 28/119 (23%), Positives = 56/119 (47%)

Query: 114 AEKAAEELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDK 173
            ++  ++ +++ P    N   D  + L V  +     E ++++ FE YGPI+ V++V D+
Sbjct: 19  LQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR 78

Query: 174 ETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLG 232
           ET + RGY F+++      + A    +G  +  +R+ V +             +G G G
Sbjct: 79  ETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNG 137

>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 = 55.1 bits (132), Expect = 3e-10
 Identities = 28/96 (29%), Positives = 48/96 (50%), Gaps = 5/96 (5%)

Query: 137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
           +  +FV  L Y TT++ +++ FE +G I+   ++TD++T K RGY F+        + A 
Sbjct: 10  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 69

Query: 197 KQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLG 232
           K  +   +DGR+  V+          +PR L  G  
Sbjct: 70  KDPNP-IIDGRKANVN----LAYLGAKPRSLQTGFA 100

>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 = 54.6 bits (131), Expect = 3e-10
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             L V  L ++TTE  +K  F ++G +  V++  D +T   +G+ F+ +           
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 198 QADGRKLDGRRVLVDVERGR 217
           Q     +DGR     +   +
Sbjct: 69  Q--RHMIDGRWCDCKLPNSK 86

>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 = 53.4 bits (128), Expect = 5e-10
 Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +F+  LS++TT+  +K  F  +G +    L  D  T + RG+ F+ +  +  +       
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 200 DGRKLDGRRVLV 211
              KL+G+ +  
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 53.9 bits (129), Expect = 5e-10
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           +  + LF+  LS+ETT+  ++  FE +G +    ++ D  T + RG+ F+ Y    ++ A
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 195 AYKQADGRKLDGRRVLVD 212
           A   A   K+DGR V   
Sbjct: 64  AMN-ARPHKVDGRVVEPK 80

>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 = 53.9 bits (129), Expect = 9e-10
 Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 3/89 (3%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + L++  L Y+ T  ++   F  YGPI+++R      T + RG A++ Y    D K A  
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 198 QADGRKLDGRRVLVDVERGRTVPNWRPRR 226
              G  +  R ++V              +
Sbjct: 65  HLSGFNVCNRYLVVLYYNANRAFQKMDTK 93

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

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 = 52.5 bits (125), Expect = 1e-09
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           T+ V  L     ++K+ + F+  GPI  V +       K   +A IE+       AA  +
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITK 59

Query: 199 ADGRKLDGRRVLVD 212
              + +    ++V 
Sbjct: 60  -THKVVGQNEIIVS 72

>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 = 52.5 bits (125), Expect = 1e-09
 Identities = 13/75 (17%), Positives = 31/75 (41%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
           TL++       T+  I+   +    +     +     N  R +A+I+     D +   ++
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 199 ADGRKLDGRRVLVDV 213
            +G K++G  ++  V
Sbjct: 63  LNGLKIEGYTLVTKV 77

>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 = 53.1 bits (127), Expect = 1e-09
 Identities = 23/95 (24%), Positives = 46/95 (48%), Gaps = 4/95 (4%)

Query: 126 PHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIE 185
           P        + ++ LF+  LS+ETTE  ++  +E +G +    ++ D  + + RG+ F+ 
Sbjct: 9   PLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 68

Query: 186 YMHTRDMKAAYKQA----DGRKLDGRRVLVDVERG 216
           +    ++ AA        DGR ++ +R +   E G
Sbjct: 69  FSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESG 103

>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 = 52.4 bits (125), Expect = 2e-09
 Identities = 14/88 (15%), Positives = 32/88 (36%), Gaps = 6/88 (6%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRL-----VTDKETNKPRGYAFIEYMHTRDM 192
           + L+V  + +  TE  +   F +   +  +       V   + N+ + +AF+E+    + 
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 193 KAAYKQADGRKLDGRRVLVDVERGRTVP 220
             A    DG    G+ + +         
Sbjct: 62  TQAMAF-DGIIFQGQSLKIRRPHDYQPL 88

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 24/80 (30%), Positives = 37/80 (46%), Gaps = 6/80 (7%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           K L+V  L   T+E  I++EF +  P    R        K R YAF+ + +  D   A K
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNREDAVEAMK 62

Query: 198 QADGRKLDGRRVLVDVERGR 217
             +G+ LDG  + V + +  
Sbjct: 63  ALNGKVLDGSPIEVTLAKPV 82

>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 = 52.1 bits (124), Expect = 3e-09
 Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 1/99 (1%)

Query: 119 EELKKYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKP 178
           EE++K  P       G+P K L++  LS   TE  +   F  +   K   +     T + 
Sbjct: 1   EEIRKI-PMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRM 59

Query: 179 RGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           RG AFI + +      A    +G KL G+ ++++  + +
Sbjct: 60  RGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK 98

>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 = 50.9 bits (121), Expect = 5e-09
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
           P  S + +  LFV  +  E  E +I+ +F  YG IK + L  D+ T   +GYA +EY   
Sbjct: 1   PQRSVEGW-ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 59

Query: 190 RDMKAAYKQADGRKLDGRRVLVD 212
           +   AA +  +G ++ G+ + VD
Sbjct: 60  KQALAAKEALNGAEIMGQTIQVD 82

>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 = 51.3 bits (122), Expect = 6e-09
 Identities = 26/80 (32%), Positives = 42/80 (52%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             LFV  LSY ++E  +++ F +YGP+  +    D  T KP+G+AF+ +M       AY 
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 198 QADGRKLDGRRVLVDVERGR 217
           + DG+   GR + V     +
Sbjct: 69  EVDGQVFQGRMLHVLPSTIK 88

>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 = 50.8 bits (121), Expect = 7e-09
 Identities = 17/93 (18%), Positives = 47/93 (50%), Gaps = 1/93 (1%)

Query: 125 DPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
           +P ++ +      +T+F  +L+       ++  F + G ++ VR+++D+ + + +G A++
Sbjct: 6   EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 65

Query: 185 EYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           E+   + +  A     G++L G  ++V   +  
Sbjct: 66  EFCEIQSVPLAIGL-TGQRLLGVPIIVQASQAE 97

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 7e-09
 Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 3/85 (3%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           +G+    ++V  L  +     I+  F  YG I+ + L           +AF+E+   RD 
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDA 66

Query: 193 KAAYKQADGRKLDGRRVLVDVERGR 217
           + A    DG   DG R+ V+  R  
Sbjct: 67  EDAVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 50.9 bits (121), Expect = 8e-09
 Identities = 19/96 (19%), Positives = 33/96 (34%), Gaps = 1/96 (1%)

Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
             +   P  T F+  L Y+ TE  IK  F                  + +G+ + E+   
Sbjct: 8   SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDL 67

Query: 190 RDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPR 225
             + +A    +   L  +R+ VDV       +  P 
Sbjct: 68  DSLLSALS-LNEESLGNKRIRVDVADQAQDKDSGPS 102

>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 = 50.2 bits (119), Expect = 9e-09
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 139 TLFVARLSYETTESKIKREFE---SYGPIKRVRLVTDKETNK---PRGYAFIEYMHTRDM 192
            +FV  LS    + ++ +  E    +G I +V +           P   A++ Y+ + D 
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 193 KAAYKQADGRKLDGRRV 209
             A +  +   +DGR +
Sbjct: 70  LRAIQCVNNVVVDGRTL 86

>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 = 50.5 bits (120), Expect = 1e-08
 Identities = 27/101 (26%), Positives = 43/101 (42%), Gaps = 13/101 (12%)

Query: 125 DPHNDPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLV--------TDKETN 176
           DP  D + S      ++V  L+   T   +   F+  G +K  +           DKET 
Sbjct: 1   DPDEDSDNS-----AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 55

Query: 177 KPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR 217
           KP+G A + Y      KAA +  DG+   G ++ V + R +
Sbjct: 56  KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 50.4 bits (120), Expect = 1e-08
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           +TL    LS+  TE ++K  FE    I+ V      +  K +G A+IE+    D +   +
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLE 71

Query: 198 QADGRKLDGRRVLVDVERGR 217
           +  G ++DGR V +     +
Sbjct: 72  EKQGAEIDGRSVSLYYTGEK 91

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           +FV  LS  TT   +K  FE +G +    L+ DK TN+ RG+ F+ +     ++    + 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CEI 60

Query: 200 DGRKLDGRRVLVD 212
              +++ + V   
Sbjct: 61  HFHEINNKMVECK 73

>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 = 50.1 bits (119), Expect = 2e-08
 Identities = 19/89 (21%), Positives = 42/89 (47%)

Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
               G     LF+  L  E  +  + + F  +G +   ++  DK+TN  + + F+ Y + 
Sbjct: 11  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 70

Query: 190 RDMKAAYKQADGRKLDGRRVLVDVERGRT 218
              +AA +  +G ++  +R+ V ++R + 
Sbjct: 71  VSAQAAIQSMNGFQIGMKRLKVQLKRSKN 99

>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 = 49.3 bits (117), Expect = 2e-08
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           K +FV  +  +T E  ++  FE YG I+ + ++TD+ + K RG+AF+ +     +     
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 198 QADGRKLDGRRVLVDV 213
           Q     ++G    V  
Sbjct: 63  Q-KYHTVNGHNCEVRK 77

>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 = 49.6 bits (118), Expect = 2e-08
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  L  + TE ++++ FE YG    V        +K +G+ FI        + A  +
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVF------IHKDKGFGFIRLETRTLAEIAKVE 63

Query: 199 ADGRKLDGRRVLVD 212
            D   L G+++ V 
Sbjct: 64  LDNMPLRGKQLRVR 77

>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 = 49.5 bits (118), Expect = 2e-08
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 4/72 (5%)

Query: 147 YETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG 206
                  ++ E   +G I+++ L        P G A + +    +     +  DGR   G
Sbjct: 29  LNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRWFGG 84

Query: 207 RRVLVDVERGRT 218
           R++      G T
Sbjct: 85  RQITAQAWDGTT 96

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 18/89 (20%), Positives = 44/89 (49%), Gaps = 2/89 (2%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
           S    K L V+ + +   +  +++ F  +G I  V ++ ++     +G+ F+ + ++ D 
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADA 64

Query: 193 KAAYKQADGRKLDGRRVLVDVERGRTVPN 221
             A ++  G  ++GR++ V+    R + N
Sbjct: 65  DRAREKLHGTVVEGRKIEVNNATARVMTN 93

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 3e-08
 Identities = 11/84 (13%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 136 PYKTLFVARLSYETTESKIKREFESY-GPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
           P  T+++  L+ +  + ++K+   +      ++  +    + K RG AF+ +        
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 195 AYKQADGRKLDGRRVLVDVERGRT 218
           A +   G     + + +   +  +
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDS 85

>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 = 48.5 bits (115), Expect = 4e-08
 Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
              +TL+V  LS + TE  I + F   GP K  +++T+        Y F+E+   RD  A
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAA 63

Query: 195 AYKQADGRKLDGRRVLVD 212
           A    +GRK+ G+ V V+
Sbjct: 64  ALAAMNGRKILGKEVKVN 81

>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 = 50.0 bits (118), Expect = 9e-08
 Identities = 18/60 (30%), Positives = 33/60 (55%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
           + LF+  LS+ETT+  ++  FE +G +    ++ D  T + RG+ F+ Y    ++ AA  
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

>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 = 48.5 bits (114), Expect = 3e-07
 Identities = 32/172 (18%), Positives = 56/172 (32%), Gaps = 19/172 (11%)

Query: 59  KPPPEKRKC-----PPLTGMAQFVSHFAEPGDPLYAPPVEKAETPVERRARIHKLRLEKG 113
           K P + RK         T      SHF + G       +    T   R          + 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 114 AEKAAEELK-------------KYDPHNDPNVSGDPYKTLFVARLSYETTESKIKREFES 160
            + A                       +    +    K +FV  +  +T E  ++  FE 
Sbjct: 61  VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 120

Query: 161 YGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD 212
           YG I+ + ++TD+ + K RG+AF+ +     +     Q     ++G    V 
Sbjct: 121 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 171

>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 = 47.8 bits (113), Expect = 1e-07
 Identities = 17/87 (19%), Positives = 31/87 (35%), Gaps = 4/87 (4%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKR--VRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
            LF+  +       +I  E           +   +  +  K RG+AF+EY   R    A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 197 KQADGR--KLDGRRVLVDVERGRTVPN 221
           ++      +L G ++ VD        +
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDVD 89

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 6/86 (6%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P   L+V  L   T+ + + REF+ +G I+ +         K   +A+I+Y      +AA
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTID------HVKGDSFAYIQYESLDAAQAA 69

Query: 196 YKQADGRKLDGRRVLVDVERGRTVPN 221
             +  G  L G    + V+  ++ P+
Sbjct: 70  CAKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 16/90 (17%), Positives = 33/90 (36%), Gaps = 9/90 (10%)

Query: 127 HNDPNVSGDPYKTLFVAR--LSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFI 184
           H          ++L VA   L    + +++    E  G +  +           + Y+F 
Sbjct: 8   HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL------MPPNKPYSFA 61

Query: 185 EYMHTRDMKAAYKQADGRKL-DGRRVLVDV 213
            Y  T + K AY   +G+++ D     + +
Sbjct: 62  RYRTTEESKRAYVTLNGKEVVDDLGQKITL 91

>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 = 46.6 bits (110), Expect = 2e-07
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 130 PNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT 189
           P++       +F+  L        +   F ++G I   ++V D+     +GY F+ +   
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQ 58

Query: 190 RDMKAAYKQADGRKLDGRRVLVDVERGR 217
              + A ++ +G  L+ R+V V   + R
Sbjct: 59  EAAERAIEKMNGMLLNDRKVFVGRFKSR 86

>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 = 45.8 bits (108), Expect = 3e-07
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L++  LS   T   +++ F               +     GYAF++Y        A + 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 199 ADGR-KLDGRRVLVDVERGR 217
             G+ +L G+ + VD    +
Sbjct: 57  LSGKVELHGKIMEVDYSVSK 76

>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 = 46.6 bits (110), Expect = 3e-07
 Identities = 13/83 (15%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
            P   + V  L Y  T   + + F  +G + ++       T   +  A ++Y      + 
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQH 60

Query: 195 AYKQADGRKLDGRRVLVDVERGR 217
           A    DG+ +      + ++  +
Sbjct: 61  AKLSLDGQNIYNACCTLRIDFSK 83

>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 = 45.8 bits (108), Expect = 3e-07
 Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
            TL+V     + T + ++  F  +G I  +        + PR  AF+ Y        A  
Sbjct: 6   NTLYVY--GEDMTPTLLRGAFSPFGNIIDLS------MDPPRNCAFVTYEKMESADQAVA 57

Query: 198 QADGRKLDGRRVLVDVERGR 217
           + +G +++  ++ V++ R +
Sbjct: 58  ELNGTQVESVQLKVNIARKQ 77

>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 = 45.9 bits (108), Expect = 3e-07
 Identities = 8/81 (9%), Positives = 27/81 (33%), Gaps = 7/81 (8%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             + V  L  ++   ++    + Y              ++ +  AF+  ++    + A +
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 198 QADGRKLDGRRVLVDVERGRT 218
                   G+ ++V ++    
Sbjct: 59  MFHQYSFRGKDLIVQLQPTDA 79

>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 = 45.4 bits (107), Expect = 5e-07
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             +FV R + + TE +++  F  YG +  V           R +AF+ +   +  ++   
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIAQSLCG 60

Query: 198 QADGRKLDGRRVLVDVERGR 217
             +   + G  V +     +
Sbjct: 61  --EDLIIKGISVHISNAEPK 78

>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 = 45.1 bits (106), Expect = 6e-07
 Identities = 28/74 (37%), Positives = 45/74 (60%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            LFV  LS++T E  +++ F  YG I  V +V D+ET + RG+ F+ + +  D K A   
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 199 ADGRKLDGRRVLVD 212
            +G+ +DGR++ VD
Sbjct: 67  MNGKSVDGRQIRVD 80

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 1e-06
 Identities = 34/101 (33%), Positives = 48/101 (47%), Gaps = 1/101 (0%)

Query: 129 DPNVSGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMH 188
           DP V     +++FV  + YE TE ++K  F   GP+   RLV D+ET KP+GY F EY  
Sbjct: 1   DPAVDRSL-RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 189 TRDMKAAYKQADGRKLDGRRVLVDVERGRTVPNWRPRRLGG 229
                +A +  +GR+  GR + VD                G
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>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 = 43.2 bits (101), Expect = 2e-06
 Identities = 16/70 (22%), Positives = 31/70 (44%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           L++  L   TT+  + +  + YG I   + + DK TNK +GY F+++      + A    
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 200 DGRKLDGRRV 209
               +  +  
Sbjct: 61  KASGVQAQMA 70

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {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 protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.3 bits (101), Expect = 4e-06
 Identities = 16/99 (16%), Positives = 35/99 (35%), Gaps = 4/99 (4%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
                  +  + +  T+  + +  E     +    V      +  G A +++ +  D + 
Sbjct: 6   SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 65

Query: 195 AYKQADGRKLDGRRVLVDV---ERGRTVPNWRPRRLGGG 230
           + +    +KL+GR   V V   E  R +    P +   G
Sbjct: 66  SERL-HRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSG 103

>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 = 4e-06
 Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 2/70 (2%)

Query: 145 LSYETTESKIKREFESYGPIKRVRLVTDKET--NKPRGYAFIEYMHTRDMKAAYKQADGR 202
             YE     ++ E   YG +K + +    +       G  F+E+    D + A +   GR
Sbjct: 22  EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR 81

Query: 203 KLDGRRVLVD 212
           K   R V+  
Sbjct: 82  KFANRVVVTK 91

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 5e-06
 Identities = 15/83 (18%), Positives = 27/83 (32%), Gaps = 5/83 (6%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P  TL ++ +    +E  +K  F S G + +          K R  A I+     +   A
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQA 64

Query: 196 YKQADGRKL-DGRRVLVDVERGR 217
                   L +   + V   +  
Sbjct: 65  LIDLHNHDLGENHHLRVSFSKST 87

>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 = 42.1 bits (98), Expect = 9e-06
 Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 6/89 (6%)

Query: 135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKA 194
              KT+F+  LS+++ E  +    + +G +K VR+V   +T   +G AF ++M     + 
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 195 AYKQA------DGRKLDGRRVLVDVERGR 217
               A       G KLDGR++ VD+   R
Sbjct: 66  CLAAASLEAEGGGLKLDGRQLKVDLAVTR 94

>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 = 41.1 bits (95), Expect = 2e-05
 Identities = 15/80 (18%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             LF+  L+   + +++K           +  V D  T   R + ++++    D++ A +
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDLEKALE 72

Query: 198 QADGRKLDGRRVLVDVERGR 217
              G K+ G  + ++  +GR
Sbjct: 73  L-TGLKVFGNEIKLEKPKGR 91

>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 = 41.7 bits (97), Expect = 2e-05
 Identities = 23/109 (21%), Positives = 43/109 (39%), Gaps = 8/109 (7%)

Query: 138 KTLFVARLSYE-TTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAY 196
             L V+ L+ E  T   +   F  YG ++RV++         +  A ++       + A 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI-----LFNKKENALVQMADGNQAQLAM 57

Query: 197 KQADGRKLDGRRVLVDVERGRTVPNWRPRRLGGGLGTTRVGGEEVNQRY 245
              +G KL G+ + + + + + V    PR      G T+  G     R+
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQ--LPREGQEDQGLTKDYGNSPLHRF 104

>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 = 39.5 bits (92), Expect = 5e-05
 Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 9/77 (11%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            + V      +    I  +F  YG I +  +           +  I Y      + A  +
Sbjct: 6   WVTVFGFPQASAS-YILLQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKALSK 58

Query: 199 ADGRKLDGRRVLVDVER 215
            DGR      +++ V+ 
Sbjct: 59  -DGRIFGE-SIMIGVKP 73

>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 = 39.4 bits (91), Expect = 9e-05
 Identities = 9/81 (11%), Positives = 21/81 (25%), Gaps = 1/81 (1%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            L+++ L     E ++               +    +   RG  F     T   +A    
Sbjct: 20  NLYISNLPLSMDEQEL-ENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 199 ADGRKLDGRRVLVDVERGRTV 219
            +G+ +     +         
Sbjct: 79  FNGKFIKTPPGVSAPTEPLLC 99

>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 = 38.6 bits (89), Expect = 1e-04
 Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 3/78 (3%)

Query: 138 KTLFVARLSYETTESKIKREF--ESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           + + +  LS E  +  + RE         K       KE +     AF+ + +    + A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 196 YKQADGRKLDGRRVLVDV 213
            +  +   L  R + V +
Sbjct: 65  LQ-MNRSLLGNREISVSL 81

>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 = 38.6 bits (89), Expect = 2e-04
 Identities = 7/92 (7%), Positives = 22/92 (23%), Gaps = 11/92 (11%)

Query: 139 TLFVARLSYETTESK-----IKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMK 193
            L     + +           +  F +Y      +        K      I + +     
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY------FKSFKRVRINFSNPLSAA 60

Query: 194 AAYKQADGRKLDGRRVLVDVERGRTVPNWRPR 225
            A  +    +  G+ + +   +   + +    
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIGSSHLA 92

>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 = 37.8 bits (87), Expect = 3e-04
 Identities = 17/87 (19%), Positives = 29/87 (33%), Gaps = 3/87 (3%)

Query: 139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQ 198
            + +  L Y  TE+ I   F    P++           +  G A +E+    D  AA  +
Sbjct: 17  CVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEADVEFATHEDAVAAMAK 74

Query: 199 ADGRKLDGRRVLVDVERGRTVPNWRPR 225
            D   +  R V + +          P 
Sbjct: 75  -DKANMQHRYVELFLNSTAGTSGSGPS 100

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 36.0 bits (82), Expect = 9e-04
 Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 5/75 (6%)

Query: 136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAA 195
           P + LF+  L  ET E  +   F  +   K       +        AF+E+       AA
Sbjct: 7   PNQILFLTNLPEETNEMMLSMLFNQFPGFKE-----VRLVPNRHDIAFVEFTTELQSNAA 61

Query: 196 YKQADGRKLDGRRVL 210
            +   G K+     +
Sbjct: 62  KEALQGFKITPTHAM 76

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-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: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.1 bits (82), Expect = 9e-04
 Identities = 12/74 (16%), Positives = 26/74 (35%), Gaps = 7/74 (9%)

Query: 140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA 199
           + +  L  + T  ++      Y              +K +G AF+  ++    +AA    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELK-------YCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 200 DGRKLDGRRVLVDV 213
              +L  R + V +
Sbjct: 54  HQSRLRERELSVQL 67

>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 = 36.5 bits (83), Expect = 0.001
 Identities = 11/75 (14%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK 197
             +    L   T  ++I+  F  +G + RV         +    A +E++   + + A++
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVL------LPEGGITAIVEFLEPLEARKAFR 64

Query: 198 QADGRKLDGRRVLVD 212
                K     + ++
Sbjct: 65  HLAYSKFHHVPLYLE 79

>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 = 35.5 bits (81), Expect = 0.002
 Identities = 13/93 (13%), Positives = 24/93 (25%), Gaps = 6/93 (6%)

Query: 133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDM 192
                  + V  L     E+ +    E +G I  V +         +  A +E+ +    
Sbjct: 11  KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSA 64

Query: 193 KAAYKQADGRKLDGRRVLVDVERGRTVPNWRPR 225
           K     A    +             +    RP 
Sbjct: 65  KECVTFAADVPVYIAGQQAFFNYSTSKRITRPG 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	480
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.84
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.84
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.82
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.82
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.82
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.82
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.82
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.81
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.8
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.8
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.8
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.79
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.79
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.78
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.78
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.78
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.77
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.76
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.76
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.76
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.76
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.76
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.76
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.75
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.74
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.74
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.74
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.73
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.72
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.72
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.72
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.72
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.71
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.71
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.71
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.71
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.71
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.7
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.7
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.69
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.69
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.68
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.68
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.67
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.67
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.67
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.64
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.63
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.59
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.59
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.57
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.57
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.51
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.48
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.44
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.4
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.39
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.35
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.35
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.82
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.51
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.38
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.91

>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=99.84  E-value=7e-21  Score=163.94  Aligned_cols=85  Identities=26%  Similarity=0.511  Sum_probs=80.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+++|+++|.++|++||.|..|.|+.++.|+.++|||||+|.+.++|..||..|||..|+|+.|+|.||.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 011668          216 GRTVP  220 (480)
Q Consensus       216 ~~~~~  220 (480)
                      .....
T Consensus       121 ~~~~~  125 (139)
T d1u6fa1         121 SGHQR  125 (139)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            65543

>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=99.84  E-value=3.8e-21  Score=152.74  Aligned_cols=85  Identities=28%  Similarity=0.442  Sum_probs=80.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..++.++|||+|||+.+++++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|+
T Consensus         4 ~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~   83 (90)
T d2cq0a1           4 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCC
Q 011668          213 VERGR  217 (480)
Q Consensus       213 ~a~~~  217 (480)
                      ||+++
T Consensus        84 ~akp~   88 (90)
T d2cq0a1          84 WAKPS   88 (90)
T ss_dssp             ESSCC
T ss_pred             eeeCC
Confidence            99864

>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=99.84  E-value=9.4e-21  Score=151.35  Aligned_cols=81  Identities=33%  Similarity=0.527  Sum_probs=78.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .++||||+|||+++|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|.|+|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      +
T Consensus        86 ~   86 (93)
T d1h2vz_          86 G   86 (93)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.83  E-value=6.4e-21  Score=148.71  Aligned_cols=80  Identities=28%  Similarity=0.469  Sum_probs=77.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.||++
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            36899999999999999999999999999999999999999999999999999999999999999999999999999964

>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=99.83  E-value=8.5e-21  Score=151.59  Aligned_cols=84  Identities=25%  Similarity=0.412  Sum_probs=79.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|..||..|||..|+|+.|+|.||
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            35579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 011668          215 RGRT  218 (480)
Q Consensus       215 ~~~~  218 (480)
                      .+..
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            7643

>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=99.83  E-value=2.1e-20  Score=151.22  Aligned_cols=83  Identities=31%  Similarity=0.600  Sum_probs=79.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+|+++|.++|++||.|..|.|+.++.|+.++|||||+|.+.++|..||..|||..|+|+.|+|.++.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      .+.
T Consensus        87 ~~~   89 (99)
T d1whwa_          87 IKK   89 (99)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>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=99.82  E-value=9.1e-21  Score=150.20  Aligned_cols=82  Identities=28%  Similarity=0.496  Sum_probs=78.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+|+++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|..||..|||..|+|+.|.|.||.
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            35789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.82  E-value=1.7e-20  Score=148.28  Aligned_cols=82  Identities=30%  Similarity=0.467  Sum_probs=78.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ...+|||+|||+.+|+++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|..||..|||..|+|+.|.|+||.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      ++
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            53

>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=99.82  E-value=1.6e-20  Score=152.73  Aligned_cols=86  Identities=22%  Similarity=0.438  Sum_probs=80.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..++.++|||+|||+.+++++|.++|+.||.|..|.|+.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|+
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      |+.++.
T Consensus        94 ~a~~k~   99 (102)
T d2cpza1          94 LKRSKN   99 (102)
T ss_dssp             CCCCSC
T ss_pred             EeCCCC
Confidence            998654

>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=99.82  E-value=1.8e-20  Score=146.14  Aligned_cols=79  Identities=29%  Similarity=0.510  Sum_probs=76.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ++|||+|||+.+++++|.++|++||.|..|.|+.+..++.++|||||+|.+.++|+.|+..|||..|+|+.|.|.||++
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            5799999999999999999999999999999999998999999999999999999999999999999999999999874

>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=99.82  E-value=1.3e-20  Score=146.20  Aligned_cols=77  Identities=25%  Similarity=0.457  Sum_probs=75.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +|||+|||+.+|+++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|..||..|||..|+|+.|+|.||+
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

>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=99.82  E-value=2.1e-20  Score=146.11  Aligned_cols=78  Identities=41%  Similarity=0.660  Sum_probs=74.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      +.|.++|||+|||+.+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|+|
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            446789999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.82  E-value=5.4e-20  Score=149.77  Aligned_cols=84  Identities=30%  Similarity=0.603  Sum_probs=77.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+++++|.++|++||.|..|.|+.+..||.++|||||+|.+.++|.+||..+|+ .|+|+.|.|.++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            446799999999999999999999999999999999999999999999999999999999998876 7999999999998


Q ss_pred             CCCCC
Q 011668          216 GRTVP  220 (480)
Q Consensus       216 ~~~~~  220 (480)
                      ....+
T Consensus        88 ~~~~p   92 (103)
T d2cqda1          88 LGAKP   92 (103)
T ss_dssp             TTCCC
T ss_pred             CCCCC
Confidence            65443

>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=99.81  E-value=2.7e-20  Score=146.01  Aligned_cols=80  Identities=29%  Similarity=0.506  Sum_probs=77.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      .+|||+|||+.+|+++|.++|++||+|..|.|+.++.||.++|||||+|.+.++|..|+..|||..|+|+.|.|.||...
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999999999753

>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=99.80  E-value=3.1e-20  Score=150.45  Aligned_cols=79  Identities=20%  Similarity=0.495  Sum_probs=75.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+|||+.+|+++|.++|+.||.|..|.|+.+..||.++|||||+|.+.++|.+||. |||..|+|+.|.|.++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            3689999999999999999999999999999999999999999999999999999999996 999999999999999764

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.80  E-value=4.9e-20  Score=143.26  Aligned_cols=79  Identities=16%  Similarity=0.292  Sum_probs=69.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      +||||+|||+++|+++|.++|+.||.|..+.++.+..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.++.+
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999999998888888899999999999999999999999999999999999999875

>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=99.80  E-value=8.8e-20  Score=142.70  Aligned_cols=79  Identities=30%  Similarity=0.597  Sum_probs=75.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+++|+++|.++|++||.|..|.|+.+..||.++|||||+|.+.++|.+||. ++++.|+|+.|.|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            34689999999999999999999999999999999999999999999999999999999998 69999999999998874

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=5.9e-20  Score=144.08  Aligned_cols=78  Identities=27%  Similarity=0.463  Sum_probs=74.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC--eEEEEeee
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG--RRVLVDVE  214 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g--r~l~V~~a  214 (480)
                      .++|||+|||+.+|+++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++|..||+.|||..|.|  .+|.|.||
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            4689999999999999999999999999999999999999999999999999999999999999999998  45999886

>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=99.80  E-value=1.2e-19  Score=143.61  Aligned_cols=81  Identities=22%  Similarity=0.427  Sum_probs=75.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+++|+++|.++|+.||.|..|.|+.++.||.++|||||+|.+.++|.+||..  +..|+|+.|.|.++.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            557899999999999999999999999999999999999999999999999999999999984  458999999999987


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ++.
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            644

>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=99.80  E-value=1.2e-19  Score=145.21  Aligned_cols=83  Identities=23%  Similarity=0.553  Sum_probs=77.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCC-CCCccceEEEEEechhhHHHHHHHc-CCceeCCeEEEEee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKE-TNKPRGYAFIEYMHTRDMKAAYKQA-DGRKLDGRRVLVDV  213 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~-t~~~~g~afV~F~~~~~a~~A~~~l-~g~~i~gr~l~V~~  213 (480)
                      +.++|||+|||+.+++++|..+|++||.|..|.|+.+.. +|.++|||||+|.+.++|..||..| ||..|+|+.|.|+|
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            567899999999999999999999999999999988754 7999999999999999999999988 89999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      |....
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            97643

>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=99.80  E-value=1.3e-19  Score=139.61  Aligned_cols=76  Identities=25%  Similarity=0.475  Sum_probs=73.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .|||+|||+.+++++|.++|++||.|..|.|+.+. ++.++|||||+|.+.++|..||..|||..|+|+.|.|+++.
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            69999999999999999999999999999999886 69999999999999999999999999999999999999985

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.80  E-value=8.6e-20  Score=143.21  Aligned_cols=79  Identities=25%  Similarity=0.467  Sum_probs=75.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC--eEEEEee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG--RRVLVDV  213 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g--r~l~V~~  213 (480)
                      ..++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|.|  ++|.|.|
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            34689999999999999999999999999999999999999999999999999999999999999999977  8899998


Q ss_pred             e
Q 011668          214 E  214 (480)
Q Consensus       214 a  214 (480)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.79  E-value=2.6e-20  Score=143.16  Aligned_cols=76  Identities=22%  Similarity=0.506  Sum_probs=73.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      |+|||+|||+.+|+++|.++|++||.|..|.|+.++.||.++|||||+|.+.++|.+||. +|++.|+|+.|.|.+|
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            579999999999999999999999999999999999999999999999999999999998 7999999999999986

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=9.3e-20  Score=142.35  Aligned_cols=79  Identities=25%  Similarity=0.473  Sum_probs=74.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEE-EecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCCC
Q 011668          140 LFVARLSYETTESKIKREFESYGPIKRV-RLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRT  218 (480)
Q Consensus       140 l~V~nL~~~~te~~L~~~F~~~G~i~~v-~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~~  218 (480)
                      |||+|||+++|+++|.++|++||.|..+ .|+.+..||.++|||||+|.+.++|..||..|||..|+|+.|.|.||.++.
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            8999999999999999999999998664 788899999999999999999999999999999999999999999997644

>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=99.79  E-value=1.1e-19  Score=142.59  Aligned_cols=79  Identities=30%  Similarity=0.558  Sum_probs=73.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCC---CccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETN---KPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       140 l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~---~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      |||+|||+++|+++|.++|++||.|..|.|+.++.++   .++|||||+|.+.++|..||..|||..|+|+.|.|.|+..
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            8999999999999999999999999999999887665   4689999999999999999999999999999999999864


Q ss_pred             CC
Q 011668          217 RT  218 (480)
Q Consensus       217 ~~  218 (480)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            33

>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=99.79  E-value=1.2e-19  Score=147.37  Aligned_cols=80  Identities=28%  Similarity=0.552  Sum_probs=76.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      ++|||+|||+++|+++|.++|++||.|..+.|+.++.++.++|||||+|.+.++|.+||. |+|..|+|+.|.|.+|.++
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECccc
Confidence            689999999999999999999999999999999999999999999999999999999997 8999999999999998865


Q ss_pred             C
Q 011668          218 T  218 (480)
Q Consensus       218 ~  218 (480)
                      .
T Consensus       100 e  100 (103)
T d1x4ba1         100 E  100 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.79  E-value=4.8e-19  Score=141.30  Aligned_cols=83  Identities=19%  Similarity=0.498  Sum_probs=76.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ...++|||+|||+.+++++|.++|++||.|..|.|+.+..  .++|||||+|.+.++|..||..|||..|+|+.|+|.||
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3567899999999999999999999999999999998864  46899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 011668          215 RGRTV  219 (480)
Q Consensus       215 ~~~~~  219 (480)
                      .++..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            87543

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.1e-19  Score=144.15  Aligned_cols=83  Identities=34%  Similarity=0.638  Sum_probs=78.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ...+|||+|||+.+|+++|.++|++||.|..|.++.+..++.++|||||+|.+.++|..||..|||..|+|+.|.|++|.
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            34689999999999999999999999999999999998999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      +..
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.79  E-value=3.2e-19  Score=141.42  Aligned_cols=81  Identities=33%  Similarity=0.546  Sum_probs=74.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .+.++|||+|||+.+|+++|.++|+.||.|..|.|+.+..++  +|||||+|.+.++|..||..|||..|.|+.|+|.||
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            356799999999999999999999999999999999887554  789999999999999999999999999999999999


Q ss_pred             cCC
Q 011668          215 RGR  217 (480)
Q Consensus       215 ~~~  217 (480)
                      .+.
T Consensus        84 ~~~   86 (90)
T d2cqia1          84 TTP   86 (90)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            753

>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=99.78  E-value=1.5e-19  Score=138.27  Aligned_cols=75  Identities=23%  Similarity=0.483  Sum_probs=71.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .|||+|||+++|+++|.++|++||+|..|.|+.++.|+.++|||||+|.+.++|.+||. +++..|+|+.|.|..|
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            49999999999999999999999999999999999999999999999999999999998 8999999999998653

>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=99.78  E-value=8.3e-20  Score=149.00  Aligned_cols=81  Identities=37%  Similarity=0.703  Sum_probs=77.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      .++|||+|||+++|+++|.++|++||+|..|.|+.++.||.++|||||+|.+.++|..||..|||..|.|+.|+|.++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             C
Q 011668          217 R  217 (480)
Q Consensus       217 ~  217 (480)
                      .
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.78  E-value=1e-19  Score=138.92  Aligned_cols=75  Identities=28%  Similarity=0.502  Sum_probs=71.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .|||+|||+.+|+++|.++|++||.|..|.|+.++.|+.++|||||+|.+.++|.+||. ++++.|+|+.|.|.+|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999997 6788999999999865

>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=99.78  E-value=5e-19  Score=136.78  Aligned_cols=77  Identities=25%  Similarity=0.486  Sum_probs=73.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .++|||+|||+++|+++|.++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+. |||..|+|+.|.|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3689999999999999999999999999999999999999999999999999999999996 8999999999999876

>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=99.77  E-value=3.6e-19  Score=140.83  Aligned_cols=79  Identities=23%  Similarity=0.487  Sum_probs=73.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..+|||+|||+.+|+++|.++|++||.|..|.|+.+.  +.++|||||+|.+.++|..||..|||..|+|+.|.|.++.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4589999999999999999999999999999999886  44789999999999999999999999999999999999975


Q ss_pred             C
Q 011668          217 R  217 (480)
Q Consensus       217 ~  217 (480)
                      +
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.77  E-value=4.3e-19  Score=139.44  Aligned_cols=81  Identities=20%  Similarity=0.373  Sum_probs=70.7

Q ss_pred             CCCEEEEcCCCCCCC-HHHHHHHhhcCCCeeEEEeccc-CCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          136 PYKTLFVARLSYETT-ESKIKREFESYGPIKRVRLVTD-KETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       136 ~~~~l~V~nL~~~~t-e~~L~~~F~~~G~i~~v~i~~d-~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..++|||+|||+.+| ++.|.++|++||.|..|.|+.+ ..++.++|||||+|.+.++|.+||+ |||..|+|+.|.|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            357999999999876 5669999999999999998764 5689999999999999999999996 999999999999999


Q ss_pred             ecCC
Q 011668          214 ERGR  217 (480)
Q Consensus       214 a~~~  217 (480)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9864

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=9.1e-19  Score=141.91  Aligned_cols=83  Identities=28%  Similarity=0.453  Sum_probs=76.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCee--------EEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCe
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIK--------RVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGR  207 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~--------~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr  207 (480)
                      ..++|||+|||+.+|+++|.++|+.||.|.        .+.++.+..+|.++|||||+|.+.++|..||..|||..|+|+
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr   86 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGS   86 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCE
Confidence            567999999999999999999999999874        566778888899999999999999999999999999999999


Q ss_pred             EEEEeeecCCC
Q 011668          208 RVLVDVERGRT  218 (480)
Q Consensus       208 ~l~V~~a~~~~  218 (480)
                      .|.|.+|+.+.
T Consensus        87 ~i~V~~a~~~~   97 (101)
T d2cpea1          87 KLKVSLARKKP   97 (101)
T ss_dssp             ECEEECSSCCC
T ss_pred             EEEEEEcCCCC
Confidence            99999998644

>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=99.76  E-value=1.1e-18  Score=144.59  Aligned_cols=78  Identities=26%  Similarity=0.450  Sum_probs=72.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+++|||+|||+.+|+++|.++|++||.|..|.|+.+   +.++|||||+|.+.++|..||..|||..|+|+.|.|.|+.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4679999999999999999999999999999999764   6678999999999999999999999999999999999986


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      .
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
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=99.76  E-value=1.1e-18  Score=140.52  Aligned_cols=83  Identities=31%  Similarity=0.569  Sum_probs=77.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcC------CceeCCeEE
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD------GRKLDGRRV  209 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~------g~~i~gr~l  209 (480)
                      ..++|||+|||+++|+++|.++|++||.|..+.++.+..++.++|||||+|.+.++|..||..||      |..|+|+.|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999886      677999999


Q ss_pred             EEeeecCCC
Q 011668          210 LVDVERGRT  218 (480)
Q Consensus       210 ~V~~a~~~~  218 (480)
                      .|.|+.++.
T Consensus        87 ~v~~a~~k~   95 (98)
T d1x4ha1          87 KVDLAVTRD   95 (98)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999997643

>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=99.76  E-value=2.2e-18  Score=140.36  Aligned_cols=83  Identities=27%  Similarity=0.469  Sum_probs=73.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccC-CCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDK-ETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~-~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ..|.++|||+|||+.+|+++|+++|+.|| |+.+.|+.+. .++.++|||||+|.+.++|++|+. ||+..|+|+.|+|.
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            34678999999999999999999999999 7778777665 478899999999999999987775 99999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      +|....
T Consensus        90 ~a~~~~   95 (104)
T d1wi8a_          90 VADQAQ   95 (104)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            997654

>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=99.76  E-value=2.1e-18  Score=138.11  Aligned_cols=80  Identities=28%  Similarity=0.473  Sum_probs=73.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+.+|+++|.++|+.||.|..|.+..+   +..++||||+|.+.++|..||..|||..|.|+.|+|+|
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            346679999999999999999999999999999988654   55789999999999999999999999999999999999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      |+.
T Consensus        88 a~~   90 (95)
T d1x4aa1          88 PRS   90 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            874

>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=99.76  E-value=5.6e-19  Score=135.02  Aligned_cols=75  Identities=25%  Similarity=0.447  Sum_probs=72.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .|||+|||+++|+++|.++|++||.|..+.++.+..++.++|||||+|.+.++|.+||+ |||..|+|+.|.|.+|
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            49999999999999999999999999999999999999999999999999999999997 9999999999999876

>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=99.75  E-value=2.4e-19  Score=145.67  Aligned_cols=85  Identities=25%  Similarity=0.383  Sum_probs=79.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..|+++|||+|||..+++++|.++|++||.|..+.|+.+..+|.++|||||+|.+.++|..||..|||..|.|+.|.|.|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45788999999999999999999999999999999988888899999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      |+++.
T Consensus        95 ak~k~   99 (102)
T d2cpxa1          95 GKNKK   99 (102)
T ss_dssp             CCCCS
T ss_pred             CCCcc
Confidence            98643

>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=99.74  E-value=3.1e-18  Score=137.24  Aligned_cols=75  Identities=17%  Similarity=0.428  Sum_probs=70.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||..+++++|.++|++||.|..|.|+.+      +|||||+|.+.++|..||..|||..|+|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4578999999999999999999999999999999865      6899999999999999999999999999999999987


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      .
T Consensus        91 ~   91 (96)
T d1x4ga1          91 E   91 (96)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.74  E-value=3.7e-19  Score=141.22  Aligned_cols=80  Identities=16%  Similarity=0.332  Sum_probs=73.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ....+|||+|||+.+|+++|+.+|+.||.|..|.|+. ..+|.++|||||+|.+.++|..||+ |||..|+|+.|.|.+|
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~-~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCE-EEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeee-cCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            3456899999999999999999999999999888864 4579999999999999999999996 9999999999999998


Q ss_pred             cC
Q 011668          215 RG  216 (480)
Q Consensus       215 ~~  216 (480)
                      ++
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.74  E-value=4.1e-18  Score=132.77  Aligned_cols=78  Identities=26%  Similarity=0.399  Sum_probs=71.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee-CCeEEEE
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL-DGRRVLV  211 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i-~gr~l~V  211 (480)
                      ..+|+++|||+|||+.+|+++|..+|++||.|..|.|+.+     .+|||||+|.+.++|..|+..|||..| +|+.|+|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            4457899999999999999999999999999999999754     358999999999999999999999988 5689999


Q ss_pred             eeec
Q 011668          212 DVER  215 (480)
Q Consensus       212 ~~a~  215 (480)
                      .||+
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9986

>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=99.73  E-value=5.6e-18  Score=132.55  Aligned_cols=77  Identities=14%  Similarity=0.277  Sum_probs=72.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .++|||+|||+.+|+++|.++|+.||.|..|.|+.+. ++.++|||||+|.+.++|.+||+ ++|..|.|+.|.|.|+.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4699999999999999999999999999999998775 79999999999999999999997 89999999999999864

>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=99.72  E-value=6e-18  Score=133.40  Aligned_cols=78  Identities=19%  Similarity=0.251  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee-CCeEEEEee
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL-DGRRVLVDV  213 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i-~gr~l~V~~  213 (480)
                      +|+++|||+|||+.+|+++|.++|+.||.|..+.+..    +..+|||||+|.+.++|..|+..|||..| +|+.|+|.|
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            4678999999999999999999999999998887754    44578999999999999999999999988 589999999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      ++.
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            875

>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=99.72  E-value=4.7e-18  Score=136.25  Aligned_cols=80  Identities=28%  Similarity=0.429  Sum_probs=72.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+.++|||+|||+++|+++|.++|++||.|..+..     ++.++|||||+|.+.++|..||..|||..|+|+.|.|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999998876643     578899999999999999999999999999999999999


Q ss_pred             ecCCC
Q 011668          214 ERGRT  218 (480)
Q Consensus       214 a~~~~  218 (480)
                      +.++.
T Consensus        88 a~~k~   92 (96)
T d1fjca_          88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             eCCCC
Confidence            98644

>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=99.72  E-value=3.8e-18  Score=134.75  Aligned_cols=77  Identities=19%  Similarity=0.361  Sum_probs=70.3

Q ss_pred             CCCEEEEcCCCCCCCHHHH---HHHhhcCCCeeEEEecccCCCCCc---cceEEEEEechhhHHHHHHHcCCceeCCeEE
Q 011668          136 PYKTLFVARLSYETTESKI---KREFESYGPIKRVRLVTDKETNKP---RGYAFIEYMHTRDMKAAYKQADGRKLDGRRV  209 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L---~~~F~~~G~i~~v~i~~d~~t~~~---~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l  209 (480)
                      ..++|||+|||+.+++++|   .++|++||.|..|.|+.++.++..   .|||||+|.+.++|..||..|||..|+|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4568999999999999999   678999999999999998876654   4899999999999999999999999999999


Q ss_pred             EEe
Q 011668          210 LVD  212 (480)
Q Consensus       210 ~V~  212 (480)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            984

>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=99.72  E-value=1e-17  Score=131.41  Aligned_cols=76  Identities=32%  Similarity=0.490  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+|+++|.++|++||.|..+.+.      .++|||||+|.+.++|..||..|||..|+|+.|.|.||+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            45799999999999999999999999998877763      457899999999999999999999999999999999997


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      +.
T Consensus        81 P~   82 (86)
T d2cpda1          81 PV   82 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.72  E-value=9.3e-18  Score=134.89  Aligned_cols=73  Identities=25%  Similarity=0.529  Sum_probs=67.0

Q ss_pred             CCCEEEEcCCC-CCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLS-YETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~-~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ..++|||+||+ ..+++++|+.+|++||.|..|.|.        +|||||+|.+.++|.+||..|||..|.|+.|+|+|+
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45679999997 568889999999999999999883        589999999999999999999999999999999998


Q ss_pred             cC
Q 011668          215 RG  216 (480)
Q Consensus       215 ~~  216 (480)
                      ..
T Consensus        86 ~~   87 (98)
T d1wf2a_          86 AE   87 (98)
T ss_dssp             TS
T ss_pred             CC
Confidence            75

>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=99.72  E-value=5.6e-18  Score=134.43  Aligned_cols=79  Identities=18%  Similarity=0.362  Sum_probs=71.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHH----HHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEE
Q 011668          136 PYKTLFVARLSYETTESKIK----REFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLV  211 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~----~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V  211 (480)
                      |++||||+|||+.+++++|.    .+|++||+|..|.+..   ++.++|||||+|.+.++|..||..|||..|+|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            67899999999999998886    4689999999998864   4678899999999999999999999999999999999


Q ss_pred             eeecCC
Q 011668          212 DVERGR  217 (480)
Q Consensus       212 ~~a~~~  217 (480)
                      .||+..
T Consensus        79 ~~ak~~   84 (91)
T d1nu4a_          79 QYAKTD   84 (91)
T ss_dssp             EECSSC
T ss_pred             EEeCCC
Confidence            999754

>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=99.71  E-value=4.2e-18  Score=137.90  Aligned_cols=80  Identities=15%  Similarity=0.313  Sum_probs=73.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+++++|.++|++||.|..+.++.+. ++.++|||||+|.+.++|..||..|||..|.|++|.|.++.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            45789999999999999999999999999999988774 68899999999999999999999999999999999887765


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      +
T Consensus        96 P   96 (101)
T d1x5oa1          96 P   96 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.71  E-value=9.3e-18  Score=138.26  Aligned_cols=76  Identities=16%  Similarity=0.264  Sum_probs=70.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+++++|.++|++||+|..|.|.      ..+|||||+|.+.++|..||..|||..|.|+.|.|+|+.
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            34689999999999999999999999999999884      346899999999999999999999999999999999987


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.71  E-value=6.4e-18  Score=132.65  Aligned_cols=79  Identities=18%  Similarity=0.242  Sum_probs=70.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ..++|||+|||+.+++++|.++|..||.|..+.++....++.++|||||+|.+.++|..||..|||..|+|+.|+|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4567999999999999999999999999876434444457999999999999999999999999999999999999875

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=1.3e-17  Score=127.10  Aligned_cols=74  Identities=22%  Similarity=0.301  Sum_probs=68.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      ++|||+|||+.+++++|+++|+.||.|..|.|+.+..  ...+||||+|.+.++|.+||. ||+..|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4899999999999999999999999999999998865  345799999999999999996 8999999999999865

>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=99.71  E-value=2.2e-17  Score=135.48  Aligned_cols=77  Identities=21%  Similarity=0.418  Sum_probs=70.5

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          137 YKTLFVARLSY-ETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       137 ~~~l~V~nL~~-~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .++|||+||++ .+|+++|.++|+.||.|..|.|+.+.     +|||||+|.+.++|.+||..|||..|.|+.|.|.|+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            46999999965 59999999999999999999998763     6899999999999999999999999999999999987


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            544

>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=99.71  E-value=1.2e-17  Score=131.54  Aligned_cols=76  Identities=12%  Similarity=0.290  Sum_probs=66.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+++++|.++|++|| |..+.+      +..+|||||+|.+.++|..||..|||..|.|+.|.|+|+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            456899999999999999999999999 323333      4467899999999999999999999999999999999997


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ...
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            544

>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=99.71  E-value=8e-18  Score=132.63  Aligned_cols=76  Identities=18%  Similarity=0.328  Sum_probs=68.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ..++|||+|||+.+|+++|+++|++||.|..|.++.     .++|||||+|.+.++|+.||.  +++.|+|+.|.|.++.
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 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            567999999999999999999999999999998753     457899999999999999985  7889999999999997


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ++.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=1.4e-17  Score=130.49  Aligned_cols=76  Identities=26%  Similarity=0.407  Sum_probs=70.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +.++|||+|||+.+++++|.++|++||.|..|.++.+      +|||||+|.+.++|..||..|||..|+|+.|+|+||.
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            3468999999999999999999999999999999754      5799999999999999999999999999999999987


Q ss_pred             CC
Q 011668          216 GR  217 (480)
Q Consensus       216 ~~  217 (480)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1e-17  Score=129.14  Aligned_cols=75  Identities=21%  Similarity=0.414  Sum_probs=68.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      .+++|||+||+  +|+++|.++|++||.|..|.+..      .+|||||+|.+.++|..||..|||..|+|+.|+|.|++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET------TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeecc------CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            56799999996  89999999999999999999864      35799999999999999999999999999999999997


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      +.+
T Consensus        76 ~~P   78 (79)
T d2bz2a1          76 KQP   78 (79)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.70  E-value=1.4e-17  Score=133.50  Aligned_cols=83  Identities=22%  Similarity=0.280  Sum_probs=74.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCC-eeEEEecccC-CCCCccceEEEEEechhhHHHHHHHcCC--ceeCCeEEEEee
Q 011668          138 KTLFVARLSYETTESKIKREFESYGP-IKRVRLVTDK-ETNKPRGYAFIEYMHTRDMKAAYKQADG--RKLDGRRVLVDV  213 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~-i~~v~i~~d~-~t~~~~g~afV~F~~~~~a~~A~~~l~g--~~i~gr~l~V~~  213 (480)
                      |.|||+|||..+++++|.++|+.||+ |..|.|+.+. .++.++|||||+|.+.++|..||..|++  ..++|+.|.|.|
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            68999999999999999999999995 9999998875 4688999999999999999999999864  456899999999


Q ss_pred             ecCCCCC
Q 011668          214 ERGRTVP  220 (480)
Q Consensus       214 a~~~~~~  220 (480)
                      |.+...+
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9875543

>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=99.70  E-value=2.5e-18  Score=130.24  Aligned_cols=71  Identities=23%  Similarity=0.414  Sum_probs=68.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       140 l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      |||+|||+.+|+++|.++|++||.|..+.++.++.++.++|||||+|.+.++|..||..|||..|+|+.|+
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            89999999999999999999999999999999999999999999999999999999999999999998763

>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=99.70  E-value=3.7e-17  Score=132.94  Aligned_cols=83  Identities=12%  Similarity=0.137  Sum_probs=75.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ...+|||+|||+.+|+++|+++|..||.|..+.++.+..++.++|||||+|.+.++|.+||. ||+..|+|+.|.|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            45679999999999999999999999999887777777789999999999999999999997 89999999999999998


Q ss_pred             CCCC
Q 011668          216 GRTV  219 (480)
Q Consensus       216 ~~~~  219 (480)
                      ....
T Consensus        93 ~~~~   96 (104)
T d1wg5a_          93 RAEV   96 (104)
T ss_dssp             TTTS
T ss_pred             HHHh
Confidence            6543

>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=99.70  E-value=1.6e-17  Score=134.65  Aligned_cols=83  Identities=20%  Similarity=0.229  Sum_probs=73.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ......+|||+|||+++|+++|.++|..|| |..|.++.+. ++..+|||||+|.+.++|++||. ||+..|+|+.|.|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            344567999999999999999999999998 4577777775 48899999999999999999997 89999999999999


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      ++....
T Consensus        88 ~s~~~~   93 (102)
T d1weza_          88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             EcCCCC
Confidence            988654

>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=99.69  E-value=5.2e-18  Score=133.41  Aligned_cols=73  Identities=18%  Similarity=0.257  Sum_probs=67.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGR  217 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~  217 (480)
                      ++|||+|||+.+|+++|.++|++||.|..|.|+.+       |||||+|.+.++|..||..|||..|.|+.|.|.++...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            36999999999999999999999999999998754       79999999999999999999999999999999887643

>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=99.69  E-value=9.3e-18  Score=129.74  Aligned_cols=75  Identities=21%  Similarity=0.352  Sum_probs=67.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCc-eeCCeEEEEeeecC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGR-KLDGRRVLVDVERG  216 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~-~i~gr~l~V~~a~~  216 (480)
                      ++|||+|||+.+|+++|.++|++||.|..+.++.      .+|||||+|.+.++|..||+.|||. .|+|+.|.|+|+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999987766643      4689999999999999999999996 69999999999986


Q ss_pred             CC
Q 011668          217 RT  218 (480)
Q Consensus       217 ~~  218 (480)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.68  E-value=5e-17  Score=130.39  Aligned_cols=78  Identities=29%  Similarity=0.540  Sum_probs=70.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCC--eEEEE
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDG--RRVLV  211 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~g--r~l~V  211 (480)
                      ..|+++|||+|||+++++++|+++|++||.|..|.|+.+      ++||||+|.+.++|..|+..|||..|.|  ..|+|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            357889999999999999999999999999999999754      5799999999999999999999999986  57999


Q ss_pred             eeecCC
Q 011668          212 DVERGR  217 (480)
Q Consensus       212 ~~a~~~  217 (480)
                      +|++..
T Consensus        88 ~~ak~~   93 (97)
T d1whya_          88 DFAKSG   93 (97)
T ss_dssp             EECCCC
T ss_pred             EeCCCC
Confidence            998753

>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=99.68  E-value=6.2e-17  Score=129.98  Aligned_cols=76  Identities=17%  Similarity=0.228  Sum_probs=70.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          136 PYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       136 ~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      ...+|||+|||+.+++++|.++|++||+|+.|.|..       +|||||+|.+.++|..||+.|||..|.|+.|.|.++.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            456899999999999999999999999999999864       4899999999999999999999999999999999987


Q ss_pred             CCC
Q 011668          216 GRT  218 (480)
Q Consensus       216 ~~~  218 (480)
                      ...
T Consensus        87 ~~~   89 (98)
T d1wg4a_          87 VYP   89 (98)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            644

>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=99.67  E-value=8.8e-17  Score=122.46  Aligned_cols=72  Identities=18%  Similarity=0.337  Sum_probs=65.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecCCC
Q 011668          140 LFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERGRT  218 (480)
Q Consensus       140 l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~~~  218 (480)
                      |||+|||+.+++++|.++|++|| |..+.+      +.++|||||+|.+.++|.+|+..|||..|.|+.|.|+|+....
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            89999999999999999999999 555554      4567999999999999999999999999999999999997543

>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=99.67  E-value=1.6e-16  Score=124.98  Aligned_cols=80  Identities=15%  Similarity=0.271  Sum_probs=71.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHc--CCceeCCeEEE
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA--DGRKLDGRRVL  210 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l--~g~~i~gr~l~  210 (480)
                      ...|+++|||+|||+.+++++|.++|++||.|..|.++.+      ++||||+|.+.++|..|+..|  ++..|.|+.|.
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            3568899999999999999999999999999999998754      479999999999999999865  67899999999


Q ss_pred             EeeecCCC
Q 011668          211 VDVERGRT  218 (480)
Q Consensus       211 V~~a~~~~  218 (480)
                      |.|++.+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99997544

>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=99.67  E-value=4.7e-17  Score=132.15  Aligned_cols=79  Identities=15%  Similarity=0.228  Sum_probs=70.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ..+|||+|||+.+|+++|.++|..||.|..+.++....+|.++|||||+|.+.++|+.||. |||..|+|+.|.|.++..
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECH
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCH
Confidence            4579999999999999999999999998775455555679999999999999999999997 999999999999998754

>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=99.65  E-value=6.7e-17  Score=132.36  Aligned_cols=80  Identities=18%  Similarity=0.303  Sum_probs=71.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee--CCeEEEEe
Q 011668          135 DPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL--DGRRVLVD  212 (480)
Q Consensus       135 ~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i--~gr~l~V~  212 (480)
                      .+..+|||+|||+.+|+++|.++|++||.|..|.|+.++    .+|||||+|.+.++|+.||..|||..|  .+..|.|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            366789999999999999999999999999999998653    479999999999999999999999998  57888998


Q ss_pred             eecCCC
Q 011668          213 VERGRT  218 (480)
Q Consensus       213 ~a~~~~  218 (480)
                      |++...
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            887543

>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=99.64  E-value=7.5e-16  Score=125.07  Aligned_cols=80  Identities=15%  Similarity=0.213  Sum_probs=71.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHc--CCceeCCeEEE
Q 011668          133 SGDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA--DGRKLDGRRVL  210 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l--~g~~i~gr~l~  210 (480)
                      ...|+.+|||+|||+.+|+++|.++|+.||.|..|.|..      .++||||+|.+.++|..||..|  ++..|.|+.|.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe------cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            345789999999999999999999999999999999864      3689999999999999999977  56778999999


Q ss_pred             EeeecCCC
Q 011668          211 VDVERGRT  218 (480)
Q Consensus       211 V~~a~~~~  218 (480)
                      |.|+....
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99997644

>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=99.63  E-value=8.4e-17  Score=132.60  Aligned_cols=82  Identities=16%  Similarity=0.234  Sum_probs=73.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ..+..+|||+|||+.+|+++|.++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||. |||..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3456799999999999999999999999998776666666789999999999999999999997 999999999999988


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      +..
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            753

>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=99.61  E-value=5.3e-16  Score=124.70  Aligned_cols=78  Identities=24%  Similarity=0.297  Sum_probs=69.7

Q ss_pred             CCCCCCEEEEcCCCCC-CCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHH--HcCCceeCCeEE
Q 011668          133 SGDPYKTLFVARLSYE-TTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYK--QADGRKLDGRRV  209 (480)
Q Consensus       133 ~~~~~~~l~V~nL~~~-~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~--~l~g~~i~gr~l  209 (480)
                      ...++++|||+|||.. +|+++|..+|+.||.|..|.|+.+      +|||||+|.+.++|..||.  .+++..|+|+.|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            3456789999999985 899999999999999999999754      5799999999999999997  578999999999


Q ss_pred             EEeeecC
Q 011668          210 LVDVERG  216 (480)
Q Consensus       210 ~V~~a~~  216 (480)
                      .|.|++.
T Consensus        88 ~V~~s~~   94 (99)
T d1x4fa1          88 KVDLSEK   94 (99)
T ss_dssp             EEEEECS
T ss_pred             EEEEcCC
Confidence            9999974

>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=99.59  E-value=1.6e-15  Score=122.79  Aligned_cols=77  Identities=10%  Similarity=0.100  Sum_probs=68.6

Q ss_pred             CCCEEEEcCCCCCC-CH----HHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEE
Q 011668          136 PYKTLFVARLSYET-TE----SKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVL  210 (480)
Q Consensus       136 ~~~~l~V~nL~~~~-te----~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~  210 (480)
                      ..++|||+||+..+ ++    ++|..+|+.||.|+.|.++.      +++||||+|.+.++|..||..|||..|+|+.|+
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 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            46789999999886 33    57999999999999999874      467999999999999999999999999999999


Q ss_pred             EeeecCCC
Q 011668          211 VDVERGRT  218 (480)
Q Consensus       211 V~~a~~~~  218 (480)
                      |.|+....
T Consensus        78 v~~a~~~~   85 (104)
T d1weya_          78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EeecccCC
Confidence            99997654

>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=99.59  E-value=1.9e-15  Score=118.87  Aligned_cols=77  Identities=18%  Similarity=0.222  Sum_probs=69.2

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHc--CCceeCCeEEE
Q 011668          134 GDPYKTLFVARLSYE-TTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQA--DGRKLDGRRVL  210 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~-~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l--~g~~i~gr~l~  210 (480)
                      ..++.+|||+|||.. +|+++|.++|+.||.|..|.|+.+      ++||||+|.+.++|..|+..|  ++..|.|++|.
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            457789999999986 789999999999999999999764      469999999999999999965  78899999999


Q ss_pred             EeeecC
Q 011668          211 VDVERG  216 (480)
Q Consensus       211 V~~a~~  216 (480)
                      |.||+.
T Consensus        79 V~~s~~   84 (89)
T d1x4da1          79 VHLSQK   84 (89)
T ss_dssp             EEEECC
T ss_pred             EEECCC
Confidence            999974

>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=99.57  E-value=4.1e-17  Score=129.05  Aligned_cols=77  Identities=17%  Similarity=0.340  Sum_probs=67.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEec-----ccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEe
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLV-----TDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVD  212 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~-----~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~  212 (480)
                      ++|||+|||+.+|+++|.++|+.||.|..+.++     .+..++.++|||||+|.+.++|+.|+. |||..|.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            589999999999999999999999988766553     344568889999999999999999996 99999999999997


Q ss_pred             eec
Q 011668          213 VER  215 (480)
Q Consensus       213 ~a~  215 (480)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            544

>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=99.57  E-value=3.5e-15  Score=133.55  Aligned_cols=82  Identities=23%  Similarity=0.427  Sum_probs=77.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEee
Q 011668          134 GDPYKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDV  213 (480)
Q Consensus       134 ~~~~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~  213 (480)
                      ....++|||+|||+.+|+++|..+|+.||.|..+.|+.+..+|.++|||||+|.+.++|.+||. +++..|+|+.|.|.+
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            3456899999999999999999999999999999999999999999999999999999999997 799999999999999


Q ss_pred             ecC
Q 011668          214 ERG  216 (480)
Q Consensus       214 a~~  216 (480)
                      |.+
T Consensus       173 A~~  175 (183)
T d1u1qa_         173 ALS  175 (183)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.5e-15  Score=123.01  Aligned_cols=75  Identities=13%  Similarity=0.254  Sum_probs=70.1

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeee
Q 011668          139 TLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVE  214 (480)
Q Consensus       139 ~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a  214 (480)
                      .|+|.++...++++.|.++|++||.|..|.|+.+ .++.++|||||+|.+.++|.+|+..|||..|+|+.|.|+|+
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            4778888888999999999999999999999876 47999999999999999999999999999999999999985

>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=99.48  E-value=4.7e-14  Score=113.45  Aligned_cols=66  Identities=21%  Similarity=0.400  Sum_probs=59.4

Q ss_pred             CCCCCCEEEEcC--CCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee
Q 011668          133 SGDPYKTLFVAR--LSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       133 ~~~~~~~l~V~n--L~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      ...|+.+|||+|  ||+.+|+++|..+|++||.|..|.++.+      ++||||+|.+.++|..|+..|||..|
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            345778999955  9999999999999999999999988764      57999999999999999999999887

>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=99.44  E-value=7.1e-14  Score=114.85  Aligned_cols=74  Identities=20%  Similarity=0.189  Sum_probs=65.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEech-hhHHHHHHHcCCceeCCeEEEEeeec
Q 011668          137 YKTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHT-RDMKAAYKQADGRKLDGRRVLVDVER  215 (480)
Q Consensus       137 ~~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~-~~a~~A~~~l~g~~i~gr~l~V~~a~  215 (480)
                      +..+||||||+.+|+++|..+|++||+|..|.|+.+      +|||||.|.+. ++|..|+..||+..|.++.+.|.|+.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            445699999999999999999999999999999854      68999999986 67899999999999988888887765


Q ss_pred             C
Q 011668          216 G  216 (480)
Q Consensus       216 ~  216 (480)
                      .
T Consensus        85 ~   85 (113)
T d1owxa_          85 L   85 (113)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.40  E-value=3.7e-13  Score=120.03  Aligned_cols=78  Identities=31%  Similarity=0.607  Sum_probs=72.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      ++|||+|||+.+|+++|.++|++||.|..+.|+.+..++.++|||||+|.+.++|.+|+. +++..+++..|.+.....
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            689999999999999999999999999999999999999999999999999999999998 667788898888876543

>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=99.39  E-value=5e-13  Score=106.91  Aligned_cols=79  Identities=18%  Similarity=0.403  Sum_probs=67.7

Q ss_pred             CCCEEEEcCC--CCCC---------CHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCcee
Q 011668          136 PYKTLFVARL--SYET---------TESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKL  204 (480)
Q Consensus       136 ~~~~l~V~nL--~~~~---------te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i  204 (480)
                      ..++|+|.||  |..+         ..++|.+.|++||.|..|.++.+    .++|||||+|.+.++|..|+..|||..|
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            5689999999  5432         13678999999999999988764    4579999999999999999999999999


Q ss_pred             CCeEEEEeeecCCC
Q 011668          205 DGRRVLVDVERGRT  218 (480)
Q Consensus       205 ~gr~l~V~~a~~~~  218 (480)
                      +|+.|.|.|+.+++
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            99999999987543

>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=99.35  E-value=6.7e-13  Score=101.80  Aligned_cols=70  Identities=17%  Similarity=0.220  Sum_probs=59.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeE-EEEeeec
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRR-VLVDVER  215 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~-l~V~~a~  215 (480)
                      +.|+|+|||+.++++.| .+|++||+|..+.+.      ..+|||||+|.+.++|++||. |||..|+|+. |.|..+.
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            57999999999886555 689999999999874      346899999999999999997 9999999975 5576654

>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=99.35  E-value=4.4e-13  Score=108.29  Aligned_cols=81  Identities=21%  Similarity=0.336  Sum_probs=69.1

Q ss_pred             CCCCEEEEcCC--CCCCC--------HHHHHHHhhcCCCeeEEEecccCCC--CCccceEEEEEechhhHHHHHHHcCCc
Q 011668          135 DPYKTLFVARL--SYETT--------ESKIKREFESYGPIKRVRLVTDKET--NKPRGYAFIEYMHTRDMKAAYKQADGR  202 (480)
Q Consensus       135 ~~~~~l~V~nL--~~~~t--------e~~L~~~F~~~G~i~~v~i~~d~~t--~~~~g~afV~F~~~~~a~~A~~~l~g~  202 (480)
                      .|+++|+|.||  +..+.        .++|++.|++||.|..|.|+.+..+  ....|++||+|.+.++|..|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            57889999999  44332        3578999999999999999876544  334689999999999999999999999


Q ss_pred             eeCCeEEEEeeec
Q 011668          203 KLDGRRVLVDVER  215 (480)
Q Consensus       203 ~i~gr~l~V~~a~  215 (480)
                      .|+|+.|.|.|..
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCeEEEEEEcC
Confidence            9999999999975

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.82  E-value=2.7e-05  Score=58.19  Aligned_cols=74  Identities=23%  Similarity=0.335  Sum_probs=59.3

Q ss_pred             CCCCCCCEEEEcCCCCCC------CH---HHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCc
Q 011668          132 VSGDPYKTLFVARLSYET------TE---SKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGR  202 (480)
Q Consensus       132 ~~~~~~~~l~V~nL~~~~------te---~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~  202 (480)
                      ..++|-.||.|.=+.+..      .+   .+|.+.|..||+|.-|+++.+        -..|+|.+-..|.+|+. |+|.
T Consensus        10 ~qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~   80 (95)
T d1ufwa_          10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGM   80 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGS
T ss_pred             ccCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCe
Confidence            345566788886554332      22   468888999999999999875        67999999999999999 9999


Q ss_pred             eeCCeEEEEeee
Q 011668          203 KLDGRRVLVDVE  214 (480)
Q Consensus       203 ~i~gr~l~V~~a  214 (480)
                      .|.|+.|+|...
T Consensus        81 ~v~G~~l~It~~   92 (95)
T d1ufwa_          81 KVKGRAVKISGP   92 (95)
T ss_dssp             EETTEEEEEECC
T ss_pred             EEcceEEEEecC
Confidence            999999999753

>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=97.51  E-value=0.00016  Score=54.86  Aligned_cols=78  Identities=13%  Similarity=0.233  Sum_probs=62.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCc--cceEEEEEechhhHHHHHHHcCCceeCC-----eEEE
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKP--RGYAFIEYMHTRDMKAAYKQADGRKLDG-----RRVL  210 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~--~g~afV~F~~~~~a~~A~~~l~g~~i~g-----r~l~  210 (480)
                      ++|.|.+||+.+|++++.+.+...|++..+..+....+.++  -.-|||.|.+.+++......++|+.|-+     ..-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            57999999999999999999999999988777665544333  3568999999999999999999988732     2345


Q ss_pred             Eeeec
Q 011668          211 VDVER  215 (480)
Q Consensus       211 V~~a~  215 (480)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66653

>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=97.38  E-value=0.00042  Score=49.02  Aligned_cols=62  Identities=19%  Similarity=0.334  Sum_probs=52.9

Q ss_pred             HHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcCCceeCCeEEEEeeecC
Q 011668          152 SKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQADGRKLDGRRVLVDVERG  216 (480)
Q Consensus       152 ~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~g~~i~gr~l~V~~a~~  216 (480)
                      +.|..+|.++|.|..+.|..... +  .-.|-|...+..+|..|+..|+-..|+++.|.|.++.+
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-Y--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-T--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-C--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            45778899999999998865432 2  34799999999999999999999999999999999864

>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=94.91  E-value=0.019  Score=43.23  Aligned_cols=55  Identities=16%  Similarity=0.340  Sum_probs=44.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCCeeEEEecccCCCCCccceEEEEEechhhHHHHHHHcC
Q 011668          138 KTLFVARLSYETTESKIKREFESYGPIKRVRLVTDKETNKPRGYAFIEYMHTRDMKAAYKQAD  200 (480)
Q Consensus       138 ~~l~V~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~t~~~~g~afV~F~~~~~a~~A~~~l~  200 (480)
                      .-||.-.+|..+...+|.++|+.||.|. |.++-+       .-|||...+.++|..++..++
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd-------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC-------ceEEEEecCHHHHHHHHHHhc
Confidence            3488889999999999999999999885 434433       279999999999998887543