Citrus Sinensis ID: 012034

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470--
Protein Sequence
MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS
Secondary Structure (PSIPRED)
cccccEEEEEccccccHHHHHHHHHccccEEEEccccccccHHHHHHHHcccccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHcccccccEEEEEccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccccccccHHHHHHHHcccccEEEEEEEEccccccccEEEEccccHHHHHHHHHHHcccccccEEEEEEEcccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEEEEccccccHHHccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEccccHHHHHHHHHHHHHHHHHHHcccccEEEEEEcccccccHHHHHHHHcccccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHcccccccccEEEEEccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHccccHHcHEEcccccccc
Coil and Loop (DISEMBL)
MLINDKQVFVGHFLRKQERETVAIKTKFNNVFvknldesttdedLKKIFGEYGTITSAVvmrdgdgkskcfgfvnfenADDAAKAVEALngkkfddrewyvgkaqkksEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFgtitsckvmrdpsgiskgsgfvafstPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFsqmrpvamgpsvpprmpmyppgpsglgqqflygqappaiippqagfgyqqqlvpgmrpagapmpnffvpvvsqgqqgqrpggrrgagpvqqtqqplpimphqmpprghayryplgrnmqdfpfdmgagsmlpvpvdmgagiprrdasvgqpmpITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQqannpadqlaslslnenlvs
Flexible Loop (DISEMBL)
mlindkqvfvghflrkqeretvaiktkfnnvfvknldesttdedlkkiFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEalngkkfddrewyvgkaqkksereqeLKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLqaqfsqmrpvamgpsvpPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQannpadqlaslslnenlvs
Low Complexity Region (SEG)
MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMgpsvpprmpmyppgpsgLGQQFLYGqappaiippqaGFGYQQQLVPGMRPAGAPMPNFFvpvvsqgqqgqrpggrrgagpvqqTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS
Disordered region (IsUnstruct)
******QVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV************************VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMR**********FV*****************KMIVSKPLYVAV********************************************FLYGQAPPAIIPPQAGFGYQQQLV***********NFFVP*******************************************************************************************************LGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLE******************************************
Disordered Region (DISOPRED)
MLINDKQVFVGH*****************NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG***************************QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPE*A**ALAEMNGKMIVSKPLYVA**********************************YPPGPSGLGQQFLYGQAPPAIIPPQA*******************************************************************************************************************************LLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEV***************************
Disordered Region (DISEMBL)
MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK**************FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA**********QAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVV*******************QTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS
Disordered Region (DISPRO)
*LINDKQVFVGHFLRKQERET**IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQG*****RRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSML*********************PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQAN*****************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKxxxxxxxxxxxxxxxxxxxxxTVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	472	2.2.26 [Sep-21-2011]
P42731	629	Polyadenylate-binding pro	no	no	0.938	0.704	0.672	1e-170
O64380	660	Polyadenylate-binding pro	no	no	0.904	0.646	0.508	1e-112
Q05196	682	Polyadenylate-binding pro	no	no	0.970	0.671	0.504	1e-111
P29341	636	Polyadenylate-binding pro	no	no	0.925	0.687	0.413	1e-83
Q5R8F7	636	Polyadenylate-binding pro	yes	no	0.925	0.687	0.413	2e-83
P11940	636	Polyadenylate-binding pro	no	no	0.925	0.687	0.413	3e-83
P61286	636	Polyadenylate-binding pro	yes	no	0.925	0.687	0.413	3e-83
Q9EPH8	636	Polyadenylate-binding pro	yes	no	0.932	0.691	0.413	7e-83
Q6DEY7	629	Embryonic polyadenylate-b	no	no	0.915	0.686	0.392	6e-82
Q6IP09	633	Polyadenylate-binding pro	N/A	no	0.927	0.691	0.410	9e-82

>sp|P42731|PABP2_ARATH Polyadenylate-binding protein 2 OS=Arabidopsis thaliana GN=PAB2 PE=1 SV=1

 Score =  598 bits (1542), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 314/467 (67%), Positives = 372/467 (79%), Gaps = 24/467 (5%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           ML+NDKQV+VG FLR+QER++ A KTKF NV+VKNL ESTTD+DLK  FGEYG ITSAVV
Sbjct: 187 MLLNDKQVYVGPFLRRQERDSTANKTKFTNVYVKNLAESTTDDDLKNAFGEYGKITSAVV 246

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           M+DG+GKSK FGFVNFENADDAA+AVE+LNG KFDD+EWYVG+AQKKSERE EL+ ++EQ
Sbjct: 247 MKDGEGKSKGFGFVNFENADDAARAVESLNGHKFDDKEWYVGRAQKKSERETELRVRYEQ 306

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
            +KE  DKFQ  NLY+KNL  SI DEKLKE+FS FGT+TS KVMRDP+G SKGSGFVAF+
Sbjct: 307 NLKEAADKFQSSNLYVKNLDPSISDEKLKEIFSPFGTVTSSKVMRDPNGTSKGSGFVAFA 366

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           TPEEA+ A+++++GKMI SKPLYVA+AQRKE+RR RLQAQFSQ+RPVAM PSV PRMP+Y
Sbjct: 367 TPEEATEAMSQLSGKMIESKPLYVAIAQRKEDRRVRLQAQFSQVRPVAMQPSVGPRMPVY 426

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
           PPG  G+GQQ  YGQAPPA+IPPQ G+GYQQQLVPGMRP G P+P+FF+P+V   QQ   
Sbjct: 427 PPGGPGIGQQMFYGQAPPAMIPPQPGYGYQQQLVPGMRPGGGPVPSFFMPMVQPQQQRPG 486

Query: 301 PGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGA 360
               R  G +Q +QQ  P+M  QM PRG  +RYP GR         G    +P P DMG 
Sbjct: 487 G--GRRPGGIQHSQQQNPMMQQQMHPRGRMFRYPQGR---------GGSGDVP-PYDMGN 534

Query: 361 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 420
            +         P+ I AL++ L+NA+PEQQRT+LGE LYPLVEQ+E ++AAKVTGMLLEM
Sbjct: 535 NM---------PLTIGALASNLSNATPEQQRTMLGEVLYPLVEQVEAESAAKVTGMLLEM 585

Query: 421 DQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLN 467
           DQTEVLHLLESPEALKAKVAEAM+VLRSVA   A    +QLASL+L+
Sbjct: 586 DQTEVLHLLESPEALKAKVAEAMDVLRSVA---AGGATEQLASLNLS 629

Binds the poly(A) tail of mRNA.
Arabidopsis thaliana (taxid: 3702)

>sp|O64380|PABP3_ARATH Polyadenylate-binding protein 3 OS=Arabidopsis thaliana GN=PAB3 PE=2 SV=1

 Score =  406 bits (1044), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 237/466 (50%), Positives = 301/466 (64%), Gaps = 39/466 (8%)

Query: 1   MLINDKQVFVGHFLRKQER--ETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
           ML+NDKQVFVGHF+R+QER  +      +F NV+VKNL +   +++L+K FG++G I+SA
Sbjct: 199 MLMNDKQVFVGHFIRRQERARDENTPTPRFTNVYVKNLPKEIGEDELRKTFGKFGVISSA 258

Query: 59  VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
           VVMRD  G S+CFGFVNFE  + AA AVE +NG    D   YVG+AQKKSERE+EL+ +F
Sbjct: 259 VVMRDQSGNSRCFGFVNFECTEAAASAVEKMNGISLGDDVLYVGRAQKKSEREEELRRKF 318

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
           EQ      +K QG NLY+KNL DS+DDEKLKE+FSE+G +TS KVM +P G+S+G GFVA
Sbjct: 319 EQERINRFEKSQGANLYLKNLDDSVDDEKLKEMFSEYGNVTSSKVMLNPQGMSRGFGFVA 378

Query: 179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMP 238
           +S PEEA RAL+EMNGKMI  KPLY+A+AQRKE+RRA LQA FSQ+R             
Sbjct: 379 YSNPEEALRALSEMNGKMIGRKPLYIALAQRKEDRRAHLQALFSQIR------------- 425

Query: 239 MYPPGP-SGLG-----------QQFLYGQAPPAIIPPQ-AGFGYQQQLVPGMRPAGAPMP 285
              PGP SG             Q    GQ   +++P Q  G+G+Q Q +PGMRP   P  
Sbjct: 426 --APGPMSGFHHPPGGPMPGPPQHMYVGQNGASMVPSQPIGYGFQPQFMPGMRPGSGP-G 482

Query: 286 NFFV--PVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPL--GRNMQD 341
           NF V  P+  Q Q G R G RRGA  VQQ  Q   +M H+ P  G  Y      GRN  D
Sbjct: 483 NFIVPYPLQRQPQTGPRMGFRRGATNVQQHIQQQQLM-HRNPSPGMRYMNGASNGRNGMD 541

Query: 342 FPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPL 401
                G    +       + I  + A +   +PI+ L+++LA+ASP  +  +LGE LYPL
Sbjct: 542 SSVPQGILPPIIPLPIDASSISHQKAPL---LPISKLTSSLASASPADRTRMLGEQLYPL 598

Query: 402 VEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLR 447
           VE+ E    AKVTGMLLEMDQ E+LHL+ESPEALK+KV+EA++VLR
Sbjct: 599 VERHEPLHVAKVTGMLLEMDQAEILHLMESPEALKSKVSEALDVLR 644

Binds the poly(A) tail of mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q05196|PABP5_ARATH Polyadenylate-binding protein 5 OS=Arabidopsis thaliana GN=PAB5 PE=1 SV=3

 Score =  401 bits (1031), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 244/484 (50%), Positives = 320/484 (66%), Gaps = 26/484 (5%)

Query: 1   MLINDKQVFVGHFLRKQER---ETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS 57
           ML+NDKQVFVGHF+R+Q+R   E+ A+ + F NV+VKNL +  TD++LKK FG+YG I+S
Sbjct: 209 MLLNDKQVFVGHFVRRQDRARSESGAVPS-FTNVYVKNLPKEITDDELKKTFGKYGDISS 267

Query: 58  AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQ 117
           AVVM+D  G S+ FGFVNF + + AA AVE +NG    +   YVG+AQKKS+RE+EL+ +
Sbjct: 268 AVVMKDQSGNSRSFGFVNFVSPEAAAVAVEKMNGISLGEDVLYVGRAQKKSDREEELRRK 327

Query: 118 FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFV 177
           FEQ      +K QG NLY+KNL DS++DEKLKE+FSE+G +TSCKVM +  G+S+G GFV
Sbjct: 328 FEQERISRFEKLQGSNLYLKNLDDSVNDEKLKEMFSEYGNVTSCKVMMNSQGLSRGFGFV 387

Query: 178 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMR-PVAMGPSVPPR 236
           A+S PEEA  A+ EMNGKMI  KPLYVA+AQRKEER+A LQ+ F+Q+R P  M P VP  
Sbjct: 388 AYSNPEEALLAMKEMNGKMIGRKPLYVALAQRKEERQAHLQSLFTQIRSPGTMSP-VPSP 446

Query: 237 MP---MYPPGP--SGLGQQFLYGQAPPAIIPPQ-AGFGYQQQLVPGMRPAGAPMPNFFV- 289
           M     +PPG   SG       G     ++P Q  G+GYQ Q +PGMRP   P PNF + 
Sbjct: 447 MSGFHHHPPGGPMSGPHHPMFIGHNGQGLVPSQPMGYGYQVQFMPGMRPGAGP-PNFMMP 505

Query: 290 -PVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGA 348
            P+  Q Q G R G RRGA  +QQ  Q       Q   + +A R+  G   +    +  A
Sbjct: 506 FPLQRQTQPGPRVGFRRGANNMQQQFQ------QQQMLQQNASRFMGGAGNRRNGMEASA 559

Query: 349 -GSMLPVPVDMGA---GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQ 404
              ++P+P++  A     P+R +    P+ I+ L++ LA ASP++   +LG+ LYPLVEQ
Sbjct: 560 PQGIIPLPLNASANSHNAPQR-SHKPTPLTISKLASDLALASPDKHPRMLGDHLYPLVEQ 618

Query: 405 LERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASL 464
            E   AAKVTGMLLEMDQ E+LHLLESPEALKAKV+EA++VLR  A   A +  D   +L
Sbjct: 619 QEPANAAKVTGMLLEMDQAEILHLLESPEALKAKVSEALDVLRRSADPAAVSSVDDQFAL 678

Query: 465 SLNE 468
           S +E
Sbjct: 679 SSSE 682

Binds the poly(A) tail of mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|P29341|PABP1_MOUSE Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2

 Score =  310 bits (794), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 198/479 (41%), Positives = 281/479 (58%), Gaps = 42/479 (8%)

Query: 1   MLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
           ML+ND++VFVG F  ++ERE    A   +F NV++KN  E   DE LK++FG++G   S 
Sbjct: 161 MLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSV 220

Query: 59  VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
            VM D  GKSK FGFV+FE  +DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +F
Sbjct: 221 KVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF 280

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
           EQ  ++ + ++QG+NLY+KNL D IDDE+L++ FS FGTITS KVM +  G SKG GFV 
Sbjct: 281 EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVC 339

Query: 179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMP 238
           FS+PEEA++A+ EMNG+++ +KPLYVA+AQRKEER+A L  Q+ Q          P   P
Sbjct: 340 FSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINP 399

Query: 239 MYPPGPSGLGQQFL-YGQAPPAIIPP--------------QAGFGYQQQLVPG-MRPAGA 282
             P  PSG     +   Q   A  PP              Q    +  Q +PG +RPA A
Sbjct: 400 YQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPA-A 458

Query: 283 PMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDF 342
           P P F     +  Q  +    +R A    QT  P P           A   P  R +  +
Sbjct: 459 PRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAA-------AAAAATPAVRTVPQY 511

Query: 343 PFDMGAGSMLPVPVDMGAGIPRRDASVGQPM-------PITALSTALANASPEQQRTLLG 395
            +  G  +    P       P+   ++ QP        P+TA  + LA+A P++Q+ +LG
Sbjct: 512 KYAAGVRN----PQQHLNAQPQ--VTMQQPAVHVQGQEPLTA--SMLASAPPQEQKQMLG 563

Query: 396 ESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA 454
           E L+PL++ +    A K+TGMLLE+D +E+LH+LESPE+L++KV EA+ VL++   ++A
Sbjct: 564 ERLFPLIQAMHPSLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA 622

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Mus musculus (taxid: 10090)

>sp|Q5R8F7|PABP1_PONAB Polyadenylate-binding protein 1 OS=Pongo abelii GN=PABPC1 PE=2 SV=1

 Score =  309 bits (792), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 198/479 (41%), Positives = 280/479 (58%), Gaps = 42/479 (8%)

Query: 1   MLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
           ML+ND++VFVG F  ++ERE    A   +F NV++KN  E   DE LK +FG++G   S 
Sbjct: 161 MLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSV 220

Query: 59  VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
            VM D  GKSK FGFV+FE  +DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +F
Sbjct: 221 KVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF 280

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
           EQ  ++ + ++QG+NLY+KNL D IDDE+L++ FS FGTITS KVM +  G SKG GFV 
Sbjct: 281 EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVC 339

Query: 179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMP 238
           FS+PEEA++A+ EMNG+++ +KPLYVA+AQRKEER+A L  Q+ Q          P   P
Sbjct: 340 FSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINP 399

Query: 239 MYPPGPSGLGQQFL-YGQAPPAIIPP--------------QAGFGYQQQLVPG-MRPAGA 282
             P  PSG     +   Q   A  PP              Q    +  Q +PG +RPA A
Sbjct: 400 YQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPA-A 458

Query: 283 PMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDF 342
           P P F     +  Q  +    +R A    QT  P P           A   P  R +  +
Sbjct: 459 PRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAA-------AAAAATPAVRTVPQY 511

Query: 343 PFDMGAGSMLPVPVDMGAGIPRRDASVGQPM-------PITALSTALANASPEQQRTLLG 395
            +  G  +    P       P+   ++ QP        P+TA  + LA+A P++Q+ +LG
Sbjct: 512 KYAAGVRN----PQQHLNAQPQ--VTMQQPAVHVQGQEPLTA--SMLASAPPQEQKQMLG 563

Query: 396 ESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA 454
           E L+PL++ +    A K+TGMLLE+D +E+LH+LESPE+L++KV EA+ VL++   ++A
Sbjct: 564 ERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA 622

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Pongo abelii (taxid: 9601)

>sp|P11940|PABP1_HUMAN Polyadenylate-binding protein 1 OS=Homo sapiens GN=PABPC1 PE=1 SV=2

 Score =  309 bits (791), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 198/479 (41%), Positives = 280/479 (58%), Gaps = 42/479 (8%)

Query: 1   MLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
           ML+ND++VFVG F  ++ERE    A   +F NV++KN  E   DE LK +FG++G   S 
Sbjct: 161 MLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSV 220

Query: 59  VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
            VM D  GKSK FGFV+FE  +DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +F
Sbjct: 221 KVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF 280

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
           EQ  ++ + ++QG+NLY+KNL D IDDE+L++ FS FGTITS KVM +  G SKG GFV 
Sbjct: 281 EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVC 339

Query: 179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMP 238
           FS+PEEA++A+ EMNG+++ +KPLYVA+AQRKEER+A L  Q+ Q          P   P
Sbjct: 340 FSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINP 399

Query: 239 MYPPGPSGLGQQFL-YGQAPPAIIPP--------------QAGFGYQQQLVPG-MRPAGA 282
             P  PSG     +   Q   A  PP              Q    +  Q +PG +RPA A
Sbjct: 400 YQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPA-A 458

Query: 283 PMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDF 342
           P P F     +  Q  +    +R A    QT  P P           A   P  R +  +
Sbjct: 459 PRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAA-------AAAAATPAVRTVPQY 511

Query: 343 PFDMGAGSMLPVPVDMGAGIPRRDASVGQPM-------PITALSTALANASPEQQRTLLG 395
            +  G  +    P       P+   ++ QP        P+TA  + LA+A P++Q+ +LG
Sbjct: 512 KYAAGVRN----PQQHLNAQPQ--VTMQQPAVHVQGQEPLTA--SMLASAPPQEQKQMLG 563

Query: 396 ESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA 454
           E L+PL++ +    A K+TGMLLE+D +E+LH+LESPE+L++KV EA+ VL++   ++A
Sbjct: 564 ERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA 622

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Homo sapiens (taxid: 9606)

>sp|P61286|PABP1_BOVIN Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1

 Score =  309 bits (791), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 198/479 (41%), Positives = 280/479 (58%), Gaps = 42/479 (8%)

Query: 1   MLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
           ML+ND++VFVG F  ++ERE    A   +F NV++KN  E   DE LK +FG++G   S 
Sbjct: 161 MLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSV 220

Query: 59  VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
            VM D  GKSK FGFV+FE  +DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +F
Sbjct: 221 KVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF 280

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
           EQ  ++ + ++QG+NLY+KNL D IDDE+L++ FS FGTITS KVM +  G SKG GFV 
Sbjct: 281 EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVC 339

Query: 179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMP 238
           FS+PEEA++A+ EMNG+++ +KPLYVA+AQRKEER+A L  Q+ Q          P   P
Sbjct: 340 FSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINP 399

Query: 239 MYPPGPSGLGQQFL-YGQAPPAIIPP--------------QAGFGYQQQLVPG-MRPAGA 282
             P  PSG     +   Q   A  PP              Q    +  Q +PG +RPA A
Sbjct: 400 YQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPA-A 458

Query: 283 PMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDF 342
           P P F     +  Q  +    +R A    QT  P P           A   P  R +  +
Sbjct: 459 PRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAA-------AAAAATPAVRTVPQY 511

Query: 343 PFDMGAGSMLPVPVDMGAGIPRRDASVGQPM-------PITALSTALANASPEQQRTLLG 395
            +  G  +    P       P+   ++ QP        P+TA  + LA+A P++Q+ +LG
Sbjct: 512 KYAAGVRN----PQQHLNAQPQ--VTMQQPAVHVQGQEPLTA--SMLASAPPQEQKQMLG 563

Query: 396 ESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA 454
           E L+PL++ +    A K+TGMLLE+D +E+LH+LESPE+L++KV EA+ VL++   ++A
Sbjct: 564 ERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA 622

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Bos taurus (taxid: 9913)

>sp|Q9EPH8|PABP1_RAT Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=2 SV=1

 Score =  308 bits (788), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 197/476 (41%), Positives = 279/476 (58%), Gaps = 36/476 (7%)

Query: 1   MLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
           ML+ND++VFVG F  ++ERE    A   +F NV++KN  E   DE LK++FG++G   S 
Sbjct: 161 MLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSV 220

Query: 59  VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
            VM D  GKSK FGFV+FE  +DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +F
Sbjct: 221 KVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF 280

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
           EQ  ++ + ++QG+NLY+KNL D IDDE+L++ FS FGTITS KVM +  G SKG GFV 
Sbjct: 281 EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVC 339

Query: 179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMP 238
           FS+PEEA++A+ EMNG+++ +KPLYVA+AQRKEER+A L  Q+ Q          P   P
Sbjct: 340 FSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINP 399

Query: 239 MYPPGPSGLGQQFL-YGQAPPAIIPP--------------QAGFGYQQQLVPG-MRPAGA 282
             P  PSG     +   Q   A  PP              Q    +  Q +PG +RPA A
Sbjct: 400 YQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPA-A 458

Query: 283 PMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDF 342
           P P F     +  Q  +    +R A    QT          M PR  A        ++  
Sbjct: 459 PRPPFSTMRPASSQVPRVMSTQRVANTSTQT----------MGPRPAAAATAATPAVRTV 508

Query: 343 P-FDMGAGSMLP---VPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESL 398
           P +   AG   P   +       + +    V    P+TA  + LA+A P++Q+ +LGE L
Sbjct: 509 PQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTA--SMLASAPPQEQKQMLGERL 566

Query: 399 YPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA 454
           +PL++ +    A K+TGMLLE+D +E+LH+LESPE+L++KV EA+ VL++   ++A
Sbjct: 567 FPLIQAMHPSLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA 622

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Rattus norvegicus (taxid: 10116)

>sp|Q6DEY7|EPAB_XENTR Embryonic polyadenylate-binding protein OS=Xenopus tropicalis GN=epabp PE=2 SV=1

 Score =  305 bits (781), Expect = 6e-82,   Method: Compositional matrix adjust.
 Identities = 197/502 (39%), Positives = 285/502 (56%), Gaps = 70/502 (13%)

Query: 1   MLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
           ML+ND++VFVGHF  ++ERE    A   +F NV++KN  E   D+ L++IF  +G   S 
Sbjct: 161 MLLNDRKVFVGHFKSRRERELEYGAKVMEFTNVYIKNFGEDMDDKRLREIFSAFGNTLSV 220

Query: 59  VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
            VM D  G+S+ FGFVN+ N ++A KAV  +NGK+ + R  YVG+AQK+ ER+ ELK +F
Sbjct: 221 KVMMDDTGRSRGFGFVNYGNHEEAQKAVSEMNGKEVNGRMIYVGRAQKRIERQGELKRKF 280

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
           EQ  +E ++++QG+NLY+KNL D IDD++L++ FS +GTITS KVM +  G SKG GFV 
Sbjct: 281 EQIKQERINRYQGVNLYVKNLDDGIDDDRLRKEFSPYGTITSAKVMTE-GGHSKGFGFVC 339

Query: 179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQ----MRPVAMGPSV- 233
           FS+PEEA++A+ EMNG+++ +KPLYVA+AQRKEER+A L  Q+ Q    MR +  GP + 
Sbjct: 340 FSSPEEATKAVTEMNGRIVSTKPLYVALAQRKEERKAILTNQYMQRLATMRAMP-GPLLG 398

Query: 234 ---------------PPRMPMYPPGPSG---LGQQFLYGQA------PPA----IIPPQA 265
                          PP    Y P P        Q+   Q+      PPA     +PP+ 
Sbjct: 399 SFQQPANYFLPAMPQPPNRTFYSPNPVAPVRQAPQWTSHQSRPPQYQPPAPLMRAVPPRR 458

Query: 266 GFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMP 325
                   +  M+ A   +P     V    Q+    G +      Q     +  MPH   
Sbjct: 459 ----MSSNISTMKQASTQVPR----VAPHSQRVANIGTQTAGARAQVNPSIMRTMPH--- 507

Query: 326 PRGHAYRYPLG-RNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALAN 384
                Y+Y    RN+Q    +     ++   V M           GQ  P+TA  ++LA+
Sbjct: 508 -----YKYSCAVRNVQPIGTNTHLQQVMEPAVLMQ----------GQE-PLTA--SSLAS 549

Query: 385 ASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAME 444
           A P++Q+ +LGE LYPL+ ++    A K+TGMLLE+D +E+LH+LESPE+L +KV EA+ 
Sbjct: 550 APPQEQKQMLGERLYPLIHEMHPTLAGKITGMLLEIDNSELLHMLESPESLHSKVEEAVA 609

Query: 445 VLRSVAQQQANNPADQLASLSL 466
           VL++    QA   + + A  SL
Sbjct: 610 VLQA---HQAKENSQKSAQQSL 628

Binds and protects the poly(A) tail of mRNA with or without an AU-rich element (ARE) and prevents mRNA deadenylation. Stimulates the translation of mRNAs to which it is bound during early development.

Xenopus tropicalis (taxid: 8364)

>sp|Q6IP09|PABPB_XENLA Polyadenylate-binding protein 1-B OS=Xenopus laevis GN=pabpc1-b PE=2 SV=1

 Score =  304 bits (779), Expect = 9e-82,   Method: Compositional matrix adjust.
 Identities = 203/495 (41%), Positives = 281/495 (56%), Gaps = 57/495 (11%)

Query: 1   MLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
           ML+ND++VFVG F  ++ERE    A   +F NV++KN  E   DE LK+ FG+YG   S 
Sbjct: 161 MLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKEWFGQYGAALSV 220

Query: 59  VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
            VM D  GKS+ FGFV+FE  +DA KAV+ +NGK  + +  +VG+AQKK ER+ ELK +F
Sbjct: 221 KVMTDDHGKSRGFGFVSFERHEDAQKAVDDMNGKDLNGKAIFVGRAQKKVERQTELKRKF 280

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
           EQ  ++ + ++QG+NLY+KNL D IDDE+L++ F+ FG+ITS KVM +  G SKG GFV 
Sbjct: 281 EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFTPFGSITSAKVMME-GGRSKGFGFVC 339

Query: 179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMP 238
           FS+PEEA++A+ EMNG+++ +KPLYVA+AQRKEER+A L  Q+ Q       P+  P + 
Sbjct: 340 FSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRVPN--PVIN 397

Query: 239 MYPPGPSGLGQQFLYGQAPP-----AIIPPQAGFGYQQQLVP-------GMRP------A 280
            Y P PS     +     PP     A  PP    G   QL P       G RP      A
Sbjct: 398 PYQPPPSS----YFMAAIPPAQNRAAYYPP----GQIAQLRPSPRWTAQGARPHPFQNMA 449

Query: 281 G-----APMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGH----AY 331
           G     AP P  F  +    Q  +    +R A    QT  P P                Y
Sbjct: 450 GAIRPSAPRPPTFSTMRPTSQVPRVMSAQRVANTSTQTMGPRPTTAAAAATSAVRTVPQY 509

Query: 332 RYPLG-RNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQ 390
           +Y  G RN Q         +M    V +           GQ  P+TA  + LA A P++Q
Sbjct: 510 KYAAGVRNTQQHLNTQPQVAMQQPAVHVQ----------GQE-PLTA--SMLAAAPPQEQ 556

Query: 391 RTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVA 450
           + +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE+L++KV EA+ VL++  
Sbjct: 557 KQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQA-- 614

Query: 451 QQQANNPADQLASLS 465
             QA   A ++ S +
Sbjct: 615 -HQAKEAAQKVVSAT 628

Binds the poly(A) tail of mRNA. Prevents mRNA deadenylation and confers poly(A) stability. Stimulates the translation of mRNAs to which it is bound, acting, at least in part, with dazl.

Xenopus laevis (taxid: 8355)

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	472
356564176	654	PREDICTED: polyadenylate-binding protein	0.993	0.717	0.798	0.0
225438781	654	PREDICTED: polyadenylate-binding protein	0.997	0.720	0.799	0.0
255538240	658	polyadenylate-binding protein, putative	0.995	0.714	0.813	0.0
225458678	640	PREDICTED: polyadenylate-binding protein	0.995	0.734	0.824	0.0
224137600	632	predicted protein [Populus trichocarpa]	0.993	0.742	0.826	0.0
356552218	652	PREDICTED: polyadenylate-binding protein	0.993	0.719	0.805	0.0
386780450	657	poly(A)-binding protein [Nicotiana tabac	0.993	0.713	0.800	0.0
356499763	646	PREDICTED: polyadenylate-binding protein	0.991	0.724	0.780	0.0
356521524	651	PREDICTED: polyadenylate-binding protein	0.995	0.721	0.786	0.0
224063493	657	predicted protein [Populus trichocarpa]	0.993	0.713	0.822	0.0

>gi|356564176|ref|XP_003550332.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score =  753 bits (1943), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/472 (79%), Positives = 419/472 (88%), Gaps = 3/472 (0%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           MLINDKQV+VGHFLRKQ+RE    KTKFNNV+VKNL ESTTDE+L   FGEYGTITSA++
Sbjct: 186 MLINDKQVYVGHFLRKQDRENALSKTKFNNVYVKNLSESTTDEELMINFGEYGTITSALI 245

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           MRD DGKS+CFGFVNFEN DDAAKAVE LNGKKFDD+EWYVGKAQKKSEREQELKG+FEQ
Sbjct: 246 MRDADGKSRCFGFVNFENPDDAAKAVEGLNGKKFDDKEWYVGKAQKKSEREQELKGRFEQ 305

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           ++KE  DK+ GLNLY+KNL D+I DEKLKE+F+++GTITSCKVMRDP+GIS+GSGFVAFS
Sbjct: 306 SIKEAADKYPGLNLYLKNLDDTISDEKLKEMFADYGTITSCKVMRDPTGISRGSGFVAFS 365

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           TPEEA+RAL EMNGKM   KPLYVA+AQRKEERRARLQAQFSQMRPVA+ PSV PRMP+Y
Sbjct: 366 TPEEATRALGEMNGKMFAGKPLYVALAQRKEERRARLQAQFSQMRPVAITPSVAPRMPLY 425

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
           PPG  GLGQQFLYGQ PPA++PPQAGFGYQQQLVPGMRP G PMP+FFVP+V QGQQGQR
Sbjct: 426 PPGAPGLGQQFLYGQGPPAMMPPQAGFGYQQQLVPGMRPGGGPMPSFFVPMVQQGQQGQR 485

Query: 301 PGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGA 360
           P GRRG GPVQQ QQP+P+M  QM PRG  YRYP GRNMQD P  + AG ML VP DMG 
Sbjct: 486 PVGRRGTGPVQQPQQPMPMMQQQMLPRGRVYRYPPGRNMQDVPLQVAAGGMLSVPYDMG- 544

Query: 361 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 420
           G+P RDA VGQPMPI AL+TALANA PEQQRT+LGE+LYPLV+QLE D+AAKVTGMLLEM
Sbjct: 545 GLPMRDA-VGQPMPIQALATALANAPPEQQRTMLGEALYPLVDQLEHDSAAKVTGMLLEM 603

Query: 421 DQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS 472
           DQ EVLHL+ESP+ALKAKVAEAM+VLR+VAQQQ  NPADQLASLSLN+NLVS
Sbjct: 604 DQPEVLHLIESPDALKAKVAEAMDVLRNVAQQQT-NPADQLASLSLNDNLVS 654

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225438781|ref|XP_002283105.1| PREDICTED: polyadenylate-binding protein 2 [Vitis vinifera] gi|296082381|emb|CBI21386.3| unnamed protein product [Vitis vinifera]

 Score =  745 bits (1923), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/473 (79%), Positives = 414/473 (87%), Gaps = 2/473 (0%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           ML+NDKQV+VG F+RKQERE+   KTKFNNV+VKNL ESTTDEDLK IFGEYG ITSAVV
Sbjct: 183 MLLNDKQVYVGPFVRKQERESATNKTKFNNVYVKNLLESTTDEDLKNIFGEYGPITSAVV 242

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           M+DGDGKSKCFGFVNFENADDAA++VEALNGKKFDD+EWYVGKAQKK+ERE ELKG+FEQ
Sbjct: 243 MQDGDGKSKCFGFVNFENADDAARSVEALNGKKFDDKEWYVGKAQKKTEREVELKGRFEQ 302

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           ++KE VDKFQGLNLY+KNL DSI D+KL+ELFSEFGTITSCKVMRDP+GIS+GSGFVAFS
Sbjct: 303 SLKEAVDKFQGLNLYVKNLDDSIADDKLRELFSEFGTITSCKVMRDPNGISRGSGFVAFS 362

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           T EEASRALA+MNGKM+ SKPLYVA+AQRKE+RRARLQAQFSQMRP AM PSV PRM MY
Sbjct: 363 TAEEASRALADMNGKMVASKPLYVALAQRKEDRRARLQAQFSQMRPAAMAPSVGPRMSMY 422

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
           PPG  GLGQQ  YGQ PPA+IPPQ GFGYQ QLVPGMRP  APMPNFFVP+V  GQ  QR
Sbjct: 423 PPGAPGLGQQLFYGQGPPALIPPQPGFGYQHQLVPGMRPGAAPMPNFFVPMVQPGQPNQR 482

Query: 301 PGGRR-GAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMG 359
           PGGRR G GPVQQTQQPLP+M  QM PRG  YRYP GRNM D P     G ML  P DM 
Sbjct: 483 PGGRRSGTGPVQQTQQPLPLMQQQMLPRGRVYRYPPGRNMADVPIPGVPGGMLSAPYDM- 541

Query: 360 AGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLE 419
           AG+P RDA+V QPMPI AL+TALANA P+QQRTLLGE+LYPLV+QLE + AAKVTGMLLE
Sbjct: 542 AGMPFRDAAVSQPMPIGALATALANAPPDQQRTLLGENLYPLVDQLEHEMAAKVTGMLLE 601

Query: 420 MDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS 472
           MDQTEVLHLLESPEALKAKVAEAMEVLR+VAQQQANNP D++ASLSLN+ L S
Sbjct: 602 MDQTEVLHLLESPEALKAKVAEAMEVLRNVAQQQANNPTDRMASLSLNDTLTS 654

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255538240|ref|XP_002510185.1| polyadenylate-binding protein, putative [Ricinus communis] gi|223550886|gb|EEF52372.1| polyadenylate-binding protein, putative [Ricinus communis]

 Score =  732 bits (1889), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 385/473 (81%), Positives = 417/473 (88%), Gaps = 3/473 (0%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           ML+NDKQV+VGHFLRK ER++ + K KFNNV+VKNL ESTT+EDLK IFGEYG ITSAV+
Sbjct: 188 MLLNDKQVYVGHFLRKHERDSASNK-KFNNVYVKNLSESTTEEDLKNIFGEYGEITSAVI 246

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           MRD DGKSKCFGFVNFEN D AAKAVE+LNGKK DD+EWYVGKAQKKSERE ELK QFEQ
Sbjct: 247 MRDADGKSKCFGFVNFENTDAAAKAVESLNGKKIDDKEWYVGKAQKKSERELELKSQFEQ 306

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           +MKE VDK+QG+NLYIKNL DSI DE LKELFS+FG ITSCKVMRDPSGIS+GSGFVAFS
Sbjct: 307 SMKEAVDKYQGVNLYIKNLDDSISDENLKELFSDFGMITSCKVMRDPSGISRGSGFVAFS 366

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           TPEEASRALAEMNGKM+VSKPLYVA+AQRKEERRARLQAQFSQMRPVAM PSV PRMP+Y
Sbjct: 367 TPEEASRALAEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPVAMAPSVGPRMPIY 426

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
            PG  G+GQQFLYGQ PP +IPPQ GFGYQQQLVPG+RP GAPMPNFFVP+V QGQQGQR
Sbjct: 427 SPGAPGMGQQFLYGQGPPTMIPPQGGFGYQQQLVPGIRPGGAPMPNFFVPMVQQGQQGQR 486

Query: 301 PGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGA 360
            GGRRGA PVQQ QQP+P+M  QM PRG  YRYP GRNM D P    AG ML VP DMG 
Sbjct: 487 HGGRRGAVPVQQNQQPVPLMHQQMLPRGRVYRYPPGRNMPDVPMPGVAGGMLSVPYDMG- 545

Query: 361 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 420
           G+P RDA+ GQP+PITAL+TALANASPE QRTLLGESLYPLV+QLE ++AAKVTGMLLEM
Sbjct: 546 GMPIRDAAAGQPVPITALATALANASPEHQRTLLGESLYPLVDQLEHESAAKVTGMLLEM 605

Query: 421 DQTEVLHLLESPEALKAKVAEAMEVLRSV-AQQQANNPADQLASLSLNENLVS 472
           DQTEVLHLLESPEALKAKVAEAMEVLRSV AQQ ANN ADQL SLSLN+ LVS
Sbjct: 606 DQTEVLHLLESPEALKAKVAEAMEVLRSVAAQQHANNTADQLTSLSLNDGLVS 658

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225458678|ref|XP_002284923.1| PREDICTED: polyadenylate-binding protein 2 [Vitis vinifera] gi|147773643|emb|CAN76464.1| hypothetical protein VITISV_017035 [Vitis vinifera]

 Score =  729 bits (1881), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 389/472 (82%), Positives = 426/472 (90%), Gaps = 2/472 (0%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           MLINDKQV+VG FLRKQERET   KTKFNNV+VKNL ESTT+EDLK IFGE+G ITS VV
Sbjct: 169 MLINDKQVYVGQFLRKQERETALNKTKFNNVYVKNLSESTTEEDLKNIFGEFGIITSVVV 228

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           MRDGDGKSKCFGFVNFENADDAA+AVEALNGKKFD++EWYVGKAQKK ERE ELKG+FEQ
Sbjct: 229 MRDGDGKSKCFGFVNFENADDAAEAVEALNGKKFDEKEWYVGKAQKKYERELELKGRFEQ 288

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           +MKE VDKFQG+NLYIKNL DSI D+KLKELFSEFGTITSCKVMRDPSGIS+GSGFVAFS
Sbjct: 289 SMKEVVDKFQGVNLYIKNLDDSIGDDKLKELFSEFGTITSCKVMRDPSGISRGSGFVAFS 348

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           T EEASRAL EMNGKM+VSKPLYVA+AQRKEERRARLQAQFSQMRPV+M PSV PRMPMY
Sbjct: 349 TSEEASRALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPVSMAPSVAPRMPMY 408

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
           PPG  GLGQQ  YGQ PPAIIPPQAGFGYQQQLVPGMRP GAPMPNFFVP+V QGQQGQR
Sbjct: 409 PPGAPGLGQQLFYGQGPPAIIPPQAGFGYQQQLVPGMRPGGAPMPNFFVPLVQQGQQGQR 468

Query: 301 PGGRRGAGPVQQTQQPLPIMPHQMPPR-GHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMG 359
           PGGRRGAGPVQQ QQP+P+M  QM PR G  YRYP GRNM D P    AG ML +P DMG
Sbjct: 469 PGGRRGAGPVQQNQQPVPLMQQQMLPRGGRVYRYPPGRNMPDVPMPGVAGGMLSIPYDMG 528

Query: 360 AGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLE 419
            G+P RDA++GQPMPI+AL++ALANA+P+QQRT+LGESLYPLV+QLE + AAKVTGMLLE
Sbjct: 529 -GVPLRDAAIGQPMPISALASALANATPDQQRTMLGESLYPLVDQLEHEMAAKVTGMLLE 587

Query: 420 MDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLV 471
           MDQTEVLHLLESPEALK+KVAEAM+VLR+VAQQQAN+P +QLASLSLN++LV
Sbjct: 588 MDQTEVLHLLESPEALKSKVAEAMDVLRNVAQQQANSPTEQLASLSLNDSLV 639

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224137600|ref|XP_002327166.1| predicted protein [Populus trichocarpa] gi|222835481|gb|EEE73916.1| predicted protein [Populus trichocarpa]

 Score =  727 bits (1876), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/473 (82%), Positives = 422/473 (89%), Gaps = 4/473 (0%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           ML+NDKQV+VGHFLRKQ+R+      KFNNVFVKNL ESTTDE+LK IF E+G ITSAVV
Sbjct: 163 MLVNDKQVYVGHFLRKQDRDGALYSIKFNNVFVKNLAESTTDEELKNIFAEHGAITSAVV 222

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           MRD DGKSKCFGFVNFE+ADDAAKAVEALNGKK D  EWYVGKAQKKSERE ELKG+FEQ
Sbjct: 223 MRDADGKSKCFGFVNFESADDAAKAVEALNGKKIDGEEWYVGKAQKKSERELELKGRFEQ 282

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           +MKETVDKFQGLNLYIKNL DSI+DEKLKELFS+FG ITSCKVMRDPSGIS+GSGFVAFS
Sbjct: 283 SMKETVDKFQGLNLYIKNLDDSINDEKLKELFSDFGAITSCKVMRDPSGISRGSGFVAFS 342

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           TPEEASRALAEMNGKM++SKPLYVA+AQRKEERRARLQAQFSQMRPV M PSV  RMPMY
Sbjct: 343 TPEEASRALAEMNGKMLISKPLYVALAQRKEERRARLQAQFSQMRPVTMAPSVASRMPMY 402

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
           PPG  G+GQQFLYGQ PPA++PPQAGFGYQQQLVPGMRP GAPMPNFFVP+V QGQQGQR
Sbjct: 403 PPGAPGMGQQFLYGQGPPAMMPPQAGFGYQQQLVPGMRPGGAPMPNFFVPLVQQGQQGQR 462

Query: 301 PGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGA 360
           PGGRRG GPVQQTQQP+P+M  QM PRG  YRYP GRNM D P    AG ML VP DMG 
Sbjct: 463 PGGRRGGGPVQQTQQPVPLMQQQMLPRGRVYRYPPGRNMPDVPMPGVAGGMLSVPYDMG- 521

Query: 361 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 420
           G+P RDA+  QPMPITAL+TALANA+PEQQRT+LGESLYP+V+QLE D+AAKVTGMLLEM
Sbjct: 522 GMPIRDAA--QPMPITALATALANATPEQQRTMLGESLYPIVDQLEHDSAAKVTGMLLEM 579

Query: 421 DQTEVLHLLESPEALKAKVAEAMEVLRSV-AQQQANNPADQLASLSLNENLVS 472
           DQTEVLHLLESPEALKAKVAEAMEVLR+V AQQQ NN ADQL SLSLN+NLVS
Sbjct: 580 DQTEVLHLLESPEALKAKVAEAMEVLRTVAAQQQINNQADQLGSLSLNDNLVS 632

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552218|ref|XP_003544466.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score =  725 bits (1872), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 380/472 (80%), Positives = 421/472 (89%), Gaps = 3/472 (0%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           MLINDKQV+VGHFLRKQ+RE    KTKFNNV+VKNL ESTTDE+L K FGEYGTITSAV+
Sbjct: 184 MLINDKQVYVGHFLRKQDRENALSKTKFNNVYVKNLSESTTDEELMKFFGEYGTITSAVI 243

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           MRD DGKS+CFGFVNFEN DDAAKAVE LNGKK DD+EWYVGKAQKKSEREQELKG+FEQ
Sbjct: 244 MRDADGKSRCFGFVNFENPDDAAKAVEGLNGKKVDDKEWYVGKAQKKSEREQELKGRFEQ 303

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           ++KE+ DK+QG+NLY+KNL D+I DEKLKE+F+E+GTITSCKVMRDP+GI +GSGFVAFS
Sbjct: 304 SIKESADKYQGVNLYLKNLDDTISDEKLKEMFAEYGTITSCKVMRDPTGIGRGSGFVAFS 363

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           TPEEASRAL EMNGKMI  KPLYVA+AQRKE+RRARLQAQFSQMRPVA+ PSV PRMP+Y
Sbjct: 364 TPEEASRALGEMNGKMIAGKPLYVALAQRKEDRRARLQAQFSQMRPVAITPSVAPRMPLY 423

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
           PPG  GLGQQFLYGQ PPA++PPQAGFGYQQQLVPGMRP G PMP+FFVP+V QGQQGQR
Sbjct: 424 PPGAPGLGQQFLYGQGPPAMMPPQAGFGYQQQLVPGMRPGGGPMPSFFVPMVQQGQQGQR 483

Query: 301 PGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGA 360
           PGGRRG GPVQQ QQP+P+M  QM PRG  YRYP GRNMQD P    AG M+ VP DMG 
Sbjct: 484 PGGRRGTGPVQQPQQPMPMMQQQMLPRGRVYRYPPGRNMQDVPLQGVAGGMMSVPYDMG- 542

Query: 361 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 420
           G+P RDA VGQPMPI AL+TALANA PEQQRT+LGE+LYPLV+QLE DAAAKVTGMLLEM
Sbjct: 543 GLPIRDA-VGQPMPIQALATALANAPPEQQRTMLGEALYPLVDQLEHDAAAKVTGMLLEM 601

Query: 421 DQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS 472
           DQ EVLHL+ESP+ALKAKVAEAM+VLR+VAQQQ  NPADQLASLSLN+NLVS
Sbjct: 602 DQPEVLHLIESPDALKAKVAEAMDVLRNVAQQQT-NPADQLASLSLNDNLVS 652

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|386780450|dbj|BAM15222.1| poly(A)-binding protein [Nicotiana tabacum]

 Score =  722 bits (1863), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/472 (80%), Positives = 420/472 (88%), Gaps = 3/472 (0%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           ML+NDKQV+VGHFLRKQERE+    TKF NV+VKNL ESTTD++LKK+FGE+G ITSAVV
Sbjct: 189 MLMNDKQVYVGHFLRKQERESTTGMTKFQNVYVKNLSESTTDDELKKVFGEFGNITSAVV 248

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           MRD DGKSKCFGF+NFE A+DAAKAVE+LNGKKFDD+EWYVGKAQKKSEREQELK +FEQ
Sbjct: 249 MRDADGKSKCFGFINFETAEDAAKAVESLNGKKFDDKEWYVGKAQKKSEREQELKSKFEQ 308

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
             KE VDK+QGLNLY+KNL D+IDDEKLKELFSEFGTITSCKVMRDPSGIS+GSGFVAFS
Sbjct: 309 TAKEAVDKYQGLNLYVKNLDDTIDDEKLKELFSEFGTITSCKVMRDPSGISRGSGFVAFS 368

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           T EEASRAL+EMNGKMIVSKPLYVA+AQRKEERRA+LQAQFSQ+RPVAM PS+ PRMP+Y
Sbjct: 369 TSEEASRALSEMNGKMIVSKPLYVALAQRKEERRAKLQAQFSQLRPVAMPPSLAPRMPIY 428

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
           PPG  G+GQQ  YGQ PPA+IPPQAGFGYQQQLVPGMRP GAPMPNFF+P+V QGQQGQR
Sbjct: 429 PPGAPGIGQQLFYGQGPPAMIPPQAGFGYQQQLVPGMRPGGAPMPNFFMPLVQQGQQGQR 488

Query: 301 PGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGA 360
           PGGRRGAGPVQQTQQP+P+M  QM PRG  YRYP GRN  + P     G ML VP DMG 
Sbjct: 489 PGGRRGAGPVQQTQQPMPLMQQQMLPRGRMYRYPPGRNGPEGPMPGVPGGMLSVPYDMGG 548

Query: 361 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 420
            +P RD+++GQPMPI+ L++ALANA PEQQRT+LGESLYPLV+QLE + AAKVTGMLLEM
Sbjct: 549 MLP-RDSAMGQPMPISTLASALANAPPEQQRTMLGESLYPLVDQLEHEHAAKVTGMLLEM 607

Query: 421 DQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS 472
           DQTEVLHLLESPEALKAKVAEAMEVLR+V  QQ  NPADQLASLSLN+NLVS
Sbjct: 608 DQTEVLHLLESPEALKAKVAEAMEVLRNV--QQTTNPADQLASLSLNDNLVS 657

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499763|ref|XP_003518706.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score =  721 bits (1861), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/470 (78%), Positives = 407/470 (86%), Gaps = 2/470 (0%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           ML+NDKQV+VG FLRKQERE+ A K KFNNVFVKNL ESTTD++LK +FGE+GTITSAVV
Sbjct: 179 MLLNDKQVYVGPFLRKQERESTADKAKFNNVFVKNLSESTTDDELKNVFGEFGTITSAVV 238

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           MRDGDGKSKCFGFVNFENADDAA+AVEALNGKKFDD+EWYVGKAQKKSERE ELK +FEQ
Sbjct: 239 MRDGDGKSKCFGFVNFENADDAARAVEALNGKKFDDKEWYVGKAQKKSERENELKQRFEQ 298

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           +MKE  DK+QG NLY+KNL DS+ D+KLKELFS FGTITSCKVMRDP+GIS+GSGFVAFS
Sbjct: 299 SMKEAADKYQGANLYVKNLDDSLGDDKLKELFSPFGTITSCKVMRDPNGISRGSGFVAFS 358

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           TP+EASRAL EMNGKM+VSKPLYV +AQRKE+RRARLQAQF+QMRPV M PSV PR+PMY
Sbjct: 359 TPDEASRALLEMNGKMVVSKPLYVTLAQRKEDRRARLQAQFAQMRPVGMPPSVGPRVPMY 418

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
           PPG  G+GQQ  Y Q PPAIIP Q GFGYQQQLVPGMRP  AP+PNFFVP+V QGQQGQR
Sbjct: 419 PPGGPGIGQQIFYAQGPPAIIPSQPGFGYQQQLVPGMRPGAAPVPNFFVPMVQQGQQGQR 478

Query: 301 PGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGA 360
             G R  G VQQ+QQP+P+MP QM PRG  YRYP GR M D      AG M  VP D+G 
Sbjct: 479 -PGGRRTGAVQQSQQPVPMMPQQMLPRGRVYRYPPGRGMPDVSMPGVAGGMFSVPYDVG- 536

Query: 361 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 420
           G+P RDAS+ Q +P+ AL+TALANASPEQQRT+LGE+LYPLVEQLE D AAKVTGMLLEM
Sbjct: 537 GMPLRDASISQQIPVGALATALANASPEQQRTMLGENLYPLVEQLEPDNAAKVTGMLLEM 596

Query: 421 DQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENL 470
           DQTEVLHLLESPEALKAKVAEAM+VLR+VAQQQA   ADQLASLSLN+NL
Sbjct: 597 DQTEVLHLLESPEALKAKVAEAMDVLRNVAQQQAGGTADQLASLSLNDNL 646

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521524|ref|XP_003529405.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score =  721 bits (1861), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/472 (78%), Positives = 410/472 (86%), Gaps = 2/472 (0%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           ML+NDKQV+VG FLRKQERE+ A K KFNNVFVKNL ESTTD++LK  FGE+GTITSAVV
Sbjct: 182 MLLNDKQVYVGPFLRKQERESAADKAKFNNVFVKNLSESTTDDELKNTFGEFGTITSAVV 241

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           MRDGDGKSKCFGFVNFENADDAA+AVEALNGK FDD+EWYVGKAQKKSERE ELK +FEQ
Sbjct: 242 MRDGDGKSKCFGFVNFENADDAARAVEALNGKNFDDKEWYVGKAQKKSERENELKQRFEQ 301

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           +MKE  DK+QG NLY+KNL DSI DEKLKELFS FGTITSCKVMRDP+G+S+GSGFVAFS
Sbjct: 302 SMKEAADKYQGANLYVKNLDDSIGDEKLKELFSPFGTITSCKVMRDPNGLSRGSGFVAFS 361

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           TPEEASRAL EMNGKM+VSKPLYV +AQRKE+RRARLQAQF+QMRPV M PSV PR+PMY
Sbjct: 362 TPEEASRALLEMNGKMVVSKPLYVTLAQRKEDRRARLQAQFAQMRPVGMPPSVGPRVPMY 421

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
           PPG  G+GQQ  Y Q PPAIIP Q GFGYQQQL+PGMRP  AP+PNFFVP+V QGQQGQR
Sbjct: 422 PPGGPGIGQQLFYSQGPPAIIPSQPGFGYQQQLMPGMRPGAAPVPNFFVPMVQQGQQGQR 481

Query: 301 PGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGA 360
           PGGRR    VQQ+QQP+P+MP QM PRG  YRYP GR + D P    AG M  VP D+G 
Sbjct: 482 PGGRRPGA-VQQSQQPVPMMPQQMLPRGRVYRYPPGRGIPDVPIPGVAGGMFSVPYDVG- 539

Query: 361 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 420
           G+P RDAS+ Q +P+ AL+TALANASPEQQRT+LGE+LYPLVEQLE D AAKVTGMLLEM
Sbjct: 540 GMPLRDASISQQIPVGALATALANASPEQQRTMLGENLYPLVEQLEPDNAAKVTGMLLEM 599

Query: 421 DQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLVS 472
           DQTEVLHLLESPEALKAKVAEAM+VLR+VAQQQA   ADQLASLSLN+NLVS
Sbjct: 600 DQTEVLHLLESPEALKAKVAEAMDVLRNVAQQQAGGTADQLASLSLNDNLVS 651

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224063493|ref|XP_002301171.1| predicted protein [Populus trichocarpa] gi|222842897|gb|EEE80444.1| predicted protein [Populus trichocarpa]

 Score =  718 bits (1854), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 389/473 (82%), Positives = 422/473 (89%), Gaps = 4/473 (0%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           MLINDKQV+VG+FLRKQER++     KFNN++VKNL ESTTDEDLK IF E+G ITSAVV
Sbjct: 182 MLINDKQVYVGNFLRKQERDSALSNIKFNNIYVKNLAESTTDEDLKSIFEEHGAITSAVV 241

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           MRD DGKSKCFGFVNFEN DDAAKAVEALNGKKFDD+EWYVGKAQKKSERE ELKG+FEQ
Sbjct: 242 MRDADGKSKCFGFVNFENVDDAAKAVEALNGKKFDDKEWYVGKAQKKSERELELKGRFEQ 301

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           ++ E+V+K+Q +NLYIKNL DS++DEKLKELFS+FGTITSCKVM DPSGIS+GSGFVAFS
Sbjct: 302 SL-ESVEKYQAVNLYIKNLDDSVNDEKLKELFSDFGTITSCKVMHDPSGISRGSGFVAFS 360

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMY 240
           TPEEASRALAE+NGKM+VSKPLYVA AQRKEERRARLQAQFSQMRPVAM PSV PRM MY
Sbjct: 361 TPEEASRALAELNGKMVVSKPLYVAPAQRKEERRARLQAQFSQMRPVAMAPSVAPRMQMY 420

Query: 241 PPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQR 300
           PPG  GLGQQFLYGQ PPA+I PQAGFGYQQQLVPGMRP GAPMPNFFVP+V QGQQGQR
Sbjct: 421 PPGAPGLGQQFLYGQGPPAMI-PQAGFGYQQQLVPGMRPGGAPMPNFFVPLVQQGQQGQR 479

Query: 301 PGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGA 360
           PGGRRG GPVQQTQQP+P+M  QM PRG  YRYP GRNM D P    AG ML VP DMG 
Sbjct: 480 PGGRRGGGPVQQTQQPVPLMQQQMLPRGRVYRYPPGRNMPDVPMPGVAGGMLSVPYDMGV 539

Query: 361 GIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEM 420
            +P RDA+ GQPMPITAL+TALANA+PEQQRT+LGE LYPLV+QLE D+AAKVTGMLLEM
Sbjct: 540 -MPIRDAAGGQPMPITALATALANATPEQQRTMLGEGLYPLVDQLEHDSAAKVTGMLLEM 598

Query: 421 DQTEVLHLLESPEALKAKVAEAMEVLRSV-AQQQANNPADQLASLSLNENLVS 472
           DQTEVLHLLESPEALKAKVAEAMEVLR+V AQQQ NNPAD LASLSLNENLVS
Sbjct: 599 DQTEVLHLLESPEALKAKVAEAMEVLRTVAAQQQINNPADHLASLSLNENLVS 651

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	472
TAIR|locus:2012161	671	PAB8 "AT1G49760" [Arabidopsis	0.989	0.695	0.626	1.8e-149
TAIR|locus:2124261	629	PAB2 "AT4G34110" [Arabidopsis	0.75	0.562	0.599	6.2e-142
TAIR|locus:2058573	662	PAB4 "AT2G23350" [Arabidopsis	0.961	0.685	0.606	2.4e-138
TAIR|locus:2199700	660	PAB3 "poly(A) binding protein	0.476	0.340	0.616	6.7e-100
UNIPROTKB|F1NH81	573	PABPC1 "Uncharacterized protei	0.470	0.387	0.546	2.2e-82
UNIPROTKB|F1SV06	631	PABPC4 "Uncharacterized protei	0.470	0.351	0.56	4.5e-82
UNIPROTKB|A4IFC3	645	PABPC4 "Uncharacterized protei	0.470	0.344	0.56	5.8e-82
UNIPROTKB|E2R9I0	631	PABPC4 "Uncharacterized protei	0.470	0.351	0.56	5.8e-82
UNIPROTKB|B1ANR0	615	PABPC4 "Polyadenylate-binding	0.470	0.360	0.56	5.8e-82
UNIPROTKB|Q13310	644	PABPC4 "Polyadenylate-binding	0.470	0.344	0.56	5.8e-82

TAIR|locus:2012161 PAB8 "AT1G49760" [Arabidopsis thaliana (taxid:3702)]

 Score = 1459 (518.7 bits), Expect = 1.8e-149, P = 1.8e-149
 Identities = 300/479 (62%), Positives = 353/479 (73%)

Query:     1 MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
             ML+NDKQV+VG F+ K +R+    K KF NV+VKNL ES +DE+L K+FGE+G  TS V+
Sbjct:   196 MLLNDKQVYVGPFVHKLQRDPSGEKVKFTNVYVKNLSESLSDEELNKVFGEFGVTTSCVI 255

Query:    61 MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
             MRDG+GKSK FGFVNFEN+DDAA+AV+ALNGK FDD+EW+VGKAQKKSERE ELK +FEQ
Sbjct:   256 MRDGEGKSKGFGFVNFENSDDAARAVDALNGKTFDDKEWFVGKAQKKSERETELKQKFEQ 315

Query:   121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
             ++KE  DK QG NLY+KNL +S+ D+KL+E F+ FGTITSCKVMRDPSG+S+GSGFVAFS
Sbjct:   316 SLKEAADKSQGSNLYVKNLDESVTDDKLREHFAPFGTITSCKVMRDPSGVSRGSGFVAFS 375

Query:   181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMXXXXXXXXXXX 240
             TPEEA+RA+ EMNGKMIV+KPLYVA+AQRKE+R+ARLQAQFSQMRPV M           
Sbjct:   376 TPEEATRAITEMNGKMIVTKPLYVALAQRKEDRKARLQAQFSQMRPVNMPPAVGPRMQMY 435

Query:   241 XXXXXXLGQQFLYGXXXXXXXXXXXGFGYQQQLVPGMRPAGAPMPNFFXXXXXXXXXXXX 300
                   +GQQ  YG           GFGYQQQLVPGMRP G+PMPNFF            
Sbjct:   436 PPGGPPMGQQLFYGQGPPAMIPQP-GFGYQQQLVPGMRPGGSPMPNFFMPMMQQGQQQQQ 494

Query:   301 XXXXXXX------XXXXXTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPV 354
                                QQP P+M  QM PRG  YRYP  R++   P      +ML V
Sbjct:   495 QQQQQQRPGGGRRGALPQPQQPSPMMQQQMHPRGRMYRYPQ-RDVNTMPGP--TQNMLSV 551

Query:   355 PVDM--GAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAK 412
             P D+  G G+  RD+   QP+PI AL+T LANA+PEQQRT+LGE+LYPLVEQLE ++AAK
Sbjct:   552 PYDVSSGGGVHHRDSPTSQPVPIVALATRLANAAPEQQRTMLGENLYPLVEQLEPESAAK 611

Query:   413 VTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQANNPADQLASLSLNENLV 471
             VTGMLLEMDQTEVLHLLESPEALKAKV EAM+VLRSVAQQQA   ADQLASLSL +N+V
Sbjct:   612 VTGMLLEMDQTEVLHLLESPEALKAKVTEAMDVLRSVAQQQAGGAADQLASLSLGDNIV 670

GO:0003723 "RNA binding" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0046686 "response to cadmium ion" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0006164 "purine nucleotide biosynthetic process" evidence=RCA

TAIR|locus:2124261 PAB2 "AT4G34110" [Arabidopsis thaliana (taxid:3702)]

 Score = 1061 (378.5 bits), Expect = 6.2e-142, Sum P(2) = 6.2e-142
 Identities = 217/362 (59%), Positives = 259/362 (71%)

Query:     1 MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
             ML+NDKQV+VG FLR+QER++ A KTKF NV+VKNL ESTTD+DLK  FGEYG ITSAVV
Sbjct:   187 MLLNDKQVYVGPFLRRQERDSTANKTKFTNVYVKNLAESTTDDDLKNAFGEYGKITSAVV 246

Query:    61 MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
             M+DG+GKSK FGFVNFENADDAA+AVE+LNG KFDD+EWYVG+AQKKSERE EL+ ++EQ
Sbjct:   247 MKDGEGKSKGFGFVNFENADDAARAVESLNGHKFDDKEWYVGRAQKKSERETELRVRYEQ 306

Query:   121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
              +KE  DKFQ  NLY+KNL  SI DEKLKE+FS FGT+TS KVMRDP+G SKGSGFVAF+
Sbjct:   307 NLKEAADKFQSSNLYVKNLDPSISDEKLKEIFSPFGTVTSSKVMRDPNGTSKGSGFVAFA 366

Query:   181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMXXXXXXXXXXX 240
             TPEEA+ A+++++GKMI SKPLYVA+AQRKE+RR RLQAQFSQ+RPVAM           
Sbjct:   367 TPEEATEAMSQLSGKMIESKPLYVAIAQRKEDRRVRLQAQFSQVRPVAMQPSVGPRMPVY 426

Query:   241 XXXXXXLGQQFLYGXXXXXXXXXXXGFGYQQQLVPGMRPAGAPMPNFFXXXXXXXXXXXX 300
                   +GQQ  YG           G+GYQQQLVPGMRP G P+P+FF            
Sbjct:   427 PPGGPGIGQQMFYGQAPPAMIPPQPGYGYQQQLVPGMRPGGGPVPSFFMPMVQPQQQRPG 486

Query:   301 XXXXXXXXXXXXTQQPLPIMPHQMPPRGHAYRYPLGRNMQ-DFP-FDMGAGSMLPVPVDM 358
                         +QQ  P+M  QM PRG  +RYP GR    D P +DMG      +P+ +
Sbjct:   487 GGRRPGGIQH--SQQQNPMMQQQMHPRGRMFRYPQGRGGSGDVPPYDMGNN----MPLTI 540

Query:   359 GA 360
             GA
Sbjct:   541 GA 542

GO:0003723 "RNA binding" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0009651 "response to salt stress" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0006486 "protein glycosylation" evidence=RCA

GO:0006413 "translational initiation" evidence=ISS

TAIR|locus:2058573 PAB4 "AT2G23350" [Arabidopsis thaliana (taxid:3702)]

 Score = 1354 (481.7 bits), Expect = 2.4e-138, P = 2.4e-138
 Identities = 291/480 (60%), Positives = 339/480 (70%)

Query:     2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVM 61
             ++NDKQ+FVG FLRK+ERE+ A K KF NV+VKNL E+TTD++LK  FG+YG+I+SAVVM
Sbjct:   198 VLNDKQIFVGPFLRKEERESAADKMKFTNVYVKNLSEATTDDELKTTFGQYGSISSAVVM 257

Query:    62 RDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQA 121
             RDGDGKS+CFGFVNFEN +DAA+AVEALNGKKFDD+EWYVGKAQKKSERE EL  ++EQ 
Sbjct:   258 RDGDGKSRCFGFVNFENPEDAARAVEALNGKKFDDKEWYVGKAQKKSERELELSRRYEQG 317

Query:   122 MKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFST 181
               +  +KF GLNLY+KNL D++ DEKL+ELF+EFGTITSCKVMRDPSG SKGSGFVAFS 
Sbjct:   318 SSDGGNKFDGLNLYVKNLDDTVTDEKLRELFAEFGTITSCKVMRDPSGTSKGSGFVAFSA 377

Query:   182 PEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMXXXXXXXXXXXX 241
               EASR L EMNGKM+  KPLYVA+AQRKEERRA+LQAQFSQMRP A             
Sbjct:   378 ASEASRVLNEMNGKMVGGKPLYVALAQRKEERRAKLQAQFSQMRP-AFIPGVGPRMPIFT 436

Query:   242 XXXXXLGQQFLYGXXXXXXXXXXXGFGYQQQLVPGMRPA--GAPMPNFFXXXXXXXXXXX 299
                  LGQQ  YG           GFGYQ QLVPGMRPA  G PM               
Sbjct:   437 GGAPGLGQQIFYGQGPPPIIPHQPGFGYQPQLVPGMRPAFFGGPMMQ-----PGQQGPRP 491

Query:   300 XXXXXXXXXXXXXTQQPLPIMPHQMPPRGHAYRYPLG-RNMQDFPFDMGAGSMLPVPVDM 358
                           QQP+P M  QM PRG  YRYP G RNM D P     G M+PV  DM
Sbjct:   492 GGRRSGDGPMRHQHQQPMPYMQPQMMPRGRGYRYPSGGRNMPDGPMP---GGMVPVAYDM 548

Query:   359 GAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLL 418
                +P       QPM    L+T+LANA+P QQRTLLGESLYPLV+Q+E + AAKVTGMLL
Sbjct:   549 NV-MP-----YSQPMSAGQLATSLANATPAQQRTLLGESLYPLVDQIESEHAAKVTGMLL 602

Query:   419 EMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQ--------QQANNPADQLASLSLNENL 470
             EMDQTEVLHLLESPEAL AKV+EA++VLR+V Q         ++ +P+D LASLS+N++L
Sbjct:   603 EMDQTEVLHLLESPEALNAKVSEALDVLRNVNQPSSQGSEGNKSGSPSDLLASLSINDHL 662

GO:0003723 "RNA binding" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0046686 "response to cadmium ion" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2199700 PAB3 "poly(A) binding protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 713 (256.0 bits), Expect = 6.7e-100, Sum P(2) = 6.7e-100
 Identities = 140/227 (61%), Positives = 176/227 (77%)

Query:     1 MLINDKQVFVGHFLRKQER--ETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
             ML+NDKQVFVGHF+R+QER  +      +F NV+VKNL +   +++L+K FG++G I+SA
Sbjct:   199 MLMNDKQVFVGHFIRRQERARDENTPTPRFTNVYVKNLPKEIGEDELRKTFGKFGVISSA 258

Query:    59 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
             VVMRD  G S+CFGFVNFE  + AA AVE +NG    D   YVG+AQKKSERE+EL+ +F
Sbjct:   259 VVMRDQSGNSRCFGFVNFECTEAAASAVEKMNGISLGDDVLYVGRAQKKSEREEELRRKF 318

Query:   119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
             EQ      +K QG NLY+KNL DS+DDEKLKE+FSE+G +TS KVM +P G+S+G GFVA
Sbjct:   319 EQERINRFEKSQGANLYLKNLDDSVDDEKLKEMFSEYGNVTSSKVMLNPQGMSRGFGFVA 378

Query:   179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMR 225
             +S PEEA RAL+EMNGKMI  KPLY+A+AQRKE+RRA LQA FSQ+R
Sbjct:   379 YSNPEEALRALSEMNGKMIGRKPLYIALAQRKEDRRAHLQALFSQIR 425

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0006397 "mRNA processing" evidence=IGI

UNIPROTKB|F1NH81 PABPC1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 632 (227.5 bits), Expect = 2.2e-82, Sum P(2) = 2.2e-82
 Identities = 123/225 (54%), Positives = 169/225 (75%)

Query:     1 MLINDKQVFVGHFLRKQERET-VAIKTK-FNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
             ML+ND++VFVG F  ++ERE  +  + K F NV++KN  E   DE LK++FG++G   S 
Sbjct:    97 MLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSV 156

Query:    59 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
              VM D  GKSK FGFV+FE  +DA KAV+ +NGK+ + ++ YVG+AQKK ER+ ELK +F
Sbjct:   157 KVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF 216

Query:   119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
             EQ  ++ + ++QG+NLY+KNL D IDDE+L++ FS FGTITS KVM +  G SKG GFV 
Sbjct:   217 EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVC 275

Query:   179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQ 223
             FS+PEEA++A+ EMNG+++ +KPLYVA+AQRKEER+A L  Q+ Q
Sbjct:   276 FSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQ 320

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1SV06 PABPC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 635 (228.6 bits), Expect = 4.5e-82, Sum P(2) = 4.5e-82
 Identities = 126/225 (56%), Positives = 169/225 (75%)

Query:     1 MLINDKQVFVGHFLRKQERET-VAIKTK-FNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
             ML+ND++VFVG F  ++ERE  +  K K F NV++KN  E   DE+LK++F ++G   S 
Sbjct:   161 MLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDENLKELFSQFGKTLSV 220

Query:    59 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
              VMRD  GKSK FGFV++E  +DA KAVE +NGK+   +  +VG+AQKK ER+ ELK +F
Sbjct:   221 KVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKF 280

Query:   119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
             EQ  +E + ++QG+NLYIKNL D+IDDEKL++ FS FG+ITS KVM +  G SKG GFV 
Sbjct:   281 EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLE-DGRSKGFGFVC 339

Query:   179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQ 223
             FS+PEEA++A+ EMNG+++ SKPLYVA+AQRKEER+A L  Q+ Q
Sbjct:   340 FSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQ 384

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|A4IFC3 PABPC4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 634 (228.2 bits), Expect = 5.8e-82, Sum P(2) = 5.8e-82
 Identities = 126/225 (56%), Positives = 169/225 (75%)

Query:     1 MLINDKQVFVGHFLRKQERET-VAIKTK-FNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
             ML+ND++VFVG F  ++ERE  +  K K F NV++KN  E   DE+LK++F ++G   S 
Sbjct:   161 MLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDENLKELFSQFGKTLSV 220

Query:    59 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
              VMRD  GKSK FGFV++E  +DA KAVE +NGK+   +  +VG+AQKK ER+ ELK +F
Sbjct:   221 KVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEITGKVIFVGRAQKKVERQAELKRKF 280

Query:   119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
             EQ  +E + ++QG+NLYIKNL D+IDDEKL++ FS FG+ITS KVM +  G SKG GFV 
Sbjct:   281 EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLE-DGRSKGFGFVC 339

Query:   179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQ 223
             FS+PEEA++A+ EMNG+++ SKPLYVA+AQRKEER+A L  Q+ Q
Sbjct:   340 FSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQ 384

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2R9I0 PABPC4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 634 (228.2 bits), Expect = 5.8e-82, Sum P(2) = 5.8e-82
 Identities = 126/225 (56%), Positives = 168/225 (74%)

Query:     1 MLINDKQVFVGHFLRKQERET-VAIKTK-FNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
             ML+ND++VFVG F  ++ERE  +  K K F NV++KN  E   DE LK++F ++G   S 
Sbjct:   161 MLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKELFSQFGKTLSV 220

Query:    59 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
              VMRD  GKSK FGFV++E  +DA KAVE +NGK+   +  +VG+AQKK ER+ ELK +F
Sbjct:   221 KVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKF 280

Query:   119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
             EQ  +E + ++QG+NLYIKNL D+IDDEKL++ FS FG+ITS KVM +  G SKG GFV 
Sbjct:   281 EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLE-DGRSKGFGFVC 339

Query:   179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQ 223
             FS+PEEA++A+ EMNG+++ SKPLYVA+AQRKEER+A L  Q+ Q
Sbjct:   340 FSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQ 384

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|B1ANR0 PABPC4 "Polyadenylate-binding protein 4" [Homo sapiens (taxid:9606)]

 Score = 634 (228.2 bits), Expect = 5.8e-82, Sum P(2) = 5.8e-82
 Identities = 126/225 (56%), Positives = 169/225 (75%)

Query:     1 MLINDKQVFVGHFLRKQERET-VAIKTK-FNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
             ML+ND++VFVG F  ++ERE  +  K K F NV++KN  E   DE LK++F ++G   S 
Sbjct:   161 MLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKELFSQFGKTLSV 220

Query:    59 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
              VMRD +GKSK FGFV++E  +DA KAVE +NGK+   +  +VG+AQKK ER+ ELK +F
Sbjct:   221 KVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKF 280

Query:   119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
             EQ  +E + ++QG+NLYIKNL D+IDDEKL++ FS FG+ITS KVM +  G SKG GFV 
Sbjct:   281 EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLE-DGRSKGFGFVC 339

Query:   179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQ 223
             FS+PEEA++A+ EMNG+++ SKPLYVA+AQRKEER+A L  Q+ Q
Sbjct:   340 FSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQ 384

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q13310 PABPC4 "Polyadenylate-binding protein 4" [Homo sapiens (taxid:9606)]

 Score = 634 (228.2 bits), Expect = 5.8e-82, Sum P(2) = 5.8e-82
 Identities = 126/225 (56%), Positives = 169/225 (75%)

Query:     1 MLINDKQVFVGHFLRKQERET-VAIKTK-FNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
             ML+ND++VFVG F  ++ERE  +  K K F NV++KN  E   DE LK++F ++G   S 
Sbjct:   161 MLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKELFSQFGKTLSV 220

Query:    59 VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
              VMRD +GKSK FGFV++E  +DA KAVE +NGK+   +  +VG+AQKK ER+ ELK +F
Sbjct:   221 KVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKF 280

Query:   119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
             EQ  +E + ++QG+NLYIKNL D+IDDEKL++ FS FG+ITS KVM +  G SKG GFV 
Sbjct:   281 EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLE-DGRSKGFGFVC 339

Query:   179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQ 223
             FS+PEEA++A+ EMNG+++ SKPLYVA+AQRKEER+A L  Q+ Q
Sbjct:   340 FSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQ 384

GO:0000166 "nucleotide binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0017130 "poly(C) RNA binding" evidence=IDA

GO:0006401 "RNA catabolic process" evidence=TAS

GO:0006396 "RNA processing" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0007596 "blood coagulation" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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

Fail to connect to STRING server

---

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	472
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-153
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-51
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-49
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-46
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	6e-35
pfam00658	72	pfam00658, PABP, Poly-adenylate binding protein, u	1e-31
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-31
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	9e-30
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-29
smart00360	73	smart00360, RRM, RNA recognition motif	4e-27
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-26
smart00517	64	smart00517, PolyA, C-terminal domain of Poly(A)-bi	1e-26
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-26
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-25
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	4e-24
smart00360	73	smart00360, RRM, RNA recognition motif	6e-24
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-23
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-21
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-20
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-20
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-20
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-20
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-19
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	9e-19
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-18
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-18
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	4e-18
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	9e-18
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-17
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-17
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-17
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	7e-17
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-17
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-16
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-16
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-16
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	8e-16
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-15
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	2e-15
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-15
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-15
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	4e-15
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	6e-15
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	6e-15
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	9e-15
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-14
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-14
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-14
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-14
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-14
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-14
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-14
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	5e-14
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	6e-14
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	7e-14
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	8e-14
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	8e-14
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-13
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-13
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-13
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-13
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-13
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-13
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-13
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	3e-13
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	3e-13
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	3e-13
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	3e-13
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	4e-13
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	5e-13
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	6e-13
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	7e-13
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	7e-13
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-12
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-12
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-12
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-12
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-12
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-12
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-12
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-12
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-12
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-12
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-12
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-12
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-12
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-12
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-12
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	3e-12
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-12
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	5e-12
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	6e-12
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	6e-12
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	6e-12
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	8e-12
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	9e-12
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	9e-12
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-11
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-11
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-11
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-11
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-11
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-11
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-11
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-11
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-11
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-11
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	3e-11
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	3e-11
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-11
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	4e-11
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-11
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-11
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	5e-11
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-11
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	6e-11
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	6e-11
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	6e-11
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	7e-11
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	7e-11
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	7e-11
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	8e-11
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-10
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-10
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	1e-10
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	1e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-10
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	1e-10
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	1e-10
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-10
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	1e-10
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-10
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	1e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-10
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-10
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-10
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	2e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-10
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-10
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-10
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	4e-10
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	4e-10
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	4e-10
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	4e-10
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	5e-10
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	5e-10
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	6e-10
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	7e-10
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	7e-10
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	7e-10
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	7e-10
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-10
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	8e-10
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	8e-10
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	8e-10
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	9e-10
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-09
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	1e-09
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	1e-09
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	1e-09
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-09
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-09
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	1e-09
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-09
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-09
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	1e-09
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-09
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-09
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-09
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-09
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-09
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-09
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	2e-09
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-09
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	2e-09
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	2e-09
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-09
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-09
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	3e-09
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	3e-09
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-09
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	3e-09
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	3e-09
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	3e-09
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	3e-09
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-09
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	4e-09
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	4e-09
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	4e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-09
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	5e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	5e-09
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	5e-09
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-09
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	5e-09
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	6e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	7e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	7e-09
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	7e-09
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	8e-09
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	8e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-09
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	9e-09
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	9e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-08
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	1e-08
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-08
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-08
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	1e-08
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-08
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	1e-08
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-08
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-08
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	1e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-08
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-08
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	3e-08
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	3e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-08
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-08
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	4e-08
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	4e-08
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	4e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	4e-08
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	5e-08
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-08
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	5e-08
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	5e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	6e-08
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	6e-08
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	6e-08
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	7e-08
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	7e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	7e-08
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	7e-08
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	8e-08
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	9e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	9e-08
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	9e-08
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	9e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-07
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	1e-07
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-07
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	1e-07
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-07
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	1e-07
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	1e-07
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-07
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-07
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-07
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	2e-07
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	2e-07
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-07
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	3e-07
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	3e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-07
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	3e-07
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	3e-07
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	3e-07
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	3e-07
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	3e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	4e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	4e-07
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	5e-07
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-07
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	5e-07
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	5e-07
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	6e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	6e-07
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	6e-07
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	6e-07
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	6e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	6e-07
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	6e-07
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	7e-07
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	7e-07
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	7e-07
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	8e-07
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	8e-07
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	8e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-07
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	9e-07
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	9e-07
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	9e-07
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	9e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-06
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	1e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	1e-06
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	1e-06
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	1e-06
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	1e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-06
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	1e-06
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	1e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-06
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-06
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-06
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-06
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-06
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-06
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	2e-06
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	2e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-06
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	2e-06
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	2e-06
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-06
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	2e-06
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	2e-06
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-06
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	3e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	3e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	3e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	3e-06
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	3e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	3e-06
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	3e-06
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	3e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-06
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	3e-06
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	3e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	4e-06
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	4e-06
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	4e-06
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	4e-06
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	4e-06
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	4e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	5e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	5e-06
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	5e-06
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	5e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	5e-06
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	6e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	6e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	6e-06
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	6e-06
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	7e-06
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	7e-06
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	8e-06
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	8e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	8e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	9e-06
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	1e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-05
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	1e-05
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	1e-05
cd12602	76	cd12602, RRM2_SF2_plant_like, RNA recognition moti	1e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-05
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	1e-05
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	1e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	2e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	2e-05
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-05
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	2e-05
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	2e-05
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	2e-05
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	2e-05
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	2e-05
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	2e-05
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	2e-05
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	2e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-05
cd12425	76	cd12425, RRM4_PTBP1_like, RNA recognition motif 4	3e-05
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	3e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	3e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	3e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	3e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	3e-05
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	3e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	3e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	4e-05
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	4e-05
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	4e-05
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	4e-05
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	4e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	5e-05
cd12349	74	cd12349, RRM2_SHARP, RNA recognition motif 2 in SM	5e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	5e-05
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	5e-05
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	5e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-05
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	5e-05
cd12626	77	cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in	5e-05
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	5e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	5e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	6e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	6e-05
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	6e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	6e-05
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	6e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	6e-05
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	6e-05
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	6e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	7e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	7e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	8e-05
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	8e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	8e-05
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	8e-05
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	8e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	8e-05
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	9e-05
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	9e-05
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	1e-04
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	1e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	1e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	1e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	1e-04
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	1e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	1e-04
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	1e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	1e-04
pfam03154	979	pfam03154, Atrophin-1, Atrophin-1 family	1e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-04
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	1e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-04
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	1e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	2e-04
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	2e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-04
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	2e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	2e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	2e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-04
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	2e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	2e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-04
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	2e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-04
cd12435	71	cd12435, RRM_GW182_like, RNA recognition motif in	2e-04
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	2e-04
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	2e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	2e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	3e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-04
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	3e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	3e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	3e-04
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	3e-04
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	3e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	3e-04
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	3e-04
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	3e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-04
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	3e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	4e-04
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	4e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	4e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	4e-04
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	4e-04
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	4e-04
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	4e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	5e-04
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	5e-04
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	5e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	5e-04
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	5e-04
cd12289	93	cd12289, RRM_LARP6, RNA recognition motif in La-re	5e-04
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	5e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	6e-04
cd12452	88	cd12452, RRM_ARP_like, RNA recognition motif in ye	6e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	6e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	6e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	7e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	7e-04
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	7e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	7e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	8e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	8e-04
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	8e-04
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	8e-04
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	8e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.001
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	0.001
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	0.001
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.001
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.001
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	0.001
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.001
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	0.001
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	0.001
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	0.001
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	0.001
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.001
cd12292	75	cd12292, RRM2_La_like, RNA recognition motif 2 in	0.001
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.001
cd12625	77	cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in	0.001
pfam08777	102	pfam08777, RRM_3, RNA binding motif	0.001
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.002
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.002
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	0.002
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	0.002
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.002
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	0.002
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.002
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.002
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.002
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	0.002
cd12541	76	cd12541, RRM2_La, RNA recognition motif 2 in La au	0.002
cd12443	73	cd12443, RRM_MCM3A_like, RNA recognition motif in	0.002
cd12356	79	cd12356, RRM_PPARGC1B, RNA recognition motif in pe	0.002
cd12540	105	cd12540, RRM_U2AFBPL, RNA recognition motif in U2	0.002
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.002
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	0.002
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	0.003
cd12349	74	cd12349, RRM2_SHARP, RNA recognition motif 2 in SM	0.003
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.003
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.003
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.003
cd12255	73	cd12255, RRM1_LKAP, RNA recognition motif 1 in Lim	0.003
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	0.003
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	0.003
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	0.003
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.003

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

 Score =  448 bits (1153), Expect = e-153
 Identities = 206/452 (45%), Positives = 277/452 (61%), Gaps = 46/452 (10%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           ML+NDK+V+VG F++K ERE  A   KF N++VKNLD S  ++ L+++F ++G ITSA V
Sbjct: 152 MLLNDKEVYVGRFIKKHERE-AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAV 210

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREW----YVGKAQKKSEREQELKG 116
           M+DG G+S+ F FVNFE  +DAAKAVE +NGKK    +     YVG+AQK++ERE EL+ 
Sbjct: 211 MKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRR 270

Query: 117 QFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGF 176
           +FE+  +E   K QG+NLY+KNL D++ DEKL+ELFSE G ITS KVM D  G+S+G GF
Sbjct: 271 KFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGF 330

Query: 177 VAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPR 236
           V FS PEEA+RA+ EM+G+M+  KPLYVA+AQRKE+RRA LQ QF Q++P         +
Sbjct: 331 VCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRM------RQ 384

Query: 237 MPMYPPGPSGLGQQFLYGQAPPAIIPPQA-GFGYQQQLVPGMRPAGAPMPNFFVPVVSQG 295
           +PM  P    +GQ   YGQ P      Q  G+     +   M P G   PN   P+ +  
Sbjct: 385 LPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVR 444

Query: 296 QQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVP 355
                    R A   Q   Q  P+ P   PP   +                     LP+ 
Sbjct: 445 APS------RNA---QNAAQKPPMQPVMYPPNYQS---------------------LPLS 474

Query: 356 VDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTG 415
            D+    P+  ++  Q      L+  LA+A+P+ Q+ +LGE L+PLVE +E   AAK+TG
Sbjct: 475 QDL----PQPQSTASQGGQNKKLAQVLASATPQMQKQVLGERLFPLVEAIEPALAAKITG 530

Query: 416 MLLEMDQTEVLHLLESPEALKAKVAEAMEVLR 447
           MLLEMD +E+LHLLESPE LK+KV EA+EVL+
Sbjct: 531 MLLEMDNSELLHLLESPELLKSKVDEALEVLK 562

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

 Score =  182 bits (464), Expect = 2e-51
 Identities = 86/216 (39%), Positives = 130/216 (60%), Gaps = 17/216 (7%)

Query: 14  LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGF 73
           +   +R+    ++   N+FVKNLD+S  ++ L   F ++G I S  V  D +GKS+ +GF
Sbjct: 74  IMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGF 133

Query: 74  VNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN 133
           V+FE  + A  A++ +NG   +D+E YVG+  KK ERE     +F              N
Sbjct: 134 VHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFT-------------N 180

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY+KNL  S++++KL+ELF++FG ITS  VM+D SG S+G  FV F   E+A++A+ EMN
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240

Query: 194 GKMI----VSKPLYVAVAQRKEERRARLQAQFSQMR 225
           GK I      K LYV  AQ++ ER A L+ +F +++
Sbjct: 241 GKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQ 276

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

 Score =  162 bits (412), Expect = 3e-49
 Identities = 55/79 (69%), Positives = 66/79 (83%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           G+NLY+KNL DSIDDE+L+E FS FGTITS KVM D  G SKG GFV FS+PEEA++A+ 
Sbjct: 1   GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60

Query: 191 EMNGKMIVSKPLYVAVAQR 209
           EMNG++I  KPLYVA+AQR
Sbjct: 61  EMNGRIIGGKPLYVALAQR 79

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

 Score =  154 bits (391), Expect = 5e-46
 Identities = 51/80 (63%), Positives = 63/80 (78%)

Query: 28  FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
           F NV+VKNL E   DE LK++FG+YG ITSA VM+D +GKSK FGFVNFEN + A KAVE
Sbjct: 1   FTNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVE 60

Query: 88  ALNGKKFDDREWYVGKAQKK 107
            LNGK+ + ++ YVG+AQKK
Sbjct: 61  ELNGKEVNGKKLYVGRAQKK 80

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

 Score =  124 bits (314), Expect = 6e-35
 Identities = 45/78 (57%), Positives = 57/78 (73%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           N+Y+KNLG+ +DDEKLKELF ++G ITS KVM+D  G SKG GFV F   E A +A+ E+
Sbjct: 3   NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 193 NGKMIVSKPLYVAVAQRK 210
           NGK +  K LYV  AQ+K
Sbjct: 63  NGKEVNGKKLYVGRAQKK 80

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|201378 pfam00658, PABP, Poly-adenylate binding protein, unique domain

 Score =  115 bits (291), Expect = 1e-31
 Identities = 41/69 (59%), Positives = 55/69 (79%)

Query: 378 LSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKA 437
            ++ALA A P++Q+ +LGE LYPL++ +  + A K+TGMLLEMD +E+LHLLES EALKA
Sbjct: 4   TASALAAAPPQEQKQMLGERLYPLIQAMHPELAGKITGMLLEMDNSELLHLLESDEALKA 63

Query: 438 KVAEAMEVL 446
           KV EA+ VL
Sbjct: 64  KVDEALAVL 72

The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family. Length = 72

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

 Score =  125 bits (316), Expect = 4e-31
 Identities = 65/204 (31%), Positives = 106/204 (51%), Gaps = 17/204 (8%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
           ++V +LD   T+  L  +F  +G + S  V RD    +S  +G+VNF+N  DA +A+E +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 90  NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 149
           N K+   +   +  +Q+     +   G                N+++KNL  S+D++ L 
Sbjct: 63  NFKRLGGKPIRIMWSQRDPSLRRSGVG----------------NIFVKNLDKSVDNKALF 106

Query: 150 ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR 209
           + FS+FG I SCKV  D +G S+G GFV F   E A  A+ ++NG ++  K +YV    +
Sbjct: 107 DTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIK 166

Query: 210 KEERRARLQAQFSQMRPVAMGPSV 233
           K ER A    +F+ +    + PSV
Sbjct: 167 KHEREAAPLKKFTNLYVKNLDPSV 190

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

 Score =  110 bits (278), Expect = 9e-30
 Identities = 36/73 (49%), Positives = 49/73 (67%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           N++IKNL  SID++ L + FS FG I SCKV  D +G SKG GFV F T E A RA+ ++
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 193 NGKMIVSKPLYVA 205
           NG ++  K ++V 
Sbjct: 64  NGMLLNDKKVFVG 76

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

 Score =  110 bits (276), Expect = 2e-29
 Identities = 38/77 (49%), Positives = 52/77 (67%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           N++VKNLD+S  DE L++ F  +GTITSA VM D  G+SK FGFV F + ++A KAV  +
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 90  NGKKFDDREWYVGKAQK 106
           NG+    +  YV  AQ+
Sbjct: 63  NGRIIGGKPLYVALAQR 79

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|214636 smart00360, RRM, RNA recognition motif

 Score =  103 bits (259), Expect = 4e-27
 Identities = 35/73 (47%), Positives = 51/73 (69%), Gaps = 1/73 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
            +FV NL   TT+E+L+++F ++G + S  ++RD + GKSK F FV FE+ +DA KA+EA
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 89  LNGKKFDDREWYV 101
           LNGK+ D R   V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score =  102 bits (256), Expect = 1e-26
 Identities = 36/70 (51%), Positives = 48/70 (68%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           +FV NL   TT+EDLK +F ++G I S  ++RD  G+SK F FV FE+ +DA KA+EALN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 91  GKKFDDREWY 100
           GK+   RE  
Sbjct: 61  GKELGGRELR 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|197769 smart00517, PolyA, C-terminal domain of Poly(A)-binding protein

 Score =  101 bits (254), Expect = 1e-26
 Identities = 40/63 (63%), Positives = 51/63 (80%)

Query: 386 SPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEV 445
            P++Q+  LGE LYP V+ LE + A K+TGMLLEMD +E+LHLLESPE L+AKV EA+EV
Sbjct: 1   PPQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRAKVDEALEV 60

Query: 446 LRS 448
           L+S
Sbjct: 61  LKS 63

Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly). Length = 64

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

 Score =  101 bits (253), Expect = 2e-26
 Identities = 38/71 (53%), Positives = 52/71 (73%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           +FV NL   TT+EDL+++F ++G I S  ++RD DGKSK F FV FE+ +DA KA+EALN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 91  GKKFDDREWYV 101
           GK+ D R+  V
Sbjct: 61  GKELDGRKLKV 71

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

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

 Score =  103 bits (258), Expect = 7e-25
 Identities = 59/191 (30%), Positives = 96/191 (50%), Gaps = 8/191 (4%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
           N +FV NL    T+EDL+++F ++G +    ++RD + GKS+ F FV FE+ + A KA+E
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKF------QGLNLYIKNLGD 141
            LNGK+ + R   V KAQ  S+   EL    + +  + + +       +  NLY+ NL  
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPL 235

Query: 142 SIDDEKLKELFSEFGTITSCKVMRDPSG-ISKGSGFVAFSTPEEASRALAEMNGKMIVSK 200
              +E+L +LF   G I    +     G I K   FV     ++A  + +  N K I+ +
Sbjct: 236 KTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILGR 295

Query: 201 PLYVAVAQRKE 211
               A +Q + 
Sbjct: 296 GPRKAFSQPRL 306

Length = 306

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

 Score = 94.9 bits (237), Expect = 4e-24
 Identities = 30/74 (40%), Positives = 47/74 (63%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           N+F+KNLD+S  ++ L   F  +G I S  V  D +G SK +GFV+FE  + A +A+E +
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 90  NGKKFDDREWYVGK 103
           NG   +D++ +VG 
Sbjct: 64  NGMLLNDKKVFVGP 77

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|214636 smart00360, RRM, RNA recognition motif

 Score = 94.6 bits (236), Expect = 6e-24
 Identities = 31/73 (42%), Positives = 48/73 (65%), Gaps = 1/73 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            L++ NL     +E+L+ELFS+FG + S +++RD  +G SKG  FV F + E+A +AL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 192 MNGKMIVSKPLYV 204
           +NGK +  +PL V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 91.6 bits (228), Expect = 6e-23
 Identities = 32/71 (45%), Positives = 46/71 (64%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL     +E L+ELFS+FG I S +++RD  G SKG  FV F +PE+A +AL  +N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 194 GKMIVSKPLYV 204
           GK +  + L V
Sbjct: 61  GKELDGRKLKV 71

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

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

 Score = 86.5 bits (215), Expect = 4e-21
 Identities = 30/70 (42%), Positives = 44/70 (62%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL     +E LK+LFS+FG I S +++RD +G SKG  FV F   E+A +AL  +N
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 194 GKMIVSKPLY 203
           GK +  + L 
Sbjct: 61  GKELGGRELR 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

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

 Score = 85.0 bits (211), Expect = 2e-20
 Identities = 32/78 (41%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           +FV+NL   TTDE L++ F E G I    V++D G  K + FG+V F   +DA +A+E  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 90  NGKKFDDREWYVGKAQKK 107
              KF  R+ +V  A+KK
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

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

 Score = 84.6 bits (210), Expect = 2e-20
 Identities = 35/78 (44%), Positives = 52/78 (66%), Gaps = 1/78 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           N++V NL  + T+EDLK +FG++G +TSA V+ D + G+S+ FGFV  E A++A  A+E 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 89  LNGKKFDDREWYVGKAQK 106
           LNG  F  R   V +A+ 
Sbjct: 61  LNGTDFGGRTLTVNEARP 78

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|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 = 83.4 bits (207), Expect = 7e-20
 Identities = 28/80 (35%), Positives = 49/80 (61%), Gaps = 1/80 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           G  L++  L     +++L+ LFS+FG +    +M+DP +G S+G GFV F + E+A  A+
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 190 AEMNGKMIVSKPLYVAVAQR 209
            ++NGK +  + + V  A+R
Sbjct: 61  RDLNGKELEGRVIKVEKAKR 80

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

 Score = 89.6 bits (221), Expect = 9e-20
 Identities = 45/242 (18%), Positives = 89/242 (36%), Gaps = 15/242 (6%)

Query: 13  FLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFG 72
               +   +     K  ++    L E    E+   +        +  V            
Sbjct: 3   SKNLKGPHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPP 62

Query: 73  FVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGL 132
                 + +  +  E    ++ D    Y  + +++  R  E              K +  
Sbjct: 63  SKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPK------SRQKSKEENN 116

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            L++ NL   + +E L+ELF +FG +   +++RD  +G S+G  FV F + E A +A+ E
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176

Query: 192 MNGKMIVSKPLYV----AVAQRKEERR----ARLQAQFSQMRPVAMGPSVPPRMPMYPPG 243
           +NGK +  +PL V      +Q + E      A    + S+ + + +  S    +   P  
Sbjct: 177 LNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLK 236

Query: 244 PS 245
            +
Sbjct: 237 TA 238

Length = 306

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

 Score = 89.2 bits (221), Expect = 2e-19
 Identities = 54/167 (32%), Positives = 89/167 (53%), Gaps = 20/167 (11%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L ++ T E+++ +F   G I S  ++RD   G+S  +GFVN+   +DA KAV +
Sbjct: 5   NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS 64

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
           LNG +  ++   V  A+  S                  D  +G NLY+  L  ++   +L
Sbjct: 65  LNGLRLQNKTIKVSYARPSS------------------DSIKGANLYVSGLPKTMTQHEL 106

Query: 149 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNG 194
           + +FS FG I + +++ D  +G+SKG GF+ F   +EA RA+  +NG
Sbjct: 107 ESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG 153

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

 Score = 80.4 bits (199), Expect = 9e-19
 Identities = 32/83 (38%), Positives = 54/83 (65%), Gaps = 2/83 (2%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTI-TSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           G NL+I NL   +D++ L + FS FG I  + K+MRDP +G SKG  F+++ + E +  A
Sbjct: 1   GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60

Query: 189 LAEMNGKMIVSKPLYVAVAQRKE 211
           +  MNG+ + ++P+ V+ A +K+
Sbjct: 61  IEAMNGQYLCNRPITVSYAFKKD 83

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 83

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 87.6 bits (217), Expect = 1e-18
 Identities = 59/202 (29%), Positives = 91/202 (45%), Gaps = 9/202 (4%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           VFV  L     + DL + F + G +     ++D    +SK   +V F + +   KA+ AL
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-AL 150

Query: 90  NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 149
            G+    R   V  +Q +  R  +       A  +  D    L LY+ NL  +I +++L+
Sbjct: 151 TGQMLLGRPIIVQSSQAEKNRAAKA------ATHQPGDIPNFLKLYVGNLHFNITEQELR 204

Query: 150 ELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 208
           ++F  FG I   ++ RDP +G SKG GF+ F   EEA  AL  MNG  +  +P+ V  AQ
Sbjct: 205 QIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ 264

Query: 209 RKEERRARLQAQFSQMRPVAMG 230
                           +   MG
Sbjct: 265 DSTYLLDAANTFEDIDKQQQMG 286

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

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 25/74 (33%), Positives = 41/74 (55%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + +KNL   + +++L+E F   G +T  KVMR   G S+  GFV F + E+A +A+   N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 194 GKMIVSKPLYVAVA 207
              I +  + V +A
Sbjct: 63  KTFIDTSKISVELA 76

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 85.1 bits (210), Expect = 4e-18
 Identities = 68/248 (27%), Positives = 111/248 (44%), Gaps = 37/248 (14%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L +  TD +L  +F   G I +  +MRD   G S  + FV+F +  D+ +A++ 
Sbjct: 109 NLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKN 168

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
           LNG    ++   V  A+   E           ++K+T       NLY+ NL  +I D++L
Sbjct: 169 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 210

Query: 149 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVA 205
             +F ++G I    ++RD  +G  +G  FV F+  EEA  A++ +N  +    S+PL V 
Sbjct: 211 DTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVR 270

Query: 206 VAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQA 265
           +A+  E  +A+     SQM    M             G  G G   + G +      P A
Sbjct: 271 LAE--EHGKAKAHHYMSQMGHGNM-------------GNMGHGNMGMAGGSGMNPPNPPA 315

Query: 266 GFGYQQQL 273
             G    +
Sbjct: 316 FMGMNNMV 323

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

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

 Score = 77.3 bits (191), Expect = 9e-18
 Identities = 27/65 (41%), Positives = 40/65 (61%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + VKNL +  T++ L++ F   G +T   VMR  DGKS+ FGFV F++ +DA +AV+  N
Sbjct: 3  IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 91 GKKFD 95
              D
Sbjct: 63 KTFID 67

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 76.9 bits (190), Expect = 1e-17
 Identities = 28/67 (41%), Positives = 39/67 (58%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + V+NL    T+ DLKK+F  +G +    + R  DGK K F FV F +  DA KA++ +N
Sbjct: 2  LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 91 GKKFDDR 97
          GKK   R
Sbjct: 62 GKKIKGR 68

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

 Score = 75.5 bits (186), Expect = 3e-17
 Identities = 30/76 (39%), Positives = 49/76 (64%), Gaps = 1/76 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
            L++ NL  S+DDE LK  F +FGT+   +V+ D  +G S+G G+V F +PE+A +A+  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 192 MNGKMIVSKPLYVAVA 207
           M+GK +  +P+ V  +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 75.3 bits (186), Expect = 4e-17
 Identities = 32/77 (41%), Positives = 49/77 (63%), Gaps = 1/77 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NLY+ NL  ++ +E LK+LF +FG +TS +V+ D  +G S+G GFV   T EEA+ A+ +
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG     + L V  A+
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|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 = 75.3 bits (186), Expect = 4e-17
 Identities = 30/79 (37%), Positives = 51/79 (64%), Gaps = 1/79 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 87
           N +FV  L   TT+++L+ +F ++G +   ++M+D   G+S+ FGFV FE+ +DA  A+ 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 88  ALNGKKFDDREWYVGKAQK 106
            LNGK+ + R   V KA++
Sbjct: 62  DLNGKELEGRVIKVEKAKR 80

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

 Score = 74.7 bits (184), Expect = 7e-17
 Identities = 25/71 (35%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           ++++ +L   ID E L+  F+ FG I+  +V++D  +G SKG GFV+F   E+A  A+  
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 192 MNGKMIVSKPL 202
           MNG+ +  + +
Sbjct: 61  MNGQWLGGRAI 71

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 74.1 bits (183), Expect = 8e-17
 Identities = 25/67 (37%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          ++V+NL  S T+EDL++ F  YG +    ++R+ D + + F FV F + +DA  A++ LN
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 91 GKKFDDR 97
          G   D R
Sbjct: 60 GLVLDGR 66

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

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

 Score = 74.1 bits (183), Expect = 1e-16
 Identities = 24/64 (37%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNG 91
          V NL E   ++DL+++F  +G I+   + +D + G+S+ F FV F   +DA +A+E LNG
Sbjct: 4  VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 92 KKFD 95
            +D
Sbjct: 64 FGYD 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 73.2 bits (180), Expect = 2e-16
 Identities = 33/76 (43%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
            +FV NL  S  DE LK  F ++GT+  A V+ D + G+S+ FG+V+FE+ +DA KA+EA
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 89  LNGKKFDDREWYVGKA 104
           ++GK+ D R   V  +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 73.4 bits (181), Expect = 2e-16
 Identities = 26/68 (38%), Positives = 42/68 (61%), Gaps = 7/68 (10%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          ++V+NL  STT+E L+++F EYG +     ++D       + FV+FE  DDA KA+E +N
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 91 GKKFDDRE 98
          GK+ +   
Sbjct: 57 GKELEGSP 64

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|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 = 71.8 bits (176), Expect = 8e-16
 Identities = 32/77 (41%), Positives = 50/77 (64%), Gaps = 1/77 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 89
           +F+  L   T ++ L+++F +YG I+  VV++D + + S+ FGFV FEN DDA  A+ A+
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 90  NGKKFDDREWYVGKAQK 106
           NGK  D R+  V +A K
Sbjct: 63  NGKSVDGRQIRVDQAGK 79

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

 Score = 71.2 bits (175), Expect = 1e-15
 Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           +FV NL  S   +DL++ F E G +    + +D DG+SK FG V F   + A KA+E  +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-KS 60

Query: 91  GKKFDDREWYVGKAQKK 107
           G++   RE  V  A ++
Sbjct: 61  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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 70.7 bits (174), Expect = 2e-15
 Identities = 28/70 (40%), Positives = 47/70 (67%), Gaps = 1/70 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +++ +LG+ + DE L   FS++ +    KV+RD  +G SKG GFV+FS P +  +A+ EM
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 193 NGKMIVSKPL 202
           NGK + ++P+
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|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 = 70.4 bits (173), Expect = 2e-15
 Identities = 26/62 (41%), Positives = 43/62 (69%), Gaps = 1/62 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          +F+ +L    TD+DL ++F  +G + SA V  D + G+SKCFGFV+++N + A  A++A+
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 90 NG 91
          NG
Sbjct: 61 NG 62

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

 Score = 70.1 bits (172), Expect = 3e-15
 Identities = 29/76 (38%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           NL +  L   +  E+L+ LF   G I SCK++RD  +G S G GFV +    +A +A+  
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 192 MNGKMIVSKPLYVAVA 207
           +NG  I +K L V+ A
Sbjct: 62  LNGFEIRNKRLKVSYA 77

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

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 69.6 bits (171), Expect = 4e-15
 Identities = 32/68 (47%), Positives = 43/68 (63%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV+NL  S T +DLK +F E G +  A V  D DG+SK FG V FE+ +DA +A+E  N
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 91 GKKFDDRE 98
          G   + RE
Sbjct: 61 GYDLEGRE 68

This subfamily corresponds to the RRM3 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. hnRNP M 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 = 72

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

 Score = 69.2 bits (170), Expect = 6e-15
 Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           V+V NL    T  +L+  F +YG + S  V R+  G    F FV FE+  DA  AV AL+
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPG----FAFVEFEDPRDAEDAVRALD 57

Query: 91  GKKFDDREWYVGKA 104
           G++       V  +
Sbjct: 58  GRRICGNRVRVELS 71

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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 69.3 bits (170), Expect = 6e-15
 Identities = 27/71 (38%), Positives = 39/71 (54%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L +KNL   I ++KL++LF  FGTIT  ++     G  +  GFV + T EEA +AL   N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 194 GKMIVSKPLYV 204
              I +  + V
Sbjct: 63  NSFIDTSKITV 73

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

 Score = 68.9 bits (169), Expect = 9e-15
 Identities = 26/77 (33%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL  S + + L+E F E G +   ++ +D  G SKG G V F+T E A +AL E +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EKS 60

Query: 194 GKMIVSKPLYVAVAQRK 210
           G+ ++ + + V +A  +
Sbjct: 61  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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 68.3 bits (168), Expect = 1e-14
 Identities = 24/70 (34%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY++NL  S+ +E L+E FS +G +   +++R+     +G  FV F++PE+A  AL ++N
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 194 GKMIVSKPLY 203
           G ++  + L 
Sbjct: 60  GLVLDGRTLR 69

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

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

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVV------MRDGDGKSKCFGFVNFENADDAAK 84
          +FVKNL+  TT+E LKK F + G + S  +         G   S  +GFV F++ + A K
Sbjct: 3  LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 85 AVEALNGKKFDDR 97
          A++ L G   D  
Sbjct: 63 ALKRLQGTVLDGH 75

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

 Score = 68.4 bits (168), Expect = 1e-14
 Identities = 28/72 (38%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           LY+ NL  +I ++ L+ +F  FG I   ++ RDP +G SKG GF+ F+  E+A +AL ++
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 193 NGKMIVSKPLYV 204
           NG  +  +P+ V
Sbjct: 61  NGFELAGRPIKV 72

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

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

 Score = 68.2 bits (167), Expect = 1e-14
 Identities = 28/76 (36%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  ++++ LFS  G I SCK++RD  +G S G GFV +  PE+A +A+  
Sbjct: 3   NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

Query: 192 MNGKMIVSKPLYVAVA 207
           +NG  + +K + V+ A
Sbjct: 63  LNGLRLQNKTIKVSYA 78

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

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

 Score = 68.2 bits (167), Expect = 1e-14
 Identities = 25/71 (35%), Positives = 38/71 (53%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           +FV NLD     + LK++F   G +  A +  D +GKS+  G V FE+  +A +A+   N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 91  GKKFDDREWYV 101
           G+   DR   V
Sbjct: 61  GQMLFDRPMRV 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 68.0 bits (167), Expect = 2e-14
 Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L+++NL     DE+L+E FSE G I  C V++D  S   +G G+V F+  E+A RAL E 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 193 NGKMIVSKPLYVAVAQRK 210
                  + ++V  A++K
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

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

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L ++NL     +  LK+LFS FG +    + R P G  KG  FV F++  +A +A+  +N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 194 GKMIVSKPLYVAV 206
           GK I  +P  VAV
Sbjct: 62  GKKIKGRP--VAV 72

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

 Score = 67.2 bits (165), Expect = 3e-14
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA-- 88
          F+  L   TT+E L++ F +YG +   V+M+D   G+S+ FGFV F +     K + A  
Sbjct: 2  FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61

Query: 89 --LNGKKFD 95
            L+G++ D
Sbjct: 62 HVLDGREID 70

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

 Score = 66.4 bits (163), Expect = 5e-14
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          VFV NL     +E+L+K F + G + +  ++RD   G  K FG+V F+  D  A A+  L
Sbjct: 2  VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 90 NGKKFDDRE 98
          NG K   R+
Sbjct: 61 NGIKLKGRK 69

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

 Score = 66.9 bits (164), Expect = 6e-14
 Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 87
           N +FV  L+  TTDEDL+ IF  +G I S  V+RD   G S  + F+ FE  +D  +A  
Sbjct: 4   NVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYF 63

Query: 88  ALNGKKFDDREWYV 101
            ++    DDR  +V
Sbjct: 64  KMDNVLIDDRRIHV 77

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|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 = 66.1 bits (162), Expect = 7e-14
 Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L+I +L +   D+ L +LF+ FG + S KV  D  +G SK  GFV++  PE A  A+  M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 193 NGKMIVSKPLYV 204
           NG  +  K L 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 66.2 bits (162), Expect = 8e-14
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
          N+ V  L +  T E+L+ +F   G I S  ++RD   G+S  +GFV++ + +DA KA+  
Sbjct: 2  NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 89 LNG 91
          LNG
Sbjct: 62 LNG 64

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

 Score = 66.3 bits (162), Expect = 8e-14
 Identities = 21/69 (30%), Positives = 41/69 (59%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          + +FV  L  S T E+L+K+F ++G + S  ++ +  GK K   +V +EN   A++AV  
Sbjct: 3  HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLK 62

Query: 89 LNGKKFDDR 97
          ++G +  ++
Sbjct: 63 MDGTEIKEK 71

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

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 24/61 (39%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           ++I+NL     +E+LKELFS+FG +   ++++D  +G SKG+ FV F T E A + L   
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 193 N 193
           +
Sbjct: 63  D 63

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

 Score = 65.8 bits (161), Expect = 1e-13
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 9/83 (10%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           N +FV  +   TT+E+L+  F  +G++    ++ D  G SK +GFV FE  +DA K +  
Sbjct: 3   NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAM 62

Query: 89  ----LNGKKFDDREWYVGKAQKK 107
                 GKK +     +G A +K
Sbjct: 63  GNLNFRGKKLN-----IGPAIRK 80

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

 Score = 65.9 bits (161), Expect = 1e-13
 Identities = 29/76 (38%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           NL I  L  ++ DE+ + LF   G + +CK++RD  +G S G GFV + + E+A RA+  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 192 MNGKMIVSKPLYVAVA 207
           +NG  + +K + VA A
Sbjct: 62  LNGLQLQNKRIKVAYA 77

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

 Score = 65.6 bits (161), Expect = 1e-13
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           LY+ +L   + +  L E+FS  G + S +V RD  +  S G  +V F  P +A RAL  +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 193 NGKMIVSKPLYVAVAQR 209
           N  +I  KP+ +  +QR
Sbjct: 62  NFDVIKGKPIRIMWSQR 78

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

 Score = 64.7 bits (158), Expect = 2e-13
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
          ++FV +L      E L+  F  +G I+ A V++D   GKSK +GFV+F   +DA  A+++
Sbjct: 1  HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 89 LNGKKFDDRE 98
          +NG+    R 
Sbjct: 61 MNGQWLGGRA 70

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

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
           +FV NL     +  L ++F  +G +T+  V+RD    K K +GFV   N ++A  A+ +
Sbjct: 3  CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 89 LNGKKFDDR 97
          LNG +   R
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|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 30/69 (43%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
          VF   L   TT+ DL+++F  YG I    V+ D   G+S+ FGFV FE+ +DA +A E L
Sbjct: 4  VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 90 NGKKFDDRE 98
          NG + D R 
Sbjct: 62 NGMEIDGRR 70

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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 27/71 (38%), Positives = 40/71 (56%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           ++++NL  S+  + LK+LF E G +    V  D  G SKG G V F +PE+A RA+   N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 194 GKMIVSKPLYV 204
           G  +  + L V
Sbjct: 61  GYDLEGRELEV 71

This subfamily corresponds to the RRM3 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. hnRNP M 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 = 72

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

 Score = 64.6 bits (158), Expect = 3e-13
 Identities = 27/67 (40%), Positives = 42/67 (62%), Gaps = 1/67 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
          NV+++ L  +TTDEDL+K+   +G I S   + D    K K +GFV+F++ + A KA+E 
Sbjct: 2  NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

Query: 89 LNGKKFD 95
          LNG+   
Sbjct: 62 LNGRGVQ 68

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

 Score = 64.6 bits (158), Expect = 3e-13
 Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
            ++++ +L   + D  L+E F   + ++   KV+ DP +G SKG GFV F   +E  RAL
Sbjct: 2   HSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRAL 61

Query: 190 AEMNGKMIVSKPLYVAVA 207
            EMNG    S+P+ V+ A
Sbjct: 62  TEMNGVYCSSRPMRVSPA 79

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

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

 Score = 64.6 bits (158), Expect = 3e-13
 Identities = 26/72 (36%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEM 192
           L + NL     DE+ +EL S FG +  C ++   S G SKG GFV +++   A +A  ++
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 193 NGKMIVSKPLYV 204
           +GK I  + L V
Sbjct: 62  DGKQIGGRKLQV 73

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

 Score = 64.3 bits (157), Expect = 4e-13
 Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L++ +L   +DD +L E FS+ + +    KV+ D +G S+G GFV FS   E  RAL EM
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEM 63

Query: 193 NGKMIV-SKPLYVAVA 207
            G   +  KP+ V++A
Sbjct: 64  QGASGLGGKPIRVSLA 79

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 63.8 bits (156), Expect = 5e-13
 Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 7/76 (9%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVV-----MRDGDGKSKCFGFVNFENADDAAKA 85
           ++V+NLD    ++DL+ IF ++G + S  +      + G   +  F FV F++A  A  A
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGR-LNNGFAFVTFKDASSAENA 61

Query: 86  VEALNGKKFDDREWYV 101
           ++ LNG +   R+  V
Sbjct: 62  LQ-LNGTELGGRKISV 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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 63.4 bits (155), Expect = 6e-13
 Identities = 25/69 (36%), Positives = 40/69 (57%), Gaps = 5/69 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 191
           L+I  L     +E L+E FS++G +  C +M+DP +G S+G GFV F+ P    + LA  
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 192 ---MNGKMI 197
              ++G+ I
Sbjct: 61  PHVLDGREI 69

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

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

 Score = 63.5 bits (155), Expect = 7e-13
 Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY+ NL  ++ ++ L ELFS+ G I SCK++R+         FV +     A+ AL  MN
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEYYDHRSAAAALQTMN 58

Query: 194 GKMIVSKPLYV 204
           G++I+ + + V
Sbjct: 59  GRLILGQEIKV 69

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

 Score = 63.4 bits (155), Expect = 7e-13
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L + NL   + +E L+ELF   G +   K+  D SG S+G+  V F   E+A RA+ + N
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 194 GKMIVSKPLYVAV 206
           G ++  +P+ V +
Sbjct: 63  GVLLDGQPMQVEL 75

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

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

 Score = 62.3 bits (152), Expect = 1e-12
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 7/74 (9%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY++NL  S  +E+L+ELFSE+G +   K ++D         FV F   ++A +A+ EMN
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 194 GKMIVSKPLYVAVA 207
           GK +   P+ V++A
Sbjct: 57  GKELEGSPIEVSLA 70

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

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

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 29/75 (38%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           G  +++ NL    D+  L +LFS FG +T+ KV+RD  +   KG GFV  +  EEA  A+
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 190 AEMNGKMIVSKPLYV 204
           A +NG  +  + L V
Sbjct: 61  ASLNGYRLGGRVLQV 75

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

 Score = 62.9 bits (153), Expect = 1e-12
 Identities = 27/71 (38%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           N+++ +L   + D  L   FS F + +  +VM D  SG S+G GFV+F + ++A  A+ E
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 192 MNGKMIVSKPL 202
           MNGK + S+P+
Sbjct: 61  MNGKWLGSRPI 71

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

 Score = 62.0 bits (151), Expect = 2e-12
 Identities = 24/71 (33%), Positives = 40/71 (56%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +++ NL   +  +KLKE+F   G +    +  D  G S+G G V F  P EA +A++  N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 194 GKMIVSKPLYV 204
           G+M+  +P+ V
Sbjct: 61  GQMLFDRPMRV 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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVM--RDPSGISKG--SGFVAFSTPEEASRA 188
           NLY+ NL   + +E L + F  FG + S K+M  R      +    GFVAF    +A RA
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

Query: 189 LAEMNGKMIVSKPLYVA 205
           L E++GK ++   L + 
Sbjct: 63  LDELDGKDVMGYELKLG 79

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

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVM--RDGDGKSK---CFGFVNFENADDAAK 84
           N++V NL+   T+E L + FG +G + S  +M  R  + + +   C GFV F N  DA +
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC-GFVAFMNRADAER 61

Query: 85  AVEALNGKKFDDREWYVG 102
           A++ L+GK     E  +G
Sbjct: 62  ALDELDGKDVMGYELKLG 79

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

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 6/87 (6%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           +FV  L   TT+E L+++F  YG I    ++RD   G SK + FV +E+  DA +A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 90  NGKKFDDREWYVGKAQKKSEREQELKG 116
           +    D  E +V       ERE+ L G
Sbjct: 66  HKLVIDGSEIFV-----DFERERTLPG 87

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

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 26/65 (40%), Positives = 43/65 (66%), Gaps = 7/65 (10%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV NL ++TT E+L+ +F +YGT+T   V+++       +GFV+ E  +DA  A++ALN
Sbjct: 2  LFVGNLPDATTSEELRALFEKYGTVTECDVVKN-------YGFVHMEEEEDAEDAIKALN 54

Query: 91 GKKFD 95
          G +F 
Sbjct: 55 GYEFM 59

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|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 = 61.9 bits (151), Expect = 2e-12
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          FV+NL  +TT+E+L+++F  +G I+   + +     +SK F FV+F   + A KA   L+
Sbjct: 3  FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELD 62

Query: 91 GKKFDDR 97
          G  F  R
Sbjct: 63 GSIFQGR 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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 62.1 bits (151), Expect = 2e-12
 Identities = 30/79 (37%), Positives = 47/79 (59%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           N +FV  +D  T + DL+K F +YGT+    ++ D  G SK +GFV FE  +DA K ++ 
Sbjct: 3   NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQE 62

Query: 89  LNGKKFDDREWYVGKAQKK 107
            N   F D++  +G+A +K
Sbjct: 63  ANRLCFRDKKLNIGQAIRK 81

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

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 27/61 (44%), Positives = 41/61 (67%), Gaps = 1/61 (1%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALN 90
          +V NL  + T++DL+ IF  +G I    + RD + G+SK +GF+ F +A+DA KA+E LN
Sbjct: 2  YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 91 G 91
          G
Sbjct: 62 G 62

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

 Score = 61.8 bits (151), Expect = 3e-12
 Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          VF++NL    T+E+LK++F ++G +  A +++D   G SK   FV F+  + A K +EA 
Sbjct: 3  VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 90 NGKKFDD 96
          +  +   
Sbjct: 63 DNAEDSG 69

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

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 28/70 (40%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 89
          V+V NL  S T+ DL KIF +YG +    +++D +  KSK   F+ F + +DA K V+AL
Sbjct: 4  VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 90 NGKKFDDREW 99
          N K+   R  
Sbjct: 64 NNKELFGRTL 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 27/68 (39%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
          +FV  L   TTD+ L+K F ++G I  AVV+ D   GKS+ +GFV F++ + A +A +  
Sbjct: 3  IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 90 NGKKFDDR 97
          N    D R
Sbjct: 63 N-PIIDGR 69

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|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGE-YGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          + VKNL  S T+ +LK+ F +  G IT   ++R  DGKS+   F+ ++  ++A KA +  
Sbjct: 3  LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 90 NG 91
          N 
Sbjct: 63 NN 64

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 61.8 bits (150), Expect = 3e-12
 Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L+++NL  S+  E L + FS+   I    V+ DP +G S+G GFV F+  E+A  ALA++
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 193 NGKMIVSKPLYVAVAQRK 210
             K +  + L + +A+R+
Sbjct: 62  KNKKLHGRILRLDIAERR 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAE 191
           NLY+  L  ++  ++L+ LFS +G I + +++ D   G+S+G GF+ F    EA RA+  
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 192 MNGK 195
           +NG 
Sbjct: 62  LNGT 65

This subfamily corresponds to the RRM2 of 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. Moreover, 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 = 79

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

 Score = 61.4 bits (150), Expect = 4e-12
 Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 4/75 (5%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEM 192
           L++  L  +  +E ++ LF E+G I    ++RD   G SKG  FV FS+ EEA +A+  +
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 193 NGKMI---VSKPLYV 204
           +GK+     S+PL V
Sbjct: 62  HGKVTMPGASRPLQV 76

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|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 = 61.1 bits (149), Expect = 4e-12
 Identities = 31/75 (41%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           VFV N+    T+E L +IF E G + S  ++ D D GK K +GF  FE+ + AA A+  L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 90  NGKKFDDREWYVGKA 104
           NG +F+ R   V  A
Sbjct: 61  NGYEFNGRALRVDFA 75

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

>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 61.2 bits (149), Expect = 5e-12
 Identities = 21/65 (32%), Positives = 38/65 (58%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           NLYI NL   +D++ L+ +   +G + S +++RD  G S+G GF    + E+    +++ 
Sbjct: 2   NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKF 61

Query: 193 NGKMI 197
           NGK +
Sbjct: 62  NGKYL 66

This subfamily corresponds to the RRM2 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, they 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 = 79

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

 Score = 61.1 bits (149), Expect = 6e-12
 Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 8/73 (10%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           +FV +L    TDE L + F +Y +   A V+RD   GKSK +GFV+F + +D  KA++ +
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 90  NGKKFDDREWYVG 102
           NGK       YVG
Sbjct: 69  NGK-------YVG 74

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

 Score = 61.1 bits (149), Expect = 6e-12
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 6/70 (8%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMR--DPSG----ISKGSGFVAFSTPEEASR 187
           L++KNL     +E LK+ F + G + S  + +  DP G    +S G GFV F + E A +
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 188 ALAEMNGKMI 197
           AL  + G ++
Sbjct: 63  ALKRLQGTVL 72

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|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 60.7 bits (148), Expect = 6e-12
 Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEF-GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L +KNL  S+ + +LKE FS+  G IT  K++R   G S+   F+ + T EEA +A    
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 193 NGKMI 197
           N   I
Sbjct: 63  NNTYI 67

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 60.4 bits (147), Expect = 8e-12
 Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 2/81 (2%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAV-VMRDGD-GKSKCFGFVNFENADDAAKAVE 87
           N+F+ NLD    ++ L   F  +G I     +MRD D G SK F F+++++ + +  A+E
Sbjct: 3   NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 88  ALNGKKFDDREWYVGKAQKKS 108
           A+NG+   +R   V  A KK 
Sbjct: 63  AMNGQYLCNRPITVSYAFKKD 83

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 83

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

 Score = 60.2 bits (147), Expect = 9e-12
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 90
          +V +L    T+  L +IF   G + S  V RD    +S  + +VNF+N  DA +A++ LN
Sbjct: 3  YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

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

 Score = 60.3 bits (147), Expect = 9e-12
 Identities = 22/68 (32%), Positives = 36/68 (52%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + V NL    T+EDL+++FG  G +    +  D  G+S+    V FE  +DA +A++  N
Sbjct: 3  LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 91 GKKFDDRE 98
          G   D + 
Sbjct: 63 GVLLDGQP 70

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

 Score = 59.9 bits (146), Expect = 1e-11
 Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 1/60 (1%)

Query: 136 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNG 194
           + NL +  D++ L+ELF  FG I+   + +D  +G S+G  FV F T E+A RA+ ++NG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

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

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 23/63 (36%), Positives = 37/63 (58%)

Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
          VKNL +   ++ L+K+F  +GTIT   +    DGK + FGFV ++  ++A KA++  N  
Sbjct: 5  VKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNS 64

Query: 93 KFD 95
            D
Sbjct: 65 FID 67

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|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 = 59.9 bits (146), Expect = 1e-11
 Identities = 28/64 (43%), Positives = 43/64 (67%), Gaps = 1/64 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          +FV  L ++ T+ED++ +F EYG I    ++RD D G+SK   FV F + ++A KA+EAL
Sbjct: 2  LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 90 NGKK 93
          +GK 
Sbjct: 62 HGKV 65

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

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

 Score = 60.1 bits (146), Expect = 1e-11
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 7/78 (8%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
            +FV NL+ + T+E+L++ F  YG +    + R   G+   + FV F N D A +A  A+
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 90  NGKKFDDREWYVGKAQKK 107
           +G+       Y+G+ Q K
Sbjct: 64  SGQ-------YIGRNQIK 74

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

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

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 23/61 (37%), Positives = 34/61 (55%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L + NL   + D+ +KELF+EFG +    V  D SG S G+  V F    +A +A+ + N
Sbjct: 3   LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYN 62

Query: 194 G 194
           G
Sbjct: 63  G 63

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

 Score = 59.9 bits (146), Expect = 1e-11
 Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L++  L  +++ + LKE+FS +GT+    +  D    + +G  +V F +PE+A +A+  M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 193 NGKMI 197
           +G  I
Sbjct: 61  DGGQI 65

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

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 28/68 (41%), Positives = 41/68 (60%), Gaps = 7/68 (10%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          VFV NLD S  +++L+K+F + G IT   ++++  GKSK + +V FEN +      EAL 
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEE---SVQEAL- 57

Query: 91 GKKFDDRE 98
           K   DRE
Sbjct: 58 -KL--DRE 62

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

 Score = 58.6 bits (142), Expect = 3e-11
 Identities = 23/63 (36%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
          N+ V  L ++ T ++++ +F   G I S  ++RD   G+S  +GFVN+ + +DA KA+  
Sbjct: 3  NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

Query: 89 LNG 91
          LNG
Sbjct: 63 LNG 65

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

 Score = 58.7 bits (142), Expect = 3e-11
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
          N+FV +L    TD  L   F  + + + A VM D   G+S+ +GFV+F +  DA  A+  
Sbjct: 1  NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 89 LNGKKFDDR 97
          +NGK    R
Sbjct: 61 MNGKWLGSR 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|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 = 58.5 bits (142), Expect = 3e-11
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEM 192
           L+++NL  +  +E+L+ELF  FG I+   +  D     SKG  FV+F  PE A +A +E+
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 193 NGKMIVSKPLYV 204
           +G +   + L+V
Sbjct: 62  DGSIFQGRLLHV 73

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

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNG 91
          V NL   TT +DL+++F +YG +    + RD    +S+ F FV F +  DA  A++A++G
Sbjct: 3  VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 92 KKFDDRE 98
          K+ D RE
Sbjct: 63 KELDGRE 69

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

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 134 LYIKNL-GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L++  L     D   L++LFS+ G  T C++   P+G  +G  FV ++T E+A  A   +
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQAL 64

Query: 193 NGKMIVSKPLYVA 205
           NG  +   P+ V+
Sbjct: 65  NGHSLQGSPIRVS 77

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

 Score = 58.6 bits (142), Expect = 3e-11
 Identities = 26/61 (42%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVE 87
            +FV  L+  T+D  L++ F  YG +T  VVM D + K S+ FGF+ F +AD+A +A+E
Sbjct: 3  CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

Query: 88 A 88
          A
Sbjct: 63 A 63

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

 Score = 58.7 bits (142), Expect = 4e-11
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++  L    ++  ++ +F+ FG+I  C V+RD +G S+G  FV F++ + A  A+  M+
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63

Query: 194 GKMIV---SKPLYVAVA 207
               +   S PL V  A
Sbjct: 64  HSQTMEGCSSPLVVKFA 80

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 58.6 bits (142), Expect = 4e-11
 Identities = 28/68 (41%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          +FV+NL  S  ++DL+K+F ++G ++   V  D   GKSK F +V F + +DA KA + L
Sbjct: 5  LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 90 NGKKFDDR 97
          +GK F  R
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|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 58.4 bits (142), Expect = 4e-11
 Identities = 29/76 (38%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS----GFVAFSTPEEASRA 188
            L+I NL   + +  L +LFS++G I     +   SG  KG      FV F T EEA +A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 189 LAEMNGKMIVSKPLYV 204
           L  +NGK  + K L V
Sbjct: 61  LKSLNGKTALGKKLVV 76

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

 Score = 58.0 bits (141), Expect = 5e-11
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
           +++  L     D+ L++ FS+FG I    V+ D  +G S+G GFV F   E A RA  + 
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 193 NGKMIVSKPLYVAVA 207
           N  +I  +   V +A
Sbjct: 63  N-PIIDGRKANVNLA 76

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|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 = 58.0 bits (141), Expect = 5e-11
 Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            +Y+ NL   + +E+L+  FS FG I   +V +D     KG  FV F T E A+ A+  +
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 193 NGKMI 197
           NG  I
Sbjct: 57  NGTSI 61

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

 Score = 58.2 bits (141), Expect = 6e-11
 Identities = 22/63 (34%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
          N+ +  L ++ TDE+ + +F   G + +  ++RD   G S  FGFV++++A+DA +A+  
Sbjct: 2  NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 89 LNG 91
          LNG
Sbjct: 62 LNG 64

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

 Score = 58.3 bits (142), Expect = 6e-11
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 33 VKNLDESTTDEDLKKIFGEYG--TITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          ++ LD  TT+ED+ +         I    ++RD   G S+ F FV F + +DA + ++AL
Sbjct: 7  LRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDAL 66

Query: 90 NGK---KFDDRE 98
          N       D R 
Sbjct: 67 NNLDPFVIDGRV 78

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 57.9 bits (140), Expect = 6e-11
 Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 134 LYIKNLGDSIDDEKLKELF-SEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           +++ +L   +++  L  LF S F +  S K+M DP +G+S+G GFV FS   +  RAL E
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 192 MNGKMIVSKPLYVAVA 207
           M G     +P+ ++ A
Sbjct: 64  MQGVYCGGRPMRISTA 79

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

 Score = 57.7 bits (140), Expect = 7e-11
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV--- 86
          +FV  L E  T+EDL++ F +YG + S  ++ D + GK + F FV F++ D   K V   
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61

Query: 87 -EALNGKKFD 95
             +NG + +
Sbjct: 62 YHTINGHRVE 71

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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 58.2 bits (140), Expect = 7e-11
 Identities = 26/69 (37%), Positives = 42/69 (60%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           NLYI NL  S+D+++L+ +   FG + S +++RD SG S+G GF    + E+    ++  
Sbjct: 2   NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHF 61

Query: 193 NGKMIVSKP 201
           NGK I + P
Sbjct: 62  NGKFIKTPP 70

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has 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. MSSP-1 contains 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 as well as induction of apoptosis. . Length = 85

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

 Score = 57.8 bits (140), Expect = 7e-11
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             + V N+     D DL+++FG++G I    ++ +  G SK FGFV F N+ DA +A E 
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREK 59

Query: 89  LNGKKFDDREWYVGKA 104
           L+G   + R+  V  A
Sbjct: 60  LHGTVVEGRKIEVNNA 75

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

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

 Score = 58.0 bits (141), Expect = 8e-11
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 86
          F  +FV  L+  TT+  L++ F EYG I    ++RD   GK + + F+ FE+  D   A 
Sbjct: 1  FKTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAY 60

Query: 87 EALNGKKFDDR 97
          +  +GKK D R
Sbjct: 61 KYADGKKIDGR 71

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

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +Y+ NLG      +L++ F ++G + S  V R+P G      FV F  P +A  A+  ++
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGF----AFVEFEDPRDAEDAVRALD 57

Query: 194 GKMIVSKPLYVAVAQR 209
           G+ I    + V +++ 
Sbjct: 58  GRRICGNRVRVELSRG 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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          + V  L  +   + LK+IF  YGT+    + +       + + +V FE+ +DA KA++ +
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 90 NGKKFDDRE 98
          +G + D +E
Sbjct: 61 DGGQIDGQE 69

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

 Score = 57.2 bits (139), Expect = 1e-10
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFG--TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
           L ++ L     +E + +  S      I   +++RD  +G S+G  FV F + E+A++ + 
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 191 EMNGKM 196
            +N   
Sbjct: 65  ALNNLD 70

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|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 23/63 (36%), Positives = 35/63 (55%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++  L     ++ ++ LF  FGTI  C ++R P G SKG  FV FS+  EA  A+  ++
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63

Query: 194 GKM 196
           G  
Sbjct: 64  GSQ 66

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being 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, being 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 a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 3/71 (4%)

Query: 140 GDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV 198
           G S+ ++ L+E F+ FG I    V++D  +  SKG  +V F+    A+RA+ EMNGK + 
Sbjct: 11  GKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLG 70

Query: 199 S--KPLYVAVA 207
              KPL V +A
Sbjct: 71  GDTKPLKVLIA 81

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 4/60 (6%)

Query: 148 LKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA 207
           L +LFS FG +   K+++       G  FV FST E A +A+  +NG +   +PL V  +
Sbjct: 1   LYKLFSPFGNVEKIKLLKK----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

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

 Score = 57.3 bits (138), Expect = 1e-10
 Identities = 25/62 (40%), Positives = 40/62 (64%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +F+ NLD + T+ DL++ F  +G IT   + R G G++  +GF+ FEN D A +A  A++
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69

Query: 91 GK 92
          GK
Sbjct: 70 GK 71

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

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

 Score = 57.4 bits (138), Expect = 1e-10
 Identities = 31/84 (36%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 189
           G  ++I NLG   D+  L ++F  FG +T+ KV+RD  +   KG GFV  +  EEA+ A+
Sbjct: 1   GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60

Query: 190 AEMNGKMIVSKPLYVAVAQRKEER 213
           A +NG  +  K L V+    K  +
Sbjct: 61  ASLNGYRLGDKILQVSFKTSKSHK 84

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

 Score = 57.4 bits (138), Expect = 1e-10
 Identities = 30/81 (37%), Positives = 44/81 (54%), Gaps = 1/81 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           +FV NL     +  L ++FG +G +T+  V+RD    K K FGFV   N D+AA A+ +L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 90  NGKKFDDREWYVGKAQKKSER 110
           NG +  DR   V     K+ +
Sbjct: 66  NGYRLGDRVLQVSFKTNKTHK 86

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

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 7/81 (8%)

Query: 129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 188
            +G  LY+   G  + +E LK+ FS FG I +  + ++     K  GFV F   E A RA
Sbjct: 2   RKGNTLYVH--GYGLTEEILKKAFSPFGNIINISMEKE-----KNCGFVTFEKMESADRA 54

Query: 189 LAEMNGKMIVSKPLYVAVAQR 209
           +AE+NG  +    L V++A++
Sbjct: 55  IAELNGTTVQGVQLKVSLARK 75

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 57.0 bits (138), Expect = 1e-10
 Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +FV  L    T+E+ K+ F ++G +  A +M+D D G+S+ FGFV F++ + A + V + 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60

Query: 90  NGKKFDDREWYVGKA 104
              +   ++  V +A
Sbjct: 61  GMLELGGKQVEVKRA 75

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|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 134 LYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           LYI NL + I  ++LK     LFS+FG +      +      +G  FV F   E A+ AL
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLK--MRGQAFVVFKDVESATNAL 59

Query: 190 AEMNGKMIVSKPLYVAVA 207
             + G     KP+ +  A
Sbjct: 60  RALQGFPFYDKPMRIQYA 77

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains 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. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

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

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 27/68 (39%), Positives = 41/68 (60%), Gaps = 3/68 (4%)

Query: 144 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPL 202
            +E+L++ FS FG++   K++ D +G+SKG GFV F T E+A + LA   G +    K L
Sbjct: 15  TEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAM--GNLNFRGKKL 72

Query: 203 YVAVAQRK 210
            +  A RK
Sbjct: 73  NIGPAIRK 80

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

 Score = 56.8 bits (137), Expect = 2e-10
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          +FV+NL  S T EDL   F +   I  AVV+ D + G+S+ +GFV F   +DA +A+  L
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 90 NGKKFDDR 97
            KK   R
Sbjct: 62 KNKKLHGR 69

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 26/65 (40%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L++ +L   +D+  +   F+E G +TS K++R+  +G S G GFV F+T E A +AL  +
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 193 NGKMI 197
           NGK I
Sbjct: 62  NGKPI 66

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

 Score = 56.6 bits (136), Expect = 2e-10
 Identities = 29/81 (35%), Positives = 44/81 (54%), Gaps = 1/81 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           +FV NL   + +  L ++FG +G + +  V+RD    K K FGFV   N D+AA A+ +L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 90  NGKKFDDREWYVGKAQKKSER 110
           NG +  DR   V     K+ +
Sbjct: 66  NGYRLGDRVLQVSFKTNKTHK 86

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

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 23/74 (31%), Positives = 44/74 (59%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++  L  S+  E+L++LF + G + S +++ + SG  KG  +V +     AS+A+ +M+
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 194 GKMIVSKPLYVAVA 207
           G  I  K + VA++
Sbjct: 65  GTEIKEKTISVAIS 78

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|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 = 55.7 bits (135), Expect = 3e-10
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           V+V NL    T+E+L++ F  +G I    V +D     K + FV F+  + AA A+ A+
Sbjct: 2  TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 90 NGKKFDDR 97
          NG   + +
Sbjct: 57 NGTSINGQ 64

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

 Score = 62.0 bits (150), Expect = 3e-10
 Identities = 85/425 (20%), Positives = 151/425 (35%), Gaps = 70/425 (16%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
           V+V ++     ++ +++ F  +G I S  +  D   GK K F FV +E  + A  A+E +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 90  NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-LYIKNLGDSIDDEKL 148
           NG+    R   VG+             Q +  +    ++ +  N +Y+ ++   + +  +
Sbjct: 170 NGQMLGGRNIKVGRPSNM--------PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDI 221

Query: 149 KELFSEFGTITSCKVMRDPSGIS-KGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA 207
           K +F  FG I  C++ R P+G   KG GF+ ++  +  S A+A MN   +  + L V   
Sbjct: 222 KSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV--- 278

Query: 208 QRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPG-PSGLGQQFLYGQAPPAIIPPQAG 266
                                 G  V P   +  P   S +         P A     A 
Sbjct: 279 ----------------------GKCVTPPDALLQPATVSAI---------PAAAAVAAAA 307

Query: 267 FGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPP 326
              +      +  A    P    P           G +      ++  + +P +P   P 
Sbjct: 308 ATAKIMAAEAVAGAAVLGPRAQSPATPSSSLPTDIGNKAVVSSAKKEAEEVPPLPQAAPA 367

Query: 327 RGHAYRYPLGRNMQDFPFDMGAGSMLPVPV-DMGAGIPRRDASVGQPMPITALSTALANA 385
                       ++  P +      +P PV   G  IP   A  G   P     + LA+ 
Sbjct: 368 V-----------VKPGPME------IPTPVPPPGLAIPSLVAPPGLVAPTEINPSFLASP 410

Query: 386 SPEQQRTLLGESLYPLVEQL------ERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKV 439
             + +R  L  +   L + L      + D  ++   ML  M +      LE  +  K K 
Sbjct: 411 RKKMKREKLPVTFGALDDTLAWKEPSKEDQTSEDGKMLAIMGEAAAALALEPKKKKKEKE 470

Query: 440 AEAME 444
            E ++
Sbjct: 471 GEELQ 475

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

 Score = 55.8 bits (135), Expect = 3e-10
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          +FV NL     ++ + + FGEYG I+S  +      G+ K FG+V F + + A  A++AL
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 90 NGKKFDDR 97
           G     R
Sbjct: 61 GGTDLLGR 68

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

 Score = 55.6 bits (135), Expect = 4e-10
 Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 193
           ++ NL   I++E+L++ F + G + + +++RD  +GI KG G+V F T +  + AL    
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62

Query: 194 GKM 196
            K+
Sbjct: 63  IKL 65

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

 Score = 55.3 bits (134), Expect = 4e-10
 Identities = 26/64 (40%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           N+YI+ L  +  DE L++L   FG I S K + D  +   KG GFV F +PE A +A+  
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

Query: 192 MNGK 195
           +NG+
Sbjct: 62  LNGR 65

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

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 56.2 bits (135), Expect = 4e-10
 Identities = 26/69 (37%), Positives = 41/69 (59%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           NLYI NL  S+D+++L+ +   FG + S +++RD SG S+G GF    + E+    +   
Sbjct: 2   NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITHF 61

Query: 193 NGKMIVSKP 201
           NGK I + P
Sbjct: 62  NGKYIKTPP 70

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has 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. MSSP-2 contains 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 as well as induction of apoptosis. . Length = 86

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 55.9 bits (135), Expect = 4e-10
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGT----ITSAVVMRDGDGKSKCFG--FVNFENADDAAK 84
           V++ NL  S+++EDL++   ++      I S  V      + +  G  +  F + + A K
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61

Query: 85  AVEALNGKKFDDREWYV 101
            V+ LNGK F +R+ +V
Sbjct: 62  VVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 55.8 bits (135), Expect = 4e-10
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           +FV  L    T E+L + F  +G I    +++  +  +  F F+ FE    AA+AVE+ N
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN-AFAFIKFEREQAAARAVESEN 64

Query: 91  GKKFDDREWYV 101
                ++  +V
Sbjct: 65  HSMLKNKTMHV 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|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 = 55.6 bits (134), Expect = 5e-10
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
           L+I  L    +++ L+++FS++G I+   V++D  +  S+G GFV F  P++A  A+  M
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 193 NGKMIVSKPLYVAVAQR 209
           NGK +  + + V  A +
Sbjct: 63  NGKSVDGRQIRVDQAGK 79

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

 Score = 55.3 bits (134), Expect = 5e-10
 Identities = 26/67 (38%), Positives = 37/67 (55%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + V NLD   +D+D+K++F E+G +  A V  D  G+S     V FE   DA KA++  N
Sbjct: 3  LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYN 62

Query: 91 GKKFDDR 97
          G   D R
Sbjct: 63 GVPLDGR 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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 55.3 bits (134), Expect = 6e-10
 Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 45 LKKIFGE--YGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD 95
          L+KIF +   G I    +  D  GK+K + FV F   ++A +AV+ALNG K D
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLD 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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 55.2 bits (133), Expect = 7e-10
 Identities = 26/68 (38%), Positives = 40/68 (58%)

Query: 143 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL 202
            ++  L++ FS++GT+   K++ D +G+SKG GFV F T E+A + L E N      K L
Sbjct: 14  TNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEANRLCFRDKKL 73

Query: 203 YVAVAQRK 210
            +  A RK
Sbjct: 74  NIGQAIRK 81

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|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 55.0 bits (132), Expect = 7e-10
 Identities = 27/71 (38%), Positives = 39/71 (54%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           +FV NLD     + LK++F   GT+  A +  D DGKS+  G V FE   +A +A+   N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 91  GKKFDDREWYV 101
           G+   DR  +V
Sbjct: 63  GQFLFDRPMHV 73

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 55.0 bits (132), Expect = 7e-10
 Identities = 27/63 (42%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 88
          N+F+ +L +  TD DL + F  +G + SA V  D     SKCFGFV+++N D A  A++A
Sbjct: 6  NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQA 65

Query: 89 LNG 91
          +NG
Sbjct: 66 MNG 68

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

 Score = 54.9 bits (132), Expect = 7e-10
 Identities = 25/63 (39%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
          N+F+ +L +   D +L ++F  +G + SA V  D    +SKCFGFV+F+N   A  A++A
Sbjct: 6  NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

Query: 89 LNG 91
          +NG
Sbjct: 66 MNG 68

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

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

 Score = 55.0 bits (133), Expect = 8e-10
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITS----CKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           +Y++NL   +D++ L+ +FS+FG + S     K       ++ G  FV F     A  AL
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 190 AEMNGKMIVSKPLYVA 205
            ++NG  +  + + V+
Sbjct: 63  -QLNGTELGGRKISVS 77

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

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

 Score = 55.1 bits (132), Expect = 8e-10
 Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           +F+ NL +   +  L ++FG +G +T+  V+RD    K K FGFV   N ++AA A+ +L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 90  NGKKFDDREWYVGKAQKKSER 110
           NG +  D+   V     KS +
Sbjct: 64  NGYRLGDKILQVSFKTSKSHK 84

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 55.3 bits (134), Expect = 8e-10
 Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 16/74 (21%)

Query: 33 VKNLDESTTDEDLKKIF---------GEYGTITSAVVMRD-------GDGKSKCFGFVNF 76
          ++NL +S  ++ LK++F          +   I    +MRD       G GKSK +GFV F
Sbjct: 5  IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64

Query: 77 ENADDAAKAVEALN 90
           N + A KA+ ALN
Sbjct: 65 TNHEHALKALRALN 78

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

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

 Score = 55.1 bits (132), Expect = 8e-10
 Identities = 29/77 (37%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  E+LK LF   G I SCK++RD  +G S G GFV +  P++A +A+  
Sbjct: 6   NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K + V+ A+
Sbjct: 66  LNGLRLQTKTIKVSYAR 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|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 55.0 bits (133), Expect = 9e-10
 Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 145 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMI 197
           DE L+ +FS FG I SC+V+RD  +G S    F+ F T E+   A  +M+  +I
Sbjct: 17  DEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLI 70

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

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L++ NL    D++ + E F E+G I+S ++  DP SG  KG G+V FS+ E A  AL  +
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 193 NGKMIVSKPL 202
            G  ++ +P+
Sbjct: 61  GGTDLLGRPV 70

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

 Score = 54.9 bits (132), Expect = 1e-09
 Identities = 28/80 (35%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 29  NNVFVKNLDESTTD-EDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
             + ++NL  S      LKKIFG YG +  A + R   GK   F FV  +   +A  A+E
Sbjct: 1   PKLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALE 60

Query: 88  ALNGKKFDDR----EWYVGK 103
             NG + D R    +W V K
Sbjct: 61  NTNGLEIDGRPVAVDWAVQK 80

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

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 54.7 bits (131), Expect = 1e-09
 Identities = 24/69 (34%), Positives = 42/69 (60%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           NLYI NL  S+D+++L+ +   FG + S +++RD +G+S+G GF    + E+    +   
Sbjct: 3   NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 193 NGKMIVSKP 201
           NGK + + P
Sbjct: 63  NGKYLKTPP 71

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It 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. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

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

 Score = 54.7 bits (131), Expect = 1e-09
 Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 1/68 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
          +FV NL     +  L ++FG +G +T+  V+RD    K K FGFV   N D+AA A+ +L
Sbjct: 4  IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 90 NGKKFDDR 97
          NG +  DR
Sbjct: 64 NGYRLGDR 71

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

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 24/58 (41%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
           L+I  L     D+ LK  FS++G IT C VM+DP +  S+G GFV F++  E   A+ 
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMN 59

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

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 5/72 (6%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA- 88
          +F+  L   TTD+ LK  F ++G IT  VVM+D + K S+ FGFV F +A +   A+ A 
Sbjct: 2  LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNAR 61

Query: 89 ---LNGKKFDDR 97
             ++G++ + +
Sbjct: 62 PHKVDGREVEPK 73

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|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 = 54.5 bits (132), Expect = 1e-09
 Identities = 24/59 (40%), Positives = 32/59 (54%), Gaps = 4/59 (6%)

Query: 43 EDLKKIFGEYGTITSAVVMRDGDGKSKCFG----FVNFENADDAAKAVEALNGKKFDDR 97
          ED+K+  G+YG + S V+ R         G    FV F + +DA KA  AL G+KFD R
Sbjct: 26 EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGR 84

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

 Score = 54.0 bits (130), Expect = 1e-09
 Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
           +YI +L     +++LK+ FS+FGT+ + +V R   +G SK  GF+ F  PE A+ A   M
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 193 NGKMIVSKPLYVAV 206
           N  +++ K L V V
Sbjct: 62  NNYLLMGKVLQVHV 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|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 = 54.0 bits (130), Expect = 1e-09
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 8/72 (11%)

Query: 31  VFVKNLDESTT-DEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           +FV   D  TT +ED++K+F  +G +     +R      K F FV FE+++DA KA+EAL
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVR-CDIR------KTFAFVEFEDSEDATKALEAL 54

Query: 90  NGKKFDDREWYV 101
           +G + D     V
Sbjct: 55  HGSRIDGSVLTV 66

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

 Score = 53.7 bits (129), Expect = 1e-09
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 7/71 (9%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           +FV N+DE T+ E+L+ +F  YG + S  VMR        F FV+      A +A+E LN
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ-------FAFVHLRGEAAADRAIEELN 55

Query: 91  GKKFDDREWYV 101
           G++   R+  V
Sbjct: 56  GRELHGRKLVV 66

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

 Score = 54.2 bits (130), Expect = 1e-09
 Identities = 27/78 (34%), Positives = 49/78 (62%), Gaps = 3/78 (3%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NLY+  L  ++  ++L++LFS++G I + +++RD  +G+S+G GF+ F    EA  A+  
Sbjct: 2   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 192 MNGKMIV--SKPLYVAVA 207
           +NG+     S+P+ V  A
Sbjct: 62  LNGQKPEGASEPITVKFA 79

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

 Score = 59.5 bits (144), Expect = 2e-09
 Identities = 37/124 (29%), Positives = 61/124 (49%), Gaps = 7/124 (5%)

Query: 28  FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 86
           F  ++V NL  + T+++L++IF  +G I    + RD + G+SK FGF+ F +A++A +A+
Sbjct: 186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEAL 245

Query: 87  EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 146
           E +NG +   R   VG AQ  +               E +DK Q +   +         E
Sbjct: 246 EVMNGFELAGRPIKVGYAQDSTYLLDAANTF------EDIDKQQQMGKNLNTEEREQLME 299

Query: 147 KLKE 150
           KL  
Sbjct: 300 KLDR 303

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

 Score = 54.0 bits (130), Expect = 2e-09
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           Q   L++  L     D  L+  F+ +G +T C VM DP +  S+G GF+ FS+ +EA  A
Sbjct: 1   QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

Query: 189 LAEM 192
           +   
Sbjct: 61  MEAQ 64

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 4/69 (5%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK----CFGFVNFENADDAAKA 85
           +++ NLD   T+  L K+F +YG I     +    G  K     + FV FE  ++A KA
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 86 VEALNGKKF 94
          +++LNGK  
Sbjct: 61 LKSLNGKTA 69

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

 Score = 53.6 bits (129), Expect = 2e-09
 Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ N+     D  L+++F +FG I   +++ +  G SKG GFV F+   +A RA  +++
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREKLH 61

Query: 194 GKMIVSKPLYVAVA 207
           G ++  + + V  A
Sbjct: 62  GTVVEGRKIEVNNA 75

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

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 5/71 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL + I +E+ KELFS++G ++   + ++     KG GF+   T   A +A AE++
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELD 58

Query: 194 GKMIVSKPLYV 204
           G M   + L V
Sbjct: 59  GIMRKGRQLRV 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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAE 191
           NLY+ NL   + +++L+++F  +G I  C ++RD S G+ +G  FV +   EEA  A++ 
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 192 MNGKMI--VSKPLYVAVA 207
           +NG +    + PL V  A
Sbjct: 62  LNGTIPPGSTMPLSVRYA 79

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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 53.9 bits (129), Expect = 2e-09
 Identities = 27/73 (36%), Positives = 40/73 (54%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           + VFV NLD     + LK++F   G +  A ++ D DGKS+  G V FE   +A +A+  
Sbjct: 1   STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISM 60

Query: 89  LNGKKFDDREWYV 101
            NG+   DR  +V
Sbjct: 61  FNGQLLFDRPMHV 73

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 53.7 bits (130), Expect = 2e-09
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 9/78 (11%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-------SGISKGSGFVAFSTPEEAS 186
           LY+KNL   + +E L  +F  F  + S    ++         G  KG  FV F + E A+
Sbjct: 4   LYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61

Query: 187 RALAEMNGKMIVSKPLYV 204
           +AL  +NG ++  KP+ +
Sbjct: 62  KALNLVNGYVLKGKPMVI 79

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

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

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           N++V  L  +T   DLK++F +YG +  A +V       ++CFGFV   + ++AAK ++ 
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 89  LNGKKFDDREWYV 101
           L+  +   R   V
Sbjct: 61  LHRTELHGRVISV 73

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

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 4/68 (5%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V V  L E  + +DLK    + G +T A V RD +G     G V F + +D  +A+  L+
Sbjct: 3  VVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEG----EGVVEFTSQEDMERALRKLD 58

Query: 91 GKKFDDRE 98
          G +F  R 
Sbjct: 59 GTEFRGRR 66

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +FV NL   TT+++L+  FG  G I    +M   D GK K F FV+FE  + A  A++  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK-- 58

Query: 90  NGKKFDDREWYVGKAQ 105
            GK  + R   V   +
Sbjct: 59  -GKHLNGRALRVEYGE 73

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +Y+ ++   + ++ +K +F  FG I SC +  DP +G  KG GF+ +  P+ A  A+A M
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 193 NG 194
           N 
Sbjct: 63  NL 64

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

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

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 32  FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 90
            V NL    TDE  +++   +G +    ++     G+SK +GFV + +   A KA   L+
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 91  GKKFDDREWYV 101
           GK+   R+  V
Sbjct: 63  GKQIGGRKLQV 73

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

 Score = 53.1 bits (128), Expect = 3e-09
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           ++V NLD + T++ L ++F + G I S  ++R+       + FV + +   AA A++ +N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEYYDHRSAAAALQTMN 58

Query: 91  GKKFDDREWYVGKA 104
           G+    +E  V  A
Sbjct: 59  GRLILGQEIKVNWA 72

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

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

 Score = 53.6 bits (128), Expect = 3e-09
 Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 189
           G  +++ NL    D+  L +LF  FG +T+ KV+RD  +   KG GFV  +  +EA+ A+
Sbjct: 1   GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60

Query: 190 AEMNGKMIVSKPLYVAVAQRKEER 213
           A +NG  +  + L V+    K+ +
Sbjct: 61  ASLNGYRLGDRVLQVSFKTSKQHK 84

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

 Score = 53.6 bits (128), Expect = 3e-09
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  ++L+ LFS  G + S K++RD  +G S G GFV +   ++A RA+  
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + SK + V+ A+
Sbjct: 63  LNGLRLQSKTIKVSYAR 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 53.6 bits (128), Expect = 3e-09
 Identities = 28/77 (36%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  E+ K LF   G I SCK++RD  +G S G GFV +  P +A +A+  
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K + V+ A+
Sbjct: 65  LNGLKLQTKTIKVSYAR 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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 4/68 (5%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
          ++V+NL    + E+L  +FG+YG I     +R G   +++   FV +E+  DA  A + L
Sbjct: 5  LYVRNLPFKISSEELYDLFGKYGAI---RQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61

Query: 90 NGKKFDDR 97
          +G    +R
Sbjct: 62 SGFNVANR 69

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

 Score = 52.8 bits (127), Expect = 3e-09
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V+      S    D+K++F   G +    ++       +   F+ FEN + A  A+E LN
Sbjct: 2  VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR---TVQPHAFITFENLEAAQLAIETLN 58

Query: 91 GKKFDDRE 98
          G   D   
Sbjct: 59 GASVDGNC 66

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

 Score = 52.7 bits (127), Expect = 4e-09
 Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
          N ++V ++    +++D+K +F  +G I S  +  D + GK K +GF+ +EN   A  A+ 
Sbjct: 1  NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 88 ALNGKKFD 95
          ++N   FD
Sbjct: 61 SMNL--FD 66

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

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA- 88
          +FV  L  +TT++D+KK F ++G +  A++M D    + + FGFV FE+ D   K  E  
Sbjct: 2  IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 89 ---LNGKK 93
             +N K 
Sbjct: 62 FHEINNKM 69

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

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 19/50 (38%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 143 IDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
             ++ LK+ FS FG +   +V +DP +G SKG GFV F+  E+  + L++
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

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

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

 Score = 53.0 bits (127), Expect = 4e-09
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 4/71 (5%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFEN---ADDAAKAV 86
          +F+  L+  TTD+ L++ FG++G +T   VMRD   G+S+ FGF+ F+     ++  K  
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 87 EALNGKKFDDR 97
            L+GK  D +
Sbjct: 61 HILDGKIIDPK 71

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 51.7 bits (125), Expect = 5e-09
 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 45 LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR 97
          L K+F  +G +    +++   G    F FV F   + A KAV+ LNG  F  R
Sbjct: 1  LYKLFSPFGNVEKIKLLKKKPG----FAFVEFSTEEAAEKAVQYLNGVLFGGR 49

(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|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 52.3 bits (125), Expect = 5e-09
 Identities = 25/71 (35%), Positives = 42/71 (59%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +++ NL   +  +KLKE+FS  GT+    +  D  G S+G G V F  P EA +A++  N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 194 GKMIVSKPLYV 204
           G+ +  +P++V
Sbjct: 63  GQFLFDRPMHV 73

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 52.8 bits (126), Expect = 5e-09
 Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L ++ T E+LK +FG  G I S  ++RD   G+S  +GFVN+ +  DA KA+  
Sbjct: 6   NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 89  LNGKKFDDREWYVGKAQ 105
           LNG +   +   V  A+
Sbjct: 66  LNGLRLQTKTIKVSYAR 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 52.8 bits (126), Expect = 5e-09
 Identities = 30/80 (37%), Positives = 45/80 (56%), Gaps = 1/80 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L ++ T E+ K +FG  G I S  ++RD   G+S  +GFVN+ + +DA KA+  
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 89  LNGKKFDDREWYVGKAQKKS 108
           LNG K   +   V  A+  S
Sbjct: 65  LNGLKLQTKTIKVSYARPSS 84

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

 Score = 52.6 bits (126), Expect = 5e-09
 Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 4/71 (5%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 191
           ++I  L     D+ L+E F +FG +T C VMRD  +G S+G GF+ F  P+  +  + + 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 192 --MNGKMIVSK 200
             ++GK+I  K
Sbjct: 61  HILDGKIIDPK 71

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

 Score = 52.4 bits (126), Expect = 5e-09
 Identities = 29/60 (48%), Positives = 36/60 (60%), Gaps = 5/60 (8%)

Query: 146 EKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALA----EMNGKMIVSK 200
           E L+E FS+FG I  C VMRDP+   S+G GFV FS P    + LA    E++GK I  K
Sbjct: 13  EGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKKIDPK 72

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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 52.3 bits (126), Expect = 6e-09
 Identities = 21/65 (32%), Positives = 40/65 (61%), Gaps = 1/65 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
          N++V  L ++ T ++L+ +F  YG I ++ ++ D   G S+  GF+ F+   +A +A++A
Sbjct: 2  NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 89 LNGKK 93
          LNG  
Sbjct: 62 LNGTI 66

This subfamily corresponds to the RRM2 of 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. Moreover, 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 = 79

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

 Score = 52.2 bits (126), Expect = 7e-09
 Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 8/68 (11%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           GL+LY         +  L+E+FS +G I   +V+ D  +G S+G GFV F + E+A  A 
Sbjct: 6   GLSLYT-------TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAK 58

Query: 190 AEMNGKMI 197
             +NG  I
Sbjct: 59  ERLNGMEI 66

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

 Score = 51.8 bits (125), Expect = 7e-09
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 7/71 (9%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL D+   E+L+ LF ++GT+T C V+++        GFV     E+A  A+  +N
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN-------YGFVHMEEEEDAEDAIKALN 54

Query: 194 GKMIVSKPLYV 204
           G   + K + V
Sbjct: 55  GYEFMGKRINV 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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 51.9 bits (124), Expect = 7e-09
 Identities = 24/71 (33%), Positives = 43/71 (60%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +++ NL   +  +KLKE+FS  G +    ++ D  G S+G G V F  P EA +A++  N
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFN 62

Query: 194 GKMIVSKPLYV 204
           G+++  +P++V
Sbjct: 63  GQLLFDRPMHV 73

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 52.0 bits (125), Expect = 8e-09
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 5/64 (7%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          NV++ N+D+S T+E L+  F +YG I S   +R    +  C  FVNF N  +A KA++ +
Sbjct: 5  NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLR----EKNC-AFVNFTNISNAIKAIDGV 59

Query: 90 NGKK 93
              
Sbjct: 60 KSHP 63

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

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

 Score = 51.9 bits (124), Expect = 8e-09
 Identities = 28/65 (43%), Positives = 39/65 (60%), Gaps = 2/65 (3%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FVK L E TT+E LK+ F   G+I + +V     G SK FGFV+F + +DA  A EA+ 
Sbjct: 3  LFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAME 60

Query: 91 GKKFD 95
            + D
Sbjct: 61 DGEID 65

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 = 51.8 bits (125), Expect = 8e-09
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 6/70 (8%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL--- 189
           LY+  L + +D++ L   F  FG I   ++  D  +   +G  FV F  PE+A+ A+   
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 190 --AEMNGKMI 197
             +E+ G+ I
Sbjct: 61  NESELFGRTI 70

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|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 52.1 bits (125), Expect = 9e-09
 Identities = 22/60 (36%), Positives = 36/60 (60%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 91
          FV  L +  T++D++++F  +GTI    ++R  DG SK   FV F +  +A  A+ AL+G
Sbjct: 5  FVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHG 64

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being 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, being 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 a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 51.3 bits (123), Expect = 9e-09
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY++       +  ++E+FS +G +   K++           FV F + E A RA   ++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI-------SNFAFVEFESLESAIRAKDSVH 54

Query: 194 GKMIVSKPLYV 204
           GK++ + PLYV
Sbjct: 55  GKVLNNNPLYV 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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 22/71 (30%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +++ NL  S+ +++L++LFS+ G IT  +++++  G SKG  +V F   E    AL  ++
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALK-LD 60

Query: 194 GKMIVSKPLYV 204
            ++I  +P++V
Sbjct: 61  RELIKGRPMFV 71

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

 Score = 51.6 bits (124), Expect = 1e-08
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAV 86
           + +F+    +S T++DL++ F  +G I    V++D   K SK   +V F  A  AA+A+
Sbjct: 3  NSRLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61

Query: 87 EALNGKKFDDRE 98
          E +NGK      
Sbjct: 62 EEMNGKCLGGDT 73

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

 Score = 51.6 bits (123), Expect = 1e-08
 Identities = 27/84 (32%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 189
           G  +++ NL    D+  L ++F  FG +T+ KV+RD  +   KG GFV  +  +EA+ A+
Sbjct: 3   GWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 190 AEMNGKMIVSKPLYVAVAQRKEER 213
           A +NG  +  + L V+    K  +
Sbjct: 63  ASLNGYRLGDRVLQVSFKTNKTHK 86

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 30/76 (39%), Positives = 40/76 (52%), Gaps = 16/76 (21%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGT---------ITSCKVMRD-------PSGISKGSGFV 177
           L I+NL  S+D++KLKELF +  +         I   K+MRD         G SKG GFV
Sbjct: 3   LSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFV 62

Query: 178 AFSTPEEASRALAEMN 193
            F+  E A +AL  +N
Sbjct: 63  EFTNHEHALKALRALN 78

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

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

 Score = 51.5 bits (123), Expect = 1e-08
 Identities = 22/65 (33%), Positives = 44/65 (67%), Gaps = 1/65 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
          N++V  L ++ T ++L+++F +YG I ++ ++RD   G S+  GF+ F+   +A +A++ 
Sbjct: 2  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 89 LNGKK 93
          LNG+K
Sbjct: 62 LNGQK 66

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

 Score = 51.5 bits (123), Expect = 1e-08
 Identities = 23/67 (34%), Positives = 39/67 (58%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV NL+    +E L ++F + G +T   + +D +GK K FGFV F++++    A+  LN
Sbjct: 4  LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 91 GKKFDDR 97
          G +   R
Sbjct: 64 GIRLYGR 70

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

 Score = 51.4 bits (123), Expect = 1e-08
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 7/68 (10%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV N+  + T ++L+ +F E+G +     ++D       + FV+ E  ++A  A+EALN
Sbjct: 3  IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD-------YAFVHMEREEEALAAIEALN 55

Query: 91 GKKFDDRE 98
          GK+   R 
Sbjct: 56 GKEVKGRR 63

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

 Score = 53.5 bits (128), Expect = 1e-08
 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +F+  L   T D  L+  F  +G +  A V+ D + G+S+ FGFVNF +   A  A+  +
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 90  NGKKFDDREWYVGKAQKKS 108
           +GK+ + R   V  A  + 
Sbjct: 97  DGKELNGRHIRVNPANDRP 115

Length = 144

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

 Score = 53.5 bits (128), Expect = 1e-08
 Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
           L+I  L    DD  L++ F+ FG +   KV+ D  +G S+G GFV F+    A+ A++EM
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 193 NGKMIVSKPLYVAVAQRK 210
           +GK +  + + V  A  +
Sbjct: 97  DGKELNGRHIRVNPANDR 114

Length = 144

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           VFV N+ E  +D+ ++K+  + G + S   V     GK K FGF  FE+ + A +A+  L
Sbjct: 3   VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 90  NGKKFDDREWYV 101
           NG +   ++  V
Sbjct: 63  NGLELGGKKLLV 74

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|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 = 51.5 bits (124), Expect = 1e-08
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
           ++I  L + + ++++KEL   FG + +  +++D  +G+SKG  F  +  P    +A+A +
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 193 NGKMIVSKPLYVAVA 207
           NG  +  K L V  A
Sbjct: 63  NGMQLGDKKLTVQRA 77

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

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

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
           +++  + +   +E + + F+EFG I +  +  D  +G  KG   + + T +EA  A+  +
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 193 NGKMIVSKPLYV 204
           NGK ++ + + V
Sbjct: 69  NGKELLGQTISV 80

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

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 24/68 (35%), Positives = 38/68 (55%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV NLD   T+E L ++F + G +    + +D +GK K F FV F++      A++ LN
Sbjct: 4  LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 91 GKKFDDRE 98
          G +   RE
Sbjct: 64 GIRLFGRE 71

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

 Score = 51.5 bits (123), Expect = 1e-08
 Identities = 21/63 (33%), Positives = 39/63 (61%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          N+F+ NLD + ++ +L++ F +YG I   V+ R   G+   + F+ F+N D A +A  A+
Sbjct: 10 NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAM 69

Query: 90 NGK 92
          +G+
Sbjct: 70 SGR 72

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

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

 Score = 51.3 bits (122), Expect = 2e-08
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  E+ + LF   G I SCK++RD  +G S G GFV +  P++A +A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K + V+ A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          +++  L    T+ D+  +F +YG I    ++RD   GKSK F F+ +E+      AV+ L
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 90 NGKKFDDR 97
          NG K   R
Sbjct: 72 NGIKLLGR 79

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

 Score = 50.6 bits (122), Expect = 3e-08
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           + ++V N   S    D++ +F +YG I S         K++ F +V F + + AA AV  
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVAL 60

Query: 89  LNGKKFDDREWYV 101
           LNGK  +  +  V
Sbjct: 61  LNGKLGEGYKLVV 73

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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 6/82 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP------SGISKGSGFVAFSTPEEASR 187
           L++KNL  S  ++ L + F         +V   P        +S G GFV F T E+A  
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 188 ALAEMNGKMIVSKPLYVAVAQR 209
           AL  M+G ++    L V  + R
Sbjct: 63  ALKAMDGFVLDGHTLVVKFSHR 84

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 50.5 bits (121), Expect = 3e-08
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
          +F++NL  + T+EDL+K+F +YG ++   +  D    K K F FV +   + A KA   L
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 90 NGKKFDDR 97
          +G  F  R
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|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 50.2 bits (121), Expect = 3e-08
 Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 3/69 (4%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKC-FGFVNFENADDAAKAVEA 88
          ++V NL   TT+E + ++F   G I   ++M  D   K+ C F FV +   +DA  AV+ 
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKR-IIMGLDRFTKTPCGFCFVEYYTREDAENAVKY 59

Query: 89 LNGKKFDDR 97
          LNG K DDR
Sbjct: 60 LNGTKLDDR 68

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

 Score = 54.6 bits (131), Expect = 4e-08
 Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  E+++ LF+  G I SCK++RD   G S G GFV +  PE+A +A+  
Sbjct: 5   NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS 64

Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K + V+ A+
Sbjct: 65  LNGLRLQNKTIKVSYAR 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 54.6 bits (131), Expect = 4e-08
 Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           G  +++ NL    D+  L +LF  FG + + K++RD  +   KG GFV+ +  +EA+ A+
Sbjct: 269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAI 328

Query: 190 AEMNGKMIVSKPLYVAVAQRKEER 213
             +NG  + ++ L V+    K  R
Sbjct: 329 LSLNGYTLGNRVLQVSFKTNKAYR 352

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

 Score = 50.1 bits (119), Expect = 4e-08
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 1/84 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 189
           G  +++ NL    D+  L +LF  FG + + KV+RD  +   KG GFV  +  +EA+ A+
Sbjct: 3   GWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 190 AEMNGKMIVSKPLYVAVAQRKEER 213
           A +NG  +  + L V+    K  +
Sbjct: 63  ASLNGYRLGDRVLQVSFKTNKTHK 86

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

 Score = 50.0 bits (119), Expect = 4e-08
 Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           +G NL+I +L     D  L + F  FG + S KV  D  + +SK  GFV++  P+ A  A
Sbjct: 3   EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62

Query: 189 LAEMNGKMIVSKPLYV 204
           +  MNG  I +K L V
Sbjct: 63  IQAMNGFQIGTKRLKV 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|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 49.9 bits (119), Expect = 4e-08
 Identities = 30/76 (39%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRA 188
           +G NL+I +L     D +L ++F  FG + S KV  D  +  SK  GFV+F  P  A  A
Sbjct: 3   EGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAA 62

Query: 189 LAEMNGKMIVSKPLYV 204
           +  MNG  I  K L V
Sbjct: 63  IQAMNGFQIGMKRLKV 78

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

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

 Score = 50.0 bits (119), Expect = 4e-08
 Identities = 24/71 (33%), Positives = 37/71 (52%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL   + +E L ELF + G +T   + +D  G  K  GFV F   E    A+A +N
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 194 GKMIVSKPLYV 204
           G  +  +P+ V
Sbjct: 64  GIRLYGRPIKV 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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 50.1 bits (119), Expect = 4e-08
 Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L ++ T E+ + +FG  G I S  ++RD   G+S  +GFVN+ +  DA KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 89  LNGKKFDDREWYVGKAQKKS 108
           LNG +   +   V  A+  S
Sbjct: 64  LNGLRLQTKTIKVSYARPSS 83

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

 Score = 50.1 bits (119), Expect = 5e-08
 Identities = 25/57 (43%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           L+I  L     DE L+  F ++GT+T C VMRDP +  S+G GFV +S+ EE   A+
Sbjct: 5   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61

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

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

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 5/72 (6%)

Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
          +   +FV  L  + T+ DL+K F ++GT+T  VVM D + K  + FGF+ FE+ D   + 
Sbjct: 1  RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

Query: 86 V----EALNGKK 93
          V      +NGKK
Sbjct: 61 VNEHFHDINGKK 72

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

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 21/50 (42%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 39 STTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 87
          S T+EDL++ F E+G I    +++D   G+SK FG+V F     AA A+E
Sbjct: 11 SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

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

 Score = 49.7 bits (118), Expect = 5e-08
 Identities = 28/70 (40%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
          +VFV +L    T ED+K  F  +G I+ A V++D   GKSK +GFV+F N  DA  A+  
Sbjct: 3  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 89 LNGKKFDDRE 98
          + G+    R+
Sbjct: 63 MGGQWLGGRQ 72

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

 Score = 49.5 bits (118), Expect = 6e-08
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
          N++V NL    T+++L+KIF  YG I    ++RD   G  +   FV ++  ++A  A+ +
Sbjct: 2  NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 89 LNGKKFDDR 97
          LNG      
Sbjct: 62 LNGTIPPGS 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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 49.7 bits (118), Expect = 6e-08
 Identities = 27/70 (38%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
          +VFV +L    T +D+K  F  +G I+ A V++D   GKSK +GFV+F N  DA  A++ 
Sbjct: 3  HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 89 LNGKKFDDRE 98
          + G+    R+
Sbjct: 63 MGGQWLGGRQ 72

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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 49.7 bits (118), Expect = 6e-08
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L+I  +    ++  ++ +FS FG I  C+++R P G+S+G  FV F+T   A  A+  M+
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63

Query: 194 GKMIV---SKPLYVAVA 207
               +   S P+ V  A
Sbjct: 64  QAQTMEGCSSPIVVKFA 80

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), 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 binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 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 preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

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

 Score = 49.2 bits (118), Expect = 7e-08
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGE-YGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          +FV +L     D  L + F + Y +   A V+ D +G S+ +GFV F +  +  +A+  +
Sbjct: 4  LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEM 63

Query: 90 NG 91
           G
Sbjct: 64 QG 65

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 49.3 bits (117), Expect = 7e-08
 Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L ++ T ++L+ +F   G + SA ++RD   G S  +GFVN+ NA DA +A+  
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 89  LNGKKFDDREWYVGKAQ 105
           LNG +   +   V  A+
Sbjct: 63  LNGLRLQSKTIKVSYAR 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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 49.1 bits (118), Expect = 7e-08
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +YI +L     + +L++ FS+FGT+T  ++ R   +G SKG  FV F +PE A      M
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 193 NGKMIVSKPL 202
           N  ++  + L
Sbjct: 62  NNYLLFERLL 71

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|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 = 49.1 bits (118), Expect = 7e-08
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 33  VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
           VKNL   TT+E+L+++F ++G++   +++      S+    V F    DA KA ++L  K
Sbjct: 5   VKNLPFGTTEEELRELFEKFGSLG-RLLL----PPSRTIALVEFLEPSDARKAFKSLAYK 59

Query: 93  KFDDREWYVGKA 104
           +F     Y+  A
Sbjct: 60  RFKHVPLYLEWA 71

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

 Score = 48.8 bits (117), Expect = 8e-08
 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 5/61 (8%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          VFV  LD + T+++L+ +FG +G I   V +  G    K  GFV F +   A  A++ L 
Sbjct: 4  VFVGGLDPAVTEDELRSLFGPFGEIVY-VKIPPG----KGCGFVQFVHRAAAEAAIQQLQ 58

Query: 91 G 91
          G
Sbjct: 59 G 59

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

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

 Score = 48.9 bits (117), Expect = 9e-08
 Identities = 26/63 (41%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L+++NL  S  ++ L++LFS+FG ++   V  D  SG SKG  +V F  PE+A +A  E+
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 193 NGK 195
           +GK
Sbjct: 65  DGK 67

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

 Score = 48.9 bits (117), Expect = 9e-08
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 9/76 (11%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSC-----KVMRDPSGISKGSGFVAFSTPEEASRA 188
           L+I+NL  +  +E L++LFS++G ++       K+ + P    KG  FV +  PE A +A
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKP----KGFAFVTYMIPEHAVKA 60

Query: 189 LAEMNGKMIVSKPLYV 204
            AE++G +   + L++
Sbjct: 61  FAELDGTVFQGRLLHL 76

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

 Score = 49.2 bits (117), Expect = 9e-08
 Identities = 24/59 (40%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 40 TTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDR 97
          TT+ DL+++F  YG +    V+ D   G+S+ F FV FE  DD+ +A+E  NG + D R
Sbjct: 11 TTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGR 69

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

 Score = 49.3 bits (118), Expect = 9e-08
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           ++V+N+ ++T  +DL+++FG+YG I    +  D    + + F +V FE+  DA  A+  L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 90  NGKKFDDREWYVGKAQ 105
           +  +F  RE  +  AQ
Sbjct: 63  DRTRFLGREIEIQFAQ 78

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 190
           L L++  L     +E L+E+FS +G I   +++RD  +G SKG  FV +    +A RA  
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 191 EMNGKMIVSKPLYV 204
           + +  +I    ++V
Sbjct: 64  DAHKLVIDGSEIFV 77

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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 18/66 (27%), Positives = 33/66 (50%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          N+++ NL     ++DL+ +   YG + S  ++RD  G+S+  GF   E+ +     +   
Sbjct: 2  NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKF 61

Query: 90 NGKKFD 95
          NGK   
Sbjct: 62 NGKYLK 67

This subfamily corresponds to the RRM2 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, they 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 = 79

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 20/72 (27%), Positives = 34/72 (47%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L++ NL  +I +E+L+  F  +G +    + R P G      FV F   + A RA   M
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 193 NGKMIVSKPLYV 204
           +G+ I    + +
Sbjct: 64  SGQYIGRNQIKI 75

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

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

 Score = 48.7 bits (116), Expect = 1e-07
 Identities = 18/60 (30%), Positives = 35/60 (58%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV  L +   + D++ +F  +G+I    V+RD +G+S+   FV F +   A  A++A++
Sbjct: 4  LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA-- 88
          F+  L   TT E L++ F ++G I   +VMRD   K S+ FGFV F +     K +    
Sbjct: 2  FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGP 61

Query: 89 --LNGKKFD 95
            L+GKK D
Sbjct: 62 HELDGKKID 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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEM 192
           +++ N+ + + D+ +++L  + G + S K ++DPS G  K  GF  F  PE A RAL  +
Sbjct: 3   VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 193 NGKMIVSKPLYVAVAQR 209
           NG  +  K L V V  +
Sbjct: 63  NGLELGGKKLLVKVDAK 79

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

 Score = 48.5 bits (115), Expect = 1e-07
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
          +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV + + ++   A
Sbjct: 1  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60

Query: 86 VEA 88
          + A
Sbjct: 61 MNA 63

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

 Score = 49.3 bits (117), Expect = 1e-07
 Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 40 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 97
          TT+ DL+++F +YG I    ++ D   + S+ F FV FEN DDA +A E  NG + D R
Sbjct: 21 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 79

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          V+V+ L ++ T E LK +F +YGT+    + R    G  K F F+ FE  ++A KA + L
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 90 NGKKFDDREW 99
          N       + 
Sbjct: 62 NNPPETATDK 71

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

 Score = 48.9 bits (116), Expect = 1e-07
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 5/72 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           L+I  L     D+ L+E F ++GT+T C VMRDP +  S+G GFV +S  EE   A++  
Sbjct: 5   LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSAR 64

Query: 191 --EMNGKMIVSK 200
             +++G+++  K
Sbjct: 65  PHKVDGRVVEPK 76

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 8/70 (11%)

Query: 134 LYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           +++ NL  D +  E L+E+FS++G I    +        KG GFV F   E+A  A+A  
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL-------HKGYGFVQFDNEEDARAAVAGE 55

Query: 193 NGKMIVSKPL 202
           NG+ I  + L
Sbjct: 56  NGREIAGQKL 65

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

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 7/87 (8%)

Query: 126 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 185
           +DK+   ++++  L   +  E+L E FS  G I    +++  +  +  + F+ F   + A
Sbjct: 1   IDKY---SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFA-FIKFEREQAA 56

Query: 186 SRALAEMNGKMIVSKPLYVAVAQRKEE 212
           +RA+   N  M+ +K ++V   Q KE 
Sbjct: 57  ARAVESENHSMLKNKTMHV---QYKEI 80

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS-KGSGFVAFSTPEEASRALAEM 192
           +Y++ L  +   E LK +FS++GT+    + R       KG  F+ F TPEEA +A   +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 193 N 193
           N
Sbjct: 62  N 62

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|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 = 48.4 bits (116), Expect = 2e-07
 Identities = 18/63 (28%), Positives = 33/63 (52%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
            + V+N+    T ++L+++F  +G + S  + +  DG  + F FV F    +A  A+EA
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 89 LNG 91
          L  
Sbjct: 61 LKS 63

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|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 = 48.3 bits (115), Expect = 2e-07
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           VFV N+    T+E LK IF E G + S  ++ D + GK K +GF  +++ + A  A+  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 90  NGKKFDDREWYVGKA 104
           NG + + R+  V  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 53.3 bits (128), Expect = 2e-07
 Identities = 51/298 (17%), Positives = 92/298 (30%), Gaps = 43/298 (14%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE--A 88
           V V+NL +   + DL +    +G ++  +++       K    V FE+ + A   V    
Sbjct: 5   VHVRNLPQDVVEADLVEALIPFGPVSYVMML-----PGKRQALVEFEDEESAKACVNFAT 59

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQ--FEQAMKETVDKFQGLNLYIKNLGDSIDDE 146
                   +  +       + +E +  G   F+ A    V     L + ++N    I  +
Sbjct: 60  SVPIYIRGQPAFF---NYSTSQEIKRDGNSDFDSAGPNKV-----LRVIVENPMYPITLD 111

Query: 147 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV-------- 198
            L ++F+ +G +         +        V F +   A  A A +NG  I         
Sbjct: 112 VLYQIFNPYGKVLRIVTFTKNNVF---QALVEFESVNSAQHAKAALNGADIYNGCCTLKI 168

Query: 199 --SKPLYVAVAQRKEERRARLQAQFSQMRPVAMGP----SVPPRMPMYPPGPSGLGQQFL 252
             +KP  + V    ++ R          R   +        P  +  +P      G    
Sbjct: 169 EYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSH 228

Query: 253 YGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPV 310
            G   P     + G        P   P     P +    ++       P G  G G V
Sbjct: 229 GGPLAPLAGGDRMG--------PPHGPPSRYRPAYEAAPLAPAISSYGPAG-GGPGSV 277

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). Length = 481

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

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 25/67 (37%), Positives = 37/67 (55%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV NLD   T+E + ++F + G +    + +D DGK K F FVNF++      A+  LN
Sbjct: 4  LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 91 GKKFDDR 97
          G K   R
Sbjct: 64 GIKLYGR 70

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

 Score = 49.2 bits (117), Expect = 2e-07
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRAL 189
              L+++NL     +E L   FS+FG++     + D S G +KG+GFV F      +  L
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

Query: 190 A 190
            
Sbjct: 61  K 61

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++  L     +++++E+FS +G +    +MRD    S+G  FV +S+ E A  A+  +N
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 194 GKMIV---SKPLYVAVA 207
           G   +    +PL V  A
Sbjct: 62  GVYTMRGCDQPLIVRFA 78

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
          +FV N+D  TT E+L++ F   GTI    ++ D   G+ K F ++ F +      A+  L
Sbjct: 2  IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60

Query: 90 NGKKFDDRE 98
          N  +F  R+
Sbjct: 61 NESEFRGRQ 69

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

 Score = 52.3 bits (125), Expect = 3e-07
 Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 1/81 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           +FV NL   T +  L ++FG +G + +  ++RD    + K +GFV+  N D+AA A+ +L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 90  NGKKFDDREWYVGKAQKKSER 110
           NG    +R   V     K+ R
Sbjct: 332 NGYTLGNRVLQVSFKTNKAYR 352

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 51.6 bits (123), Expect = 3e-07
 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 189
           G NL +  L   + D +L  LF   G I +C++MRD  +G S G  FV F +  ++ RA+
Sbjct: 107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAI 166

Query: 190 AEMNGKMIVSKPLYVAVAQ 208
             +NG  + +K L V+ A+
Sbjct: 167 KNLNGITVRNKRLKVSYAR 185

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

>gnl|CDD|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 = 47.6 bits (114), Expect = 3e-07
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 193
           ++ N+     +E+L E+FSE G + S +++ D  +G  KG GF  F   E A+ A+  +N
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 194 GKMIVSKPLYV 204
           G     + L V
Sbjct: 62  GYEFNGRALRV 72

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          +++ +L     +++LKK F ++GT+ +  V R    G SK +GF+ F N + AA A +++
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 90 NG 91
          N 
Sbjct: 62 NN 63

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

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 10/73 (13%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKV---MRDPSGISKGSGFVAFSTPEEASRAL 189
           NL++  L  +     LK+LFS++G +   K+    R P   ++  GFV  ++ EEA++ +
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPG--ARCFGFVTMASVEEAAKCI 58

Query: 190 A-----EMNGKMI 197
                 E++G++I
Sbjct: 59  QHLHRTELHGRVI 71

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

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

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
          +FV  + E   +ED+   F E+G I +  +  D   G  K +  + +E   +A  A+E L
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 90 NGKKF 94
          NGK+ 
Sbjct: 69 NGKEL 73

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

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 21/71 (29%), Positives = 35/71 (49%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL   + +E L ELF + G +   K+ +DP+G  K   FV F        A+  +N
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 194 GKMIVSKPLYV 204
           G  +  + L +
Sbjct: 64  GIRLFGRELRI 74

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

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

 Score = 48.1 bits (114), Expect = 3e-07
 Identities = 30/87 (34%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           +G NL+I +L     D+ L ++F  FG + S KV  D  + +SK  GFV++  P  A  A
Sbjct: 6   EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 65

Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRA 215
           +  MNG  I  K L V + + K + + 
Sbjct: 66  IQAMNGFQIGMKRLKVQLKRSKNDSKP 92

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 22/68 (32%), Positives = 41/68 (60%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          ++V NLD   T++ LK+IF   G + +  ++ D + K   +GFV +  + DA  A++ LN
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 91 GKKFDDRE 98
          G++ ++ E
Sbjct: 61 GRQIENNE 68

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

 Score = 47.7 bits (113), Expect = 3e-07
 Identities = 22/65 (33%), Positives = 40/65 (61%), Gaps = 7/65 (10%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV+NL  + T+E L+K FG++G +     ++D       + F++F+  D A KA+E +N
Sbjct: 4  LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 56

Query: 91 GKKFD 95
          GK+ +
Sbjct: 57 GKELE 61

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

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 48.0 bits (115), Expect = 3e-07
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 19/86 (22%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITS----------------AVVMRDG--DGKSKCF 71
           VFV NL  +T  +DLKK+F ++G I S                   ++    D K    
Sbjct: 2  TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61

Query: 72 GFVNFENADDAAKAVEALNGKKFDDR 97
           +V F+  + A KA++ LNG +F+  
Sbjct: 62 AYVVFKEEESAEKALK-LNGTEFEGH 86

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

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +++  +   + +++L  LF + G I   ++M D SG+++G  FV ++  E A RA+ +++
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 194 GKMI-VSKPLYV 204
              I   K L V
Sbjct: 64  NYEIRPGKRLGV 75

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

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 25/57 (43%), Positives = 38/57 (66%), Gaps = 1/57 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 189
           L++ NL  ++  ++LKE FS+FG + SC V  D  +G+SKG GFV+FS+ +    AL
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENAL 58

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

 Score = 47.6 bits (113), Expect = 3e-07
 Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 10/84 (11%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV--- 86
           +FV  L     + DL + F ++G +  A V+ D   GK + FGFV F+N D A KA    
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61

Query: 87  -EALNGKKFDDREWYVGKAQKKSE 109
              +NG + +     V KA  K E
Sbjct: 62  FHPINGHRVE-----VKKAVPKEE 80

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

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV NL    T+E+ K++F +YG ++   + ++     K FGF+  +   +A KA   L+
Sbjct: 4  LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELD 58

Query: 91 GKKFDDRE 98
          G     R+
Sbjct: 59 GIMRKGRQ 66

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

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +++  L  ++ +++L+ LF  FG I   K+   P G  KG GFV F     A  A+ ++ 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKI---PPG--KGCGFVQFVHRAAAEAAIQQLQ 58

Query: 194 GKMIVSKPLYVA 205
           G +I    + ++
Sbjct: 59  GTIIGGSRIRLS 70

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

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 47.3 bits (112), Expect = 4e-07
 Identities = 25/71 (35%), Positives = 45/71 (63%), Gaps = 5/71 (7%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NLY+  L  ++  +++++LFS++G I + +++ D  +GIS+G GF+ F    EA  A+  
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 192 MNGKMIVSKPL 202
           +NG+    KPL
Sbjct: 63  LNGQ----KPL 69

This subgroup corresponds to the RRM2 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 = 81

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

 Score = 47.0 bits (112), Expect = 5e-07
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 10/71 (14%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           N+YI N+ DS+ +EKL+  FS++G I S   +R+     K   FV F+    A +A+  +
Sbjct: 5   NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLRE-----KNCAFVNFTNISNAIKAIDGV 59

Query: 193 NGKMIVSKPLY 203
                 S PL+
Sbjct: 60  K-----SHPLF 65

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

>gnl|CDD|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 = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L+I +L   + +E LK LF E+G I S  ++       +G  +V   T ++A RAL ++ 
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI-----PPRGCAYVCMETRQDAHRALQKLR 59

Query: 194 GKMIVSKPLYVAVAQRKE 211
              +  K + VA A  K 
Sbjct: 60  NVKLAGKKIKVAWAPNKG 77

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

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTIT--SAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 87
          ++V NL   TTDEDL+    E G +   S        +GKSK F +V F +   AA   E
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 88 ALNGKKFDDRE 98
           L G++F+ ++
Sbjct: 61 KLEGREFNGKK 71

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 47.0 bits (111), Expect = 5e-07
 Identities = 22/64 (34%), Positives = 42/64 (65%), Gaps = 1/64 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NLY+  L  ++  ++L++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  
Sbjct: 4   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 192 MNGK 195
           +NG+
Sbjct: 64  LNGQ 67

This subgroup corresponds to the RRM2 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 also regulates 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 = 81

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

 Score = 51.2 bits (122), Expect = 6e-07
 Identities = 25/65 (38%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 85
           K  N++V NL  + TD+ L  IFG+YG I    ++RD   G  +   FV F   ++A +A
Sbjct: 192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEA 251

Query: 86  VEALN 90
           + ALN
Sbjct: 252 ISALN 256

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

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

 Score = 46.9 bits (112), Expect = 6e-07
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 36 LDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKK 93
          L+    +  +   F E G +TS  ++R+   GKS  +GFV F   + A +A+++LNGK 
Sbjct: 7  LEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKP 65

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

 Score = 46.4 bits (111), Expect = 6e-07
 Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 8/63 (12%)

Query: 31 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          VFV NL+ +  + EDL++IF +YG I   + +  G      +GFV F+N +DA  AV   
Sbjct: 3  VFVGNLNTDKVSKEDLEEIFSKYGKIL-GISLHKG------YGFVQFDNEEDARAAVAGE 55

Query: 90 NGK 92
          NG+
Sbjct: 56 NGR 58

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

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

 Score = 47.0 bits (111), Expect = 6e-07
 Identities = 25/63 (39%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 88
          N+F+ +L +   D+DL ++F  +G + SA V  D     SKCFGFV+++N   A  A++A
Sbjct: 9  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQA 68

Query: 89 LNG 91
          +NG
Sbjct: 69 MNG 71

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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 47.0 bits (111), Expect = 6e-07
 Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
           L+I  L     +E L+  + ++G +T C VMRDP S  S+G GFV FS   E   A+A
Sbjct: 5   LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

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

 Score = 46.7 bits (111), Expect = 6e-07
 Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +Y+ ++   + ++ +++ FS FG I S  +  DP +   KG  FV +  PE A  AL +M
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 193 NGKMI 197
           NG M+
Sbjct: 63  NGVML 67

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|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 51.7 bits (124), Expect = 6e-07
 Identities = 25/121 (20%), Positives = 32/121 (26%), Gaps = 10/121 (8%)

Query: 214 RARLQAQFSQMRPVAM--GPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQ 271
           + R QA      P  +      P +      GP        Y Q P           +  
Sbjct: 164 QQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPG--YPQPPQGHPEQVQPQQFLP 221

Query: 272 QLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMP----HQMPPR 327
              P   PA  P+P          QQ Q PG  +   P           P     Q PP+
Sbjct: 222 A--PSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQ 279

Query: 328 G 328
            
Sbjct: 280 N 280

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

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

 Score = 46.5 bits (111), Expect = 7e-07
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY++NL   I  E+L +LF ++G I   ++       ++G+ FV +    +A  A   ++
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKE--TRGTAFVVYEDIYDAKNACDHLS 62

Query: 194 G 194
           G
Sbjct: 63  G 63

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

 Score = 46.6 bits (111), Expect = 7e-07
 Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 31 VFVKNLDESTTDEDL----KKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 86
          VFV +L  S +D++L     + F +YGT+    V+RD   +   + FV F N DDA  A+
Sbjct: 5  VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRP--YAFVQFTNDDDAKNAL 62

Query: 87 EALNGKKFDDR 97
              G   D R
Sbjct: 63 AKGQGTILDGR 73

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

 Score = 46.5 bits (110), Expect = 7e-07
 Identities = 22/58 (37%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 87
          +FV  L  +TT ED+K+ F ++G +  A++M D    + + FGFV FE+ D   K  E
Sbjct: 2  IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

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

 Score = 46.5 bits (111), Expect = 8e-07
 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 31  VFVKNLDESTTDEDLKKIF-GEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           +FV +L    TD  L++ F   Y ++  A VVM    G+SK +GFV F + D+  +A+  
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 89  LNGKKFDDREWYVGKA 104
           +NG     R   V  A
Sbjct: 64  MNGVYCSSRPMRVSPA 79

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 46.7 bits (110), Expect = 8e-07
 Identities = 25/84 (29%), Positives = 50/84 (59%), Gaps = 3/84 (3%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NLY+  L  ++  ++L++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  
Sbjct: 7   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66

Query: 192 MNGKMI--VSKPLYVAVAQRKEER 213
           +NG+     ++P+ V  A    ++
Sbjct: 67  LNGQKPPGATEPITVKFANNPSQK 90

This subgroup corresponds to the RRM2 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 = 90

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 46.1 bits (110), Expect = 8e-07
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V VKNL + TT+  +++ F + G I    ++    G       + FE  D+A  A+   +
Sbjct: 3  VKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGG---LVAVIEFETEDEALAALTK-D 58

Query: 91 GKKFDDRE 98
           K+    E
Sbjct: 59 HKRLGGNE 66

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

 Score = 50.3 bits (120), Expect = 9e-07
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTI-TSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           N++V  L ++ T  +L+ IF  +G I TS ++  +  G SK  GF+ F+  D+A +A++ 
Sbjct: 91  NLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKT 150

Query: 89  LNGKK 93
           LNG  
Sbjct: 151 LNGTT 155

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

 Score = 46.5 bits (110), Expect = 9e-07
 Identities = 21/71 (29%), Positives = 36/71 (50%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL  ++ +  L+  F  FG IT   + R   G +   GF+ F   + A RA   M+
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69

Query: 194 GKMIVSKPLYV 204
           GK++   P+ +
Sbjct: 70  GKVLRRNPIKI 80

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

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 46.4 bits (110), Expect = 9e-07
 Identities = 19/61 (31%), Positives = 38/61 (62%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV  L++  T+++++++F  YG +    +MRD   +S+   FV + + + A  A++ALN
Sbjct: 2  LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 91 G 91
          G
Sbjct: 62 G 62

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

 Score = 46.0 bits (109), Expect = 9e-07
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 3/67 (4%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FVKNL  + T ++LK++F +   I   +     DG SK   ++ F+   +A KA+E   
Sbjct: 6  LFVKNLPYNITVDELKEVFEDAVDIR--LPSGK-DGSSKGIAYIEFKTEAEAEKALEEKQ 62

Query: 91 GKKFDDR 97
          G + D R
Sbjct: 63 GAEVDGR 69

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|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 46.1 bits (109), Expect = 9e-07
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L I NL  +   ++ +EL   FG +  C  V  + +G SKG GFV +   + A+RA +++
Sbjct: 2   LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61

Query: 193 NGKMIVSKPLYV 204
            GK + S+ LYV
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|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 = 45.7 bits (109), Expect = 1e-06
 Identities = 19/61 (31%), Positives = 33/61 (54%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L ++N+      ++L+ELFS FG + S ++ +   G  +G  FV F T +EA  A+  + 
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALK 62

Query: 194 G 194
            
Sbjct: 63  S 63

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + V NLD   +D++L+ +F ++G +    +       S+   FV F +   A  A++ALN
Sbjct: 4  LLVFNLDSPISDQELRSLFSQFGEVKD--IRETPLRPSQK--FVEFYDIRAAEAALDALN 59

Query: 91 GKKFDDREW 99
          G+ F     
Sbjct: 60 GRPFLGGRL 68

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

 Score = 45.9 bits (108), Expect = 1e-06
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 10/75 (13%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVM---RDPSGISKGSGFVAFSTPEEASR 187
           G NL++  L  +     LK LFS++G +   KV+   R P   ++  GFV  ST EEA++
Sbjct: 1   GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPG--ARCYGFVTMSTSEEATK 58

Query: 188 ALA-----EMNGKMI 197
            +      E++G+MI
Sbjct: 59  CINHLHRTELHGRMI 73

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

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

 Score = 45.8 bits (108), Expect = 1e-06
 Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY+ NL   + +  + +LFS+ G   SCK++ D +G +    FV F     A+ +LA MN
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAG-NDPYCFVEFFEHRHAAASLAAMN 60

Query: 194 GKMIVSKPLYV 204
           G+ I+ K + V
Sbjct: 61  GRKIMGKEVKV 71

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V+VK   +  T +D+++ F ++G + +  + RD D K K   FV F+  +DA K +E   
Sbjct: 2  VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK-E 60

Query: 91 GKKFDDRE 98
            K+ ++E
Sbjct: 61 KLKYKEKE 68

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 20/62 (32%), Positives = 32/62 (51%)

Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
          VKNL    ++E L++ F ++G +  AVV+ D  G+S   G V F     A  A++  +  
Sbjct: 4  VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCSEG 63

Query: 93 KF 94
           F
Sbjct: 64 CF 65

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

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

 Score = 50.3 bits (120), Expect = 1e-06
 Identities = 38/192 (19%), Positives = 78/192 (40%), Gaps = 25/192 (13%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 87
           + +++ NL     ++ +K++   +G + +  +++D   G SK + F  +++      A+ 
Sbjct: 296 DRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIA 355

Query: 88  ALNGKKFDDREWYV-----GKAQKKSEREQELKGQFEQAMKETVDKFQG-------LNLY 135
           ALNGK   D + +V     G  Q   +    +      A   +    Q        + L 
Sbjct: 356 ALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLT 415

Query: 136 IKNLGDSIDD--------EKLKELFSEFGTITSCKVMRDPSGISKGSG----FVAFSTPE 183
               GD + D        E +K  FS++G + +  + R     +   G    F+ ++   
Sbjct: 416 NLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVR 475

Query: 184 EASRALAEMNGK 195
            A +A+  MNG+
Sbjct: 476 SAEKAMEGMNGR 487

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

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 5/60 (8%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          NV++ NL ES ++E+L++   ++G I    ++++     K   FV+F +  +A K V  L
Sbjct: 5  NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTL 59

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

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

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 7/68 (10%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV+NL  + T+E L+K F E+G +     ++D       + FV+FE  D A +A++ +N
Sbjct: 4  LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEERDAAVRAMDEMN 56

Query: 91 GKKFDDRE 98
          GK+ +  E
Sbjct: 57 GKEIEGEE 64

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

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

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDA-AKAVEA 88
          +FV  L  S T+ DL++ F  +GT++   ++ +   G  + F +++   ++    K    
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 89 LNGKKF 94
          LNG K+
Sbjct: 62 LNGTKW 67

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

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +Y+ NL  S+ +  L ++FS++G +    +++D  +  SKG  F+ F   E+A + +  +
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 193 NGKMIVSKPLYVAVA 207
           N K +  + L  ++A
Sbjct: 64  NNKELFGRTLKCSIA 78

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 32 FVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          FV  L ++  D   L+K+F + G  T   +    +G+ + F FV +  A+DA +A +ALN
Sbjct: 6  FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALN 65

Query: 91 GKKF 94
          G   
Sbjct: 66 GHSL 69

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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 45.2 bits (108), Expect = 2e-06
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 9/76 (11%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-------DGKSKCFGFVNFENADD 81
            ++VKNL +  T+EDL  IFG +  + S+   ++        +G+ K   FV F + + 
Sbjct: 2  KRLYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEI 59

Query: 82 AAKAVEALNGKKFDDR 97
          A KA+  +NG     +
Sbjct: 60 ATKALNLVNGYVLKGK 75

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

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

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKA 85
          V  L   TT++DLK  F  +G +    V +D   G+SK FGFV F + +D  K 
Sbjct: 4  VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV 57

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

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
          ++V  L E   ++ L   F  +G I    +  D    K + F FV FE  +DAA A++ +
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 90 NG 91
          N 
Sbjct: 61 NE 62

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

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

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           ++V+     T++  +++IF  YG +    ++         F FV FE+ + A +A ++++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI-------SNFAFVEFESLESAIRAKDSVH 54

Query: 91  GKKFDDREWYV 101
           GK  ++   YV
Sbjct: 55  GKVLNNNPLYV 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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 21/49 (42%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 142 SIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           S  +E L+E F EFG I    +++D  +G SKG G+V F  P +A+ AL
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 45.5 bits (107), Expect = 2e-06
 Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFE--NADDAA 83
          +F  +F+  L   TT+E L+  + ++G +T  VVMRD    +S+ FGFV F   N  DAA
Sbjct: 1  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAA 60

Query: 84 KA 85
           A
Sbjct: 61 MA 62

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 4/60 (6%)

Query: 134 LYIKNLG--DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
           +Y+K      ++DD  ++E F +FG + + ++ RD     KGS FV F T E+A + L +
Sbjct: 2   VYVKGFPKDATLDD--IQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK 59

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 8/68 (11%)

Query: 31 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          +FV N D  +T   DL++ F  YG + +  + R+       F FV +E  +DA KA+E+ 
Sbjct: 2  LFVINFDPINTRTRDLERHFEPYGKLVNVRIRRN-------FAFVQYETQEDATKALEST 54

Query: 90 NGKKFDDR 97
          N  K  DR
Sbjct: 55 NMSKVLDR 62

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +Y+ NL + + +E L ELF + G + +  + +D  +   +G GFV F + E+A  A+  M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 193 NGKMIVSKPLYV 204
           N   +  KP+ V
Sbjct: 61  NMIKLYGKPIRV 72

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

 Score = 45.7 bits (108), Expect = 2e-06
 Identities = 30/98 (30%), Positives = 50/98 (51%), Gaps = 16/98 (16%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 87
           +++FV+N+ + T  EDL++ FG YG I    V  D    + + F +V FE+  DA  A+ 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKET 125
            L      DR+W  G+         +++ QF Q  ++T
Sbjct: 61  NL------DRKWICGR---------QIEIQFAQGDRKT 83

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

 Score = 45.2 bits (108), Expect = 2e-06
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           + ++ L  S  +E +++ FS          ++ D  G   G  +V F++PE+A RAL + 
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 193 NGKM 196
           N KM
Sbjct: 62  NNKM 65

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

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

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 88
          N++V  L  +T   DLK +FG+YG + SA V+ +     +KC+G V   ++ + A+ +  
Sbjct: 1  NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISH 60

Query: 89 LN 90
          L+
Sbjct: 61 LH 62

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

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
           ++V  +   TT  +L++ F  +G I    +    DG +  +GFV +  A DA +A+E
Sbjct: 4  VIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN--YGFVTYRYACDAFRAIE 59

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           NLYI  L  ++  + ++++FS FG I + +V+ D  +G+S+G  F+ F    EA  A+  
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 192 MNG 194
            NG
Sbjct: 62  FNG 64

This subgroup corresponds to the RRM2 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|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 4/52 (7%)

Query: 41 TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
          ++++L+KIF +YG + S VV+     K K    V F +   A  AVE   G 
Sbjct: 17 SEDELRKIFSKYGDV-SDVVVSS---KKKGSAIVEFASKKAAEAAVENECGL 64

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

>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 = 44.7 bits (106), Expect = 3e-06
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA-- 190
           +++  L   + +E+ KE FS+FG +   ++M+D  +G S+G GFV F +     R  +  
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 191 --EMNGKMIVSKP 201
             E+ GK +  K 
Sbjct: 62  MLELGGKQVEVKR 74

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

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISK------GSGFVAFSTPEEASR 187
           +YI NL  S  +E L+E   +F  ++     +   G         G  +  FS+PE+A +
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61

Query: 188 ALAEMNGKMIVSKPLYV 204
            + ++NGK+  ++ L+V
Sbjct: 62  VVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>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 = 44.9 bits (107), Expect = 3e-06
 Identities = 17/77 (22%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
           N +F+  L    +++ +K++   +G + +  +++D   G SK + F  + +     +A+ 
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 88  ALNGKKFDDREWYVGKA 104
            LNG +  D++  V +A
Sbjct: 61  GLNGMQLGDKKLTVQRA 77

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

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

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 190
            ++++ +L   I  + +K  F+ FG I+  +V++D  +G SKG GFV+F    +A  A+ 
Sbjct: 2   FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

Query: 191 EMNGKMIVSKPLYVAVAQR 209
           +M G+ +  + +    A R
Sbjct: 62  QMGGQWLGGRQIRTNWATR 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|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 19/64 (29%), Positives = 34/64 (53%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY+ NL   + ++ LK++F   G + + K++ D +      GFV +    +A  AL  +N
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 194 GKMI 197
           G+ I
Sbjct: 61  GRQI 64

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|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 = 44.6 bits (106), Expect = 3e-06
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 9/65 (13%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITS--AVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          +++ +L +  T+EDLK +F EYG I S   +  R       C  +V  E   DA +A++ 
Sbjct: 5  LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRG------C-AYVCMETRQDAHRALQK 57

Query: 89 LNGKK 93
          L   K
Sbjct: 58 LRNVK 62

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

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 88
          N++V  L  +T   DLK +F +YG +  A V+ +     ++C+GFV    +++A K +  
Sbjct: 3  NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINH 62

Query: 89 LNGKKFDDR 97
          L+  +   R
Sbjct: 63 LHRTELHGR 71

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

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

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 7/75 (9%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L+++NL  ++ +E L++ FSEFG +   K ++D         FV F   + A RA+ EMN
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEERDAAVRAMDEMN 56

Query: 194 GKMIVSKPLYVAVAQ 208
           GK I  + + + +A+
Sbjct: 57  GKEIEGEEIEIVLAK 71

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

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 86
          +FV  + E T +  L+  F +YG I    +M D G GK + F FV F++ D   K V
Sbjct: 3  IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 59

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

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V+V NL  +    +L++ FG YG + S  V R+  G    F FV FE+  DAA AV  L+
Sbjct: 7  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 62

Query: 91 GK 92
          G+
Sbjct: 63 GR 64

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L +++L   + ++  ++L   FG  +S +VM    G  K + F  F   + AS+AL+ ++
Sbjct: 2   LLVRHLPPELSEDDKEDLLKHFG-ASSVRVMS-RRGKLKNTAFATFDNEQAASQALSRLH 59

Query: 194 GKMIVSKPLYV 204
              I+ K L V
Sbjct: 60  QLKILGKRLVV 70

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

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

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFEN 78
          +FV  L   TT E L++ F +YG +   V+M+D    +S+ FGFV F++
Sbjct: 2  LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50

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|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 136 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK 195
           I N+   +  E L  L S +GT+ +C+ +  P+     +  V + +PE+A +A+ ++NG 
Sbjct: 5   ISNIPPHVRWEDLDSLLSTYGTVKNCEQV--PTKSETATVNVTYESPEQAQQAVNKLNGH 62

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 22/56 (39%), Positives = 36/56 (64%), Gaps = 5/56 (8%)

Query: 41 TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD 96
          + E+L ++F +YGT+   +VM  G  K  CF  V++ + +DAA A +ALNGK+ + 
Sbjct: 16 SREELLRVFEKYGTVED-LVMPPG--KPYCF--VSYSSIEDAAAAYDALNGKELEL 66

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 44.4 bits (105), Expect = 4e-06
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 31  VFVKNLDESTTDEDLKKIF-GEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           +FV +L     + DL  +F   + +  SA +M D   G S+ +GFV F + +D  +A+  
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 89  LNGKKFDDREWYVGKA 104
           + G     R   +  A
Sbjct: 64  MQGVYCGGRPMRISTA 79

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

 Score = 44.2 bits (105), Expect = 4e-06
 Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 190
           L++  L + + +E L+E FS++G + S +++ D  +G  +G  FV F   +   + + 
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVL 59

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

 Score = 44.2 bits (105), Expect = 4e-06
 Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 7/62 (11%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V++  L     + D+++ F  YG I   + +++G      FGFV FE+  DA  AV  LN
Sbjct: 2  VYIGRLPYRARERDVERFFKGYGRIRE-INLKNG------FGFVEFEDPRDADDAVYELN 54

Query: 91 GK 92
          GK
Sbjct: 55 GK 56

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 = 44.3 bits (104), Expect = 4e-06
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAK 84
          T+   +FV  L  +T  ED+K+ F ++G +  A++M D    + + FGFV FEN D   K
Sbjct: 1  TRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK 60

Query: 85 AVE 87
            E
Sbjct: 61 VCE 63

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

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)

Query: 29 NNV-FVKNLDESTTDEDLKKIFGEY-GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 86
          N + F++NL E TT E L+ +F ++ G     +V        +   FV FE  + A  A+
Sbjct: 2  NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVAL 55

Query: 87 EALNGKK 93
          +AL G K
Sbjct: 56 QALQGFK 62

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

 Score = 44.3 bits (104), Expect = 4e-06
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAE 191
           ++I  L      + L++ FS+FG I  C VMRDP+   S+G GFV F+ P    + LA+
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

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

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 44.2 bits (104), Expect = 4e-06
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV+NL    T + LK  F E G +  A +  + +GKSK  G V FE+ + A +A   +N
Sbjct: 2  IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVRFESPEVAERACRMMN 60

Query: 91 GKKFDDRE 98
          G K + RE
Sbjct: 61 GYKLNGRE 68

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L + NL      + L+ +F ++G +    + RD  +  S+G  FV F    +A  A+  M
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 193 NGKMIVSKPLYVA 205
           +GK +  + L 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|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 44.1 bits (105), Expect = 5e-06
 Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 6/67 (8%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS---GFVAFSTPEEASRALA 190
           L++ N   S D   +++LF ++G I S   +R PS     +    +V F++PE A+ A+A
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILS---IRFPSLRFNKTRRFCYVQFTSPESAAAAVA 59

Query: 191 EMNGKMI 197
            +NGK+ 
Sbjct: 60  LLNGKLG 66

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

 Score = 44.2 bits (104), Expect = 5e-06
 Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 7/75 (9%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L+++NL +++ +E L++ F +FG +   K ++D         F+ F   + A +A+ EMN
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 56

Query: 194 GKMIVSKPLYVAVAQ 208
           GK +  + + +  A+
Sbjct: 57  GKELEGENIEIVFAK 71

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

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 44.3 bits (104), Expect = 5e-06
 Identities = 22/65 (33%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          N++V  L ++ T ++L+++F +YG  ITS +++    G S+  GF+ F+   +A +A++ 
Sbjct: 4  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 89 LNGKK 93
          LNG+K
Sbjct: 64 LNGQK 68

This subgroup corresponds to the RRM2 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 also regulates 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 = 81

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

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY+  LG+ + ++ L++ F +FG I S  V+       +   FV F+T E A +A   + 
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVVP-----RQQCAFVTFTTREAAEKAAERLF 58

Query: 194 GKMIV 198
            K+I+
Sbjct: 59  NKLII 63

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

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 44.1 bits (104), Expect = 6e-06
 Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK------SKCFGFVNFENADDAAK 84
           +FVKNL+ STT++ L   F        A V    D K      S  FGFV F+  + A  
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 85  AVEALNGKKFDDREWYVGKAQK 106
           A++A++G   D     V  + +
Sbjct: 63  ALKAMDGFVLDGHTLVVKFSHR 84

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 43.9 bits (103), Expect = 6e-06
 Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 190
            ++++ +L   I  E +K  F+ FG I+  +V++D  +G SKG GFV+F    +A  A+ 
Sbjct: 2   FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61

Query: 191 EMNGKMIVSKPLYVAVAQR 209
            M G+ +  + +    A R
Sbjct: 62  HMGGQWLGGRQIRTNWATR 80

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 43.9 bits (104), Expect = 6e-06
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 31  VFVKNLDESTTDEDLK----KIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKA 85
           +FVK  D S  ++D++    + F   G IT   +  D + G SK F ++ F++ D   KA
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 86  VEALNGKKFDDREWYVGKA 104
           +E L+G         V +A
Sbjct: 62  LE-LDGSDLGGGNLVVDEA 79

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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 48.5 bits (115), Expect = 6e-06
 Identities = 57/247 (23%), Positives = 95/247 (38%), Gaps = 31/247 (12%)

Query: 22  VAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV------MRDGDGKSKCFGFVN 75
           V I      +FV  + ++   E+   I  E+  +T  VV            K++ F FV 
Sbjct: 132 VCISVDNCRLFVGGIPKNKKREE---ILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVE 188

Query: 76  FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLY 135
           +E+   AA A   L   +   + W    A   +E E+E+       +K          LY
Sbjct: 189 YESHRAAAMARRKLMPGRI--QLWGHVIAVDWAEPEEEVDEDVMAKVKI---------LY 237

Query: 136 IKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           ++NL  +  +E +++ FSEF  G +   K +RD         FV F   E+A +A+ E+N
Sbjct: 238 VRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD-------YAFVHFEDREDAVKAMDELN 290

Query: 194 GKMIVSKPLYVAVAQR-KEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFL 252
           GK +    + V +A+   ++   R                      +Y P    L  +  
Sbjct: 291 GKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQ-VYDPASRSLAYEDY 349

Query: 253 YGQAPPA 259
           Y   P A
Sbjct: 350 YYHPPYA 356

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|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 43.8 bits (103), Expect = 7e-06
 Identities = 20/65 (30%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          N++V  L ++ + ++++++F +YG  ITS +++    G S+  GF+ F+   +A +A++ 
Sbjct: 3  NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 89 LNGKK 93
          LNG+K
Sbjct: 63 LNGQK 67

This subgroup corresponds to the RRM2 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 = 81

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

 Score = 43.9 bits (104), Expect = 7e-06
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 134 LYIKNLGDSIDDEKL----KELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           +++ +L  S  D++L     E FS++GT+   KV+RD     +   FV F+  ++A  AL
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQ--RPYAFVQFTNDDDAKNAL 62

Query: 190 AEMNGKMIVSKPL 202
           A+  G ++  + +
Sbjct: 63  AKGQGTILDGRHI 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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 43.7 bits (103), Expect = 8e-06
 Identities = 26/79 (32%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 134 LYIKNLGDSIDD-EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L I+NL  SI    KLK++F  +G +    + R   G   G  FV     + A  AL   
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENT 62

Query: 193 NGKMIVSKPLYVAVAQRKE 211
           NG  I  +P+ V  A +K 
Sbjct: 63  NGLEIDGRPVAVDWAVQKN 81

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

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 43.6 bits (102), Expect = 8e-06
 Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 87
           N++++ L   TTD+DL K+   YG I S   + D    K K +GFV+F++   A KAV 
Sbjct: 2  TNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 61

Query: 88 AL 89
          AL
Sbjct: 62 AL 63

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has 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. MSSP-2 contains 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 as well as induction of apoptosis. . Length = 75

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

 Score = 43.1 bits (102), Expect = 8e-06
 Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 5/67 (7%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 91
          ++ NL     + DL+++F E+    S+V+++ G      + FV+  +   A KA+E LNG
Sbjct: 2  YIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGG-----YAFVDCPDQSWADKAIEKLNG 56

Query: 92 KKFDDRE 98
          K    + 
Sbjct: 57 KILQGKV 63

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

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

 Score = 43.3 bits (102), Expect = 9e-06
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          N VFV  +D    + +++  F +YG++    ++ D  G SK +GFV+F +  D  K VE+
Sbjct: 6  NTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVES 65

Query: 89 ---LNGKKF 94
              +GKK 
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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 6/56 (10%)

Query: 146 EKLKE----LFSEFGTITSCKVM--RDPSGISKGSGFVAFSTPEEASRALAEMNGK 195
           EKLK+    +FS+FG      +    D +G +KG  FV F+TPEEA  A+  +NG 
Sbjct: 18  EKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGY 73

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

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

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 7/71 (9%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +++ N+  +   ++L+ LF EFG +  C  +       K   FV     EEA  A+  +N
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKV-------KDYAFVHMEREEEALAAIEALN 55

Query: 194 GKMIVSKPLYV 204
           GK +  + + V
Sbjct: 56  GKEVKGRRINV 66

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
           LY++N+ D+   + L+ LF ++G I    +  D  +   +G  +V F    +A  AL  +
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 193 NGKMIVSKPLYVAVAQ--RK 210
           +    + + + +  AQ  RK
Sbjct: 63  DRTRFLGREIEIQFAQGDRK 82

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

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
          +   +F+  L   TTD+ L++ F ++GT+T  VVMRD   K S+ FGFV +   ++   A
Sbjct: 1  QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60

Query: 86 VEA 88
          + A
Sbjct: 61 MSA 63

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKA 85
          +FV NL  +   ++LK+ F ++G + S  V  D + G SK +GFV+F + D    A
Sbjct: 2  LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENA 57

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|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 22/65 (33%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          N++V  L ++ T ++L+++F +YG  ITS +++    G S+  GF+ F+   +A +A++ 
Sbjct: 7  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66

Query: 89 LNGKK 93
          LNG+K
Sbjct: 67 LNGQK 71

This subgroup corresponds to the RRM2 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 = 90

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 43.4 bits (103), Expect = 1e-05
 Identities = 21/60 (35%), Positives = 31/60 (51%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L +KNL   + +E L++ FS+FG +    V+ D  G S G G V FS    A  A+   +
Sbjct: 2   LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCS 61

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

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

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           L++  L      E L+  FS++G +  C +M+D  +  S+G GFV F  P      LA  
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 191 --EMNGKMIVSKP 201
              ++G+ I  KP
Sbjct: 62  PHTLDGRTIDPKP 74

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|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           ++++NL   +  +KLKE FS+ G +   ++  + +G SKG G V F +PE A +A   MN
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME-NGKSKGCGTVRFDSPESAEKACRLMN 60

Query: 194 GKMI 197
           G  I
Sbjct: 61  GIKI 64

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|241046 cd12602, RRM2_SF2_plant_like, RNA recognition motif 2 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 8/69 (11%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V V  L  S + +DLK      G +  + V RDG G +   G V+F N DD   A+    
Sbjct: 3  VLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGRGTT---GIVDFTNYDDMKYAI---- 55

Query: 91 GKKFDDREW 99
           +K DD E+
Sbjct: 56 -RKLDDTEF 63

This subfamily corresponds to the RRM2 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 = 76

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 191
           +++  L      + LK+ F++FG +T C +  DP +G S+G GF+ F       + L + 
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 192 ---MNGKMIVSK 200
              ++G++I  K
Sbjct: 62  EHRLDGRLIDPK 73

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 134 LYIKNL-GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           L ++N+  +  +  KL E FS+FGTI + +V       +  S  V FST EEA +A  
Sbjct: 4   LEVRNIPPELNNITKLNEHFSKFGTIVNIQV-----NYNPESALVQFSTSEEAKKAYR 56

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + LA  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 191 --EMNGKMIVSK 200
             E++ K I  K
Sbjct: 63  RHELDSKTIDPK 74

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          V++ +L     + +L+K F ++GT+T   + R    GKSK + FV FE+ + A    E +
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 90 NG 91
          N 
Sbjct: 62 NN 63

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEAL 89
          V ++ L  S T+ED++  F         + +  D DG+     +V F + +DA +A+   
Sbjct: 2  VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRAL-RK 60

Query: 90 NGKKFDDR 97
          +  K   R
Sbjct: 61 HNNKMGGR 68

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

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 25/68 (36%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV+NL    T + LK+ F + G +  A +  + +GKSK  G V F++ + A KA   +N
Sbjct: 2  IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME-NGKSKGCGTVRFDSPESAEKACRLMN 60

Query: 91 GKKFDDRE 98
          G K + RE
Sbjct: 61 GIKINGRE 68

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 21/66 (31%), Positives = 38/66 (57%), Gaps = 3/66 (4%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTIT-SCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           L++ +L   +D+  +K++++  G    + KV+R   SG++ G  FV F +P  A  AL+ 
Sbjct: 2   LWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALS- 60

Query: 192 MNGKMI 197
           +NG  I
Sbjct: 61  LNGTPI 66

This subgroup corresponds to the RRM1 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), 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 carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, 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 = 81

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

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 21/61 (34%), Positives = 32/61 (52%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + VKNL    T +D++ +F  YG + S  V +  D  ++ F FV F  A +A  A+ AL 
Sbjct: 3  ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 91 G 91
           
Sbjct: 63 D 63

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 22/71 (30%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +Y+ ++   + +E+L  LFS  G +  C+V  DP+ + + + F+ F T EE +RA   ++
Sbjct: 5   VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFA-FIEF-TDEEGARAALSLS 62

Query: 194 GKMIVSKPLYV 204
           G M+   P+ V
Sbjct: 63  GTMLGFYPVRV 73

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L + NL  S   E+ +EL   +G I  C  V  + +G SKG GFV +   + AS+A  E+
Sbjct: 2   LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61

Query: 193 NGKMIVSKPLYV 204
            GK +    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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY+ NL   + +  + +LFS+ G   SCK++ + +  +    FV F    +A+ ALA MN
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMN 60

Query: 194 GKMIVSKPLYV 204
           G+ I+ K + V
Sbjct: 61  GRKILGKEVKV 71

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|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 28/82 (34%), Positives = 40/82 (48%), Gaps = 12/82 (14%)

Query: 134 LYIKNLGDSIDDEKLKE----LFSEFG---TITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
           +YI NL D I  E+LK     LFS+FG    I + K M+      +G  FV F     A+
Sbjct: 4   IYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMK-----MRGQAFVIFKELSSAT 58

Query: 187 RALAEMNGKMIVSKPLYVAVAQ 208
            AL ++ G     KP+ +  A+
Sbjct: 59  NALRQLQGFPFYGKPMRIQYAK 80

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. 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. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NLG +  +E+L++LFS        K+     G      FV F     A++AL  + 
Sbjct: 5   LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGP---VCFVEFEDVSFATQALNSLQ 61

Query: 194 GKMIVSK 200
           G ++ S 
Sbjct: 62  GAVLSSS 68

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

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 2/66 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           L++ +L   +D+  +K  F+  G T+ S K++R+  +G   G  FV F+    A R L +
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 192 MNGKMI 197
           +NGK I
Sbjct: 62  LNGKPI 67

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             + VKN    TT E+L+ +F  +G +T  ++   G         V F N   A  A +A
Sbjct: 1   TTILVKNFPYGTTAEELRDLFEPHGKLTRVLMPPAG-----TIAIVEFANPQQARLAFKA 55

Query: 89  LNGKKFDDREWYVGKA 104
           L  ++F D   Y+ K 
Sbjct: 56  LAYRRFKDSILYLEKG 71

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

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

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 12/81 (14%)

Query: 30  NVFVKNLDEST-----TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           NV++ N+ +        +++L+K   +YG I S  ++R+     K   F+NF N  +A  
Sbjct: 4   NVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILRE-----KACAFINFMNIPNAIA 58

Query: 85  AVEALNGKK--FDDREWYVGK 103
           A++ LNGKK          GK
Sbjct: 59  ALQTLNGKKPYDTIVRINYGK 79

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

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 41.7 bits (99), Expect = 3e-05
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 10/72 (13%)

Query: 32 FVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFG--FVNFENADDAAKA 85
          ++ NL+E    ++LK+    +F ++G +   V  +      K  G  FV F++ + A  A
Sbjct: 3  YINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK----TLKMRGQAFVVFKDVESATNA 58

Query: 86 VEALNGKKFDDR 97
          + AL G  F D+
Sbjct: 59 LRALQGFPFYDK 70

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains 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. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 134 LYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L++ N+  S+ +E LKELF++  GT+ + K       ++     +   + EEA  AL  +
Sbjct: 2   LHLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKMA----LIQMGSVEEAIEALIAL 57

Query: 193 -NGKMIVSKPLYVA 205
            N ++  S  L V+
Sbjct: 58  HNYQLSESSHLRVS 71

This subfamily corresponds to the RRM4 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 25/64 (39%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          ++FV NL+ +   ++LK    E+ +  +  V     G SK FG+V+FE+A+D  KA+E L
Sbjct: 2  SLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKALE-L 60

Query: 90 NGKK 93
           GKK
Sbjct: 61 TGKK 64

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

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

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 7/64 (10%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V++  L     ++D+++ FG YG +   + +++G      +GFV FE++ DA  AV  LN
Sbjct: 2  VYIGRLSYHVREKDIQRFFGGYGKLLE-IDLKNG------YGFVEFEDSRDADDAVYELN 54

Query: 91 GKKF 94
          GK  
Sbjct: 55 GKDL 58

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

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 29/97 (29%), Positives = 50/97 (51%), Gaps = 16/97 (16%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
           ++FV+N+ ++T  EDL++ FG YG I    V  D    + + F ++ FE+  DA  A+  
Sbjct: 2   SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKET 125
           LN      R+W  G+         +++ QF Q  ++T
Sbjct: 62  LN------RKWVCGR---------QIEIQFAQGDRKT 83

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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 41.9 bits (98), Expect = 3e-05
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE-- 87
          +F+  L   TT +DLK  F ++G +    +  D   G+S+ FGFV F+ ++   K ++  
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 88 --ALNGKKFDDRE 98
             LNGK  D + 
Sbjct: 61 EHKLNGKVIDPKR 73

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is 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 = 74

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 41.9 bits (98), Expect = 3e-05
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 191
           ++I  L      + LK+ FS+FG +  C +  DP +G S+G GFV F   E   + + + 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 192 ---MNGKMIVSK 200
              +NGK+I  K
Sbjct: 61  EHKLNGKVIDPK 72

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is 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 = 74

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 142 SIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNG 194
           S+  E+L  LF     +  C + RDP +G SKG  +V +S P  A  A  ++NG
Sbjct: 10  SVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNG 63

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

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 42.1 bits (98), Expect = 3e-05
 Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 9/85 (10%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           N++++ L  +TTD+DL K+   YG I S   + D    K K +GFV+F++   A KAV A
Sbjct: 9   NLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSA 68

Query: 89  LNGKKFDDREWYVGKAQKKSEREQE 113
           L             +AQ   ++EQ+
Sbjct: 69  LKASGV--------QAQMAKQQEQD 85

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has 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. MSSP-1 contains 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 as well as induction of apoptosis. . Length = 86

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

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 134 LYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           +++K    S+ ++ ++    E FS  G IT   +  D  +G SKG  ++ F + +   +A
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 189 LAEMNGKMIVSKPLYV 204
           L E++G  +    L V
Sbjct: 62  L-ELDGSDLGGGNLVV 76

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|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 41.5 bits (97), Expect = 4e-05
 Identities = 24/64 (37%), Positives = 37/64 (57%), Gaps = 7/64 (10%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          VF+  L+ +  ++D+++ F  YG I      RD D K + FGFV F++  DA  AV  L+
Sbjct: 2  VFIGRLNPAAREKDVERFFKGYGRI------RDIDLK-RGFGFVEFDDPRDADDAVYELD 54

Query: 91 GKKF 94
          GK+ 
Sbjct: 55 GKEL 58

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that 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 it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains 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. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 9/67 (13%)

Query: 31 VFVKNLDESTTDEDLKKIFGEY--GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          ++V+NL   T+++ +KK FG++  G +     +RD       + FV+F + +DA  A+  
Sbjct: 4  LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD-------YAFVHFTSREDAVHAMNN 56

Query: 89 LNGKKFD 95
          LNG + +
Sbjct: 57 LNGTELE 63

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|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 41.3 bits (97), Expect = 4e-05
 Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 9/66 (13%)

Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN-- 90
          V NLD S +++DL +IFG YG I     +R+   K +   F+ F +   A  A++ALN  
Sbjct: 6  VFNLDPSVSNDDLHQIFGAYGEIKE---IRETPNK-RHHKFIEFYDVRSAEAALKALNRS 61

Query: 91 ---GKK 93
             GK+
Sbjct: 62 EIAGKR 67

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|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 9/73 (12%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTI-------TSAV-VMRDGD-GKSKCFGFVNFENADD 81
          VFV NL  +TT++DL + FG  G I          + + +D D G+ K    V +++   
Sbjct: 1  VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 82 AAKAVEALNGKKF 94
          A+ A+E  N K F
Sbjct: 61 ASAAIEWFNNKDF 73

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

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++K L +   +E LKE F   G+I +  V    +G SKG GFV FS+ E+A  A   M 
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAME 60

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|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 7/69 (10%)

Query: 30 NVFVKNLDESTTDEDLKK-IFGEY---GTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
           + VKNL   ++D  LK  +F E+   G +TS  V   G G  + +  V F   +DA KA
Sbjct: 1  GIIVKNLPLRSSDTSLKDGLFHEFKKHGKVTSVKVH--GTGSER-YAIVFFRKPEDAEKA 57

Query: 86 VEALNGKKF 94
          +E   GK F
Sbjct: 58 LEVSKGKLF 66

This subfamily corresponds to the RRM2 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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 193
           ++  L   + +  L E FS+ G +   +++RD  S  SKG  +V F   E    AL  + 
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-LT 61

Query: 194 GKMIVSKPLYV 204
           G+ ++ +P+ V
Sbjct: 62  GQRLLGQPIMV 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|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 12/75 (16%)

Query: 30 NVF-VKNLDESTTDEDLKK-IFGE---YGTITSAVVMRDGDGKSKCFG--FVNFENADDA 82
          N+F      E   D+++K+ +  E   +G +    V      K+   G  +V F+  + A
Sbjct: 8  NMFDPAEETEDEWDDEIKEDVLEECSKFGPVEHIKVD-----KNSPEGVVYVKFKTVEAA 62

Query: 83 AKAVEALNGKKFDDR 97
           K ++ALNG+ FD R
Sbjct: 63 QKCIQALNGRWFDGR 77

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia 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. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 41.0 bits (97), Expect = 5e-05
 Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 5/64 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++  LG      +L+  F  FG I             +   ++ + + E A  A   + 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPG-----RNYAYIEYESIEAAQAAKEALR 55

Query: 194 GKMI 197
           G  +
Sbjct: 56  GFPL 59

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 = 41.2 bits (97), Expect = 5e-05
 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 11/84 (13%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVM-RDPSGISKGSGFVAFSTPEEASRALAEM 192
           L++ NL   I +++LKE F EFG +   ++  +   G     GFV F  PE   + LA  
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILA-- 63

Query: 193 NGKMIVSKPLYVAVAQR--KEERR 214
                 +KP+Y     R   EE++
Sbjct: 64  ------NKPIYFRGDHRLNVEEKK 81

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

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 6/68 (8%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + V NL  S T++D+ ++F   G +  A ++R G  +      V +   DDA  A++  N
Sbjct: 3  LVVSNLHPSVTEDDIVELFSAIGALKRARLVRPGVAE------VVYVRKDDALTAIDKYN 56

Query: 91 GKKFDDRE 98
           ++ D + 
Sbjct: 57 NRELDGQP 64

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|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 20/65 (30%), Positives = 40/65 (61%), Gaps = 7/65 (10%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
          N +++ NL  + T EDL+++FG+    +T  V+++ G      + FV++ + + A +A+E
Sbjct: 2  NKLYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKSG------YAFVDYPDQNWAIRAIE 55

Query: 88 ALNGK 92
           L+GK
Sbjct: 56 TLSGK 60

This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 41.5 bits (98), Expect = 5e-05
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 136 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNG 194
             NL D+ID+  LK++  ++G +   K+   P +    G   V F + + A R + ++N 
Sbjct: 7   FSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQ 66

Query: 195 KMIVSKPLYV 204
             ++ K + V
Sbjct: 67  TSVMGKIIKV 76

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

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

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL   I +E  K+LF ++G  +   + RD     +G GF+   +   A  A AE++
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD 58

Query: 194 GKMIVSKPLYV 204
           G ++ ++PL +
Sbjct: 59  GTILKNRPLRI 69

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

>gnl|CDD|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 = 40.9 bits (96), Expect = 6e-05
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
           +++ N+     +E+LK++FSE G + S +++ D  +G  KG GF  +   E A  A+  +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 193 NGKMIVSKPLYVAVA 207
           NG  +  + L V  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

 Score = 41.0 bits (96), Expect = 6e-05
 Identities = 13/47 (27%), Positives = 32/47 (68%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           +++  +   +D+ +++  F+++G++   K++ D +G+SKG GFV+F 
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFY 54

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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 41.0 bits (96), Expect = 6e-05
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 33  VKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 91
           V NL  S T E+ +++   YG I    +V  +  G SK +GFV +   D A+KA   L G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 92  KKFDDREWYV 101
           K+  +   + 
Sbjct: 64  KQLGESTLFA 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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEA 88
          +FV NL    T+++LK+ F E+G +    +  + G G+   FGFV F++ +   K +  
Sbjct: 6  LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

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|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           +YI NL + +  E+LK+    +FS+FG I     ++      +G  FV F     A+ AL
Sbjct: 2   IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLK--MRGQAFVVFKDISSATNAL 59

Query: 190 AEMNGKMIVSKPLYVAVAQ 208
             M G     KP+ +A ++
Sbjct: 60  RSMQGFPFYDKPMRIAYSK 78

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila 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). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

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

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          ++V NLD +TT + L + F + G +   V M   + +   + FV F        A+  LN
Sbjct: 7  IYVGNLDPTTTADQLLEFFSQAGEV-KYVRMAGDETQPTRYAFVEFAEQTSVINAL-KLN 64

Query: 91 GKKFDDR 97
          G  F  R
Sbjct: 65 GAMFGGR 71

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

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

 Score = 40.8 bits (95), Expect = 6e-05
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 7/69 (10%)

Query: 33  VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
           V N+  S T+++L+  F EYG +    +++D       + FV+ E A+DA +A+  L+  
Sbjct: 5   VGNISSSCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLDNT 57

Query: 93  KFDDREWYV 101
           +F  +  +V
Sbjct: 58  EFQGKRMHV 66

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

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 40.9 bits (96), Expect = 6e-05
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 8/64 (12%)

Query: 32 FVKNL-DESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          F+ NL  +  + EDL +IF  YG +   V+          +GFV F++ +  A A+    
Sbjct: 3  FIGNLPTKRVSKEDLFRIFSTYGELAQIVL-------KNAYGFVQFDSPESCANAINCEQ 55

Query: 91 GKKF 94
          GK  
Sbjct: 56 GKMI 59

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

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

 Score = 44.9 bits (106), Expect = 7e-05
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
           +YI NL   + ++++KEL   FG + +  +++D  +G+SKG  F  +  P     A+A +
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 193 NGKMIVSKPLYVAVA 207
           NGK      L+V  A
Sbjct: 358 NGKDTGDNKLHVQRA 372

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

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

 Score = 40.6 bits (95), Expect = 7e-05
 Identities = 14/60 (23%), Positives = 34/60 (56%), Gaps = 7/60 (11%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV NL    T+++++ +F +YG +    ++++       +GFV+ ++   A +A+  L+
Sbjct: 3  LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN-------YGFVHMDDKTAADEAIRNLH 55

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

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 4/65 (6%)

Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
          V NL  S +++ L+++F +  +I     +   +G+ K + FV FE+A+DA +A+ + N  
Sbjct: 6  VNNLSYSASEDSLQEVFEKATSIR----IPQNNGRPKGYAFVEFESAEDAKEALNSCNNT 61

Query: 93 KFDDR 97
          + + R
Sbjct: 62 EIEGR 66

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

 Score = 40.8 bits (96), Expect = 8e-05
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAE- 191
           +++  L  ++ +  L++ FS+FGT+T   VM D      +G GF+ F + +   + + E 
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64

Query: 192 ---MNGKMIVSK 200
              +NGK +  K
Sbjct: 65  FHDINGKKVEVK 76

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          VFV  L     + DL + F + G +    ++RD +  +SK   +V F + +    A+  L
Sbjct: 2  VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60

Query: 90 NGKKF 94
           G++ 
Sbjct: 61 TGQRL 65

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 40.6 bits (95), Expect = 8e-05
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           +++  L      + LKE FS+FG +  C +  DP +G S+G GFV F       + L   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 191 --EMNGKMIVSK 200
             +++G++I  K
Sbjct: 61  EHKLDGRVIDPK 72

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|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 40.5 bits (95), Expect = 8e-05
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 2/65 (3%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          ++V NL     + D++ +F +YG I  A+ +++       F FV FE+  DA  AV   +
Sbjct: 2  IYVGNLPGDIRERDIEDLFYKYGPI-KAIDLKNRRRGPP-FAFVEFEDPRDAEDAVRGRD 59

Query: 91 GKKFD 95
          G  FD
Sbjct: 60 GYDFD 64

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 40.8 bits (95), Expect = 8e-05
 Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 5/65 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          ++V+NL  STT+E ++K   E+ +I    V R    K + + FV+F N +DA  A+ ALN
Sbjct: 11 LYVRNLMLSTTEETIEK---EFNSIKPGAVERVK--KIRDYAFVHFSNREDAVDAMNALN 65

Query: 91 GKKFD 95
          GK  D
Sbjct: 66 GKVID 70

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

 Score = 40.4 bits (94), Expect = 8e-05
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +Y   +   + ++ +++ FS FG I   +V  +     KG  F+ FST E A+ A+  +N
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFIRFSTHESAAHAIVSVN 57

Query: 194 GKMI 197
           G  I
Sbjct: 58  GTTI 61

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

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

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 4/66 (6%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 91
          FV+N++ +  DE+L+ +F ++G I +         K + F  V++ +   A +A  AL G
Sbjct: 5  FVRNINSNVEDEELRALFEQFGDIRTLY----TACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 92 KKFDDR 97
           +   R
Sbjct: 61 TELGGR 66

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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 4/54 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
          VFV  L E  T+EDL++ F ++G +T   + +        F FV F + + A  
Sbjct: 3  VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRA----FAFVTFADPEVAQS 52

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 6/65 (9%)

Query: 35 NLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK 93
          N+ ++  +E +K  F + G  +    +  D +G       V FE+  DA KA  +LNG +
Sbjct: 7  NVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEG-----ALVEFESPSDAGKASLSLNGSQ 61

Query: 94 FDDRE 98
          F  + 
Sbjct: 62 FGGKT 66

This subfamily corresponds to the RRM4 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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 17/63 (26%), Positives = 33/63 (52%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          N+++ NL  S  +++L+ +   +G + S  ++RD  G S+  GF   E+ +     +   
Sbjct: 2  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHF 61

Query: 90 NGK 92
          NGK
Sbjct: 62 NGK 64

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has 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. MSSP-1 contains 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 as well as induction of apoptosis. . Length = 85

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 17/63 (26%), Positives = 35/63 (55%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          N+++ NL  S  +++L+ +   +G + S  ++RD +G S+  GF   E+ +     ++  
Sbjct: 3  NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 90 NGK 92
          NGK
Sbjct: 63 NGK 65

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It 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. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

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

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 5/60 (8%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           N+YI NL +S  +E+L+E   +FG I   K++++     K   FV F +   A + +  +
Sbjct: 5   NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTL 59

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

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 6/61 (9%)

Query: 144 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 203
            +++L+++FS++G ++   V+       KGS  V F++ + A  A+    G    S PL 
Sbjct: 17  SEDELRKIFSKYGDVSDV-VVSSKK---KGSAIVEFASKKAAEAAVENECGL--PSNPLL 70

Query: 204 V 204
           V
Sbjct: 71  V 71

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 88
          +FV  L   T+ +DLK  F ++G +T   +  D + G+S+ FGF+ F++A    K +E  
Sbjct: 2  MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 89 ---LNGKKFDDRE 98
             L+G+  D ++
Sbjct: 62 EHRLDGRLIDPKK 74

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 20/74 (27%), Positives = 38/74 (51%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + +KNL      + ++ LFS +G + S +V +     ++G  FV FST +EA  A+  + 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 194 GKMIVSKPLYVAVA 207
              ++ + L +  A
Sbjct: 63  DTHLLGRRLVLQYA 76

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

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
            +L++ NL  + D ++LK   SEF +  +  V     G SK  G+V F + E+  +AL E
Sbjct: 1   FSLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKAL-E 59

Query: 192 MNGKMIVSKPL 202
           + GK ++   +
Sbjct: 60  LTGKKLLGNEI 70

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

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 90
          FV  + +S T E L ++F     +    + RD   GKSK F +V + N   A  A E LN
Sbjct: 4  FV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLN 62

Query: 91 GKKF 94
          G ++
Sbjct: 63 GFEY 66

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

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 40.8 bits (95), Expect = 1e-04
 Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           +YI NL + I  ++LK+    +FS FG I    V R      +G  FV F     A+ AL
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 63

Query: 190 AEMNGKMIVSKPLYVAVAQRKEE 212
             M G     KP+ +  A+   +
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSD 86

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), 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 and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +Y+  +     +++++  FS  G I    +M  P +G  +G  F+ F T E A RALA +
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-L 59

Query: 193 NGKMIVSKPLYV 204
           +G+ +  + L V
Sbjct: 60  DGEDMGGRFLKV 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|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 135 YIKNLGDSIDDEKLKELF-SEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +I N+   +  + LK+LF  + G +T  ++ +D  G S+G G V F   E   +AL  MN
Sbjct: 3   FISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETMN 62

Query: 194 GKMIVSKPLYV 204
              +  + L V
Sbjct: 63  RYELKGRKLVV 73

This subfamily corresponds to the RRM1 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. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M 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 = 76

>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family

 Score = 44.3 bits (104), Expect = 1e-04
 Identities = 32/101 (31%), Positives = 40/101 (39%), Gaps = 10/101 (9%)

Query: 226 PVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMP 285
           P +  P      P  PP P  L Q  ++ Q  P+  PPQ  FG  Q  VP +       P
Sbjct: 259 PSSRHPQSSHHGPG-PPMPHALQQGPVFLQ-HPSSNPPQ-PFGLAQSQVPPLPLPSQAQP 315

Query: 286 NFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPP 326
           +   P      Q Q+P       P +Q   P P MPH  PP
Sbjct: 316 HSHTPPSQSALQPQQP-------PREQPLPPAPSMPHIKPP 349

Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Length = 979

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 26/68 (38%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE-- 87
          +FV NL   TT EDL   F   G   S  ++ D   GKSK   FV F+ A+   KA++  
Sbjct: 3  LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 88 --ALNGKK 93
             L G+K
Sbjct: 63 HTLLKGRK 70

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

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 86
          N + ++ L  S T+ED++     +G       +MR    G S+ F FV F + ++A + +
Sbjct: 3  NTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWM 62

Query: 87 EALNGK 92
          E   GK
Sbjct: 63 ELNQGK 68

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|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           ++I  L      + L E  S FG +  C +  DP +G S+G GFV F       + L   
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 191 --EMNGKMIVSK 200
             +++GK+I  K
Sbjct: 62  EHKLDGKLIDPK 73

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which 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 = 76

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

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 9/67 (13%)

Query: 31 VFVKNLDESTTDEDLKKIFGEY--GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          ++V+NL  STT+E +K  F ++  G +     +RD       + FV+F N +DA  A+  
Sbjct: 4  LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD-------YAFVHFFNREDAVAAMSV 56

Query: 89 LNGKKFD 95
          +NGK  D
Sbjct: 57 MNGKCID 63

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|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 = 40.2 bits (95), Expect = 2e-04
 Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 11/70 (15%)

Query: 138 NLGDSIDDEKLKELF-------SEFGTITSCKVMRDPSGISKGSG----FVAFSTPEEAS 186
              +  DDE+ +E+         ++G + S  + R  +      G    FV F+  E+A 
Sbjct: 11  TPEELEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQ 70

Query: 187 RALAEMNGKM 196
           +A   + G+ 
Sbjct: 71  KAQLALAGRK 80

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

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 20/73 (27%), Positives = 36/73 (49%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           NL+I NL  ++ + +L+  F ++G I    + R   G      F+ F   + A RA   M
Sbjct: 10  NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAM 69

Query: 193 NGKMIVSKPLYVA 205
           +G++I   P+ + 
Sbjct: 70  SGRVIGRNPIKIG 82

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

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           L++  L  S+ +  L+E FS FGT++  ++++   +G  +G  ++   T E   +  
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKC 58

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
          V+V NLDE  T+E L ++F + G + +  + +D      + +GFV F + +DA  A++ +
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 90 NGKK 93
          N  K
Sbjct: 61 NMIK 64

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|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            +Y+  +       +L++ F  FG I    +     G +   GFV +    +A RA+   
Sbjct: 4   VIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN--YGFVTYRYACDAFRAIEHG 61

Query: 193 N 193
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 18/65 (27%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
          N+++  L  + T +D++ +F  +G I ++ V+ D   G S+   F+ F+   +A +A+ +
Sbjct: 2  NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 89 LNGKK 93
           NG K
Sbjct: 62 FNGHK 66

This subgroup corresponds to the RRM2 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|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 6/70 (8%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITS--AVVMRDGDGKSKCFGFVNFENADDAAKAV 86
            + + N+      EDL  +   YGT+ +   V  +  +  +     V +E+ + A +AV
Sbjct: 1  RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKS-ETATV---NVTYESPEQAQQAV 56

Query: 87 EALNGKKFDD 96
            LNG +++ 
Sbjct: 57 NKLNGHEYEG 66

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 5/68 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          ++V  L   T+  +L++ F  +G I   +    G      + ++ +E+ + A  A EAL 
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRR-IDYDPGRN----YAYIEYESIEAAQAAKEALR 55

Query: 91 GKKFDDRE 98
          G       
Sbjct: 56 GFPLGGPG 63

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 12/73 (16%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTI----TSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           L+++N+  +++DE+L+ LF +FG I    T+CK         +G   V++     A RA 
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTLYTACK--------HRGFIMVSYYDIRAARRAK 55

Query: 190 AEMNGKMIVSKPL 202
             + G  +  + L
Sbjct: 56  RALQGTELGGRKL 68

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

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

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 23/60 (38%), Positives = 34/60 (56%), Gaps = 4/60 (6%)

Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
          + NLD + + E L+ IF  YG +     +R+   K +   FV F +  DAAKA+ A+NGK
Sbjct: 6  IFNLDPTVSSETLRSIFQVYGDVKE---LRETPCK-REQRFVEFFDVRDAAKALRAMNGK 61

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|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITS--------AVVMRDGDGKSKCFGFVNFENADDA 82
          +++  L +  T++ L ++FG  G I            +  D + + K    V +++   A
Sbjct: 1  IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 83 AKAVEALNGKKF 94
            A+E  NG +F
Sbjct: 61 QAAIEWFNGYEF 72

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.8 bits (92), Expect = 2e-04
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
          N++++ L   TTD+DL K+   YG I S   + D +  + K +GFV+F++   A KAV +
Sbjct: 6  NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65

Query: 89 L 89
          L
Sbjct: 66 L 66

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It 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. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEY-GTITSAVVMRDGDGKSKC-FGFVNFENADDAAKAV 86
             +FV  L     + +L  +F  + G   S +V ++  G  K   GFV+F +A  AA A+
Sbjct: 1   RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAM 60

Query: 87  EALNGKKFDDREWYV 101
           +AL G +FD     V
Sbjct: 61  DALQGYRFDPDTSSV 75

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

>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 = 39.7 bits (93), Expect = 2e-04
 Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALN 90
          FV  +  +  ++DL+ +F ++G I    V++D   G  K   F+ +   + A KA  AL+
Sbjct: 9  FVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSALH 68

Query: 91 GKK 93
           +K
Sbjct: 69 EQK 71

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

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 15/64 (23%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L ++NL   ID   L+ L  + G + +  +      +  G+  + +S+ EEA++A + +N
Sbjct: 4   LVLRNLTPQIDGSTLRTLCMQHGPLLTFHL-----NLRHGNALIRYSSKEEAAKAQSALN 58

Query: 194 GKMI 197
             ++
Sbjct: 59  NCVL 62

This subfamily corresponds to the RRM of the GW182 family which includes three paralogs of TNRC6 (GW182-related) proteins comprising GW182/TNGW1, TNRC6B (containing three isoforms) and TNRC6C in mammal, a single Drosophila ortholog (dGW182, also called Gawky) and two Caenorhabditis elegans orthologs AIN-1 and AIN-2, which contain multiple miRNA-binding sites and have important functions in miRNA-mediated translational repression, as well as mRNA degradation in Metazoa. The GW182 family proteins directly interact with Argonaute (Ago) proteins, and thus function as downstream effectors in the miRNA pathway, responsible for inhibition of translation and acceleration of mRNA decay. Members in this family are characterized by an abnormally high content of glycine/tryptophan (G/W) repeats, one or more glutamine (Q)-rich motifs, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The only exception is the worm protein that does not contain a recognizable RRM domain. The GW182 family proteins are recruited to miRNA targets through an interaction between their N-terminal domain and an Argonaute protein. Then they promote translational repression and/or degradation of miRNA targets through their C-terminal silencing domain. . Length = 71

>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 29 NNVFVKNLDESTTDED-LKK--IFGEYGTITSAVVMRDGDGKSK---CFG-FVNFENADD 81
          N V+V  L     DE+ LKK   FG+YG I   V+ R+             +V +   +D
Sbjct: 6  NLVYVVGLPPRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKED 65

Query: 82 AAKAVEALNGKKFDDR 97
          A + ++A++G   D R
Sbjct: 66 ALRCIQAVDGFYLDGR 81

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 89
          VFV NL     +E L ++FG+ G I    ++RD      K F +V F++ +   KA+  L
Sbjct: 2  VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL-LL 60

Query: 90 NGKKF 94
          N KKF
Sbjct: 61 NEKKF 65

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|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 194
           ++  +  S+ ++ LKE FS  G +T  ++  D    ++   FV F+  E A  AL  ++G
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR-FAFVEFADAESALSAL-NLSG 61

Query: 195 KMIVSKPLYV 204
            ++   PL V
Sbjct: 62  TLLGGHPLRV 71

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + V  +D S +++DLK+ F   G +T   +  D    ++ F FV F +A+ A  A+  L+
Sbjct: 3  IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR-FAFVEFADAESALSALN-LS 60

Query: 91 GK 92
          G 
Sbjct: 61 GT 62

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V+V NL       +L++ F  YG + +  + R+  G    F FV FE+  DA  AV  L+
Sbjct: 2  VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLD 57

Query: 91 GK 92
          GK
Sbjct: 58 GK 59

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

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 15/64 (23%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
          +FV ++  + T+++++ +F E+G +    +++D   G  +   FV +   D+A +A+ AL
Sbjct: 2  LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 90 NGKK 93
          + ++
Sbjct: 62 HNQR 65

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

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAV--- 86
          +FV  + E T +  L+  F EYG I +  ++ D   GK + FGFV F++ D   K V   
Sbjct: 3  LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQK 62

Query: 87 -EALNGKKFDDRE 98
             +NG   + R+
Sbjct: 63 YHTINGHNAEVRK 75

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

 Score = 39.0 bits (91), Expect = 3e-04
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
           + +++ N+ +    E+L+ LF  +G + SC VMR          FV       A RA+ E
Sbjct: 1   VKIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ-------FAFVHLRGEAAADRAIEE 53

Query: 192 MNGKMIVSKPLYV 204
           +NG+ +  + L V
Sbjct: 54  LNGRELHGRKLVV 66

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

 Score = 39.5 bits (92), Expect = 3e-04
 Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L++  L   + +  L E FS+FG +   +V+ D  +G  +G GFV F   + A +A A +
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA-AVV 60

Query: 193 NGKMIVSKPLYVAVAQRKEE 212
               I    + V  A  KEE
Sbjct: 61  KFHPINGHRVEVKKAVPKEE 80

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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           ++++NL      + LK+ F+E G +    +  + +G SKG G V F +PE A RA   MN
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVRFESPEVAERACRMMN 60

Query: 194 G 194
           G
Sbjct: 61  G 61

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 5/67 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FV NL    T+ED KK+F +YG  +   + RD     + FGF+  E+   A  A   L+
Sbjct: 4  LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD 58

Query: 91 GKKFDDR 97
          G    +R
Sbjct: 59 GTILKNR 65

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

>gnl|CDD|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 = 3e-04
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE-- 87
          +FV  L   TT +DLK+ F ++G +    +  D   G+S+ FGFV F++A    K ++  
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 88 --ALNGKKFDDR 97
             L+G+  D +
Sbjct: 61 EHKLDGRVIDPK 72

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|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 8/80 (10%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDPSGISKGSGFVAFSTPEEA 185
           +YI  L D + ++ L ELF   G I           K+  D     KG   V +  P  A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 186 SRALAEMNGKMIVSKPLYVA 205
             A+   NG       + V+
Sbjct: 61  QAAIEWFNGYEFRGNKIKVS 80

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +Y+ NLG      +L+  FS +G + +  + R+P G +    FV F  P +A  A+  ++
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFA----FVEFEDPRDAEDAVRGLD 57

Query: 194 GKMIVSKPLYVAVA 207
           GK+I    + V ++
Sbjct: 58  GKVICGSRVRVELS 71

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|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           L ++NL   + +E L+E FS+FG +    V+ D  G S G G V F++   A +A 
Sbjct: 2   LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAF 57

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 19/63 (30%), Positives = 35/63 (55%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           G  ++I  L   + +++L  L  + G I   ++M D +G ++G  FV FS  +EA  A+ 
Sbjct: 1   GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIK 60

Query: 191 EMN 193
           ++N
Sbjct: 61  QLN 63

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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 86
          +FV  + E T +  L+  F +YG I +  VM D   GK + F FV F++ D   K V
Sbjct: 3  IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIV 59

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|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 21/56 (37%), Positives = 31/56 (55%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           L +KNL   + +E L++ FS+FG +    V+ D  G   G GFV F+    A +AL
Sbjct: 2   LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKAL 57

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>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 = 38.9 bits (91), Expect = 3e-04
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 5/70 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEA- 88
          +FV  L   TT+E +++ FG++G I    + M     K + F F+ F++ +   K +E  
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQ 61

Query: 89 ---LNGKKFD 95
             + GKK +
Sbjct: 62 FHVIGGKKVE 71

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 30 NVFVKNLDESTTDEDLKKIF-GEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           V V NL +  T+  +++ F  + G I   ++  +  GKS     + F+ A DA KA + 
Sbjct: 1  KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 89 LNGKKFDDR 97
           NG+  D  
Sbjct: 61 FNGRIDDGN 69

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

 Score = 42.6 bits (100), Expect = 4e-04
 Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 2/94 (2%)

Query: 124 ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP 182
            T  +     +++  L     +  L E FS+ G +   + ++D  S  SKG  +V F   
Sbjct: 82  LTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDV 141

Query: 183 EEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
           E   +ALA + G+M++ +P+ V  +Q ++ R A+
Sbjct: 142 ESVIKALA-LTGQMLLGRPIIVQSSQAEKNRAAK 174

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

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L++  L     + KL+  F E+G I   +++RD  +G  +G  F+ F    +   A    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 193 NGKMI 197
           +GK I
Sbjct: 64  DGKKI 68

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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 17/63 (26%), Positives = 33/63 (52%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          N+++ NL  S  +++L+ +   +G + S  ++RD  G S+  GF   E+ +     +   
Sbjct: 2  NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITHF 61

Query: 90 NGK 92
          NGK
Sbjct: 62 NGK 64

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has 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. MSSP-2 contains 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 as well as induction of apoptosis. . Length = 86

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 136 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK 195
           +  L +    + LK+   + G +T   V RD  G     G V F++ E+  RAL +++G 
Sbjct: 5   VSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGE----GVVEFTSQEDMERALRKLDGT 60

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 39.5 bits (92), Expect = 4e-04
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAV 86
          +FV+NL    T+E L   F ++G++  A  V+    G++K  GFV F++       +
Sbjct: 4  LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L + NL   I D++L+ LFS+FG +   K +R  + +     FV F     A  AL  +N
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEV---KDIR-ETPLRPSQKFVEFYDIRAAEAALDALN 59

Query: 194 GKMIVSKPLYVA 205
           G+  +   L V 
Sbjct: 60  GRPFLGGRLKVK 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|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 91
          F+  +++   +  ++  F ++G   S +V      ++KC GFV FE  + A K   A++ 
Sbjct: 6  FLFGVEDDLPEYKIRDYFEQFGKSKSVIVNH----RAKC-GFVRFETREAAEKFAAAISE 60

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

>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 25/62 (40%), Positives = 34/62 (54%), Gaps = 6/62 (9%)

Query: 42 DEDLK-KIFGE---YGTITSAVVMRDGDGKSKCF--GFVNFENADDAAKAVEALNGKKFD 95
          DEDLK +I  E   YG + + +V      ++      FV F +AD+A KAV ALNG+ F 
Sbjct: 16 DEDLKDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFFG 75

Query: 96 DR 97
           R
Sbjct: 76 GR 77

This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. 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 RRMs and a C-terminal UHM domain. . Length = 85

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 42.7 bits (100), Expect = 4e-04
 Identities = 40/181 (22%), Positives = 53/181 (29%), Gaps = 5/181 (2%)

Query: 218 QAQFSQMRPVAMGP-SVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPG 276
           Q Q   M     GP        M  PG  G G Q    Q        Q     QQQL   
Sbjct: 174 QGQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQ 233

Query: 277 MRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLG 336
                  M     P  +Q Q GQ+  G+ G  P Q     + +   Q PP+    +  LG
Sbjct: 234 Q---QQQMDQQQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLG 290

Query: 337 RNMQDF-PFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLG 395
                      G       P+      P      GQ +    +S         + R + G
Sbjct: 291 MLPNQMQQMPGGGQGGPGQPMGPPPQRPGAVPQGGQAVQQGVMSAGQQQLKQMKLRNMRG 350

Query: 396 E 396
           +
Sbjct: 351 Q 351

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

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

 Score = 38.3 bits (90), Expect = 5e-04
 Identities = 17/63 (26%), Positives = 33/63 (52%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          VFV  +     +++L  +F + G I    +M D  G ++ + FV + N + A +AV+ L+
Sbjct: 4  VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 91 GKK 93
            +
Sbjct: 64 NYE 66

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

 Score = 38.3 bits (89), Expect = 5e-04
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++KNL  +I  ++LKE+F +   I   ++     G SKG  ++ F T  EA +AL E  
Sbjct: 6   LFVKNLPYNITVDELKEVFEDAVDI---RLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQ 62

Query: 194 G 194
           G
Sbjct: 63  G 63

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|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 133 NLYIKNLGDSIDDE----KLKELFSEFGTITSCKVMRDPSGISKGS-GFVAFSTPEEASR 187
            LY+  +   + +E     L   FS+FG + S KV  + +  + G   FV F +   ASR
Sbjct: 2   TLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASR 61

Query: 188 ALAEMNGK-MIVSKPLYVAV 206
           A    NGK +    PL V  
Sbjct: 62  AQKACNGKWLFQGSPLKVRF 81

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|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 38.2 bits (89), Expect = 5e-04
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 9/68 (13%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK---CFGFVNFENADDAAKAVE 87
          ++V NL      +D++ +F +YG I      RD D K++    F FV FE+  DA  AV 
Sbjct: 2  IYVGNLPPDIRTKDIEDLFYKYGAI------RDIDLKNRRGPPFAFVEFEDPRDAEDAVY 55

Query: 88 ALNGKKFD 95
            +G  +D
Sbjct: 56 GRDGYDYD 63

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

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

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 25/67 (37%), Positives = 38/67 (56%), Gaps = 3/67 (4%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALN 90
          FV NL  +T   DL  IF +  ++ S  ++RD +  K K F +V FE+ +   +A+E  +
Sbjct: 5  FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YD 62

Query: 91 GKKFDDR 97
          G  FDDR
Sbjct: 63 GALFDDR 69

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|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6 (LARP6) and similar proteins

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 20/80 (25%), Positives = 30/80 (37%), Gaps = 17/80 (21%)

Query: 38  ESTTDEDLKKIFGEYGTITSAVVMRDGD----------------GKSKCFGFVNFENADD 81
           E +T E + ++F   G I    ++R G                 G  +C   V FE  + 
Sbjct: 11  EESTIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKEC-AVVEFEKLEA 69

Query: 82  AAKAVEALNGKKFDDREWYV 101
           A KAVE L+ +        V
Sbjct: 70  ARKAVEELSARDDWRDGIKV 89

This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 21/56 (37%), Positives = 29/56 (51%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           L +KNL   + +E L+E FS FG +    V+ D  G   G G V F+    A +AL
Sbjct: 2   LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKAL 57

This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional 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. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score = 38.3 bits (89), Expect = 6e-04
 Identities = 20/71 (28%), Positives = 34/71 (47%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL   + +E + ELF + G +   K+ +D  G  K   FV F        A+  +N
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 194 GKMIVSKPLYV 204
           G  +  +PL +
Sbjct: 64  GIKLYGRPLNI 74

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|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast asparagine-rich protein (ARP) and similar proteins

 Score = 38.6 bits (90), Expect = 6e-04
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 8/79 (10%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFG-------TITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
           LYI NL       +L+  F+++G       T+ +       S     SGF  F + EEA 
Sbjct: 3   LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62

Query: 187 RALAEMNGKMIVSKPLYVA 205
            ALA +NG+ +  + + V 
Sbjct: 63  EALA-LNGRCLGERAIEVQ 80

This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response. . Length = 88

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 148 LKELFSEFGTITSCKVMRDPSGISK--GSGFVAFSTPEEASRA 188
           L+ELFS FG + + ++ +  +G     G GFV F T ++A RA
Sbjct: 17  LRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59

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

 Score = 38.2 bits (89), Expect = 6e-04
 Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 142 SIDDEKLKELFSEFGTITSCKVMRDPS---GISKGSGFVAFSTPEEASRA 188
           S  ++ L+ELF ++G +    V+RD S     SKG  FV F T + A  A
Sbjct: 12  SWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 61

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

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

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 7/62 (11%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +V  L E  T++DL+  F ++G I S  VV R      +C  FV F   + A KA E L 
Sbjct: 5  YVGGLGERVTEKDLRDHFYQFGEIRSITVVPR-----QQC-AFVTFTTREAAEKAAERLF 58

Query: 91 GK 92
           K
Sbjct: 59 NK 60

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

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

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMN 193
           YI NL   I ++ ++E F     ITS ++  D  +G  KG G V F+  E    AL +++
Sbjct: 3   YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KLD 60

Query: 194 GKMIVSKPLYVA 205
           G ++  +P+ +A
Sbjct: 61  GTVLCGRPIRIA 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|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 37.9 bits (89), Expect = 7e-04
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 11/77 (14%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI--------SKGSGFVAFSTPEEA 185
           LY+ NL   I +E+L + F++   + +  + + P            K   FV F T EEA
Sbjct: 4   LYVGNLPPGITEEELVDFFNQ--AMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEA 61

Query: 186 SRALAEMNGKMIVSKPL 202
           + ALA ++G +   +PL
Sbjct: 62  TAALA-LDGIIFKGQPL 77

The subfamily corresponds to the RRM1 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 = 82

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

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 5/66 (7%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          N V++  LDES T++ L + F  YG +   V+ R      +    V F+  + A  AV  
Sbjct: 8  NCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDR-----QRGQALVFFDKVEAAQAAVNE 62

Query: 89 LNGKKF 94
          + G+K 
Sbjct: 63 MKGRKL 68

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

 Score = 41.6 bits (97), Expect = 8e-04
 Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKA 85
           KFN ++V ++    ++ D+K +F  +G I    + R   G   K +GF+ + N    ++A
Sbjct: 203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEA 262

Query: 86  VEALN 90
           + ++N
Sbjct: 263 IASMN 267

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

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           +++  L  +  ++ +K+ FS+FG +    +M D  +   +G GFV F + +   +     
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 191 --EMNGKMIVSK 200
             E+N KM+  K
Sbjct: 62  FHEINNKMVECK 73

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

 Score = 38.1 bits (88), Expect = 8e-04
 Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 4/64 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +Y+ NLG++ +  +L+  F  +G + S  V R+P G +    FV F  P +A+ A+ E++
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRELD 62

Query: 194 GKMI 197
           G+ +
Sbjct: 63  GRTL 66

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|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 38.1 bits (88), Expect = 8e-04
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 9/77 (11%)

Query: 134 LYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
           LY++NL  S  +E +++ F+    G +   K +RD         FV FS  E+A  A+  
Sbjct: 11  LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRD-------YAFVHFSNREDAVDAMNA 63

Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NGK+I   P+ V +A+
Sbjct: 64  LNGKVIDGSPIEVTLAK 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|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 38.2 bits (89), Expect = 8e-04
 Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 1/71 (1%)

Query: 25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAA 83
          KT +       L E    E L   F ++G + S  V  +        + FV F +A  A+
Sbjct: 1  KTLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAAS 60

Query: 84 KAVEALNGKKF 94
          +A +A NGK  
Sbjct: 61 RAQKACNGKWL 71

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

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 15/79 (18%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCK--VMRDPSGISK------GSGFVAFSTPEEA 185
           LY+ NL     +E++ ELFS  G I   K  +M    G+ +      G  FV + T E+A
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDI---KRIIM----GLDRFTKTPCGFCFVEYYTREDA 53

Query: 186 SRALAEMNGKMIVSKPLYV 204
             A+  +NG  +  + + V
Sbjct: 54  ENAVKYLNGTKLDDRIIRV 72

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|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 29/149 (19%), Positives = 41/149 (27%), Gaps = 4/149 (2%)

Query: 234 PPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVS 293
           PP+ P   P P    Q+ L  +   A +  +       Q    + P G P      P   
Sbjct: 136 PPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQG 195

Query: 294 QGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGR---NMQDFPFDMGAGS 350
             +Q           P Q   Q     P Q P         L +    +Q   F   +  
Sbjct: 196 PPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPA-QPPLPPQLPQQPPPLQQPQFPGLSQQ 254

Query: 351 MLPVPVDMGAGIPRRDASVGQPMPITALS 379
           M P P        +      QP P    +
Sbjct: 255 MPPPPPQPPQQQQQPPQPQAQPPPQNQPT 283

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

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

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 10/73 (13%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVM---RDPSGISKGSGFVAFSTPEEASRAL 189
           NL++  L  +     LK LF ++G + S KV+   R P   +K  G V  S+  E +R +
Sbjct: 1   NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPG--AKCYGIVTMSSSAEVARCI 58

Query: 190 A-----EMNGKMI 197
           +     E++G+ I
Sbjct: 59  SHLHRTELHGQQI 71

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

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAE 191
           NLYI+ L     D+ L +L   +G I S K + D +    KG GFV F +P  A +A+  
Sbjct: 3   NLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 62

Query: 192 M 192
           +
Sbjct: 63  L 63

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has 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. MSSP-2 contains 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 as well as induction of apoptosis. . Length = 75

>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 = 20/47 (42%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNF 76
          +F+  L   TT E L++ FG++G +   +VMRD   K S+ FGFV F
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49

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

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 134 LYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
           LY++NL  S  +E +K  F++F  G +   K +RD         FV F   E+A  A++ 
Sbjct: 4   LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD-------YAFVHFFNREDAVAAMSV 56

Query: 192 MNGKMIVSKPLYVAVAQ 208
           MNGK I    + V +A+
Sbjct: 57  MNGKCIDGASIEVTLAK 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|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 = 37.8 bits (88), Expect = 0.001
 Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L++  +  +++++ L+ LF +FG I    V++D  +G+ KG  F+ +   E A +A + +
Sbjct: 8   LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67

Query: 193 NGK 195
           + +
Sbjct: 68  HEQ 70

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|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 21/55 (38%), Positives = 31/55 (56%)

Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
          VKNL    ++E L++ F ++G +  AVV+ D  G+    GFV F     A KA+E
Sbjct: 4  VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALE 58

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>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 = 37.4 bits (87), Expect = 0.001
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELF-SEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
            + + NL   + + +++E F S+ G I    +  +  G S G   + F    +A++A  +
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 192 MNGKMIVSK 200
            NG++    
Sbjct: 61  FNGRIDDGN 69

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|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 5/59 (8%)

Query: 143 IDDE---KLKELFSEFGTITSCKVMRDPSGISKGS--GFVAFSTPEEASRALAEMNGKM 196
           ID++   +++E   ++G + +  V    S  +  +   FV FS  +EA +A+  +NG+ 
Sbjct: 15  IDEDLKDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRF 73

This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. 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 RRMs and a C-terminal UHM domain. . Length = 85

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 3/68 (4%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          V++ NL    T++D+++ F     ITS  +  D + G+ K FG V+F + +    A++ L
Sbjct: 2  VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK-L 59

Query: 90 NGKKFDDR 97
          +G     R
Sbjct: 60 DGTVLCGR 67

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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 19/60 (31%), Positives = 31/60 (51%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          VFV  +     +++L  +F   G I    +M D DGK++ + FV +    +A +AV  LN
Sbjct: 4  VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63

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|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 9/67 (13%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS--GFVAFSTPEEASRA 188
           G+ L I ++G  +  E +K +F++FG +            ++G+  G++ F TPE A +A
Sbjct: 1   GVILKITSIGPGVTREDIKAVFAQFGEVKYVD-------FTEGADTGYIRFKTPEAAQKA 53

Query: 189 LAEMNGK 195
                 K
Sbjct: 54  REAFVEK 60

This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), 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. LARP7 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. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

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

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 2/65 (3%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V+V NL     + +++ +F +YG I   + ++    +   + F+ FE+A DA  A+   +
Sbjct: 2  VYVGNLPGDIREREVEDLFYKYGPIVD-IDLKLPP-RPPGYAFIEFEDARDAEDAIRGRD 59

Query: 91 GKKFD 95
          G  FD
Sbjct: 60 GYDFD 64

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|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 7/65 (10%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
          N +++ NL+ES T  DL+K+F ++  + +   +++ G      + FV+  +   A KA+E
Sbjct: 2  NKLYIGNLNESVTPADLEKVFEDHKISYSGQFLVKSG------YAFVDCPDEQWAMKAIE 55

Query: 88 ALNGK 92
            +GK
Sbjct: 56 TFSGK 60

This subgroup corresponds to the RRM1 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. IGF2BP1 promotes mRNA stabilization; it functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD and stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS). . Length = 77

>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +    L++ T+ ED+K+ F ++G +   V   +GD +    G+V F+  + A KA+E   
Sbjct: 4  LKFSGLNKPTSREDIKEAFSQHGEV-KYVDFLEGDKE----GYVRFKTPEAAKKALEKAT 58

Query: 91 --GKKFDDREW 99
              K  + E 
Sbjct: 59 EAKLKIKEAEV 69

This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif. Length = 102

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

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMR-DPSGISKGSGFVAFSTPEEASRAL 189
           L++ NL     +++L+  F   G I   ++M  + SG  KG  FV F   E A+ AL
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

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|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTIT--SCKVMRD-PSGISKGSGFVAFSTPEEASRALA 190
           LY+ NL     DE L+   +E G +   S K      +G SKG  +V F++   A+    
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 191 EMNGKMIVSKPLYVA 205
           ++ G+    K   V 
Sbjct: 61  KLEGREFNGKKCVVT 75

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 33  VKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEALNG 91
           + NL  + T +  +++   +G +    +V  +  G SK +GFV +   D AA+A   L G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 92  KKFDDREWYV 101
           K+   R  YV
Sbjct: 64  KQLGSRTLYV 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|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 9/77 (11%)

Query: 134 LYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
           LY++NL     ++ +K+ F +F  G +   K +RD         FV F++ E+A  A+  
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD-------YAFVHFTSREDAVHAMNN 56

Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  +    + V +A+
Sbjct: 57  LNGTELEGSCIEVTLAK 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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 7/64 (10%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL     +++++ LF ++G +  C ++       K  GFV       A  A+  ++
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDII-------KNYGFVHMDDKTAADEAIRNLH 55

Query: 194 GKMI 197
              +
Sbjct: 56  HYKL 59

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

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 29  NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           + +++ NL+E    ++LKK    IF  +G I   +V R    + +   FV F+    A  
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 61

Query: 85  AVEALNGKKFDDREWYVGKAQKKSE 109
           A+ ++ G  F D+   +  A+  S+
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSD 86

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), 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 and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENADDAAKAV 86
          + + V+N+    T ++L+++F  +G + +  + +   G G  + FGFV+F    DA +A 
Sbjct: 1  SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 87 EAL 89
          +AL
Sbjct: 61 KAL 63

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +++  L +S+ ++ L   FS +G +    + R      +G   V F   E A  A+ EM 
Sbjct: 10  VWLDGLDESVTEQYLTRHFSRYGPVVHVVIDR-----QRGQALVFFDKVEAAQAAVNEMK 64

Query: 194 GKMIVSKPLYV 204
           G+ +  + L V
Sbjct: 65  GRKLGGRKLQV 75

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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 17/63 (26%), Positives = 34/63 (53%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           G  +++  +   + +++L  +F   G I   ++M D  G ++G  FV ++   EA RA+ 
Sbjct: 1   GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVR 60

Query: 191 EMN 193
           E+N
Sbjct: 61  ELN 63

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

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +Y   +   + ++ +++ FS FG I   +V  D     KG  FV F++ E A+ A+  +N
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD-----KGYSFVRFNSHESAAHAIVSVN 57

Query: 194 GKMI 197
           G  I
Sbjct: 58  GTTI 61

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

>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 5/63 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +    + E T+ EDLK+ F E+G + + V    G  +    G+V F+  + A +A+E L 
Sbjct: 4  LHFSGVGEQTSREDLKEAFEEFGEV-AWVDFARGQTE----GYVRFKEENAAKEALEKLK 58

Query: 91 GKK 93
            K
Sbjct: 59 EAK 61

This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 76

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 8/70 (11%)

Query: 134 LYIKNLGDSIDD-EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           +  KN+ D ++D + L+  F +FG     KV R      K S  V F     A  ALA+ 
Sbjct: 3   IQCKNIPDELNDKDWLERHFGKFG-----KVARVYCNPRKKSAVVHFFDHASA--ALAKK 55

Query: 193 NGKMIVSKPL 202
            GK++  KP+
Sbjct: 56  KGKLLQHKPI 65

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

>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +YI+NL  S+   +LK+ F  FG I  CKV+    G  +  GF+ +   E A+ +L +  
Sbjct: 5   IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRG--EKYGFITYRHSEHAALSLGKGA 62

Query: 194 GKMIVSKP 201
                ++P
Sbjct: 63  SLRKRNEP 70

This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 79

>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 11/72 (15%)

Query: 144 DDEKLKELFSEF-----------GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           D+E L   F EF           G +   KV  +     +G+ +V + + EEA  A    
Sbjct: 30  DEEDLYSDFEEFYDDVLPEFEKFGEVVQFKVCCNYEPHLRGNVYVQYQSEEEALAAFKMF 89

Query: 193 NGKMIVSKPLYV 204
           NG+    K L  
Sbjct: 90  NGRWYAGKQLTC 101

This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. . Length = 105

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 10/70 (14%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK----CFGFVNFENADDAAKAV 86
          ++V NL     ++DL+ +F +YG I      RD + K++     F FV FE+  DA  AV
Sbjct: 2  IYVGNLPSDVREKDLEDLFYKYGRI------RDIELKNRRGLVPFAFVRFEDPRDAEDAV 55

Query: 87 EALNGKKFDD 96
             NG  F  
Sbjct: 56 FGRNGYDFGQ 65

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 134 LYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           ++I NL    +    ++ +FS++G I  C V        KG  FV +     A  A+A  
Sbjct: 4   VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGE 56

Query: 193 NGKMIVSKPLYVAVA 207
           +G+MI  + L + +A
Sbjct: 57  DGRMIAGQVLDINLA 71

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

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

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 11/79 (13%)

Query: 133 NLYIKN--LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           +L + N  LG+ +  E+L  +F ++GT+    VM       K   FV++S+ E+A+ A  
Sbjct: 3   HLVVANGGLGNGVSREELLRVFEKYGTVEDL-VMP----PGKPYCFVSYSSIEDAAAAYD 57

Query: 191 EMNGKMIV----SKPLYVA 205
            +NGK +     +KPLY++
Sbjct: 58  ALNGKELELPQQNKPLYLS 76

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 26/77 (33%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 133 NLYIKNLGDSIDDEKLKE-LFSEF---GTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 188
            + +KNL     D  LK+ LF EF   G +TS KV    S   +    V F  PE+A +A
Sbjct: 1   GIIVKNLPLRSSDTSLKDGLFHEFKKHGKVTSVKVHGTGS---ERYAIVFFRKPEDAEKA 57

Query: 189 LAEMNGKMIVSKPLYVA 205
           L    GK+     + V 
Sbjct: 58  LEVSKGKLFFGAEIEVT 74

This subfamily corresponds to the RRM2 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|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 31 VFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 86
          +++ NL+E    E+LKK    IF ++G I   V ++    K +   FV F++   A  A+
Sbjct: 2  IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALK--TLKMRGQAFVVFKDISSATNAL 59

Query: 87 EALNGKKFDDR 97
           ++ G  F D+
Sbjct: 60 RSMQGFPFYDK 70

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila 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). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

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

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMR-DGDGKSKCFGFVNFENADDAAKAVEAL 89
          V+V  +   +T+++++  F   G I    +M     G+ +   F+ F+  ++AAK   AL
Sbjct: 1  VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKT-EEAAKRALAL 59

Query: 90 NGKKFDDR 97
          +G+    R
Sbjct: 60 DGEDMGGR 67

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|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 18/63 (28%), Positives = 35/63 (55%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           G  +++  +   + +++L  LF   G I   ++M + SG ++G  FV ++T EEA  A+ 
Sbjct: 1   GCEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIR 60

Query: 191 EMN 193
            +N
Sbjct: 61  ILN 63

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), 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 = 78

>gnl|CDD|240701 cd12255, RRM1_LKAP, RNA recognition motif 1 in Limkain-b1 (LKAP) and similar proteins

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 4/64 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L + NL  +ID  +++            KV+     +S G+  + F   + A RAL  MN
Sbjct: 5   LVVSNLPTNIDPSRIRNRLKRLSDNCGGKVLS----VSGGTAIIRFPNQDSARRALKRMN 60

Query: 194 GKMI 197
           G+ +
Sbjct: 61  GEDV 64

This subfamily corresponds to the RRM1 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes. . Length = 73

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 145 DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 204
           D  L+++F  FG +    ++       K  G+  ++  E A RA+  ++GK +    L V
Sbjct: 13  DYILEDVFCRFGGLIDVYLVPG-----KNYGYAKYADRESAERAITTLHGKEVNGVKLKV 67

This subfamily corresponds to the RRM4 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 = 68

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

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 7/64 (10%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          VF  N +      +++++FG+YG +   V M+ G      F FV  E+  DA  A+  L+
Sbjct: 3  VFCGNFEYDARQSEIERLFGKYGRV-DRVDMKSG------FAFVYMEDERDAEDAIRGLD 55

Query: 91 GKKF 94
            +F
Sbjct: 56 NFEF 59

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

>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 16/64 (25%), Positives = 34/64 (53%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           G  ++I  +   + +++L  LF   GT+   ++M   SG+++G  +  +S    AS A+A
Sbjct: 1   GSEVFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIA 60

Query: 191 EMNG 194
            ++ 
Sbjct: 61  TLHN 64

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that 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. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           G  +++  +   + +++L  LF + G I   ++M DP +G+++G  FV F T E A  A+
Sbjct: 1   GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60

Query: 190 AEMNGKMI 197
              N   I
Sbjct: 61  KLYNNHEI 68

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	472
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.98
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.97
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.96
smart00517	64	PolyA C-terminal domain of Poly(A)-binding protein	99.96
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.95
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.95
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.95
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
PF00658	72	PABP: Poly-adenylate binding protein, unique domai	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.93
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.93
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.92
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.92
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.92
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.92
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.92
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.92
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.91
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.91
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.9
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.87
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.87
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.84
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.81
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.8
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.76
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.76
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.74
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.71
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.7
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.7
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.68
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.64
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.64
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.63
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.63
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.62
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.61
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.61
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.6
KOG0122	270	consensus Translation initiation factor 3, subunit	99.59
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.57
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.57
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.56
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.54
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.54
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.53
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.53
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.5
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.49
PLN03120	260	nucleic acid binding protein; Provisional	99.49
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.45
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.45
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.44
PLN03213	759	repressor of silencing 3; Provisional	99.44
smart00362	72	RRM_2 RNA recognition motif.	99.43
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.41
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.4
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.4
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.4
PLN03121	243	nucleic acid binding protein; Provisional	99.39
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.38
KOG0122	270	consensus Translation initiation factor 3, subunit	99.38
PLN03120	260	nucleic acid binding protein; Provisional	99.37
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.37
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.36
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.36
smart00360	71	RRM RNA recognition motif.	99.36
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.34
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.34
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.34
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.33
smart00362	72	RRM_2 RNA recognition motif.	99.32
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.3
PLN03213	759	repressor of silencing 3; Provisional	99.28
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.27
PLN03121	243	nucleic acid binding protein; Provisional	99.26
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.26
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.25
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.25
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.24
smart00360	71	RRM RNA recognition motif.	99.23
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.23
smart00361	70	RRM_1 RNA recognition motif.	99.22
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.22
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	99.21
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.2
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.19
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.18
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.18
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.18
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.17
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.17
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.16
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.15
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.14
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.12
KOG0226	290	consensus RNA-binding proteins [General function p	99.1
smart00361	70	RRM_1 RNA recognition motif.	99.1
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.1
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.06
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.06
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.03
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.99
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.97
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.96
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.96
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.95
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.93
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.91
KOG0226	290	consensus RNA-binding proteins [General function p	98.91
KOG4210	285	consensus Nuclear localization sequence binding pr	98.87
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.83
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.83
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.82
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.81
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.76
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.75
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.69
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.69
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.65
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.61
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.6
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.58
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.54
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.48
KOG0151	877	consensus Predicted splicing regulator, contains R	98.43
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.43
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.33
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.33
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.31
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.3
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.22
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.21
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.16
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.15
KOG0151	877	consensus Predicted splicing regulator, contains R	98.08
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.08
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.07
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.04
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.04
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.04
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.9
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.7
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.67
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.64
KOG2314	698	consensus Translation initiation factor 3, subunit	97.6
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.6
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.59
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.59
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.54
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	97.44
KOG4210	285	consensus Nuclear localization sequence binding pr	97.42
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.3
KOG0943	3015	consensus Predicted ubiquitin-protein ligase/hyper	97.24
KOG3152	278	consensus TBP-binding protein, activator of basal	97.21
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.21
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.14
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.0
KOG2314	698	consensus Translation initiation factor 3, subunit	96.97
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.93
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.79
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.73
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	96.7
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.68
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.64
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.54
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.51
KOG3152	278	consensus TBP-binding protein, activator of basal	96.34
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.32
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	95.89
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.87
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.79
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.75
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.71
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.66
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.64
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.61
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.4
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.09
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.74
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	94.57
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.22
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	94.14
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.14
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.01
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.55
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.38
KOG2068	327	consensus MOT2 transcription factor [Transcription	93.29
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.2
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	92.61
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	92.58
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	92.44
KOG2893	341	consensus Zn finger protein [General function pred	92.0
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	91.87
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.88
KOG2591	684	consensus c-Mpl binding protein, contains La domai	90.79
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.01
KOG2591	684	consensus c-Mpl binding protein, contains La domai	89.72
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	89.28
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	89.14
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	88.49
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	87.87
KOG2135	526	consensus Proteins containing the RNA recognition	87.04
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	86.72
KOG2135	526	consensus Proteins containing the RNA recognition	86.51
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	86.23
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	86.03
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	85.22
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	83.91
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	81.78

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

Probab=100.00  E-value=7.2e-68  Score=568.72  Aligned_cols=405  Identities=49%  Similarity=0.771  Sum_probs=291.8

Q ss_pred             CcccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHH
Q 012034            1 MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENAD   80 (472)
Q Consensus         1 ~~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e   80 (472)
                      +.++|++|+|+.++++.+|.. .....+++|||+||+.++|+++|+++|++||.|.++.+++|.+|+++|||||+|++.+
T Consensus       152 ~~~~~~~i~v~~~~~~~~~~~-~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e  230 (562)
T TIGR01628       152 MLLNDKEVYVGRFIKKHEREA-APLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHE  230 (562)
T ss_pred             cEecCceEEEecccccccccc-ccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHH
Confidence            457899999999999888852 2346789999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHCCCccC----CcceeeeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccC
Q 012034           81 DAAKAVEALNGKKFD----DREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFG  156 (472)
Q Consensus        81 ~A~~Av~~lng~~i~----g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G  156 (472)
                      +|.+|++.|++..+.    |+.|+|.++.++.++..++...++....+......+++|||+||++++|+++|+++|+.||
T Consensus       231 ~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G  310 (562)
T TIGR01628       231 DAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECG  310 (562)
T ss_pred             HHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcC
Confidence            999999999999999    9999999999999988888777776666666677889999999999999999999999999


Q ss_pred             ceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHHHHHHHHHHhhhcCCCCCCCCCCCCC
Q 012034          157 TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPR  236 (472)
Q Consensus       157 ~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~pp~  236 (472)
                      .|++|+|+.+.+|.++|||||+|.+.++|.+|+..|||+.++|++|+|.++.+++.+...++.++.+..+....  .+. 
T Consensus       311 ~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~~~~~~~~~~q~~~~~~~--~~~-  387 (562)
T TIGR01628       311 EITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQ--LPM-  387 (562)
T ss_pred             CeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHHHHHHHHHHHHHhhhhccC--CCC-
Confidence            99999999998999999999999999999999999999999999999999999999999888887763321111  010 


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCccCccCCCCCCCCCCCCCCCCCCCCCCC
Q 012034          237 MPMYPPGPSGLGQQFLYGQAPPAIIPPQA-GFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQ  315 (472)
Q Consensus       237 ~~~~pp~~~g~g~~~~~g~~p~~~~pp~~-~~~~~~~~~p~~~p~~~~~p~~~~p~~~~~~~~~~~~~~~g~~p~~~~~~  315 (472)
                         ..+..+.++++.++++.+.+++++++ +|+..+           +++..++++.+.++     .   +..++.+++.
T Consensus       388 ---~~p~~~~~~~p~~~~~~~~~~~~~~p~~~~~~~-----------~~~~~~~~~~~~~p-----~---~~~~~~~~~~  445 (562)
T TIGR01628       388 ---GSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMS-----------MMPTPMGPGGPLRP-----N---GLAPMNAVRA  445 (562)
T ss_pred             ---CCCCCCcccCCCccCCCCcccCCCCCCCCCCCC-----------CCCCCCCCCCCCCC-----C---CCCCCCcCCC
Confidence               00111111122222222211111111 111000           00000000000000     0   0000000000


Q ss_pred             CCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCccccchhhhhcCCHHHHHHHh
Q 012034          316 PLPIMPHQMPPR-GHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLL  394 (472)
Q Consensus       316 ~~p~~~~~~~~~-~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~q~~~~  394 (472)
                      +.....+...+. .+.++++++.+.  .+          .++.    +++.+...+.+.+.++++++||+++|++||++|
T Consensus       446 ~~~~~~~~~~~~~~~~~~~~p~~~~--~~----------~~~~----~~~~~~~~~~~~~~~~~~~~la~~~p~~q~~~l  509 (562)
T TIGR01628       446 PSRNAQNAAQKPPMQPVMYPPNYQS--LP----------LSQD----LPQPQSTASQGGQNKKLAQVLASATPQMQKQVL  509 (562)
T ss_pred             CCcccccccccccCCCcCCCccccC--CC----------CCcc----cccccCCccccccchhHHHHHhhCCHHHHHHHH
Confidence            000000000000 011222222110  00          0000    110010112223456799999999999999999


Q ss_pred             hhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHH
Q 012034          395 GESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLR  447 (472)
Q Consensus       395 g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~  447 (472)
                      ||+|||+|++++|++|+||||||||||++|||+||||+|+|++||+||++||+
T Consensus       510 g~~~~~~~~~~~~~~~~~~tgm~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (562)
T TIGR01628       510 GERLFPLVEAIEPALAAKITGMLLEMDNSELLHLLESPELLKSKVDEALEVLK  562 (562)
T ss_pred             HHHhHHHHHhhChhhcCcceEEEecCCHHHHHHHhcCHHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999999999994

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.2e-33  Score=259.42  Aligned_cols=178  Identities=28%  Similarity=0.529  Sum_probs=158.9

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .-.|||+.|..+++.|+||+.|.+||+|.+++|++| .|++|||||||.|-+.++|++||..|||..|.+|.|+-.||.+
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            556999999999999999999999999999999999 6899999999999999999999999999999999999999998


Q ss_pred             chhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHH
Q 012034          107 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS  186 (472)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~  186 (472)
                      |..........+++....  ....+|++||+|+...+||++||+.|+.||.|.+|+|+++     +||+||.|++.|+|.
T Consensus       142 Kp~e~n~~~ltfdeV~NQ--ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGYaFVrF~tkEaAa  214 (321)
T KOG0148|consen  142 KPSEMNGKPLTFDEVYNQ--SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGYAFVRFETKEAAA  214 (321)
T ss_pred             CccccCCCCccHHHHhcc--CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cceEEEEecchhhHH
Confidence            874332222233433332  2345789999999999999999999999999999999998     899999999999999


Q ss_pred             HHHHHhCCcEecCeeEEEEEcccHHH
Q 012034          187 RALAEMNGKMIVSKPLYVAVAQRKEE  212 (472)
Q Consensus       187 ~Ai~~l~g~~i~gk~l~V~~a~~k~~  212 (472)
                      +||..+|+.+|+|..+++.|-+....
T Consensus       215 hAIv~mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  215 HAIVQMNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             HHHHHhcCceeCceEEEEeccccCCC
Confidence            99999999999999999999887644

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=2.7e-32  Score=272.75  Aligned_cols=169  Identities=31%  Similarity=0.553  Sum_probs=154.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||+++||++|+++|+.||+|.+|+|+.| .+++++|||||+|.++++|++||+.||+..|.++.|.|.+
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            456899999999999999999999999999999999999 5899999999999999999999999999999999999998


Q ss_pred             cccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCH
Q 012034          104 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP  182 (472)
Q Consensus       104 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~  182 (472)
                      +.....                  ....++|||+||+.++|+++|+++|++||.|++++|+++. +++++|||||+|.+.
T Consensus       184 a~p~~~------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~  245 (346)
T TIGR01659       184 ARPGGE------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKR  245 (346)
T ss_pred             cccccc------------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCH
Confidence            864321                  1124589999999999999999999999999999999886 789999999999999


Q ss_pred             HHHHHHHHHhCCcEecC--eeEEEEEcccHH
Q 012034          183 EEASRALAEMNGKMIVS--KPLYVAVAQRKE  211 (472)
Q Consensus       183 ~~A~~Ai~~l~g~~i~g--k~l~V~~a~~k~  211 (472)
                      ++|.+||+.||+..+.+  ++|.|.+++...
T Consensus       246 e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       246 EEAQEAISALNNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             HHHHHHHHHhCCCccCCCceeEEEEECCccc
Confidence            99999999999999876  689999988754

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).

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

Probab=99.98  E-value=3.7e-30  Score=276.75  Aligned_cols=196  Identities=42%  Similarity=0.662  Sum_probs=170.7

Q ss_pred             cccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHH
Q 012034            2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADD   81 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~   81 (472)
                      .|+|+.|.|....+..    .......++|||+|||.++|+++|+++|++||.|.+|+|..|.+|+++|||||+|++.++
T Consensus        66 ~i~gk~i~i~~s~~~~----~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~  141 (562)
T TIGR01628        66 RLGGKPIRIMWSQRDP----SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEES  141 (562)
T ss_pred             EECCeeEEeecccccc----cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHH
Confidence            3677877775543221    222345778999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCccCCcceeeeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEE
Q 012034           82 AAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC  161 (472)
Q Consensus        82 A~~Av~~lng~~i~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v  161 (472)
                      |.+|++.+||..+.++.|+|.+...+.++..             ......++|||+||+.++|+++|+++|+.||.|+++
T Consensus       142 A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~~-------------~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~  208 (562)
T TIGR01628       142 AKAAIQKVNGMLLNDKEVYVGRFIKKHEREA-------------APLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSA  208 (562)
T ss_pred             HHHHHHHhcccEecCceEEEecccccccccc-------------ccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEE
Confidence            9999999999999999999988766654420             112234689999999999999999999999999999


Q ss_pred             EEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec----CeeEEEEEcccHHHHH
Q 012034          162 KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV----SKPLYVAVAQRKEERR  214 (472)
Q Consensus       162 ~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~----gk~l~V~~a~~k~~~~  214 (472)
                      .++++.+|.++|||||+|.+.++|.+|++.++|..+.    |+.++|.+++.+.++.
T Consensus       209 ~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~  265 (562)
T TIGR01628       209 AVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAERE  265 (562)
T ss_pred             EEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhH
Confidence            9999999999999999999999999999999999999    9999999998887664

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

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

Probab=99.97  E-value=1.3e-30  Score=273.58  Aligned_cols=178  Identities=24%  Similarity=0.430  Sum_probs=154.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+||++++++++|+++|++||.|.+|.+++| .+|++||||||+|++.++|.+|++.|||..|.|+.|.|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            56789999999999999999999999999999999999 58999999999999999999999999999999999999876


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHH
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE  183 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~  183 (472)
                      ............     .  .......++|||+||+.++++++|+++|+.||.|++++|.++. +|+++|||||+|.+.+
T Consensus       185 ~~~p~a~~~~~~-----~--~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e  257 (612)
T TIGR01645       185 SNMPQAQPIIDM-----V--QEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQ  257 (612)
T ss_pred             cccccccccccc-----c--cccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHH
Confidence            543221110000     0  0011123589999999999999999999999999999999986 5789999999999999


Q ss_pred             HHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          184 EASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       184 ~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +|.+|++.||+..|+|+.|+|.++...
T Consensus       258 ~A~kAI~amNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       258 SQSEAIASMNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             HHHHHHHHhCCCeeCCeEEEEEecCCC
Confidence            999999999999999999999988754

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.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.97  E-value=2.2e-29  Score=245.60  Aligned_cols=184  Identities=27%  Similarity=0.451  Sum_probs=148.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccC-Ccceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFD-DREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~-g~~l~V~~  103 (472)
                      ..-+.|||+.||.|+.|++|..+|++.|+|.++++|.| -+|.+||||||.|.++++|++||+.||+++|. |+.|.|+.
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            45688999999999999999999999999999999999 68999999999999999999999999999884 66666654


Q ss_pred             cccc----------hhHHHHHHHHHHh------------------------------------hhhh-------------
Q 012034          104 AQKK----------SEREQELKGQFEQ------------------------------------AMKE-------------  124 (472)
Q Consensus       104 a~~~----------~~~~~~~~~~~~~------------------------------------~~~~-------------  124 (472)
                      +..+          ...+.++......                                    .+..             
T Consensus       161 Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~  240 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAI  240 (506)
T ss_pred             eeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcc
Confidence            4221          1111111111100                                    0000             


Q ss_pred             ------------hccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHh
Q 012034          125 ------------TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM  192 (472)
Q Consensus       125 ------------~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l  192 (472)
                                  .....+-..|||+||+.++|+|.|+++|++||.|+.|+.++|       ||||+|.+.++|.+|++.+
T Consensus       241 tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~  313 (506)
T KOG0117|consen  241 TVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKET  313 (506)
T ss_pred             eeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHh
Confidence                        000001124999999999999999999999999999999877       9999999999999999999


Q ss_pred             CCcEecCeeEEEEEcccHHHHHHH
Q 012034          193 NGKMIVSKPLYVAVAQRKEERRAR  216 (472)
Q Consensus       193 ~g~~i~gk~l~V~~a~~k~~~~~~  216 (472)
                      ||++|+|..|.|.+|+...+++..
T Consensus       314 ngkeldG~~iEvtLAKP~~k~k~~  337 (506)
T KOG0117|consen  314 NGKELDGSPIEVTLAKPVDKKKKE  337 (506)
T ss_pred             cCceecCceEEEEecCChhhhccc
Confidence            999999999999999988766544

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=9.2e-30  Score=258.23  Aligned_cols=204  Identities=27%  Similarity=0.433  Sum_probs=161.1

Q ss_pred             ccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHH
Q 012034            3 INDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADD   81 (472)
Q Consensus         3 ~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~   81 (472)
                      |.|++|.|.......      .....++|||+|||.++++++|+++|++||.|..+.++.+. ++.++|||||+|++.++
T Consensus        70 l~g~~i~v~~a~~~~------~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~  143 (352)
T TIGR01661        70 LQNKTIKVSYARPSS------DSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDE  143 (352)
T ss_pred             ECCeeEEEEeecccc------cccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHH
Confidence            556666665432221      12356789999999999999999999999999999999884 78899999999999999


Q ss_pred             HHHHHHHHCCCccCC--cceeeeccccchhHHH-HHHHH---H-----H-------------------------------
Q 012034           82 AAKAVEALNGKKFDD--REWYVGKAQKKSEREQ-ELKGQ---F-----E-------------------------------  119 (472)
Q Consensus        82 A~~Av~~lng~~i~g--~~l~V~~a~~~~~~~~-~~~~~---~-----~-------------------------------  119 (472)
                      |.+|++.|||..+.|  ..|.|.++........ .....   .     .                               
T Consensus       144 A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  223 (352)
T TIGR01661       144 ADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFT  223 (352)
T ss_pred             HHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhh
Confidence            999999999999887  4678887754331100 00000   0     0                               


Q ss_pred             h-----------------hh-----------------hhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEee
Q 012034          120 Q-----------------AM-----------------KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMR  165 (472)
Q Consensus       120 ~-----------------~~-----------------~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~  165 (472)
                      .                 ..                 ........+.+|||+||++++++++|+++|++||.|++++|++
T Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~  303 (352)
T TIGR01661       224 AVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIR  303 (352)
T ss_pred             hhhhhhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeE
Confidence            0                 00                 0000012234699999999999999999999999999999999


Q ss_pred             CC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHHH
Q 012034          166 DP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEE  212 (472)
Q Consensus       166 ~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~  212 (472)
                      |. +|.++|||||+|.+.++|.+|+..|||..|+|+.|+|.|+..+..
T Consensus       304 d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       304 DLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             cCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            97 899999999999999999999999999999999999999987753

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

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=1.8e-30  Score=260.96  Aligned_cols=224  Identities=63%  Similarity=0.954  Sum_probs=211.0

Q ss_pred             CcccCeeEEEcCcccchhhhhhhc--cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCC
Q 012034            1 MLINDKQVFVGHFLRKQERETVAI--KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFEN   78 (472)
Q Consensus         1 ~~~~~k~v~v~~~~~~~~r~~~~~--~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~   78 (472)
                      |+++|++||||.|.++.+|.....  ...++++||+|++.+.+++.|+++|+.||.|.++.++.+..|+++||+||+|++
T Consensus       138 ~ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~  217 (369)
T KOG0123|consen  138 MLLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFEN  217 (369)
T ss_pred             cccCCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecC
Confidence            578999999999999999975544  377999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHCCCccCCcceeeeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCce
Q 012034           79 ADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTI  158 (472)
Q Consensus        79 ~e~A~~Av~~lng~~i~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I  158 (472)
                      +++|..|++.|++..+.+..|+|.+++++.++...++..++.............+|||+|++..++++.|+++|+.||.|
T Consensus       218 ~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI  297 (369)
T KOG0123|consen  218 PEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEI  297 (369)
T ss_pred             hhHHHHHHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccce
Confidence            99999999999999999999999999999999999998888888888778889999999999999999999999999999


Q ss_pred             EEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHHHHHHHHHHhhhcC
Q 012034          159 TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQM  224 (472)
Q Consensus       159 ~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~~~~~~~~~~~~  224 (472)
                      ++++|+.+..|.++||+||+|.+.++|.+|+..+|+..+.+++++|.+++++..++.+++..+.+.
T Consensus       298 ~s~kv~~~~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~r~~~~~~~~~~~  363 (369)
T KOG0123|consen  298 TSAKVMVDENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKEDRRARLQAVFGAR  363 (369)
T ss_pred             eeEEEEeccCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhccchhhhhhhccee
Confidence            999999999999999999999999999999999999999999999999999988888877766554

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=2.2e-29  Score=255.52  Aligned_cols=167  Identities=34%  Similarity=0.630  Sum_probs=151.5

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      +.++|||+|||.++||++|+++|++||+|.+|+|++| .+|+++|||||+|.+.++|.+||+.|||..|.|+.|.|.++.
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            4689999999999999999999999999999999998 479999999999999999999999999999999999999986


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEE  184 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~  184 (472)
                      .+..                  ...+++|||+||+..+++++|+++|+.||.|..++++.+. ++.++|||||+|.+.++
T Consensus        82 ~~~~------------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~  143 (352)
T TIGR01661        82 PSSD------------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDE  143 (352)
T ss_pred             cccc------------------ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHH
Confidence            5321                  1234589999999999999999999999999999998875 67899999999999999


Q ss_pred             HHHHHHHhCCcEecC--eeEEEEEcccHH
Q 012034          185 ASRALAEMNGKMIVS--KPLYVAVAQRKE  211 (472)
Q Consensus       185 A~~Ai~~l~g~~i~g--k~l~V~~a~~k~  211 (472)
                      |.+|++.|||..+.|  .+|.|.++....
T Consensus       144 A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       144 ADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             HHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            999999999999876  678888886553

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

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.96  E-value=2.3e-29  Score=244.34  Aligned_cols=172  Identities=30%  Similarity=0.576  Sum_probs=150.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCc-cCC--cceee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKK-FDD--REWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~-i~g--~~l~V  101 (472)
                      ...-++||+.||+.|+|+||+++|++||.|.+|.|++|+ ++.++|||||.|.+.++|.+|+.+||+.. |.|  ..|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            456679999999999999999999999999999999994 89999999999999999999999998765 555  46777


Q ss_pred             eccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCC
Q 012034          102 GKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFST  181 (472)
Q Consensus       102 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s  181 (472)
                      ++|....++-                 ....+|||+-|+..+||.+++++|++||.|++|.|++|.++.|||||||+|++
T Consensus       112 k~Ad~E~er~-----------------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fst  174 (510)
T KOG0144|consen  112 KYADGERERI-----------------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFST  174 (510)
T ss_pred             cccchhhhcc-----------------ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEeh
Confidence            7776543321                 11236999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhCCcE-ec--CeeEEEEEcccHHHHH
Q 012034          182 PEEASRALAEMNGKM-IV--SKPLYVAVAQRKEERR  214 (472)
Q Consensus       182 ~~~A~~Ai~~l~g~~-i~--gk~l~V~~a~~k~~~~  214 (472)
                      .+.|..||+.|||.. +.  ..+|.|+||..+.++.
T Consensus       175 ke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~  210 (510)
T KOG0144|consen  175 KEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKD  210 (510)
T ss_pred             HHHHHHHHHhhccceeeccCCCceEEEecccCCCch
Confidence            999999999999965 43  5699999998875554

>smart00517 PolyA C-terminal domain of Poly(A)-binding protein

Probab=99.96  E-value=1e-29  Score=186.35  Aligned_cols=64  Identities=61%  Similarity=0.944  Sum_probs=62.1

Q ss_pred             CHHHHHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHH
Q 012034          386 SPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSV  449 (472)
Q Consensus       386 ~~~~q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~  449 (472)
                      +|++||++|||+|||+|++++|++|+||||||||||++|||+||+|+++|++||+||++||++|
T Consensus         1 ~p~~qkq~LGE~Lyp~V~~~~p~~A~KITGMLLEmd~~ell~lle~~~~L~~kv~EA~~vl~~~   64 (64)
T smart00517        1 PPQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRSKVDEALEVLKSH   64 (64)
T ss_pred             CHHHHHHHHhHHHhHHHHhhCcccCCcCeeeeeCCCHHHHHHHhcCHHHHHHHHHHHHHHHHhC
Confidence            5789999999999999999999999999999999999999999999999999999999999875

Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly)

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.95  E-value=1.5e-27  Score=250.50  Aligned_cols=179  Identities=31%  Similarity=0.500  Sum_probs=153.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      +...++|||+|||.++|+++|+++|++||.|.+|.++.| .+|+++|||||+|.+.++|.+||. |+|..+.|+.|.|..
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            345789999999999999999999999999999999999 579999999999999999999996 899999999999987


Q ss_pred             cccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCH
Q 012034          104 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP  182 (472)
Q Consensus       104 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~  182 (472)
                      +............      .........++|||+||+..+|+++|+++|+.||.|.+|.+..+. +|.++|||||+|.+.
T Consensus       165 ~~~~~~~~~~~~~------~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~  238 (457)
T TIGR01622       165 SQAEKNRAAKAAT------HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDA  238 (457)
T ss_pred             cchhhhhhhhccc------ccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCH
Confidence            6543322211000      000011125689999999999999999999999999999999886 468999999999999


Q ss_pred             HHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          183 EEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       183 ~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ++|.+|+..|||..|.|+.|.|.|+...
T Consensus       239 e~A~~A~~~l~g~~i~g~~i~v~~a~~~  266 (457)
T TIGR01622       239 EEAKEALEVMNGFELAGRPIKVGYAQDS  266 (457)
T ss_pred             HHHHHHHHhcCCcEECCEEEEEEEccCC
Confidence            9999999999999999999999998743

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.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.95  E-value=4.8e-27  Score=246.48  Aligned_cols=180  Identities=26%  Similarity=0.409  Sum_probs=143.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccC-Ccceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD-DREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~-g~~l~V~~a  104 (472)
                      ...++|||+|||+++||++|+++|++||.|.+++|+.|.+|++||||||+|.+.|+|++||+.||+..|. ++.|.|.++
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            4568999999999999999999999999999999999999999999999999999999999999998885 565555443


Q ss_pred             ccc----------hhHHHHHHHHHH----------------------------------------hh---h---------
Q 012034          105 QKK----------SEREQELKGQFE----------------------------------------QA---M---------  122 (472)
Q Consensus       105 ~~~----------~~~~~~~~~~~~----------------------------------------~~---~---------  122 (472)
                      ...          ...+.++...+.                                        ..   .         
T Consensus       136 ~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~  215 (578)
T TIGR01648       136 VDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIA  215 (578)
T ss_pred             ccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEE
Confidence            210          000000000000                                        00   0         


Q ss_pred             ------h---hhccccccceeeeecCCCCccHHHHHHHHhcc--CceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHH
Q 012034          123 ------K---ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE  191 (472)
Q Consensus       123 ------~---~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~--G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~  191 (472)
                            .   +........+|||+||++++|+++|+++|+.|  |.|++|++++       +||||+|.+.++|.+|++.
T Consensus       216 VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r-------gfAFVeF~s~e~A~kAi~~  288 (578)
T TIGR01648       216 VDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR-------DYAFVHFEDREDAVKAMDE  288 (578)
T ss_pred             EEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec-------CeEEEEeCCHHHHHHHHHH
Confidence                  0   00001123579999999999999999999999  9999998764       4999999999999999999


Q ss_pred             hCCcEecCeeEEEEEcccHHH
Q 012034          192 MNGKMIVSKPLYVAVAQRKEE  212 (472)
Q Consensus       192 l~g~~i~gk~l~V~~a~~k~~  212 (472)
                      ||+..|+|+.|.|.|+..+..
T Consensus       289 lnG~~i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       289 LNGKELEGSEIEVTLAKPVDK  309 (578)
T ss_pred             hCCCEECCEEEEEEEccCCCc
Confidence            999999999999999987543

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.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=3.2e-27  Score=215.67  Aligned_cols=169  Identities=31%  Similarity=0.607  Sum_probs=155.9

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      +...+||.|.=||.++|+|||+.+|+..|+|++|++++|+ +|.|.|||||+|.+++||++||..|||..+..+.|+|.+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            5678999999999999999999999999999999999995 899999999999999999999999999999999999999


Q ss_pred             cccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCH
Q 012034          104 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP  182 (472)
Q Consensus       104 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~  182 (472)
                      |.+.++                  ...+.+|||.+||...|..+|+.+|+.||.|..-+|..|. +|.+||.+||.|+..
T Consensus       118 ARPSs~------------------~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr  179 (360)
T KOG0145|consen  118 ARPSSD------------------SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKR  179 (360)
T ss_pred             ccCChh------------------hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecch
Confidence            987654                  3456699999999999999999999999999988888875 899999999999999


Q ss_pred             HHHHHHHHHhCCcEec--CeeEEEEEcccHH
Q 012034          183 EEASRALAEMNGKMIV--SKPLYVAVAQRKE  211 (472)
Q Consensus       183 ~~A~~Ai~~l~g~~i~--gk~l~V~~a~~k~  211 (472)
                      .+|+.||..|||..-.  ..+|.|+|+....
T Consensus       180 ~EAe~AIk~lNG~~P~g~tepItVKFannPs  210 (360)
T KOG0145|consen  180 IEAEEAIKGLNGQKPSGCTEPITVKFANNPS  210 (360)
T ss_pred             hHHHHHHHhccCCCCCCCCCCeEEEecCCcc
Confidence            9999999999998764  4689999998763

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

Probab=99.94  E-value=6.9e-26  Score=238.42  Aligned_cols=202  Identities=23%  Similarity=0.344  Sum_probs=154.5

Q ss_pred             cccCeeEEEcCcccch-hhhhh-----hccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEE
Q 012034            2 LINDKQVFVGHFLRKQ-ERETV-----AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVN   75 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~-~r~~~-----~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~   75 (472)
                      .|+|+.|+|....++. .|...     .......+|||+||++++|+++|+++|++||.|.+|.|+++.   .+|+|||+
T Consensus        64 ~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~---~~~~afVe  140 (481)
T TIGR01649        64 YIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN---NVFQALVE  140 (481)
T ss_pred             eEcCeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC---CceEEEEE
Confidence            5789999998775443 22110     112345689999999999999999999999999999998863   25799999


Q ss_pred             eCCHHHHHHHHHHHCCCccCC--cceeeeccccchh--------------------HHHHHHH----HHHhh--------
Q 012034           76 FENADDAAKAVEALNGKKFDD--REWYVGKAQKKSE--------------------REQELKG----QFEQA--------  121 (472)
Q Consensus        76 F~~~e~A~~Av~~lng~~i~g--~~l~V~~a~~~~~--------------------~~~~~~~----~~~~~--------  121 (472)
                      |++.++|.+|++.|||..|.+  +.|.|.|+.....                    ++..+..    .....        
T Consensus       141 f~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (481)
T TIGR01649       141 FESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSY  220 (481)
T ss_pred             ECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccC
Confidence            999999999999999999965  4677777653211                    0000000    00000        


Q ss_pred             ----------------------------hh-------h----h------ccccccceeeeecCCC-CccHHHHHHHHhcc
Q 012034          122 ----------------------------MK-------E----T------VDKFQGLNLYIKNLGD-SIDDEKLKELFSEF  155 (472)
Q Consensus       122 ----------------------------~~-------~----~------~~~~~~~~l~V~nL~~-~~t~e~L~~~F~~~  155 (472)
                                                  ..       .    .      .....+++|||+||++ .+|+++|+++|+.|
T Consensus       221 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~y  300 (481)
T TIGR01649       221 GHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVY  300 (481)
T ss_pred             CCcccccCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhc
Confidence                                        00       0    0      0012457899999997 69999999999999


Q ss_pred             CceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          156 GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       156 G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      |.|.+|+|+++    ++|||||+|.+.++|.+|+..|||..|.|++|+|.+++..
T Consensus       301 G~V~~vki~~~----~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       301 GNVERVKFMKN----KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CCeEEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            99999999986    4799999999999999999999999999999999987554

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).

>PF00658 PABP: Poly-adenylate binding protein, unique domain; InterPro: IPR002004 The polyadenylate-binding protein (PABP) has a conserved C-terminal domain (PABC), which is also found in the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains (IPR000569 from INTERPRO) []

Probab=99.94  E-value=2.3e-27  Score=180.65  Aligned_cols=71  Identities=61%  Similarity=0.915  Sum_probs=69.3

Q ss_pred             ccchhhhhcCCHHHHHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHH
Q 012034          376 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL  446 (472)
Q Consensus       376 ~~~~~~la~~~~~~q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l  446 (472)
                      +.+++.|+++++++||++|||+|||+|..++|++|+||||||||||++||++||+|++.|++||+||++||
T Consensus         2 ~~~~~~la~~~~~~qk~~LGe~Ly~~V~~~~p~~A~KITGMLLe~~~~ell~ll~~~~~L~~kv~eA~~vL   72 (72)
T PF00658_consen    2 PLTASALASASPEQQKQILGERLYPLVQAIYPELAGKITGMLLEMDNSELLHLLEDPELLREKVQEAIEVL   72 (72)
T ss_dssp             STSHHHHHTSCHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTSCHHHHHHHHHTHHHHHHHHHHHHHHH
T ss_pred             cchHHHHhcCCHHHHHHHHhccccHHHHHhCcchhHHHHHHHhcCCHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999997

PABP recognises the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilisation/degradation. PABC domains of PABP are peptide-binding domains that mediate PABP homo-oligomerisation and protein-protein interactions. In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail [].; GO: 0003723 RNA binding; PDB: 3KUR_E 1JH4_A 2RQH_B 3KUI_A 3KUS_A 3KUJ_A 3KTR_A 2X04_A 3PTH_A 1JGN_A ....

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

Probab=99.93  E-value=1.1e-25  Score=236.77  Aligned_cols=178  Identities=20%  Similarity=0.307  Sum_probs=144.3

Q ss_pred             CcceEEeCCCCC-CCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDE-STTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~-~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+||++ ++|+++|+++|+.||.|.+|+|+.+    ++|||||+|.+.++|.+|++.|||..|.|+.|+|.++.
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~----~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~  349 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN----KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSK  349 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            567999999997 6999999999999999999999987    36899999999999999999999999999999999875


Q ss_pred             cchhHHHH-------HH--HHHHhhhhhhc----------cccccceeeeecCCCCccHHHHHHHHhccCc--eEEEEEe
Q 012034          106 KKSEREQE-------LK--GQFEQAMKETV----------DKFQGLNLYIKNLGDSIDDEKLKELFSEFGT--ITSCKVM  164 (472)
Q Consensus       106 ~~~~~~~~-------~~--~~~~~~~~~~~----------~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~--I~~v~i~  164 (472)
                      ........       ..  ..+......+.          ....+.+|||+|||+++|+++|+++|+.||.  |+.++++
T Consensus       350 ~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~  429 (481)
T TIGR01649       350 QQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFF  429 (481)
T ss_pred             cccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEe
Confidence            54221100       00  00000000000          0123568999999999999999999999998  8889987


Q ss_pred             eCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCee------EEEEEccc
Q 012034          165 RDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP------LYVAVAQR  209 (472)
Q Consensus       165 ~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~------l~V~~a~~  209 (472)
                      .+.++ ++++|||+|.+.++|.+|+..||+..|.++.      |+|++++.
T Consensus       430 ~~~~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       430 PKDNE-RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             cCCCC-cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccC
Confidence            65444 5899999999999999999999999999885      88888865

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).

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.93  E-value=4.8e-25  Score=234.56  Aligned_cols=186  Identities=19%  Similarity=0.293  Sum_probs=147.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|+.||.|..+.|+++ .+|+++|||||+|.+.++|..|++.|||..|.|+.|.|.++
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            34579999999999999999999999999999999998 58999999999999999999999999999999999999998


Q ss_pred             ccchhHHHHHHH--------HHHh--hhhhhccccccceeeeecCCCC--c--------cHHHHHHHHhccCceEEEEEe
Q 012034          105 QKKSEREQELKG--------QFEQ--AMKETVDKFQGLNLYIKNLGDS--I--------DDEKLKELFSEFGTITSCKVM  164 (472)
Q Consensus       105 ~~~~~~~~~~~~--------~~~~--~~~~~~~~~~~~~l~V~nL~~~--~--------t~e~L~~~F~~~G~I~~v~i~  164 (472)
                      ............        ....  ............+|+|.|+...  +        ..++|+++|++||.|++|+|+
T Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~  452 (509)
T TIGR01642       373 CVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIP  452 (509)
T ss_pred             ccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEee
Confidence            543211100000        0000  0000011223457899998531  1        236899999999999999998


Q ss_pred             eCC----CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHH
Q 012034          165 RDP----SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       165 ~~~----~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      ++.    .+.+.|++||+|.+.++|.+|+..|||..|+|+.|.|.|.....
T Consensus       453 ~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~~~  503 (509)
T TIGR01642       453 RPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGEDC  503 (509)
T ss_pred             ccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCHHH
Confidence            752    34568999999999999999999999999999999999976543

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=1.6e-25  Score=222.97  Aligned_cols=183  Identities=31%  Similarity=0.464  Sum_probs=157.8

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      .||||++||.+++.++|.++|+.+|.|..++++.+. ++.+||||||+|.-.||+++|+...+++.+.|+.|.|..+.++
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            789999999999999999999999999999999984 6789999999999999999999999999999999999999876


Q ss_pred             hhHHHHHHHHHHhhhhh------hcc--ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEc
Q 012034          108 SEREQELKGQFEQAMKE------TVD--KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF  179 (472)
Q Consensus       108 ~~~~~~~~~~~~~~~~~------~~~--~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f  179 (472)
                      ...+.......+...+.      ...  ....+.|.|.||||.+.+.+|..+|+.||.|.+|.|++..+|+-.|||||.|
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~f  165 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQF  165 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEE
Confidence            65442221111111110      111  1225689999999999999999999999999999999988888889999999


Q ss_pred             CCHHHHHHHHHHhCCcEecCeeEEEEEcccHH
Q 012034          180 STPEEASRALAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       180 ~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      .+..+|.+|++.+|+..|+|++|-|.||-.+.
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            99999999999999999999999999997763

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=8.6e-25  Score=199.83  Aligned_cols=202  Identities=29%  Similarity=0.446  Sum_probs=162.2

Q ss_pred             ccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHH
Q 012034            3 INDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADD   81 (472)
Q Consensus         3 ~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~   81 (472)
                      |..|.|.|....+..+      ..+..||||.+||+.+|..||+.+|++||.|..-+|..| .+|.+||.|||.|...++
T Consensus       108 LQ~KTIKVSyARPSs~------~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~E  181 (360)
T KOG0145|consen  108 LQNKTIKVSYARPSSD------SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIE  181 (360)
T ss_pred             eccceEEEEeccCChh------hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhH
Confidence            4557777776544332      356788999999999999999999999999877778777 689999999999999999


Q ss_pred             HHHHHHHHCCCccCCc--ceeeeccccchhHH--HHHHHHH--------------------H--------hhh-----hh
Q 012034           82 AAKAVEALNGKKFDDR--EWYVGKAQKKSERE--QELKGQF--------------------E--------QAM-----KE  124 (472)
Q Consensus        82 A~~Av~~lng~~i~g~--~l~V~~a~~~~~~~--~~~~~~~--------------------~--------~~~-----~~  124 (472)
                      |+.||+.|||..-.|+  .|.|+++...+...  ..+...+                    +        ..+     .+
T Consensus       182 Ae~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d  261 (360)
T KOG0145|consen  182 AEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTID  261 (360)
T ss_pred             HHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCcccc
Confidence            9999999999987665  78998886543221  0000000                    0        000     00


Q ss_pred             ----------hccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhC
Q 012034          125 ----------TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN  193 (472)
Q Consensus       125 ----------~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~  193 (472)
                                ......+++|||-||..+.+|.-|+++|..||.|..|+|++|. ++++|||+||.+.+.++|..||..||
T Consensus       262 ~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLN  341 (360)
T KOG0145|consen  262 GMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLN  341 (360)
T ss_pred             ccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhc
Confidence                      0011235789999999999999999999999999999999996 48999999999999999999999999


Q ss_pred             CcEecCeeEEEEEcccH
Q 012034          194 GKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       194 g~~i~gk~l~V~~a~~k  210 (472)
                      |..+++|.|.|+|...+
T Consensus       342 Gy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  342 GYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             CccccceEEEEEEecCC
Confidence            99999999999987654

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.92  E-value=2.1e-25  Score=194.41  Aligned_cols=171  Identities=32%  Similarity=0.554  Sum_probs=152.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....+|||+||+..+|++-|.++|-+.|.|.++.+.+|. +...+|||||+|.++|+|.-|++-||...+-|+.|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            346789999999999999999999999999999999994 6778999999999999999999999999999999999988


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEE-EEEeeCC-CCCcccEEEEEcCCH
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS-CKVMRDP-SGISKGSGFVAFSTP  182 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~-v~i~~~~-~g~s~g~afV~f~s~  182 (472)
                      ....+                 ....+.+|||+||+.++++..|.+.|+.||.+.+ -+|++++ +|.++||+||.|.+.
T Consensus        87 s~~~~-----------------nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sf  149 (203)
T KOG0131|consen   87 SAHQK-----------------NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASF  149 (203)
T ss_pred             ccccc-----------------cccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhH
Confidence            72211                 1112358999999999999999999999998776 4788886 588999999999999


Q ss_pred             HHHHHHHHHhCCcEecCeeEEEEEcccHHHH
Q 012034          183 EEASRALAEMNGKMIVSKPLYVAVAQRKEER  213 (472)
Q Consensus       183 ~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~  213 (472)
                      +.+.+|+..+||+.++.+++.|+++.++..+
T Consensus       150 easd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  150 EASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             HHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence            9999999999999999999999999877543

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.92  E-value=9.1e-25  Score=219.75  Aligned_cols=273  Identities=36%  Similarity=0.500  Sum_probs=222.5

Q ss_pred             EEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccchhH
Q 012034           31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSER  110 (472)
Q Consensus        31 l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~~~  110 (472)
                      |||+||++++|..+|.++|+.||+|.||++..|.+| ++|| ||+|+++++|++|++.+||..+.+++|+|..+..+.++
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er  156 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEER  156 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhh
Confidence            999999999999999999999999999999999999 9999 99999999999999999999999999999999988877


Q ss_pred             HHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHH
Q 012034          111 EQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA  190 (472)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~  190 (472)
                      ...... .         ...-+++||+|++.+++++.|.+.|+.||.|.++.++.+..|.+++|+||.|.+.++|..|+.
T Consensus       157 ~~~~~~-~---------~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~  226 (369)
T KOG0123|consen  157 EAPLGE-Y---------KKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVE  226 (369)
T ss_pred             cccccc-h---------hhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHH
Confidence            654432 1         112347999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhCCcEecCeeEEEEEcccHHHHHHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 012034          191 EMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQ  270 (472)
Q Consensus       191 ~l~g~~i~gk~l~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~pp~~~~~pp~~~g~g~~~~~g~~p~~~~pp~~~~~~~  270 (472)
                      .|++..+.++.+.|.-++.+.++..-+...+.+........                    ..                 
T Consensus       227 ~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~--------------------~~-----------------  269 (369)
T KOG0123|consen  227 TLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVS--------------------LQ-----------------  269 (369)
T ss_pred             hccCCcCCccceeecccccchhhHHHHhhhhHhhhhhcccc--------------------cc-----------------
Confidence            99999999999999999997776665554433321100000                    00                 


Q ss_pred             CCCCCCCCCCCCCCCCCccCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 012034          271 QQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGS  350 (472)
Q Consensus       271 ~~~~p~~~p~~~~~p~~~~p~~~~~~~~~~~~~~~g~~p~~~~~~~~p~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~  350 (472)
                                   ..+                                                                
T Consensus       270 -------------~~n----------------------------------------------------------------  272 (369)
T KOG0123|consen  270 -------------GAN----------------------------------------------------------------  272 (369)
T ss_pred             -------------ccc----------------------------------------------------------------
Confidence                         000                                                                


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCccccchhhhhcCCHHHHHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhC
Q 012034          351 MLPVPVDMGAGIPRRDASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLE  430 (472)
Q Consensus       351 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~  430 (472)
                                 ..           +.-+...+......++.+.+|+....+|...+...+...+.+..+-++++...|.+
T Consensus       273 -----------l~-----------vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~g~skG~gfV~fs~~eeA~~A~~~  330 (369)
T KOG0123|consen  273 -----------LY-----------VKNLDETLSDEKLRKIFSSFGEITSAKVMVDENGKSKGFGFVEFSSPEEAKKAMTE  330 (369)
T ss_pred             -----------cc-----------cccCccccchhHHHHHHhcccceeeEEEEeccCCCccceEEEEcCCHHHHHHHHHh
Confidence                       00           00022234444557788888999988888888888888888888888888888888


Q ss_pred             ChHHHHHHHHHHHHHHHHHHH
Q 012034          431 SPEALKAKVAEAMEVLRSVAQ  451 (472)
Q Consensus       431 ~~~~l~~~v~~a~~~l~~~~~  451 (472)
                      -...+.......+++.+.++.
T Consensus       331 ~n~~~i~~k~l~vav~qr~~~  351 (369)
T KOG0123|consen  331 MNGRLIGGKPLYVAVAQRKED  351 (369)
T ss_pred             hChhhhcCCchhhhHHhhhcc
Confidence            888888888888888876553

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.92  E-value=1e-24  Score=231.97  Aligned_cols=178  Identities=22%  Similarity=0.373  Sum_probs=140.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcC------------CCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCC
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEY------------GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK   92 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~f------------G~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~   92 (472)
                      ....++|||+|||.++|+++|+++|+.|            +.|..+.+     ++++|||||+|.+.|+|..|| +|+|.
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~-----~~~kg~afVeF~~~e~A~~Al-~l~g~  245 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-----NKEKNFAFLEFRTVEEATFAM-ALDSI  245 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE-----CCCCCEEEEEeCCHHHHhhhh-cCCCe
Confidence            4567899999999999999999999985            23344433     345899999999999999999 59999


Q ss_pred             ccCCcceeeeccccchhHHHH---HH--------HHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEE
Q 012034           93 KFDDREWYVGKAQKKSEREQE---LK--------GQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC  161 (472)
Q Consensus        93 ~i~g~~l~V~~a~~~~~~~~~---~~--------~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v  161 (472)
                      .|.|+.|.|.+..........   ..        .................+|||+||+..+|+++|+++|+.||.|..+
T Consensus       246 ~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~  325 (509)
T TIGR01642       246 IYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAF  325 (509)
T ss_pred             EeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEE
Confidence            999999999865433210000   00        0000000001112234689999999999999999999999999999


Q ss_pred             EEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          162 KVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       162 ~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .|+.+. +|.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus       326 ~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       326 NLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             EEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            998885 78899999999999999999999999999999999999875

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.92  E-value=8.2e-24  Score=222.16  Aligned_cols=208  Identities=25%  Similarity=0.394  Sum_probs=155.6

Q ss_pred             cccCeeEEEcCcccchhhhhhhc------cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEE
Q 012034            2 LINDKQVFVGHFLRKQERETVAI------KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFV   74 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~------~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV   74 (472)
                      .|.|+.|.|........+.....      ....++|||+|||.++|+++|+++|+.||.|.+|.++.|. +|+++|||||
T Consensus       154 ~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV  233 (457)
T TIGR01622       154 MLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFI  233 (457)
T ss_pred             EECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEE
Confidence            34566666655433332221111      1236899999999999999999999999999999999985 6799999999


Q ss_pred             EeCCHHHHHHHHHHHCCCccCCcceeeeccccchhHHHH------------------------HHHHHHhhh--------
Q 012034           75 NFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQE------------------------LKGQFEQAM--------  122 (472)
Q Consensus        75 ~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~~~~~~------------------------~~~~~~~~~--------  122 (472)
                      +|.+.++|.+|++.|||..|.|+.|.|.++.........                        +........        
T Consensus       234 ~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  313 (457)
T TIGR01622       234 QFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIP  313 (457)
T ss_pred             EECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCC
Confidence            999999999999999999999999999997532211100                        000000000        


Q ss_pred             ------------------h------------------hhc----cccccceeeeecCCCCcc----------HHHHHHHH
Q 012034          123 ------------------K------------------ETV----DKFQGLNLYIKNLGDSID----------DEKLKELF  152 (472)
Q Consensus       123 ------------------~------------------~~~----~~~~~~~l~V~nL~~~~t----------~e~L~~~F  152 (472)
                                        .                  ...    ......+|+|.|+-...+          .+||++.|
T Consensus       314 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~  393 (457)
T TIGR01622       314 GTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEEC  393 (457)
T ss_pred             CccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHH
Confidence                              0                  000    113346788999954433          36899999


Q ss_pred             hccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHHH
Q 012034          153 SEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEE  212 (472)
Q Consensus       153 ~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~  212 (472)
                      ++||.|++|.|...   .+.|++||+|.+.++|.+|++.|||+.|+|+.|.|.+.....-
T Consensus       394 ~k~G~v~~v~v~~~---~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~  450 (457)
T TIGR01622       394 SKYGGVVHIYVDTK---NSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVY  450 (457)
T ss_pred             HhcCCeeEEEEeCC---CCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHH
Confidence            99999999999743   4679999999999999999999999999999999999876653

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=4.8e-25  Score=214.35  Aligned_cols=209  Identities=27%  Similarity=0.446  Sum_probs=167.7

Q ss_pred             ccCeeEEEcCcccchhhhhhhcc---CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCH
Q 012034            3 INDKQVFVGHFLRKQERETVAIK---TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENA   79 (472)
Q Consensus         3 ~~~k~v~v~~~~~~~~r~~~~~~---~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~   79 (472)
                      |++++++-|-+..-+-|-.+.+.   ...++|||+-|++.+||.+++++|++||.|++|.|++|..+.|||||||+|++.
T Consensus        96 lhn~ktlpG~~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstk  175 (510)
T KOG0144|consen   96 LHNQKTLPGMHHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTK  175 (510)
T ss_pred             hhcccccCCCCcceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehH
Confidence            45667776666555544332221   347889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHCCCc-cCCc--ceeeeccccchhHHHHHHHHH--------------------------------------
Q 012034           80 DDAAKAVEALNGKK-FDDR--EWYVGKAQKKSEREQELKGQF--------------------------------------  118 (472)
Q Consensus        80 e~A~~Av~~lng~~-i~g~--~l~V~~a~~~~~~~~~~~~~~--------------------------------------  118 (472)
                      |.|..||++||+.. ++|+  .|.|+||..+.++..+.....                                      
T Consensus       176 e~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sq  255 (510)
T KOG0144|consen  176 EMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQ  255 (510)
T ss_pred             HHHHHHHHhhccceeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccC
Confidence            99999999999876 5554  799999987665441100000                                      


Q ss_pred             --------------------------------------------------------------------------------
Q 012034          119 --------------------------------------------------------------------------------  118 (472)
Q Consensus       119 --------------------------------------------------------------------------------  118 (472)
                                                                                                      
T Consensus       256 n~g~l~g~~~L~~l~a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~  335 (510)
T KOG0144|consen  256 NVGTLGGLPPLGPLNATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGAR  335 (510)
T ss_pred             CCcccccccCCCCcchhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHh
Confidence                                                                                            


Q ss_pred             ----------------------------------------H------------------------------------hhh
Q 012034          119 ----------------------------------------E------------------------------------QAM  122 (472)
Q Consensus       119 ----------------------------------------~------------------------------------~~~  122 (472)
                                                              +                                    ...
T Consensus       336 q~~p~t~~~~n~~~~~a~a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~  415 (510)
T KOG0144|consen  336 QTFPGTPANYNLAGGMAGAGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVG  415 (510)
T ss_pred             hcCCCCchhcccccccccccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhccc
Confidence                                                    0                                    000


Q ss_pred             hhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCee
Q 012034          123 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP  201 (472)
Q Consensus       123 ~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~  201 (472)
                      ....+...+.+|||.+||.+.-+.+|-..|..||.|.+.+++-|+ +|.|+.|+||.|++..+|..||..|||+.|+.|+
T Consensus       416 ~~q~eGpeGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~Kr  495 (510)
T KOG0144|consen  416 NGQVEGPEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKR  495 (510)
T ss_pred             CccccCCCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhcccc
Confidence            000111234569999999999999999999999999999998886 8999999999999999999999999999999999


Q ss_pred             EEEEEcccHH
Q 012034          202 LYVAVAQRKE  211 (472)
Q Consensus       202 l~V~~a~~k~  211 (472)
                      ++|.+.+.+.
T Consensus       496 lkVQlk~~~~  505 (510)
T KOG0144|consen  496 LKVQLKRDRN  505 (510)
T ss_pred             ceEEeeeccC
Confidence            9999877653

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.92  E-value=4.5e-25  Score=202.35  Aligned_cols=187  Identities=30%  Similarity=0.476  Sum_probs=159.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCcc-C--Ccceeee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF-D--DREWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i-~--g~~l~V~  102 (472)
                      ...++|||+-|.+.-+|||++.+|..||.|++|.+.+..+|.+||||||.|.++-+|..||..|||... .  ...|.|+
T Consensus        17 ~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   17 GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            357889999999999999999999999999999999999999999999999999999999999999774 3  3579999


Q ss_pred             ccccchhHHHHHH-------------------------------------------------------------------
Q 012034          103 KAQKKSEREQELK-------------------------------------------------------------------  115 (472)
Q Consensus       103 ~a~~~~~~~~~~~-------------------------------------------------------------------  115 (472)
                      ++....||....-                                                                   
T Consensus        97 ~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A  176 (371)
T KOG0146|consen   97 FADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAA  176 (371)
T ss_pred             eccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccccc
Confidence            9987777651000                                                                   


Q ss_pred             --------------------------------------------------------------------HHHH--------
Q 012034          116 --------------------------------------------------------------------GQFE--------  119 (472)
Q Consensus       116 --------------------------------------------------------------------~~~~--------  119 (472)
                                                                                          ..+.        
T Consensus       177 ~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aa  256 (371)
T KOG0146|consen  177 APVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAA  256 (371)
T ss_pred             CCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhh
Confidence                                                                                0000        


Q ss_pred             -----------------hhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCC
Q 012034          120 -----------------QAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFST  181 (472)
Q Consensus       120 -----------------~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s  181 (472)
                                       .......+...+|||||-.||.+..|.+|...|-.||.|.+.+|+.|+ ++.||+|+||.|++
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN  336 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC
Confidence                             000011223367999999999999999999999999999999999997 78999999999999


Q ss_pred             HHHHHHHHHHhCCcEecCeeEEEEEcccHHH
Q 012034          182 PEEASRALAEMNGKMIVSKPLYVAVAQRKEE  212 (472)
Q Consensus       182 ~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~  212 (472)
                      +.+|+.||..|||..|+-|+|+|.+.+.|+.
T Consensus       337 p~SaQaAIqAMNGFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  337 PASAQAAIQAMNGFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             chhHHHHHHHhcchhhhhhhhhhhhcCcccc
Confidence            9999999999999999999999999888764

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.91  E-value=8e-25  Score=203.23  Aligned_cols=149  Identities=23%  Similarity=0.521  Sum_probs=139.6

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccch
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  108 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~  108 (472)
                      .+|||+|||.++++.+|+.+|++||+|.+|.|+++       ||||..+++..|+.||..||+..|.|..|.|+.++.|+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc-------cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            36999999999999999999999999999999987       99999999999999999999999999999999887663


Q ss_pred             hHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHH
Q 012034          109 EREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA  188 (472)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~A  188 (472)
                      +                    ..++|+|+||.+.++.++||..|++||.|.+|+|.+|       |+||.|+..++|..|
T Consensus        76 k--------------------~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-------y~fvh~d~~eda~~a  128 (346)
T KOG0109|consen   76 K--------------------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-------YAFVHFDRAEDAVEA  128 (346)
T ss_pred             C--------------------CccccccCCCCccccCHHHhhhhcccCCceeeeeecc-------eeEEEEeeccchHHH
Confidence            2                    3458999999999999999999999999999999976       999999999999999


Q ss_pred             HHHhCCcEecCeeEEEEEcccHH
Q 012034          189 LAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       189 i~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      +..|++.+|.|++++|.++.++-
T Consensus       129 ir~l~~~~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen  129 IRGLDNTEFQGKRMHVQLSTSRL  151 (346)
T ss_pred             Hhcccccccccceeeeeeecccc
Confidence            99999999999999999987653

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.91  E-value=1.6e-23  Score=208.92  Aligned_cols=186  Identities=33%  Similarity=0.500  Sum_probs=153.0

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      ..+|.|+|||+.|.+.+|+.+|+.||.|.+|.|.+..+|+-.|||||.|.+..+|..|++.+|+..|+|+.|-|.||-.+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            67899999999999999999999999999999998888887799999999999999999999999999999999999655


Q ss_pred             hhHHH----------------HHHH-H------------------HH--h------------------------h-hhh-
Q 012034          108 SEREQ----------------ELKG-Q------------------FE--Q------------------------A-MKE-  124 (472)
Q Consensus       108 ~~~~~----------------~~~~-~------------------~~--~------------------------~-~~~-  124 (472)
                      ...+.                +... .                  .+  .                        + ..+ 
T Consensus       197 d~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~  276 (678)
T KOG0127|consen  197 DTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKES  276 (678)
T ss_pred             ccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcc
Confidence            33221                0000 0                  00  0                        0 000 


Q ss_pred             ---------hccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHh--
Q 012034          125 ---------TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM--  192 (472)
Q Consensus       125 ---------~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l--  192 (472)
                               ..+...+.+|||.||++++|+++|.+.|+.||.|.++.|+.++ ++.|+|.|||.|.+..+|.+||+.-  
T Consensus       277 ~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Asp  356 (678)
T KOG0127|consen  277 DKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASP  356 (678)
T ss_pred             cchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCc
Confidence                     0001123579999999999999999999999999999998886 7899999999999999999999876  


Q ss_pred             ---CC-cEecCeeEEEEEcccHHHH
Q 012034          193 ---NG-KMIVSKPLYVAVAQRKEER  213 (472)
Q Consensus       193 ---~g-~~i~gk~l~V~~a~~k~~~  213 (472)
                         .| ..++|+.|.|..+-.+++-
T Consensus       357 a~e~g~~ll~GR~Lkv~~Av~RkeA  381 (678)
T KOG0127|consen  357 ASEDGSVLLDGRLLKVTLAVTRKEA  381 (678)
T ss_pred             cCCCceEEEeccEEeeeeccchHHH
Confidence               23 6789999999999777554

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=2e-23  Score=198.86  Aligned_cols=174  Identities=26%  Similarity=0.470  Sum_probs=150.6

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      -.++|||+.|.+++.|+.|+..|..||.|+||.+.+| .+++.||||||+|+-+|.|..|++.|||..++||.|+|.+.+
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            4688999999999999999999999999999999999 589999999999999999999999999999999999999765


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCC-CcccEEEEEcCCHHH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG-ISKGSGFVAFSTPEE  184 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g-~s~g~afV~f~s~~~  184 (472)
                      .-...+.......++.+     +  =..|||..+..+++++||+.+|+.||.|.+|.+-+++++ ..|||+|++|.+..+
T Consensus       192 NmpQAQpiID~vqeeAk-----~--fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs  264 (544)
T KOG0124|consen  192 NMPQAQPIIDMVQEEAK-----K--FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQS  264 (544)
T ss_pred             CCcccchHHHHHHHHHH-----h--hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccc
Confidence            44332222221111111     1  126999999999999999999999999999999999754 579999999999999


Q ss_pred             HHHHHHHhCCcEecCeeEEEEEc
Q 012034          185 ASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       185 A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      -..||..||-+.++|..|+|..+
T Consensus       265 ~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  265 QSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             hHHHhhhcchhhcccceEecccc
Confidence            99999999999999999998743

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

Probab=99.87  E-value=4.9e-21  Score=201.58  Aligned_cols=105  Identities=20%  Similarity=0.420  Sum_probs=86.9

Q ss_pred             cccCeeEEEcCcccchhhhh-----hhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEE
Q 012034            2 LINDKQVFVGHFLRKQERET-----VAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN   75 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~-----~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~   75 (472)
                      .|+|++|.|++.........     ......+++|||+||+.++++++|+++|+.||.|.++.|.+|. +|++||||||+
T Consensus       173 ~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVe  252 (612)
T TIGR01645       173 MLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIE  252 (612)
T ss_pred             EEecceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEE
Confidence            46677888875433221110     0112467899999999999999999999999999999999994 68899999999


Q ss_pred             eCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           76 FENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        76 F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      |++.++|.+||+.||+..|+|+.|+|.++..
T Consensus       253 Fe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       253 YNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             ECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            9999999999999999999999999988753

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.

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.87  E-value=5e-22  Score=204.36  Aligned_cols=178  Identities=28%  Similarity=0.473  Sum_probs=152.9

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCC----ceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK----SKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~----skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      ..++|||+||++++|.++|...|++.|.|.++.|....++.    |.|||||+|.+.++|++|++.|+|+.|+|+.|+|.
T Consensus       514 ~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk  593 (725)
T KOG0110|consen  514 TETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELK  593 (725)
T ss_pred             cchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEE
Confidence            34559999999999999999999999999999988775543    56999999999999999999999999999999999


Q ss_pred             ccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC-CCCCcccEEEEEcCC
Q 012034          103 KAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST  181 (472)
Q Consensus       103 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~-~~g~s~g~afV~f~s  181 (472)
                      .+..+....         ..........+++|+|+|||...+..+++++|..||.|.+|+|... ..+.++|||||.|-+
T Consensus       594 ~S~~k~~~~---------~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t  664 (725)
T KOG0110|consen  594 ISENKPAST---------VGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLT  664 (725)
T ss_pred             eccCccccc---------cccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccC
Confidence            987222111         0122222334679999999999999999999999999999999887 355679999999999


Q ss_pred             HHHHHHHHHHhCCcEecCeeEEEEEcccHHHH
Q 012034          182 PEEASRALAEMNGKMIVSKPLYVAVAQRKEER  213 (472)
Q Consensus       182 ~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~  213 (472)
                      ..+|.+|++.|.+..+.|+.|.+.|+......
T Consensus       665 ~~ea~nA~~al~STHlyGRrLVLEwA~~d~~~  696 (725)
T KOG0110|consen  665 PREAKNAFDALGSTHLYGRRLVLEWAKSDNTM  696 (725)
T ss_pred             cHHHHHHHHhhcccceechhhheehhccchHH
Confidence            99999999999999999999999999887553

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.84  E-value=2.1e-21  Score=188.93  Aligned_cols=174  Identities=25%  Similarity=0.460  Sum_probs=151.9

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||++|+|++|+|.|++.|+.||+|.++.+++| .+++++||+||+|.+.++..+++.. ..+.|+|+.|.+.++.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            5788999999999999999999999999999999999 4799999999999999999999864 5778999999999998


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEE  184 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~  184 (472)
                      ++.+.......            .....+||++|+.+++++++++.|++||.|..+.++.|. ...++||+||.|.+.++
T Consensus        84 ~r~~~~~~~~~------------~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~s  151 (311)
T KOG4205|consen   84 SREDQTKVGRH------------LRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDS  151 (311)
T ss_pred             Ccccccccccc------------cceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccc
Confidence            76654322111            133479999999999999999999999999999988885 67899999999999998


Q ss_pred             HHHHHHHhCCcEecCeeEEEEEcccHHHHH
Q 012034          185 ASRALAEMNGKMIVSKPLYVAVAQRKEERR  214 (472)
Q Consensus       185 A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~~  214 (472)
                      +.+++ ..+.+.|+++.+.|..|.+++...
T Consensus       152 Vdkv~-~~~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  152 VDKVT-LQKFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             cceec-ccceeeecCceeeEeeccchhhcc
Confidence            88877 688889999999999999987654

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.81  E-value=1.6e-20  Score=188.64  Aligned_cols=181  Identities=24%  Similarity=0.427  Sum_probs=153.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ++..++||+-.|....+..+|.++|+.+|.|..|.++.| .++++||.|||+|.|.++.-.|| .|.|..+.|..|.|..
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~  254 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQL  254 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecc
Confidence            577899999999999999999999999999999999999 47899999999999999999999 6999999999999987


Q ss_pred             cccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCH
Q 012034          104 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP  182 (472)
Q Consensus       104 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~  182 (472)
                      ......+.......+...  ...  ..-..|||+||..++++++|+.+|+.||.|+.|.+.+|. +|.++||+||+|.+.
T Consensus       255 sEaeknr~a~~s~a~~~k--~~~--~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~  330 (549)
T KOG0147|consen  255 SEAEKNRAANASPALQGK--GFT--GPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNK  330 (549)
T ss_pred             cHHHHHHHHhcccccccc--ccc--cchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecH
Confidence            754433322111111100  000  011129999999999999999999999999999999996 999999999999999


Q ss_pred             HHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          183 EEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       183 ~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ++|.+|+..|||.+|.|+.|+|.....+
T Consensus       331 ~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  331 EDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             HHHHHHHHHhccceecCceEEEEEeeee
Confidence            9999999999999999999999876655

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.80  E-value=1.3e-19  Score=167.13  Aligned_cols=140  Identities=32%  Similarity=0.552  Sum_probs=118.9

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..-+||||+||+.++||+-|..+|+..|.|++++|+.|                                  .|.|.|+.
T Consensus         4 ~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~----------------------------------e~~v~wa~   49 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD----------------------------------ELKVNWAT   49 (321)
T ss_pred             CCCceEEeeccChhhHHHHHHHHHHhccccccceeehh----------------------------------hhcccccc
Confidence            45789999999999999999999999999999999887                                  33444443


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEE  184 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~  184 (472)
                      .....             ......+...+||+.|..+++-|+||+.|.+||+|.+++|++|. +++||||+||.|-+.++
T Consensus        50 ~p~nQ-------------sk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~d  116 (321)
T KOG0148|consen   50 APGNQ-------------SKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKED  116 (321)
T ss_pred             CcccC-------------CCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHH
Confidence            32110             00011123469999999999999999999999999999999995 89999999999999999


Q ss_pred             HHHHHHHhCCcEecCeeEEEEEcccHHH
Q 012034          185 ASRALAEMNGKMIVSKPLYVAVAQRKEE  212 (472)
Q Consensus       185 A~~Ai~~l~g~~i~gk~l~V~~a~~k~~  212 (472)
                      |++||..|||..|++|.|+..|+.+|..
T Consensus       117 AEnAI~~MnGqWlG~R~IRTNWATRKp~  144 (321)
T KOG0148|consen  117 AENAIQQMNGQWLGRRTIRTNWATRKPS  144 (321)
T ss_pred             HHHHHHHhCCeeeccceeeccccccCcc
Confidence            9999999999999999999999998863

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.76  E-value=3.3e-18  Score=172.12  Aligned_cols=204  Identities=23%  Similarity=0.355  Sum_probs=149.2

Q ss_pred             ccCeeEEEcCcccchhhhhhhc--------cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEE
Q 012034            3 INDKQVFVGHFLRKQERETVAI--------KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGF   73 (472)
Q Consensus         3 ~~~k~v~v~~~~~~~~r~~~~~--------~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aF   73 (472)
                      +.|..|+|..-..-+.|.....        ..++..|||+||..++|+++|+.+|+.||.|..|.+..|. +|.++||||
T Consensus       245 llg~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGf  324 (549)
T KOG0147|consen  245 LLGVPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGF  324 (549)
T ss_pred             ccCceeEecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcce
Confidence            4456677766655555533221        2345559999999999999999999999999999999995 999999999


Q ss_pred             EEeCCHHHHHHHHHHHCCCccCCcceeeeccccchhHH------------------------HHHHHHHHhhh-------
Q 012034           74 VNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSERE------------------------QELKGQFEQAM-------  122 (472)
Q Consensus        74 V~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~~~~------------------------~~~~~~~~~~~-------  122 (472)
                      |+|.+.++|++|++.|||.+|.|+.|.|..-..+.+..                        ..+..+.....       
T Consensus       325 i~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~  404 (549)
T KOG0147|consen  325 ITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPST  404 (549)
T ss_pred             EEEecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccch
Confidence            99999999999999999999999999885432221110                        00000000000       


Q ss_pred             -----------------------hhhccc-------cccceeeeecCCCCcc----------HHHHHHHHhccCceEEEE
Q 012034          123 -----------------------KETVDK-------FQGLNLYIKNLGDSID----------DEKLKELFSEFGTITSCK  162 (472)
Q Consensus       123 -----------------------~~~~~~-------~~~~~l~V~nL~~~~t----------~e~L~~~F~~~G~I~~v~  162 (472)
                                             ......       ...-|+.++|+=+.-|          .||+.+.+++||.|..|.
T Consensus       405 ~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~  484 (549)
T KOG0147|consen  405 AISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIF  484 (549)
T ss_pred             hhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEE
Confidence                                   000011       2233556666633222          278889999999999888


Q ss_pred             EeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          163 VMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       163 i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      |-++    |-|+.||.|.+.++|..|+.+|||.+|.|+.|.++|-...
T Consensus       485 vd~n----s~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~~  528 (549)
T KOG0147|consen  485 VDKN----SAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPLE  528 (549)
T ss_pred             EccC----CCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeehh
Confidence            8665    5599999999999999999999999999999999986544

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.76  E-value=1.7e-17  Score=161.84  Aligned_cols=182  Identities=21%  Similarity=0.375  Sum_probs=147.9

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHh-cCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFG-EYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~-~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      .+.++.+||.|||+++.+.+||++|. +.|+|+-|.+..|.+|++||||.|+|+++|.+++|++.||.+.+.|+.|.|+.
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             ccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            35677799999999999999999997 68999999999999999999999999999999999999999999999999976


Q ss_pred             cccchhHHHH-----------------------------------------------------HHHH-------------
Q 012034          104 AQKKSEREQE-----------------------------------------------------LKGQ-------------  117 (472)
Q Consensus       104 a~~~~~~~~~-----------------------------------------------------~~~~-------------  117 (472)
                      .......+.-                                                     +...             
T Consensus       121 d~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~  200 (608)
T KOG4212|consen  121 DHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLS  200 (608)
T ss_pred             cCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccch
Confidence            5432111100                                                     0000             


Q ss_pred             --HHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCc
Q 012034          118 --FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK  195 (472)
Q Consensus       118 --~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~  195 (472)
                        |....+. ....-...+||.||...+....|.+.|.-.|.|+++.+--|+.|.++|||.++|+.+-+|..||..+++.
T Consensus       201 ~~Flr~~h~-f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~  279 (608)
T KOG4212|consen  201 ASFLRSLHI-FSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQ  279 (608)
T ss_pred             hhhhhhccC-CCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccC
Confidence              0000000 0111123589999999999999999999999999999988888999999999999999999999999987


Q ss_pred             EecCeeEEEEEc
Q 012034          196 MIVSKPLYVAVA  207 (472)
Q Consensus       196 ~i~gk~l~V~~a  207 (472)
                      -+.+++..+.+.
T Consensus       280 g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  280 GLFDRRMTVRLD  291 (608)
T ss_pred             CCccccceeecc
Confidence            777777777663

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.74  E-value=3.4e-17  Score=148.80  Aligned_cols=176  Identities=23%  Similarity=0.405  Sum_probs=143.1

Q ss_pred             CcceEEeCCCCCCCCHHHHHH----HHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           27 KFNNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~----~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      .+.||||.||+..+..++|++    +|+.||.|..|...+  +.+.||-|||.|.+.+.|..|+.+|+|..+-|+.++|.
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            345999999999999999999    999999998877664  56889999999999999999999999999999999999


Q ss_pred             ccccchhHHHHHHHHHHhhhh----h----------------------------hccccccceeeeecCCCCccHHHHHH
Q 012034          103 KAQKKSEREQELKGQFEQAMK----E----------------------------TVDKFQGLNLYIKNLGDSIDDEKLKE  150 (472)
Q Consensus       103 ~a~~~~~~~~~~~~~~~~~~~----~----------------------------~~~~~~~~~l~V~nL~~~~t~e~L~~  150 (472)
                      +|..++..-...+..+.....    +                            .........||+.|||.+++.+.|..
T Consensus        86 yA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~  165 (221)
T KOG4206|consen   86 YAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSD  165 (221)
T ss_pred             cccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHH
Confidence            998876643321110000000    0                            00122345799999999999999999


Q ss_pred             HHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec-CeeEEEEEcc
Q 012034          151 LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPLYVAVAQ  208 (472)
Q Consensus       151 ~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~-gk~l~V~~a~  208 (472)
                      +|..|....+++++..    -.+.|||+|.+...|..|...+.+..|- ...+.|.++.
T Consensus       166 lf~qf~g~keir~i~~----~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  166 LFEQFPGFKEIRLIPP----RSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHhhCcccceeEeccC----CCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            9999999999998875    3678999999999999999999998886 7777777764

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

Probab=99.71  E-value=3.5e-17  Score=144.10  Aligned_cols=83  Identities=30%  Similarity=0.576  Sum_probs=78.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++||++|+++|++||.|.++.|+.| .+++++|||||+|++.++|++|++.||+..|+|+.|.|.++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            45788999999999999999999999999999999999 58999999999999999999999999999999999999998


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus       112 ~~~~  115 (144)
T PLN03134        112 NDRP  115 (144)
T ss_pred             CcCC
Confidence            7543

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.70  E-value=4.9e-16  Score=148.26  Aligned_cols=182  Identities=19%  Similarity=0.298  Sum_probs=141.8

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCee--------EEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT--------SAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD   96 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~--------~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g   96 (472)
                      .+.+++|||.|||.++|.+++.++|++||-|.        .|++.++..|+-||-|.|+|-..|++..|++-|++..+.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            46678899999999999999999999999776        4789999999999999999999999999999999999999


Q ss_pred             cceeeeccccchhH--------------HHHHHHHHHh------hhhhhccccccceeeeecCCC----Ccc-------H
Q 012034           97 REWYVGKAQKKSER--------------EQELKGQFEQ------AMKETVDKFQGLNLYIKNLGD----SID-------D  145 (472)
Q Consensus        97 ~~l~V~~a~~~~~~--------------~~~~~~~~~~------~~~~~~~~~~~~~l~V~nL~~----~~t-------~  145 (472)
                      +.|.|++|+-....              ...+......      ...........++|.++|+=.    ..+       .
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlk  290 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLK  290 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHH
Confidence            99999988532111              1111110000      000111122345788888732    122       3


Q ss_pred             HHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          146 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       146 e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ++|++.+++||.|.+|.|...   ...|.+-|.|.+.++|..||+.|+|+.|+|+.|..++...
T Consensus       291 edl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence            688889999999999998743   4578899999999999999999999999999998886543

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.70  E-value=2.4e-16  Score=150.72  Aligned_cols=206  Identities=20%  Similarity=0.406  Sum_probs=153.7

Q ss_pred             cccCeeEEEcCcccchhhhhhh-----ccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCC-CCceeEEEEE
Q 012034            2 LINDKQVFVGHFLRKQERETVA-----IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVN   75 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~-----~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~-g~skG~aFV~   75 (472)
                      +|+|+.|.||+......-+...     ..++|++|||..+..+.+|+||+..|+.||+|.+|.+-++.+ +..||||||+
T Consensus       179 mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiE  258 (544)
T KOG0124|consen  179 MLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIE  258 (544)
T ss_pred             cccCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEE
Confidence            5788999999766554332221     247899999999999999999999999999999999999965 5689999999


Q ss_pred             eCCHHHHHHHHHHHCCCccCCcceeeeccccchhHH--------------------------------------------
Q 012034           76 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSERE--------------------------------------------  111 (472)
Q Consensus        76 F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~~~~--------------------------------------------  111 (472)
                      |++..+-..||..||-..++|..|+|.++-.....-                                            
T Consensus       259 y~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~  338 (544)
T KOG0124|consen  259 YNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGL  338 (544)
T ss_pred             eccccchHHHhhhcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccc
Confidence            999999999999999999999999998763221110                                            


Q ss_pred             --------------------------------------------------------------------HHHHHHHH--h-
Q 012034          112 --------------------------------------------------------------------QELKGQFE--Q-  120 (472)
Q Consensus       112 --------------------------------------------------------------------~~~~~~~~--~-  120 (472)
                                                                                          +++..+.+  . 
T Consensus       339 vSpA~~aa~p~~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~  418 (544)
T KOG0124|consen  339 VSPAPRAAQPLGTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEM  418 (544)
T ss_pred             cCccccccCCCCCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHH
Confidence                                                                                00000000  0 


Q ss_pred             -----------------hhhhhccccccceeeeecC--CCCcc---HHHHHHHHhccCceEEEEEeeCCCCCc-----cc
Q 012034          121 -----------------AMKETVDKFQGLNLYIKNL--GDSID---DEKLKELFSEFGTITSCKVMRDPSGIS-----KG  173 (472)
Q Consensus       121 -----------------~~~~~~~~~~~~~l~V~nL--~~~~t---~e~L~~~F~~~G~I~~v~i~~~~~g~s-----~g  173 (472)
                                       ..........++.+.++|.  |.+++   +.++++.|++||.|..+.|.....+..     --
T Consensus       419 L~~QE~msI~G~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiV  498 (544)
T KOG0124|consen  419 LSEQEHMSISGSSARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIV  498 (544)
T ss_pred             hhhhhCccccCccHHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhh
Confidence                             0001112223345667776  34444   468899999999999999987654331     22


Q ss_pred             EEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          174 SGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       174 ~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      -.||+|+...++.+|+..|+|+.|+|+++..++.
T Consensus       499 KIFVefS~~~e~~rak~ALdGRfFgGr~VvAE~Y  532 (544)
T KOG0124|consen  499 KIFVEFSIASETHRAKQALDGRFFGGRKVVAEVY  532 (544)
T ss_pred             eeeeeechhhHHHHHHHhhccceecCceeehhhh
Confidence            4699999999999999999999999999877654

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.68  E-value=5.1e-16  Score=135.90  Aligned_cols=172  Identities=20%  Similarity=0.357  Sum_probs=133.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++.|.+|.++|.+||.|..|.+.....  .-+||||+|++..||+.||..-+|..++|..|.|+++.
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g--~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPG--PPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCC--CCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4678899999999999999999999999999998866532  25699999999999999999999999999999999986


Q ss_pred             cchhHHHHHHHHHHh---------hhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEE
Q 012034          106 KKSEREQELKGQFEQ---------AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGF  176 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~af  176 (472)
                      ....... -...+..         ...-...+-....+.|.+||.+-+.+||+++..+-|.|....+.+|      |++.
T Consensus        82 ggr~s~~-~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~Gv  154 (241)
T KOG0105|consen   82 GGRSSSD-RRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGV  154 (241)
T ss_pred             CCCcccc-cccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------ccee
Confidence            5421100 0000000         0000111222346899999999999999999999999999999987      4789


Q ss_pred             EEcCCHHHHHHHHHHhCCcEe--cCeeEEEEE
Q 012034          177 VAFSTPEEASRALAEMNGKMI--VSKPLYVAV  206 (472)
Q Consensus       177 V~f~s~~~A~~Ai~~l~g~~i--~gk~l~V~~  206 (472)
                      |.|...|+-+-|+..|....+  .|...++.+
T Consensus       155 V~~~r~eDMkYAvr~ld~~~~~seGe~~yirv  186 (241)
T KOG0105|consen  155 VEYLRKEDMKYAVRKLDDQKFRSEGETAYIRV  186 (241)
T ss_pred             eeeeehhhHHHHHHhhccccccCcCcEeeEEe
Confidence            999999999999999988765  355544443

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.64  E-value=4.5e-15  Score=154.26  Aligned_cols=111  Identities=21%  Similarity=0.322  Sum_probs=93.3

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....|||||++|+++++|.+|+.+|+.||+|.+|.++..     +|||||++.+.++|.+|+.+|++..+.++.|+|.|+
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            456899999999999999999999999999999999865     899999999999999999999999999999999999


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHh
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFS  153 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~  153 (472)
                      ..+.-+. +++..            ....+-|..|||+.-.++|+.+++
T Consensus       493 ~g~G~ks-e~k~~------------wD~~lGVt~IP~~kLt~dl~~~~e  528 (894)
T KOG0132|consen  493 VGKGPKS-EYKDY------------WDVELGVTYIPWEKLTDDLEAWCE  528 (894)
T ss_pred             ccCCcch-hhhhh------------hhcccCeeEeehHhcCHHHHHhhh
Confidence            8776654 44332            334567888898766566555543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.64  E-value=1.1e-15  Score=157.89  Aligned_cols=178  Identities=28%  Similarity=0.404  Sum_probs=140.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...+-++|+|||..+..++|.+.|..||.|..+.+-  +.|.   -++|.|.+..+|+.|++.|....+....+++.|+.
T Consensus       383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~~G~---~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP  457 (725)
T KOG0110|consen  383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--PGGT---GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAP  457 (725)
T ss_pred             hhcceeeeccCccccccHHHHHHhhcccccceeecC--cccc---eeeeeecCccchHHHHHHhchhhhccCccccccCh
Confidence            456789999999999999999999999999988433  4443   48999999999999999999999999999999885


Q ss_pred             cchhHHH--------HHHHH-------H--------H--------hhhhhh-ccccccceeeeecCCCCccHHHHHHHHh
Q 012034          106 KKSEREQ--------ELKGQ-------F--------E--------QAMKET-VDKFQGLNLYIKNLGDSIDDEKLKELFS  153 (472)
Q Consensus       106 ~~~~~~~--------~~~~~-------~--------~--------~~~~~~-~~~~~~~~l~V~nL~~~~t~e~L~~~F~  153 (472)
                      ...-...        +....       .        .        ...... ......+.|||+||.+++|.++|...|.
T Consensus       458 ~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~  537 (725)
T KOG0110|consen  458 EDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFS  537 (725)
T ss_pred             hhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHH
Confidence            4322200        00000       0        0        000000 0111223499999999999999999999


Q ss_pred             ccCceEEEEEeeCCCCC----cccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          154 EFGTITSCKVMRDPSGI----SKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       154 ~~G~I~~v~i~~~~~g~----s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..|.|.++.|...++..    |.|||||+|.+.++|+.|+..|+|+.|+|+.|.|+++.
T Consensus       538 k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  538 KQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            99999999997766543    56999999999999999999999999999999999988

>PF00076 RRM_1: RNA recognition motif

Probab=99.63  E-value=1e-15  Score=117.29  Aligned_cols=70  Identities=46%  Similarity=0.785  Sum_probs=67.5

Q ss_pred             EEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        31 l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      |||+|||.++|+++|+++|++||.|..+.+..+.+++++|||||+|++.++|++|++.|+|..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999999999999988899999999999999999999999999999998874

(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 ....

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

Probab=99.63  E-value=1.8e-15  Score=133.21  Aligned_cols=81  Identities=33%  Similarity=0.580  Sum_probs=75.9

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+++|||+||++++|+++|+++|++||.|.+++|+.+. +++++|||||+|.+.++|++|++.||+..|+|+.|+|.++.
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            45689999999999999999999999999999998885 78999999999999999999999999999999999999986


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus       113 ~~  114 (144)
T PLN03134        113 DR  114 (144)
T ss_pred             cC
Confidence            53

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.62  E-value=4.3e-15  Score=147.98  Aligned_cols=177  Identities=21%  Similarity=0.277  Sum_probs=134.0

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      -.-|.+++|||++|++||.++|+.++ |+++.+.+ .+|+..|-|||+|++.|++++|+++ +...+..+.|.|-.+...
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r-~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR-RNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec-cCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEccCCc
Confidence            44588999999999999999999985 56644433 5799999999999999999999985 788889999999877554


Q ss_pred             hhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEE-EEEeeCCCCCcccEEEEEcCCHHHHH
Q 012034          108 SEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS-CKVMRDPSGISKGSGFVAFSTPEEAS  186 (472)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~-v~i~~~~~g~s~g~afV~f~s~~~A~  186 (472)
                      ... ..++.      ...........|-+++||+.||++||.++|+---.|.. +.+..+..+++.|-|||+|++.+.|+
T Consensus        87 e~d-~~~~~------~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae  159 (510)
T KOG4211|consen   87 EAD-WVMRP------GGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAE  159 (510)
T ss_pred             ccc-ccccC------CCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHH
Confidence            331 11110      00001112345889999999999999999998755555 55677778899999999999999999


Q ss_pred             HHHHHhCCcEecCeeEEEEEcccHHHHHH
Q 012034          187 RALAEMNGKMIVSKPLYVAVAQRKEERRA  215 (472)
Q Consensus       187 ~Ai~~l~g~~i~gk~l~V~~a~~k~~~~~  215 (472)
                      +|+. -|.+.|.-+-|.|-.+...+.++.
T Consensus       160 ~Al~-rhre~iGhRYIEvF~Ss~~e~~~~  187 (510)
T KOG4211|consen  160 IALG-RHRENIGHRYIEVFRSSRAEVKRA  187 (510)
T ss_pred             HHHH-HHHHhhccceEEeehhHHHHHHhh
Confidence            9994 455667777777776655555543

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.61  E-value=9.5e-16  Score=139.65  Aligned_cols=80  Identities=35%  Similarity=0.593  Sum_probs=73.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      +..+|+|||++|+|++++|+|+++|++||+|.+++|+.| .+|+|||||||+|.|.|+|.+|++. -.-.|+||+-.|+.
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccch
Confidence            578999999999999999999999999999999999999 4899999999999999999999985 45668999887776


Q ss_pred             cc
Q 012034          104 AQ  105 (472)
Q Consensus       104 a~  105 (472)
                      |.
T Consensus        88 A~   89 (247)
T KOG0149|consen   88 AS   89 (247)
T ss_pred             hh
Confidence            64

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.61  E-value=4.3e-15  Score=143.65  Aligned_cols=164  Identities=32%  Similarity=0.469  Sum_probs=123.0

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .++|||+|||.++|+++|+++|++||.|..+.+..| .+++++|||||+|.+.++|..|++.+++..|.|+.|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            599999999999999999999999999999999999 5899999999999999999999999999999999999999652


Q ss_pred             ----chhHHHH--HHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCC-cccEEEEEc
Q 012034          107 ----KSEREQE--LKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAF  179 (472)
Q Consensus       107 ----~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~-s~g~afV~f  179 (472)
                          +......  ....................+++.+++..++..++...|..+|.+....+.....+. ...+.++.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGN  274 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccch
Confidence                2221100  000001111222334456789999999999999999999999999777766554322 333444444


Q ss_pred             CCHHHHHHHHHH
Q 012034          180 STPEEASRALAE  191 (472)
Q Consensus       180 ~s~~~A~~Ai~~  191 (472)
                      .....+......
T Consensus       275 ~~~~~~~~~~~~  286 (306)
T COG0724         275 EASKDALESNSR  286 (306)
T ss_pred             hHHHhhhhhhcc
Confidence            444444444433

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.60  E-value=5e-16  Score=142.65  Aligned_cols=168  Identities=27%  Similarity=0.442  Sum_probs=132.3

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccch
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  108 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~  108 (472)
                      ..|||++||+.+.+.+|.++|..||.|..+.+..       ||+||+|++..+|..||..||++.|.+..+.|+++....
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~-------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN-------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec-------ccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            3699999999999999999999999999887754       599999999999999999999999999999999887432


Q ss_pred             hHH-HHHHH-HHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHH
Q 012034          109 ERE-QELKG-QFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS  186 (472)
Q Consensus       109 ~~~-~~~~~-~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~  186 (472)
                      ... ..... .......-....-..+.+.|.++..+++..+|.+.|..+|.++...+       .++++||+|++.++|.
T Consensus        75 ~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------~~~~~~v~Fs~~~da~  147 (216)
T KOG0106|consen   75 RGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------RRNFAFVEFSEQEDAK  147 (216)
T ss_pred             cccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------hccccceeehhhhhhh
Confidence            111 00000 00000111111223567899999999999999999999999965554       3569999999999999


Q ss_pred             HHHHHhCCcEecCeeEEEEEcccH
Q 012034          187 RALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       187 ~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +|++.+++..+.++.|.+...-..
T Consensus       148 ra~~~l~~~~~~~~~l~~~~~~~d  171 (216)
T KOG0106|consen  148 RALEKLDGKKLNGRRISVEKNSRD  171 (216)
T ss_pred             hcchhccchhhcCceeeecccCcc
Confidence            999999999999999999544333

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.59  E-value=3.2e-15  Score=136.66  Aligned_cols=102  Identities=33%  Similarity=0.490  Sum_probs=87.9

Q ss_pred             eeEEEcCcccchhhhhhh----ccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHH
Q 012034            6 KQVFVGHFLRKQERETVA----IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENAD   80 (472)
Q Consensus         6 k~v~v~~~~~~~~r~~~~----~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e   80 (472)
                      +--||.++.|...+....    .....++|.|.||+.+++|++|+++|.+||.|..+.|.+| .+|.+||||||+|++.+
T Consensus       163 ~g~yvpP~mR~ga~~~~g~~~R~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRd  242 (270)
T KOG0122|consen  163 KGKYVPPSMRAGADRASGSDMRERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRD  242 (270)
T ss_pred             CccccCccccCCcccccccccccCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHH
Confidence            345677777766421111    1246788999999999999999999999999999999999 68999999999999999


Q ss_pred             HHHHHHHHHCCCccCCcceeeeccccc
Q 012034           81 DAAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        81 ~A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      ||.+||+.|||.-++.-.|.|+|+.++
T Consensus       243 dA~rAI~~LnG~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  243 DAARAIADLNGYGYDNLILRVEWSKPS  269 (270)
T ss_pred             HHHHHHHHccCcccceEEEEEEecCCC
Confidence            999999999999999999999999764

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.57  E-value=4.8e-15  Score=156.33  Aligned_cols=149  Identities=23%  Similarity=0.265  Sum_probs=107.3

Q ss_pred             ccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcC--CCeeEEEEEECCCCCceeEEEEEeCCHH
Q 012034            3 INDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEY--GTITSAVVMRDGDGKSKCFGFVNFENAD   80 (472)
Q Consensus         3 ~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~f--G~I~~v~i~~d~~g~skG~aFV~F~~~e   80 (472)
                      |.++.|.|....+..+.. .....+.++|||+||++++|+++|+++|++|  |+|++|.+++       +||||+|++.+
T Consensus       209 l~Gr~I~VdwA~p~~~~d-~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r-------gfAFVeF~s~e  280 (578)
T TIGR01648       209 LWGHVIAVDWAEPEEEVD-EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR-------DYAFVHFEDRE  280 (578)
T ss_pred             ecCceEEEEeeccccccc-ccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec-------CeEEEEeCCHH
Confidence            445566665443332211 1112456889999999999999999999999  9999998764       49999999999


Q ss_pred             HHHHHHHHHCCCccCCcceeeeccccchhHHHHH-HH---------HHHhhhhhhccccccceeeeecCCCCccHHHHHH
Q 012034           81 DAAKAVEALNGKKFDDREWYVGKAQKKSEREQEL-KG---------QFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE  150 (472)
Q Consensus        81 ~A~~Av~~lng~~i~g~~l~V~~a~~~~~~~~~~-~~---------~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~  150 (472)
                      +|.+|++.||+..|+|+.|.|.|+......+... ..         ..+.............+++++|+++..+++.+.+
T Consensus       281 ~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~  360 (578)
T TIGR01648       281 DAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLH  360 (578)
T ss_pred             HHHHHHHHhCCCEECCEEEEEEEccCCCcccccccccccCCCcccccccccccCcccCccccccccccccccccccchhh
Confidence            9999999999999999999999997654321100 00         0000000001112346899999999999999999


Q ss_pred             HHhccCceE
Q 012034          151 LFSEFGTIT  159 (472)
Q Consensus       151 ~F~~~G~I~  159 (472)
                      +|..+|.|.
T Consensus       361 ~f~~~g~~~  369 (578)
T TIGR01648       361 FPRMPGPIR  369 (578)
T ss_pred             ccccCcccc
Confidence            999998643

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.57  E-value=1.1e-14  Score=146.10  Aligned_cols=99  Identities=29%  Similarity=0.459  Sum_probs=83.2

Q ss_pred             cccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHH
Q 012034            2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENAD   80 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e   80 (472)
                      .|.+++|.|.......      .....++|||+|||+++||++|+++|++||+|.++.|+.|. ++++||||||+|++.+
T Consensus       173 ~l~gr~i~V~~a~p~~------~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e  246 (346)
T TIGR01659       173 TVRNKRLKVSYARPGG------ESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKRE  246 (346)
T ss_pred             ccCCceeeeecccccc------cccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHH
Confidence            3556777776543221      12356789999999999999999999999999999999995 8999999999999999


Q ss_pred             HHHHHHHHHCCCccCC--cceeeecccc
Q 012034           81 DAAKAVEALNGKKFDD--REWYVGKAQK  106 (472)
Q Consensus        81 ~A~~Av~~lng~~i~g--~~l~V~~a~~  106 (472)
                      +|++||+.||+..+.+  +.|.|.++..
T Consensus       247 ~A~~Ai~~lng~~~~g~~~~l~V~~a~~  274 (346)
T TIGR01659       247 EAQEAISALNNVIPEGGSQPLTVRLAEE  274 (346)
T ss_pred             HHHHHHHHhCCCccCCCceeEEEEECCc
Confidence            9999999999999876  5788888764

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).

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.56  E-value=3.1e-14  Score=128.29  Aligned_cols=169  Identities=20%  Similarity=0.358  Sum_probs=124.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CC-CCceeEEEEEeCCHHHHHHHHHHHCCCccC---Cccee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GD-GKSKCFGFVNFENADDAAKAVEALNGKKFD---DREWY  100 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~-g~skG~aFV~F~~~e~A~~Av~~lng~~i~---g~~l~  100 (472)
                      ..-+||||.+||.|+.-.+|..+|..|--.+...+... +. .-.+-+|||+|.+..+|..|+.+|||..|+   +..|.
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            45899999999999999999999999855555555554 22 235679999999999999999999999986   56777


Q ss_pred             eeccccchhHHHH--------------------HH-HHHH----------------------------------------
Q 012034          101 VGKAQKKSEREQE--------------------LK-GQFE----------------------------------------  119 (472)
Q Consensus       101 V~~a~~~~~~~~~--------------------~~-~~~~----------------------------------------  119 (472)
                      ++.++...++.+.                    .. ...+                                        
T Consensus       112 iElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P  191 (284)
T KOG1457|consen  112 IELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAP  191 (284)
T ss_pred             eeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCC
Confidence            7776544433210                    00 0000                                        


Q ss_pred             -------hhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHh
Q 012034          120 -------QAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM  192 (472)
Q Consensus       120 -------~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l  192 (472)
                             ....-......+++|||.||..++|+++|+.+|+.|-....++|... +|  -..||+.|++.+.|..|+..|
T Consensus       192 ~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~-~g--~~vaf~~~~~~~~at~am~~l  268 (284)
T KOG1457|consen  192 SANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR-GG--MPVAFADFEEIEQATDAMNHL  268 (284)
T ss_pred             cccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC-CC--cceEeecHHHHHHHHHHHHHh
Confidence                   00000001112357999999999999999999999987777776542 33  347999999999999999999


Q ss_pred             CCcEe
Q 012034          193 NGKMI  197 (472)
Q Consensus       193 ~g~~i  197 (472)
                      +|..|
T Consensus       269 qg~~~  273 (284)
T KOG1457|consen  269 QGNLL  273 (284)
T ss_pred             hccee
Confidence            99876

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.54  E-value=1.2e-14  Score=148.44  Aligned_cols=186  Identities=21%  Similarity=0.389  Sum_probs=140.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      .....+||++||...++++++|+++.||.+....+..| .+|.++||||.+|.+......|+..|||+.+.++.|.|.+|
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            45678999999999999999999999999999999999 46999999999999999999999999999999999999998


Q ss_pred             ccchhHHHHHHHHHH----h--hhhhhccccccceeeeecC--CCCc-c-------HHHHHHHHhccCceEEEEEeeC-C
Q 012034          105 QKKSEREQELKGQFE----Q--AMKETVDKFQGLNLYIKNL--GDSI-D-------DEKLKELFSEFGTITSCKVMRD-P  167 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~----~--~~~~~~~~~~~~~l~V~nL--~~~~-t-------~e~L~~~F~~~G~I~~v~i~~~-~  167 (472)
                      ...............    .  .............|.+.|+  ++++ +       -|+++..|++||.|.+|.|.++ .
T Consensus       367 ~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~  446 (500)
T KOG0120|consen  367 IVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYP  446 (500)
T ss_pred             hccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCC
Confidence            655443222211000    0  0000001111112333332  1111 1       1577778889999999999887 3


Q ss_pred             C---CCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHH
Q 012034          168 S---GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       168 ~---g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      +   .-..|..||+|.+.+++++|.++|+|..|.++.|..+|.....
T Consensus       447 ~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeDk  493 (500)
T KOG0120|consen  447 DENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDEDK  493 (500)
T ss_pred             CCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHHH
Confidence            2   2346778999999999999999999999999999999876554

>PF00076 RRM_1: RNA recognition motif

Probab=99.54  E-value=3.6e-14  Score=108.69  Aligned_cols=70  Identities=47%  Similarity=0.797  Sum_probs=67.4

Q ss_pred             eeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEE
Q 012034          134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY  203 (472)
Q Consensus       134 l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~  203 (472)
                      |||+|||.++|+++|+++|+.||.|..+.+..+.++.++++|||+|.+.++|.+|++.++|..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999999999999987889999999999999999999999999999999885

(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 ....

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.53  E-value=3.5e-14  Score=109.20  Aligned_cols=70  Identities=40%  Similarity=0.777  Sum_probs=65.1

Q ss_pred             EEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        31 l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      |||+|||+++|+++|+++|+.||.|..+.+..++++.++|+|||+|.+.++|.+|++.+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999999999999997799999999999999999999999999999999874

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 ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.53  E-value=1.3e-14  Score=137.55  Aligned_cols=86  Identities=29%  Similarity=0.474  Sum_probs=78.8

Q ss_pred             hhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           21 TVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        21 ~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      .+..+..-++|+|.|||+...|-||+.+|++||.|.+|.|+.++.| |||||||+|++.+||++|-++|||..|.||+|.
T Consensus        89 ~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEGRkIE  167 (376)
T KOG0125|consen   89 NSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEGRKIE  167 (376)
T ss_pred             cCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeeceEEE
Confidence            3334567789999999999999999999999999999999998666 799999999999999999999999999999999


Q ss_pred             eeccccc
Q 012034          101 VGKAQKK  107 (472)
Q Consensus       101 V~~a~~~  107 (472)
                      |..+..+
T Consensus       168 Vn~ATar  174 (376)
T KOG0125|consen  168 VNNATAR  174 (376)
T ss_pred             Eeccchh
Confidence            9998765

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.50  E-value=4.1e-14  Score=123.29  Aligned_cols=78  Identities=32%  Similarity=0.515  Sum_probs=72.3

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      -.++|||+||+.++++.||..+|..||.|.+|||-..    ..|||||+|++..||..|+..|+|+.|+|..|.|+.+..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            3788999999999999999999999999999999885    467999999999999999999999999999999998765


Q ss_pred             ch
Q 012034          107 KS  108 (472)
Q Consensus       107 ~~  108 (472)
                      ..
T Consensus        85 ~~   86 (195)
T KOG0107|consen   85 RP   86 (195)
T ss_pred             Cc
Confidence            43

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.49  E-value=7.5e-13  Score=127.85  Aligned_cols=184  Identities=18%  Similarity=0.228  Sum_probs=137.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcC----CCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEY----GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~f----G~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      .+.-.|.+++||.++++.++.++|..-    |....|.++...+|+..|-|||.|..+++|..|+.+ |...|+.|.|.+
T Consensus       159 ~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIEl  237 (508)
T KOG1365|consen  159 ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIEL  237 (508)
T ss_pred             ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHH
Confidence            346678999999999999999999632    355678888888999999999999999999999986 556666677777


Q ss_pred             eccccchhHHHHHHHHHHhhhh--------------hhccccccceeeeecCCCCccHHHHHHHHhccCc-eEE--EEEe
Q 012034          102 GKAQKKSEREQELKGQFEQAMK--------------ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGT-ITS--CKVM  164 (472)
Q Consensus       102 ~~a~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~-I~~--v~i~  164 (472)
                      -++.+. +.+..+.+.......              .........+|.+++||++.+.|||.++|..|.. |..  |.+.
T Consensus       238 FRSTaa-Evqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv  316 (508)
T KOG1365|consen  238 FRSTAA-EVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMV  316 (508)
T ss_pred             HHHhHH-HHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEE
Confidence            666443 333333222211000              0001112347999999999999999999999974 444  6777


Q ss_pred             eCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHH
Q 012034          165 RDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       165 ~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      .+..|+..|-|||.|.+.++|..|....|.+...++.|.|--+.-.+
T Consensus       317 ~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~ee  363 (508)
T KOG1365|consen  317 LNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEE  363 (508)
T ss_pred             EcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHH
Confidence            88889999999999999999999999988887777777665544443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.49  E-value=1.1e-13  Score=130.50  Aligned_cols=77  Identities=22%  Similarity=0.349  Sum_probs=71.3

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      .++|||+||++++|+++|+++|+.||+|.+|.|..|..  ++|||||+|++.++|..|+. |||..|.|+.|.|.++...
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            57899999999999999999999999999999998853  57999999999999999995 9999999999999998643

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.45  E-value=4.6e-13  Score=102.91  Aligned_cols=70  Identities=40%  Similarity=0.701  Sum_probs=65.2

Q ss_pred             eeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEE
Q 012034          134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY  203 (472)
Q Consensus       134 l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~  203 (472)
                      |||+|||+++++++|+++|+.||.|..+.+..++++.++|+|||+|.+.++|.+|++.+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999999999999987789999999999999999999999999999999874

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 ....

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.45  E-value=1.1e-13  Score=126.15  Aligned_cols=78  Identities=31%  Similarity=0.482  Sum_probs=70.3

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      -++|||++|+|++.+|+|+++|++||+|+++.|+.|+ +|+||||+||+|.|.++|.+|++..| -.|+||+..|.+|.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccchhhh
Confidence            3579999999999999999999999999999999996 89999999999999999999996544 578999988887653

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.44  E-value=2.4e-13  Score=127.69  Aligned_cols=81  Identities=30%  Similarity=0.549  Sum_probs=77.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      .+.++||||..|+.+++|.+|++.|+.||.|+.|.|+.| .+|+++|||||+|+++.+...|.+..+|..|+|+.|.|..
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            478999999999999999999999999999999999999 6999999999999999999999999999999999999875


Q ss_pred             cc
Q 012034          104 AQ  105 (472)
Q Consensus       104 a~  105 (472)
                      ..
T Consensus       178 ER  179 (335)
T KOG0113|consen  178 ER  179 (335)
T ss_pred             cc
Confidence            43

>PLN03213 repressor of silencing 3; Provisional

Probab=99.44  E-value=3.7e-13  Score=133.65  Aligned_cols=80  Identities=25%  Similarity=0.421  Sum_probs=73.3

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCH--HHHHHHHHHHCCCccCCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENA--DDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~--e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      .....+|||+||++++|+++|+..|+.||.|.+|.|+++ +|  ||||||+|.+.  +++.+||+.|||..+.|+.|+|.
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            355788999999999999999999999999999999944 56  89999999987  78999999999999999999999


Q ss_pred             ccccc
Q 012034          103 KAQKK  107 (472)
Q Consensus       103 ~a~~~  107 (472)
                      .|+..
T Consensus        84 KAKP~   88 (759)
T PLN03213         84 KAKEH   88 (759)
T ss_pred             eccHH
Confidence            99754

>smart00362 RRM_2 RNA recognition motif

Probab=99.43  E-value=7e-13  Score=100.96  Aligned_cols=72  Identities=49%  Similarity=0.775  Sum_probs=67.6

Q ss_pred             eEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        30 ~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      +|||+|||.++++++|+++|++||.|..+.+..+. +.++|+|||+|.+.++|.+|++.+++..+.|+.|.|.
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            58999999999999999999999999999999887 7789999999999999999999999999999988763

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.41  E-value=2.1e-14  Score=125.57  Aligned_cols=79  Identities=30%  Similarity=0.491  Sum_probs=74.0

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..-=|||+|||.+.||.+|.-+|++||+|..|.+++| .||+|+||||++|++..+..-||..|||..|.||.|+|..-.
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            3455999999999999999999999999999999999 699999999999999999999999999999999999997543

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.40  E-value=5.5e-13  Score=126.72  Aligned_cols=80  Identities=29%  Similarity=0.532  Sum_probs=74.4

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ....|||.|||+..-|-||+..|++||.|.+|.|+.++.| ||||+||+|++.+||++|-++|||..|.||+|.|..+..
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            3457999999999999999999999999999999987554 799999999999999999999999999999999998876


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus       174 r  174 (376)
T KOG0125|consen  174 R  174 (376)
T ss_pred             h
Confidence            6

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.40  E-value=1.7e-12  Score=103.51  Aligned_cols=83  Identities=28%  Similarity=0.395  Sum_probs=74.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....+-|||+|||+++|.|+..++|.+||.|..|+|-.++  ..+|-|||.|++..+|++|++.|+|..++++.|.|...
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            3557889999999999999999999999999999887653  45899999999999999999999999999999999987


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      +....
T Consensus        93 q~~~~   97 (124)
T KOG0114|consen   93 QPEDA   97 (124)
T ss_pred             CHHHH
Confidence            65433

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.40  E-value=3e-12  Score=125.55  Aligned_cols=72  Identities=33%  Similarity=0.483  Sum_probs=67.1

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      |.|+|+|||.++|+..|++-|.+||.|.++.|+.  +|+++|  .|.|.++++|++|+..|+|..++|+.|.|.|.
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadime--~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME--NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhhc--cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            5699999999999999999999999999999965  478887  89999999999999999999999999999874

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.39  E-value=1.2e-12  Score=121.50  Aligned_cols=78  Identities=24%  Similarity=0.387  Sum_probs=71.4

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      ..++|||+||++++|+++|+++|+.||+|.+|.|++|  ++++|||||+|++.++|..|+ .|+|..|.++.|.|..+..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCcc
Confidence            4578999999999999999999999999999999988  456789999999999999999 5999999999999988754


Q ss_pred             c
Q 012034          107 K  107 (472)
Q Consensus       107 ~  107 (472)
                      .
T Consensus        81 y   81 (243)
T PLN03121         81 Y   81 (243)
T ss_pred             c
Confidence            3

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.38  E-value=2.3e-11  Score=127.03  Aligned_cols=81  Identities=22%  Similarity=0.447  Sum_probs=74.2

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      +..++||||+.|+..+++.||..+|+.||.|.+|.++..     +|||||++.+..+|.+|+.+|+...+.++.|+|.|+
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            345679999999999999999999999999999999875     899999999999999999999999999999999999


Q ss_pred             ccHHHH
Q 012034          208 QRKEER  213 (472)
Q Consensus       208 ~~k~~~  213 (472)
                      ..+..+
T Consensus       493 ~g~G~k  498 (894)
T KOG0132|consen  493 VGKGPK  498 (894)
T ss_pred             ccCCcc
Confidence            776443

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.38  E-value=1.3e-12  Score=119.65  Aligned_cols=81  Identities=33%  Similarity=0.566  Sum_probs=76.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|-|.||+.++++++|+++|.+||.|..+.|.+|+ +|.+||||||+|.+.++|.+||..|||.-++.-.|+|.|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            45679999999999999999999999999999999885 89999999999999999999999999999999999999997


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      ++
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            64

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.37  E-value=2.3e-12  Score=121.65  Aligned_cols=75  Identities=23%  Similarity=0.355  Sum_probs=69.2

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .++|||+||++.+|+++|+++|+.||.|++|.|..+.  .++|||||+|.+.++|..|+ .|+|..|.|+.|.|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~--~~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN--ERSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC--CCCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEecc
Confidence            3589999999999999999999999999999999874  35799999999999999999 599999999999999754

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=1.2e-12  Score=108.26  Aligned_cols=82  Identities=28%  Similarity=0.404  Sum_probs=74.7

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      .++.+||||+||+..++||.|.++|+++|+|..|.+--|+ +...=||+||+|.+.++|..|++.+++..++.+.|.|.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            4789999999999999999999999999999998887775 455679999999999999999999999999999999988


Q ss_pred             ccc
Q 012034          104 AQK  106 (472)
Q Consensus       104 a~~  106 (472)
                      .-.
T Consensus       113 D~G  115 (153)
T KOG0121|consen  113 DAG  115 (153)
T ss_pred             ccc
Confidence            643

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.36  E-value=1.5e-12  Score=132.63  Aligned_cols=85  Identities=33%  Similarity=0.572  Sum_probs=79.9

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      +.|||+|||++++|++|.++|+..|.|.++++++| .+|+.||||||+|.+.++|.+|++.|||..+.|++|+|.|+...
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            88999999999999999999999999999999999 58999999999999999999999999999999999999999876


Q ss_pred             hhHHHH
Q 012034          108 SEREQE  113 (472)
Q Consensus       108 ~~~~~~  113 (472)
                      ..++..
T Consensus        99 ~~~~~~  104 (435)
T KOG0108|consen   99 KNAERS  104 (435)
T ss_pred             chhHHH
Confidence            655443

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.36  E-value=8.6e-13  Score=117.81  Aligned_cols=80  Identities=33%  Similarity=0.567  Sum_probs=76.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|.|-||..-+|-++|+.+|++||.|-.|.|.+| -|+.++|||||-|.+..+|+.|+++|+|..|+|+.|.|+.|
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            46789999999999999999999999999999999999 48999999999999999999999999999999999999987


Q ss_pred             c
Q 012034          105 Q  105 (472)
Q Consensus       105 ~  105 (472)
                      .
T Consensus        91 r   91 (256)
T KOG4207|consen   91 R   91 (256)
T ss_pred             h
Confidence            4

>smart00360 RRM RNA recognition motif

Probab=99.36  E-value=3.5e-12  Score=96.65  Aligned_cols=70  Identities=49%  Similarity=0.780  Sum_probs=65.6

Q ss_pred             eCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        33 V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      |+|||.++++++|+++|+.||.|..+.+..+. +++++|||||+|.+.++|.+|++.+++..+.|+.|.|.
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            68999999999999999999999999999885 58899999999999999999999999999999998873

>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=99.34  E-value=7.4e-12  Score=95.77  Aligned_cols=74  Identities=46%  Similarity=0.750  Sum_probs=69.6

Q ss_pred             eEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        30 ~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      +|+|+|||.++++++|+++|+.||.|..+.+..+..++.+|+|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999999999999987778899999999999999999999999999999998864

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).

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.34  E-value=1.3e-12  Score=116.75  Aligned_cols=78  Identities=27%  Similarity=0.467  Sum_probs=74.0

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      -++|.|.||.+.++.++|+.+|++||.|-+|.|..|. ++.++|||||.|.+..+|+.|++.|+|.+++|+.|.|.+|.
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            3579999999999999999999999999999999997 78899999999999999999999999999999999999764

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.34  E-value=1.2e-11  Score=120.80  Aligned_cols=175  Identities=21%  Similarity=0.315  Sum_probs=135.4

Q ss_pred             cceEEeCCCC-CCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp-~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .+.|.|.||. ..+|.+.|.-+|+-||+|..|+|.+++    +--|.|.|.|...|.-|++.|+|..+.|++|+|..++.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            6778899997 568999999999999999999999974    24799999999999999999999999999999988754


Q ss_pred             chhH-------HHHHHHHHHhhhh-----hhccc-----cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCC
Q 012034          107 KSER-------EQELKGQFEQAMK-----ETVDK-----FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG  169 (472)
Q Consensus       107 ~~~~-------~~~~~~~~~~~~~-----~~~~~-----~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g  169 (472)
                      ....       ...+...+...-.     .....     .++.+|++.|+|.++++|+|++.|.+-|...+...+..   
T Consensus       373 ~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~---  449 (492)
T KOG1190|consen  373 TNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ---  449 (492)
T ss_pred             ccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC---
Confidence            3211       1111111111100     00111     23457999999999999999999999887665544432   


Q ss_pred             CcccEEEEEcCCHHHHHHHHHHhCCcEecCe-eEEEEEccc
Q 012034          170 ISKGSGFVAFSTPEEASRALAEMNGKMIVSK-PLYVAVAQR  209 (472)
Q Consensus       170 ~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk-~l~V~~a~~  209 (472)
                      +.+.++++.+.+.|+|..|+-.+|.+.+++. .++|+|++.
T Consensus       450 kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  450 KDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             CCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            2366999999999999999999999998755 899998764

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.33  E-value=3.5e-12  Score=124.35  Aligned_cols=175  Identities=17%  Similarity=0.280  Sum_probs=126.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCc--cCCcceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK--FDDREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~--i~g~~l~V~~  103 (472)
                      ...+-|.++|||++++|++|.+++.+||.|+.+...+.     +..||++|.|.++|...+.......  +.|+.|+|.+
T Consensus        26 ~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkG-----knQAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~  100 (492)
T KOG1190|consen   26 EPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKG-----KNQAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQY  100 (492)
T ss_pred             CCcceeEeccCCccccHHHHHHhcccccceeeeeeecc-----chhhhhhhcchhhhhheeecccccCccccCcceeehh
Confidence            46778999999999999999999999999999988876     3389999999999998665544333  7889999988


Q ss_pred             cccchhHH------HHHHHHHHh--hhhhhcc------cccc--------ceeeeecCCCCccHHHHHHHHhccCceEEE
Q 012034          104 AQKKSERE------QELKGQFEQ--AMKETVD------KFQG--------LNLYIKNLGDSIDDEKLKELFSEFGTITSC  161 (472)
Q Consensus       104 a~~~~~~~------~~~~~~~~~--~~~~~~~------~~~~--------~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v  161 (472)
                      +..+....      ..-+..+..  ...+...      ...|        ..++|.|+-+.++-|.|..+|++||.|..|
T Consensus       101 sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKI  180 (492)
T KOG1190|consen  101 SNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKI  180 (492)
T ss_pred             hhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEE
Confidence            64332111      000000000  0000000      0001        236788999999999999999999999998


Q ss_pred             EEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          162 KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       162 ~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .-+...++-   .|+|.|.+.+.|..|...|+|+.|...++.+++.-
T Consensus       181 iTF~Knn~F---QALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~  224 (492)
T KOG1190|consen  181 ITFTKNNGF---QALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDF  224 (492)
T ss_pred             EEEecccch---hhhhhccchhhHHHHHHhccCCcccCceeEEEeeh
Confidence            777664443   48999999999999999999999865555444433

>smart00362 RRM_2 RNA recognition motif

Probab=99.32  E-value=1e-11  Score=94.40  Aligned_cols=72  Identities=43%  Similarity=0.746  Sum_probs=67.5

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      +|||+||+..+++++|+++|+.||.|..+.+..+. +.++|+|||+|.+.++|.+|++.+++..+.|+.|.|+
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            48999999999999999999999999999998876 7789999999999999999999999999999998873

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.30  E-value=5.2e-12  Score=110.27  Aligned_cols=77  Identities=29%  Similarity=0.538  Sum_probs=71.6

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..+.|||+||+..+++.||..+|..||.|.+|.|-..    ..|||||+|++..+|..|+..|+|+.|+|..|.|++..-
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            4678999999999999999999999999999999875    588999999999999999999999999999999998765


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      .
T Consensus        85 ~   85 (195)
T KOG0107|consen   85 R   85 (195)
T ss_pred             C
Confidence            4

>PLN03213 repressor of silencing 3; Provisional

Probab=99.28  E-value=1.8e-11  Score=121.85  Aligned_cols=79  Identities=23%  Similarity=0.455  Sum_probs=72.7

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCH--HHHHHHHHHhCCcEecCeeEEEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTP--EEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~--~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ..+.+|||+||.+.+++++|+..|+.||.|.+|.|+++ +|  ||||||+|.+.  .++.+||..|||..+.|+.|+|..
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            34568999999999999999999999999999999955 55  99999999987  789999999999999999999999


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      |+..
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            9876

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.27  E-value=1.9e-12  Score=116.51  Aligned_cols=82  Identities=29%  Similarity=0.467  Sum_probs=77.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||++|..++||.-|...|-+||.|..|.+.-| .+.+.||||||+|+..|||..||..||+.++.||.|+|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            35688999999999999999999999999999999999 78999999999999999999999999999999999999999


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      .+.
T Consensus        88 kP~   90 (298)
T KOG0111|consen   88 KPE   90 (298)
T ss_pred             CCc
Confidence            754

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.26  E-value=2.3e-11  Score=113.07  Aligned_cols=76  Identities=20%  Similarity=0.372  Sum_probs=70.1

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+.+|||+||++.+|+++|+++|+.||.|.+|+|+++  +.+++||||+|.+.++|..|+ .|+|..|.+++|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            4578999999999999999999999999999999987  566789999999999999999 899999999999998544

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.26  E-value=7.1e-12  Score=104.64  Aligned_cols=83  Identities=28%  Similarity=0.421  Sum_probs=77.5

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ..-+.|||.++..++||++|.+.|..||+|+++.+--| .+|-.||||.|+|++.+.|.+|++.+||..|.|..|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            45678999999999999999999999999999999888 69999999999999999999999999999999999999998


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus       150 Fv~g  153 (170)
T KOG0130|consen  150 FVKG  153 (170)
T ss_pred             EecC
Confidence            6543

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.25  E-value=2.1e-11  Score=114.77  Aligned_cols=82  Identities=23%  Similarity=0.467  Sum_probs=76.8

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .-++|||..|+.++++.+|++.|+.||.|+.|.|+.|. +|+++|||||+|++..+...|.+..+|..|+|+.|.|.+-.
T Consensus       100 Py~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvER  179 (335)
T KOG0113|consen  100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVER  179 (335)
T ss_pred             ccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecc
Confidence            34689999999999999999999999999999999994 99999999999999999999999999999999999999866


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .+.
T Consensus       180 gRT  182 (335)
T KOG0113|consen  180 GRT  182 (335)
T ss_pred             ccc
Confidence            554

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.25  E-value=5.3e-11  Score=95.04  Aligned_cols=79  Identities=27%  Similarity=0.430  Sum_probs=71.6

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      .-|||+|||..+|.|+..++|.+||.|..|+|-..  -.-+|-|||.|++..+|.+|++.|+|..+.++.+.|-+.+...
T Consensus        19 riLyirNLp~~ITseemydlFGkyg~IrQIRiG~~--k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   19 RILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT--KETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             eeEEEecCCccccHHHHHHHhhcccceEEEEecCc--cCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHH
Confidence            46999999999999999999999999999999654  2358999999999999999999999999999999999887654


Q ss_pred             H
Q 012034          212 E  212 (472)
Q Consensus       212 ~  212 (472)
                      .
T Consensus        97 ~   97 (124)
T KOG0114|consen   97 A   97 (124)
T ss_pred             H
Confidence            4

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.24  E-value=1e-12  Score=115.09  Aligned_cols=76  Identities=25%  Similarity=0.477  Sum_probs=72.3

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      .-|||+|||+++|+.||.-+|++||.|..|.+++|. +|+|+||||+||++..+.--|+..|||..|.|+.|+|...
T Consensus        36 A~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   36 AYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             eEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            469999999999999999999999999999999996 8999999999999999999999999999999999999743

>smart00360 RRM RNA recognition motif

Probab=99.23  E-value=4.4e-11  Score=90.49  Aligned_cols=70  Identities=44%  Similarity=0.763  Sum_probs=65.0

Q ss_pred             eecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          136 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       136 V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      |+||+..+++++|+++|+.||.|..+.+..+. ++.++|+|||+|.+.++|.+|+..+++..+.|+.|.|+
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            57899999999999999999999999998876 47889999999999999999999999999999998873

>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=99.23  E-value=8.5e-11  Score=89.78  Aligned_cols=74  Identities=41%  Similarity=0.719  Sum_probs=69.5

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      +|+|+|||..+++++|+++|+.||.|..+.+..+..+..+|+|||.|.+.++|..|++.+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999999999999887777899999999999999999999999999999998864

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).

>smart00361 RRM_1 RNA recognition motif

Probab=99.22  E-value=3.4e-11  Score=92.64  Aligned_cols=60  Identities=30%  Similarity=0.527  Sum_probs=54.1

Q ss_pred             HHHHHHHHh----cCCCeeEEE-EEEC-CC--CCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           42 DEDLKKIFG----EYGTITSAV-VMRD-GD--GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        42 ee~L~~~F~----~fG~I~~v~-i~~d-~~--g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      +++|+++|+    +||.|.++. |..+ .+  ++++|||||+|++.++|.+|++.|||..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            678999998    999999996 6555 44  889999999999999999999999999999999876

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.22  E-value=1.7e-11  Score=121.02  Aligned_cols=78  Identities=38%  Similarity=0.620  Sum_probs=73.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      .+-.-|||+||+.++|||.|+++|++||.|+.|+.++|       ||||.|.+.++|.+|++.+||++|+|..|.|..|+
T Consensus       257 s~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAK  329 (506)
T KOG0117|consen  257 SKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAK  329 (506)
T ss_pred             hheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHhcCceecCceEEEEecC
Confidence            56778999999999999999999999999999999988       99999999999999999999999999999999998


Q ss_pred             cchhH
Q 012034          106 KKSER  110 (472)
Q Consensus       106 ~~~~~  110 (472)
                      ...++
T Consensus       330 P~~k~  334 (506)
T KOG0117|consen  330 PVDKK  334 (506)
T ss_pred             Chhhh
Confidence            76554

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=99.21  E-value=1.1e-09  Score=104.97  Aligned_cols=79  Identities=18%  Similarity=0.238  Sum_probs=68.7

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccC--ceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFG--TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G--~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .++||+||-|++|++||.+.+...|  .+.+++++.++ +|.|||||+|...+..+.++.++.|..++|+|..-.|.-..
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~N  160 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSYN  160 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeeccc
Confidence            4799999999999999999998887  56777888776 78999999999999999999999999999999877766554


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      +.
T Consensus       161 K~  162 (498)
T KOG4849|consen  161 KT  162 (498)
T ss_pred             hh
Confidence            44

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.20  E-value=3.2e-11  Score=99.99  Aligned_cols=83  Identities=24%  Similarity=0.347  Sum_probs=74.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+++|||+||...++||.|.++|+++|.|..|.+-.|+ +-..=|||||+|.+.++|..|+.-++|..++.++|.+.|.-
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            46799999999999999999999999999999887775 44577999999999999999999999999999999999876


Q ss_pred             cHHH
Q 012034          209 RKEE  212 (472)
Q Consensus       209 ~k~~  212 (472)
                      .-.+
T Consensus       115 GF~e  118 (153)
T KOG0121|consen  115 GFVE  118 (153)
T ss_pred             cchh
Confidence            5443

>PF13893 RRM_5: RNA recognition motif

Probab=99.19  E-value=4.7e-11  Score=87.55  Aligned_cols=56  Identities=36%  Similarity=0.704  Sum_probs=51.0

Q ss_pred             HHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           45 LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        45 L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      |+++|++||+|.++.+..+.    +++|||+|.+.++|.+|++.||+..+.|+.|.|.+|
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            68999999999999997764    589999999999999999999999999999999875

(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 ....

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.18  E-value=6.9e-11  Score=98.77  Aligned_cols=84  Identities=21%  Similarity=0.439  Sum_probs=77.8

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ...++-|||.++..+.++++|.+.|..||.|+.+.+-.|+ +|..+|||+|+|++.++|++|++.+||..+.|.+|.|.|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            3456789999999999999999999999999999998775 899999999999999999999999999999999999999


Q ss_pred             cccHH
Q 012034          207 AQRKE  211 (472)
Q Consensus       207 a~~k~  211 (472)
                      +.-+.
T Consensus       149 ~Fv~g  153 (170)
T KOG0130|consen  149 CFVKG  153 (170)
T ss_pred             EEecC
Confidence            87653

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.18  E-value=1.3e-11  Score=111.12  Aligned_cols=80  Identities=29%  Similarity=0.509  Sum_probs=75.6

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC-CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~-~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .++|||++|.+++|+.-|...|-.||.|..|.+..| .+++.|||+||+|.-.|+|..||+.||+.++.|+.|+|.++.+
T Consensus        10 KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP   89 (298)
T KOG0111|consen   10 KRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKP   89 (298)
T ss_pred             ceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCC
Confidence            458999999999999999999999999999999888 4788999999999999999999999999999999999999976


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      .
T Consensus        90 ~   90 (298)
T KOG0111|consen   90 E   90 (298)
T ss_pred             c
Confidence            4

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.18  E-value=2.5e-11  Score=112.32  Aligned_cols=83  Identities=34%  Similarity=0.548  Sum_probs=77.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      .+-+||||..||.+..+.||...|-.||.|.|.+|..| .|+.||+||||.|.+..+|+.||.+|||..|+-++|+|...
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLK  362 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLK  362 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhc
Confidence            56899999999999999999999999999999999999 58999999999999999999999999999999999999876


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus       363 RPkd  366 (371)
T KOG0146|consen  363 RPKD  366 (371)
T ss_pred             Cccc
Confidence            6553

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.17  E-value=5.9e-11  Score=114.56  Aligned_cols=79  Identities=38%  Similarity=0.685  Sum_probs=75.3

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .++|||+||+..+|+++|+++|..||.|..+.+..++ .+.++|||||+|.+.++|..|+..+++..+.|+.|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            5789999999999999999999999999999999985 899999999999999999999999999999999999999764

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.17  E-value=5.9e-12  Score=113.50  Aligned_cols=140  Identities=23%  Similarity=0.325  Sum_probs=118.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...+||||.|+-..+||+-|.|+|-.-|.|..|.|..+.+++.| ||||.|+++-+..-|++-+||..+.++.+.|..-.
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            45788999999999999999999999999999999999888888 99999999999999999999999998888775433


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA  185 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A  185 (472)
                      ..+..                           -|+..++++.+.+.|+.-|.+..+++.++.+|+.+.++|+.+......
T Consensus        86 G~sha---------------------------pld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~  138 (267)
T KOG4454|consen   86 GNSHA---------------------------PLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAV  138 (267)
T ss_pred             CCCcc---------------------------hhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcC
Confidence            22110                           156678899999999999999999999999999999999988766655


Q ss_pred             HHHHHHhC
Q 012034          186 SRALAEMN  193 (472)
Q Consensus       186 ~~Ai~~l~  193 (472)
                      -.++....
T Consensus       139 P~~~~~y~  146 (267)
T KOG4454|consen  139 PFALDLYQ  146 (267)
T ss_pred             cHHhhhhc
Confidence            55554333

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.16  E-value=1.2e-09  Score=105.67  Aligned_cols=166  Identities=21%  Similarity=0.269  Sum_probs=123.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHH--CCCccCCcceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL--NGKKFDDREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~l--ng~~i~g~~l~V~~  103 (472)
                      ...--|.|++|-..++|.+|.+.++.||.|.-+..+..     +.-|.|+|+|.+.|+.+|.--  +-..+.|..-.+.+
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~-----~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~Ny  103 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH-----KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNY  103 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc-----cceeeeeeccccchhhheehhccCcccccCchhhccc
Confidence            44567999999999999999999999999988877765     447999999999999999632  23335666555555


Q ss_pred             cccchhHHHHHHHHHHhhhhhhcccccccee--eeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCC
Q 012034          104 AQKKSEREQELKGQFEQAMKETVDKFQGLNL--YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFST  181 (472)
Q Consensus       104 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l--~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s  181 (472)
                      +..+..+         ....++  ...+..|  .|-|--+.+|.+.|..++...|.|..|.|++. +|.   .|.|+|++
T Consensus       104 Stsq~i~---------R~g~es--~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ngV---QAmVEFds  168 (494)
T KOG1456|consen  104 STSQCIE---------RPGDES--ATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NGV---QAMVEFDS  168 (494)
T ss_pred             chhhhhc---------cCCCCC--CCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cce---eeEEeech
Confidence            5322110         001111  1111123  35566688999999999999999999999986 444   69999999


Q ss_pred             HHHHHHHHHHhCCcEec--CeeEEEEEcccHH
Q 012034          182 PEEASRALAEMNGKMIV--SKPLYVAVAQRKE  211 (472)
Q Consensus       182 ~~~A~~Ai~~l~g~~i~--gk~l~V~~a~~k~  211 (472)
                      .+.|++|...|||..|.  ...|+|+||+...
T Consensus       169 v~~AqrAk~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  169 VEVAQRAKAALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             hHHHHHHHhhcccccccccceeEEEEecCcce
Confidence            99999999999998874  4678888887653

>PF13893 RRM_5: RNA recognition motif

Probab=99.15  E-value=2e-10  Score=84.19  Aligned_cols=56  Identities=36%  Similarity=0.711  Sum_probs=51.4

Q ss_pred             HHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          148 LKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       148 L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      |+++|++||.|.++.+..+.    +++|||+|.+.++|.+|++.|||..++|++|+|.|+
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            68999999999999998763    589999999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.14  E-value=1e-10  Score=119.34  Aligned_cols=84  Identities=27%  Similarity=0.476  Sum_probs=79.0

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +++||+|+++++++++|.++|+..|.|.++++..|+ +|+++|||||+|.+.++|.+|++.|||.++.|++|+|.|+...
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            689999999999999999999999999999999986 8999999999999999999999999999999999999999877


Q ss_pred             HHHHH
Q 012034          211 EERRA  215 (472)
Q Consensus       211 ~~~~~  215 (472)
                      ..+..
T Consensus        99 ~~~~~  103 (435)
T KOG0108|consen   99 KNAER  103 (435)
T ss_pred             chhHH
Confidence            65543

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.12  E-value=8.2e-11  Score=103.47  Aligned_cols=102  Identities=28%  Similarity=0.446  Sum_probs=84.9

Q ss_pred             ccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeE-EEEEECC-CCCceeEEEEEeCCHH
Q 012034            3 INDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDG-DGKSKCFGFVNFENAD   80 (472)
Q Consensus         3 ~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~-v~i~~d~-~g~skG~aFV~F~~~e   80 (472)
                      |-|+.|+|.+....++.     .....+|||+||..+++|.-|.+.|+.||.|.+ -.|++|. +|+++|||||.|.+.|
T Consensus        76 LYgrpIrv~kas~~~~n-----l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfe  150 (203)
T KOG0131|consen   76 LYGRPIRVNKASAHQKN-----LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFE  150 (203)
T ss_pred             hcCceeEEEeccccccc-----ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHH
Confidence            45677777766532222     234588999999999999999999999998765 4677874 6999999999999999


Q ss_pred             HHHHHHHHHCCCccCCcceeeeccccchh
Q 012034           81 DAAKAVEALNGKKFDDREWYVGKAQKKSE  109 (472)
Q Consensus        81 ~A~~Av~~lng~~i~g~~l~V~~a~~~~~  109 (472)
                      .+.+|++++||..++.+.+.|..+.++..
T Consensus       151 asd~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  151 ASDAAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             HHHHHHHHhccchhcCCceEEEEEEecCC
Confidence            99999999999999999999999876654

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=99.10  E-value=5.9e-11  Score=109.43  Aligned_cols=173  Identities=27%  Similarity=0.422  Sum_probs=137.0

Q ss_pred             CcceEEeCCCCCCCCHHH-H--HHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           27 KFNNVFVKNLDESTTDED-L--KKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~-L--~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      +.-.+++.++-.++..+- |  ...|+.+-......+.++..+.-++++|+.|.....-.++-..-+++.+....+++..
T Consensus        95 ~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~  174 (290)
T KOG0226|consen   95 AVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAA  174 (290)
T ss_pred             ccccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeecc
Confidence            344567777766666655 3  6778888888888888888888899999999988777777766677777777777776


Q ss_pred             cccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCH
Q 012034          104 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP  182 (472)
Q Consensus       104 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~  182 (472)
                      ++...+....            .-......||.+.|..+++++.|-+.|.+|-.....++++|. +|+++||+||.|.+.
T Consensus       175 gtswedPsl~------------ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~p  242 (290)
T KOG0226|consen  175 GTSWEDPSLA------------EWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDP  242 (290)
T ss_pred             ccccCCcccc------------cCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCH
Confidence            6655443211            011234579999999999999999999999988889999885 899999999999999


Q ss_pred             HHHHHHHHHhCCcEecCeeEEEEEcccHH
Q 012034          183 EEASRALAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       183 ~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      +++..|+.+|+|+.++.++|.+..+.-++
T Consensus       243 ad~~rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  243 ADYVRAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             HHHHHHHHhhcccccccchhHhhhhhHHh
Confidence            99999999999999999999887554443

>smart00361 RRM_1 RNA recognition motif

Probab=99.10  E-value=3.5e-10  Score=87.02  Aligned_cols=60  Identities=25%  Similarity=0.539  Sum_probs=53.2

Q ss_pred             HHHHHHHHh----ccCceEEEE-EeeCC-C--CCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEE
Q 012034          145 DEKLKELFS----EFGTITSCK-VMRDP-S--GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  204 (472)
Q Consensus       145 ~e~L~~~F~----~~G~I~~v~-i~~~~-~--g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V  204 (472)
                      +++|+++|+    .||.|.++. |..++ +  +.++|||||.|.+.++|.+|+..|||+.+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578888888    999999995 55443 4  889999999999999999999999999999999976

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.10  E-value=6.4e-10  Score=112.20  Aligned_cols=161  Identities=18%  Similarity=0.317  Sum_probs=114.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CC--Ccee---EEEEEeCCHHHHHHHHHHHCCCccCCcce
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DG--KSKC---FGFVNFENADDAAKAVEALNGKKFDDREW   99 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g--~skG---~aFV~F~~~e~A~~Av~~lng~~i~g~~l   99 (472)
                      .-.++|||++||++++|+.|...|..||.+..-+-.+.. .+  -.+|   |+|+.|+++.+++.-+.+..-   +...+
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~~~  333 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEGNY  333 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---cccce
Confidence            567889999999999999999999999997654443221 11  2456   999999999999988876432   33344


Q ss_pred             eeeccccchhHHH----H---HHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHh-ccCceEEEEEeeC-CCCC
Q 012034          100 YVGKAQKKSEREQ----E---LKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFS-EFGTITSCKVMRD-PSGI  170 (472)
Q Consensus       100 ~V~~a~~~~~~~~----~---~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~-~~G~I~~v~i~~~-~~g~  170 (472)
                      ++...........    .   ....+.  ......-....+|||++||.-++.++|..+|+ .||.|..+-|-.| +-+.
T Consensus       334 yf~vss~~~k~k~VQIrPW~laDs~fv--~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KY  411 (520)
T KOG0129|consen  334 YFKVSSPTIKDKEVQIRPWVLADSDFV--LDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKY  411 (520)
T ss_pred             EEEEecCcccccceeEEeeEeccchhh--hccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCC
Confidence            4432221111000    0   000000  00111222346899999999999999999999 7999999999988 4577


Q ss_pred             cccEEEEEcCCHHHHHHHHHH
Q 012034          171 SKGSGFVAFSTPEEASRALAE  191 (472)
Q Consensus       171 s~g~afV~f~s~~~A~~Ai~~  191 (472)
                      .+|-|-|+|++..+=.+||++
T Consensus       412 PkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  412 PKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CCCcceeeecccHHHHHHHhh
Confidence            899999999999999999864

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.06  E-value=1.8e-10  Score=118.24  Aligned_cols=178  Identities=21%  Similarity=0.367  Sum_probs=137.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcC-----------C-CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEY-----------G-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK   93 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~f-----------G-~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~   93 (472)
                      .....+||++++..++++.+..+|+.-           | .|.++.+-.     .+.|+|++|.+.++|..|+. +++..
T Consensus       173 ~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~-----~~nfa~ie~~s~~~at~~~~-~~~~~  246 (500)
T KOG0120|consen  173 RQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNL-----EKNFAFIEFRSISEATEAMA-LDGII  246 (500)
T ss_pred             hhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecc-----cccceeEEecCCCchhhhhc-ccchh
Confidence            446779999999999999999999754           2 255555543     36799999999999999985 78999


Q ss_pred             cCCcceeeeccccchhHHHHHHH-----HHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-
Q 012034           94 FDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-  167 (472)
Q Consensus        94 i~g~~l~V~~a~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-  167 (472)
                      +.|..+.+.+...+.....-...     .+...............+||++|+..++++.++++.+.||.+....++.+. 
T Consensus       247 f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~  326 (500)
T KOG0120|consen  247 FEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSA  326 (500)
T ss_pred             hCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccc
Confidence            99998888765433221111100     111111112222334579999999999999999999999999999998886 


Q ss_pred             CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          168 SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       168 ~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      +|.++||||++|.+...+..|+..|||..+.++.|.|..+-.
T Consensus       327 ~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~  368 (500)
T KOG0120|consen  327 TGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIV  368 (500)
T ss_pred             cccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhc
Confidence            589999999999999999999999999999999999986543

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.06  E-value=1.9e-09  Score=104.24  Aligned_cols=198  Identities=20%  Similarity=0.288  Sum_probs=140.7

Q ss_pred             ccCeeEEEcCcccc-hhhhhhhccCCcceEEeCCC--CCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCH
Q 012034            3 INDKQVFVGHFLRK-QERETVAIKTKFNNVFVKNL--DESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENA   79 (472)
Q Consensus         3 ~~~k~v~v~~~~~~-~~r~~~~~~~~~~~l~V~nL--p~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~   79 (472)
                      |++++-++.+..+. -+|..........-|.+.=|  =.-+|-+-|..+....|.|..|.|++. +|-   .|.|+|++.
T Consensus        94 i~gq~Al~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ngV---QAmVEFdsv  169 (494)
T KOG1456|consen   94 IAGQQALFNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NGV---QAMVEFDSV  169 (494)
T ss_pred             ccCchhhcccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cce---eeEEeechh
Confidence            55666666655332 33333222334444444433  367899999999999999999999886 443   799999999


Q ss_pred             HHHHHHHHHHCCCccC-C-cceeeeccccchhHHHH-----HH-------HHH--------------------Hh-----
Q 012034           80 DDAAKAVEALNGKKFD-D-REWYVGKAQKKSEREQE-----LK-------GQF--------------------EQ-----  120 (472)
Q Consensus        80 e~A~~Av~~lng~~i~-g-~~l~V~~a~~~~~~~~~-----~~-------~~~--------------------~~-----  120 (472)
                      +.|++|..+|||..|- | +.|+|++|+....+-..     +.       ..+                    ++     
T Consensus       170 ~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h  249 (494)
T KOG1456|consen  170 EVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGH  249 (494)
T ss_pred             HHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCC
Confidence            9999999999999874 3 47788777543221000     00       000                    00     


Q ss_pred             ---------------------hhhh------hccccccceeeeecCC-CCccHHHHHHHHhccCceEEEEEeeCCCCCcc
Q 012034          121 ---------------------AMKE------TVDKFQGLNLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISK  172 (472)
Q Consensus       121 ---------------------~~~~------~~~~~~~~~l~V~nL~-~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~  172 (472)
                                           ....      .....+++.+.|-+|+ ..++-+.|..+|..||.|+.|++++.+    .
T Consensus       250 ~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk----~  325 (494)
T KOG1456|consen  250 SGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK----P  325 (494)
T ss_pred             CCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc----c
Confidence                                 0000      0112245678898998 467789999999999999999999874    5


Q ss_pred             cEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          173 GSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       173 g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      |-|.|++.|..+.++|+..||+..+.|.+|.|.+++
T Consensus       326 gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~Sk  361 (494)
T KOG1456|consen  326 GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSK  361 (494)
T ss_pred             ceeEEEcCcHHHHHHHHHHhccCccccceEEEeecc
Confidence            679999999999999999999999999999998765

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.03  E-value=3.1e-10  Score=106.55  Aligned_cols=91  Identities=22%  Similarity=0.464  Sum_probs=81.1

Q ss_pred             cccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHH
Q 012034            2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADD   81 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~   81 (472)
                      .|+|+.|.|....+|        .+..++|+|+||...++.+||+..|++||.|.++.|++|       |+||.|+..++
T Consensus        60 tLhg~nInVeaSksK--------sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-------y~fvh~d~~ed  124 (346)
T KOG0109|consen   60 TLHGVNINVEASKSK--------SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-------YAFVHFDRAED  124 (346)
T ss_pred             eecceEEEEEecccc--------CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc-------eeEEEEeeccc
Confidence            367777777665544        256889999999999999999999999999999999987       99999999999


Q ss_pred             HHHHHHHHCCCccCCcceeeeccccc
Q 012034           82 AAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        82 A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      |..|++.|++.++.|+++.|+.+.++
T Consensus       125 a~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  125 AVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             hHHHHhcccccccccceeeeeeeccc
Confidence            99999999999999999999987654

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.99  E-value=7e-09  Score=104.15  Aligned_cols=163  Identities=19%  Similarity=0.279  Sum_probs=122.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeE-EEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~-v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      .....|.+++||+.||++||.++|+-.-.+.. +.+..|..+++.|-|||+|++.|+|+.|+.. |.+.|..+-|.|-++
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            46778999999999999999999998766665 6677788899999999999999999999986 677788888888776


Q ss_pred             ccchhHHHHHH--------HHHHh------------------------------------------------------hh
Q 012034          105 QKKSEREQELK--------GQFEQ------------------------------------------------------AM  122 (472)
Q Consensus       105 ~~~~~~~~~~~--------~~~~~------------------------------------------------------~~  122 (472)
                      .....+...-.        ..++.                                                      ..
T Consensus       180 s~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~  259 (510)
T KOG4211|consen  180 SRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNY  259 (510)
T ss_pred             HHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccccccccccccc
Confidence            54433322100        00000                                                      00


Q ss_pred             -hh-hcc-----------ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHH
Q 012034          123 -KE-TVD-----------KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL  189 (472)
Q Consensus       123 -~~-~~~-----------~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai  189 (472)
                       .+ ...           ...+..++..+||...++.++..+|+..-.+ .|.|--.++|+..|-|+|+|.+.++|..|+
T Consensus       260 ~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~TGEAdveF~t~edav~Am  338 (510)
T KOG4211|consen  260 PVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRATGEADVEFATGEDAVGAM  338 (510)
T ss_pred             CCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccCCcceeecccchhhHhhh
Confidence             00 000           0011347788999999999999999986544 677777788999999999999999999998


Q ss_pred             H
Q 012034          190 A  190 (472)
Q Consensus       190 ~  190 (472)
                      .
T Consensus       339 s  339 (510)
T KOG4211|consen  339 G  339 (510)
T ss_pred             c
Confidence            4

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.97  E-value=5.2e-10  Score=109.50  Aligned_cols=106  Identities=25%  Similarity=0.454  Sum_probs=92.5

Q ss_pred             ccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHH
Q 012034            3 INDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADD   81 (472)
Q Consensus         3 ~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~   81 (472)
                      |.++.|.+-+.+++.+...........+|||++||.++++++|+++|++||.|..+.++.| .+.+.+||+||.|.++++
T Consensus        72 ~dgr~ve~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~s  151 (311)
T KOG4205|consen   72 LDGRSVEPKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDS  151 (311)
T ss_pred             cCCccccceeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccc
Confidence            5677788888888887765444445779999999999999999999999999999999999 578999999999999999


Q ss_pred             HHHHHHHHCCCccCCcceeeeccccchh
Q 012034           82 AAKAVEALNGKKFDDREWYVGKAQKKSE  109 (472)
Q Consensus        82 A~~Av~~lng~~i~g~~l~V~~a~~~~~  109 (472)
                      +.+++. ..-+.|+++.+.|.+|.++..
T Consensus       152 Vdkv~~-~~f~~~~gk~vevkrA~pk~~  178 (311)
T KOG4205|consen  152 VDKVTL-QKFHDFNGKKVEVKRAIPKEV  178 (311)
T ss_pred             cceecc-cceeeecCceeeEeeccchhh
Confidence            999997 478889999999999988764

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.96  E-value=1.1e-09  Score=100.11  Aligned_cols=81  Identities=35%  Similarity=0.571  Sum_probs=74.7

Q ss_pred             eeeeecCCCCccHHHHHH----HHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          133 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~----~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      +|||.||.+.+..++|++    +|+.||.|.+|...+.  .+.||-|||.|++.+.|..|+..|+|..+.||++++.||.
T Consensus        11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt--~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen   11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKT--PKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCC--CCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            899999999999999998    9999999999988764  6789999999999999999999999999999999999999


Q ss_pred             cHHHHHH
Q 012034          209 RKEERRA  215 (472)
Q Consensus       209 ~k~~~~~  215 (472)
                      .+..-..
T Consensus        89 s~sdii~   95 (221)
T KOG4206|consen   89 SDSDIIA   95 (221)
T ss_pred             Cccchhh
Confidence            8865443

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.96  E-value=7.5e-10  Score=106.35  Aligned_cols=84  Identities=37%  Similarity=0.526  Sum_probs=79.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...+-|||-.|..-+|+++|.-+|+.||.|.+|.|++| ++|.+..||||+|++.+++++|.-+|++..|+.++|-|.++
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            56788999999999999999999999999999999999 79999999999999999999999999999999999999998


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      ++-+.
T Consensus       317 QSVsk  321 (479)
T KOG0415|consen  317 QSVSK  321 (479)
T ss_pred             hhhhh
Confidence            76544

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.95  E-value=4.8e-11  Score=126.24  Aligned_cols=149  Identities=25%  Similarity=0.324  Sum_probs=126.5

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEE-ECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~-~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +...++||+||+..+.+++|...|+.+|.+..+.+. ...+++-||+|||.|.+.+++.+||.- +...+.|+       
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f-~d~~~~gK-------  736 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAF-RDSCFFGK-------  736 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhh-hhhhhhhh-------
Confidence            345679999999999999999999999988887776 235678899999999999999999974 44444431       


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHH
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE  184 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~  184 (472)
                                                 ..++|.|.|...|+++|+.+|+.+|.+++..++..++|+.+|.+||.|.+..+
T Consensus       737 ---------------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~  789 (881)
T KOG0128|consen  737 ---------------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEAD  789 (881)
T ss_pred             ---------------------------hhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcch
Confidence                                       15899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhCCcEecCeeEEEEEccc
Q 012034          185 ASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       185 A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      +.+++....+..+..+.+.|.+...
T Consensus       790 ~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  790 ASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhcccchhhhhhhcCccccccCC
Confidence            9999988887777666666665443

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.93  E-value=1.5e-09  Score=95.62  Aligned_cols=77  Identities=23%  Similarity=0.404  Sum_probs=68.8

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .+.|||+|||.++-+.+|.++|.+||.|.+|.+....  ....||||+|++..+|..||..-+|..++|..|+|+++..
T Consensus         6 ~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~--g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    6 SRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP--GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             cceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC--CCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            4689999999999999999999999999999875431  2467999999999999999999999999999999998653

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.91  E-value=2.8e-09  Score=95.89  Aligned_cols=82  Identities=22%  Similarity=0.329  Sum_probs=74.9

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcC-CCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEY-GTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~f-G~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....-+||..+|.-+.+.++..+|.+| |.++.+++.++ +||+|||||||+|++.|.|.-|-+.||+..+.++.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            456779999999999999999999998 78888888666 7999999999999999999999999999999999999988


Q ss_pred             cccc
Q 012034          104 AQKK  107 (472)
Q Consensus       104 a~~~  107 (472)
                      -.+.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            7655

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.91  E-value=2.6e-09  Score=98.71  Aligned_cols=90  Identities=28%  Similarity=0.464  Sum_probs=78.6

Q ss_pred             hhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC
Q 012034           18 ERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDD   96 (472)
Q Consensus        18 ~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g   96 (472)
                      +-..........+||.+.|..+++++-|-..|++|-.....++++| ++|+++||+||.|.+..|+.+|+++|+|+.++.
T Consensus       180 dPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgs  259 (290)
T KOG0226|consen  180 DPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGS  259 (290)
T ss_pred             CcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhccccccc
Confidence            3333334567788999999999999999999999999999999999 699999999999999999999999999999999


Q ss_pred             cceeeeccccc
Q 012034           97 REWYVGKAQKK  107 (472)
Q Consensus        97 ~~l~V~~a~~~  107 (472)
                      +.|.+..+.-+
T Consensus       260 rpiklRkS~wk  270 (290)
T KOG0226|consen  260 RPIKLRKSEWK  270 (290)
T ss_pred             chhHhhhhhHH
Confidence            99877655433

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.87  E-value=1.3e-09  Score=106.27  Aligned_cols=175  Identities=23%  Similarity=0.240  Sum_probs=136.2

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..+++|++++.+++.+.++..+|.+.|....+..... ....++|+++|.|...+.+..|+.....+.+.++.+..-...
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            5889999999999999999999999998777666664 567899999999999999999998543345555555443333


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceee-eecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLY-IKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE  183 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~  183 (472)
                      ....+..        ............++| |++++..+++++|+.+|..+|.|..+++..++ .+.++||++|+|.+..
T Consensus       167 ~~~~~~~--------n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~  238 (285)
T KOG4210|consen  167 RRGLRPK--------NKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGN  238 (285)
T ss_pred             ccccccc--------chhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhch
Confidence            2221000        000111222233555 99999999999999999999999999998875 7899999999999999


Q ss_pred             HHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          184 EASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       184 ~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ++..++.. ....+.+.++.+......
T Consensus       239 ~~~~~~~~-~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  239 SKKLALND-QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             hHHHHhhc-ccCcccCcccccccCCCC
Confidence            99999987 888999999999877655

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.83  E-value=1.7e-09  Score=115.06  Aligned_cols=161  Identities=21%  Similarity=0.302  Sum_probs=136.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++||++||+..+++.+|+..|..||.|.+|.|....-+..--||||.|.+-..+-.|..++.+..|....+.+...
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            45688999999999999999999999999999999887755555569999999999999999999998887776666665


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHH
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE  184 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~  184 (472)
                      +.+..                    ..+.++|++|..|+....|...|..||.|..|.+-..     .-|++|.|++...
T Consensus       449 ~~kst--------------------~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~  503 (975)
T KOG0112|consen  449 QPKST--------------------PTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPA  503 (975)
T ss_pred             ccccc--------------------cceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCcc
Confidence            43221                    2346999999999999999999999999999877543     4599999999999


Q ss_pred             HHHHHHHhCCcEecC--eeEEEEEcccH
Q 012034          185 ASRALAEMNGKMIVS--KPLYVAVAQRK  210 (472)
Q Consensus       185 A~~Ai~~l~g~~i~g--k~l~V~~a~~k  210 (472)
                      |..|+..|.|..|++  +.+.|.|+..-
T Consensus       504 aq~a~~~~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  504 AQAATHDMRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             chhhHHHHhcCcCCCCCcccccccccCC
Confidence            999999999999975  56777776554

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.83  E-value=5.7e-09  Score=105.70  Aligned_cols=81  Identities=31%  Similarity=0.565  Sum_probs=74.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...+||||.+|...+.-.+|+.+|++||.|.-.+|+.+ .+--.++||||++.+.++|.+||+.|+.+.|.|+.|.|+++
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            45789999999999999999999999999999999988 45556899999999999999999999999999999999987


Q ss_pred             cc
Q 012034          105 QK  106 (472)
Q Consensus       105 ~~  106 (472)
                      +.
T Consensus       483 KN  484 (940)
T KOG4661|consen  483 KN  484 (940)
T ss_pred             cc
Confidence            53

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.82  E-value=1.2e-08  Score=96.34  Aligned_cols=83  Identities=33%  Similarity=0.452  Sum_probs=77.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +...++|+|.|||..+++++|+++|+.||.++.+.+.+|++|.+.|.|=|.|+..+||.+||+.+++..++|+.+.+...
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            45568899999999999999999999999999999999999999999999999999999999999999999999888776


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ...
T Consensus       160 ~~~  162 (243)
T KOG0533|consen  160 SSP  162 (243)
T ss_pred             cCc
Confidence            543

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.81  E-value=7.3e-09  Score=99.74  Aligned_cols=77  Identities=22%  Similarity=0.387  Sum_probs=69.8

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHH-CCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL-NGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~l-ng~~i~g~~l~V~~  103 (472)
                      ++.-++|||++|-..++|.+|++.|.+||+|.++.+...     +++|||+|.+.++|+.|.++. |...|+|.+|.|.|
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~W  299 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKW  299 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceEEEEEe
Confidence            467899999999999999999999999999999999876     679999999999999999764 55568999999999


Q ss_pred             ccc
Q 012034          104 AQK  106 (472)
Q Consensus       104 a~~  106 (472)
                      +..
T Consensus       300 g~~  302 (377)
T KOG0153|consen  300 GRP  302 (377)
T ss_pred             CCC
Confidence            877

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.76  E-value=1.3e-08  Score=98.02  Aligned_cols=83  Identities=30%  Similarity=0.490  Sum_probs=77.3

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ....|||--|..-++++||.-+|+.||.|.+|.|++|. +|.|..||||+|++.+++.+|.-.|.+..|+++.|+|.|++
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            34579999999999999999999999999999999995 89999999999999999999999999999999999999988


Q ss_pred             cHHH
Q 012034          209 RKEE  212 (472)
Q Consensus       209 ~k~~  212 (472)
                      +-..
T Consensus       318 SVsk  321 (479)
T KOG0415|consen  318 SVSK  321 (479)
T ss_pred             hhhh
Confidence            7654

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.75  E-value=5.7e-08  Score=78.82  Aligned_cols=78  Identities=26%  Similarity=0.355  Sum_probs=66.8

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcC--CCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccC----Ccceee
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEY--GTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFD----DREWYV  101 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~f--G~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~----g~~l~V  101 (472)
                      |||.|+|||...|.++|.+++...  |...-+.+..| .++.+.|||||+|.++++|.+..+.++|+.+.    .+...|
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            789999999999999999999764  67777888888 68889999999999999999999999998875    345666


Q ss_pred             ecccc
Q 012034          102 GKAQK  106 (472)
Q Consensus       102 ~~a~~  106 (472)
                      .+|.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            66643

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.69  E-value=4.5e-08  Score=94.37  Aligned_cols=79  Identities=27%  Similarity=0.437  Sum_probs=69.4

Q ss_pred             ccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHh-CCcEecCeeEEE
Q 012034          126 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM-NGKMIVSKPLYV  204 (472)
Q Consensus       126 ~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l-~g~~i~gk~l~V  204 (472)
                      .+...-.+|||++|.+.+++.+|+++|.+||.|.++.++..     +++|||+|.+.++|+.|.++. +...|+|.+|.|
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            34445568999999999999999999999999999999876     679999999999999998764 555679999999


Q ss_pred             EEccc
Q 012034          205 AVAQR  209 (472)
Q Consensus       205 ~~a~~  209 (472)
                      .|...
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99887

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.69  E-value=4.2e-08  Score=88.44  Aligned_cols=79  Identities=27%  Similarity=0.435  Sum_probs=72.2

Q ss_pred             ceeeeecCCCCccHHHHHHHHhcc-CceEEEEEeeC-CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEF-GTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~-G~I~~v~i~~~-~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..+||..++..+.+.++..+|.+| |.|+.+++-++ ++|.|+|||||+|++.+.|.-|-+.||+..+.++-|.|.+-..
T Consensus        50 g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmpp  129 (214)
T KOG4208|consen   50 GVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPP  129 (214)
T ss_pred             cceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCc
Confidence            468999999999999999999998 77888888676 4899999999999999999999999999999999999998766


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      .
T Consensus       130 e  130 (214)
T KOG4208|consen  130 E  130 (214)
T ss_pred             h
Confidence            5

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.65  E-value=2.5e-08  Score=101.67  Aligned_cols=174  Identities=18%  Similarity=0.223  Sum_probs=115.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|+|-|||..+++++|+++|+.||+|..|..-    -..+|..||+|.|..+|++|+++|++.+|.|+.|.....
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~  147 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGG  147 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCc
Confidence            4678999999999999999999999999999985533    345789999999999999999999999999999883222


Q ss_pred             ccchhHH---HHHHHHHHhhhhhhccccc-cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcC
Q 012034          105 QKKSERE---QELKGQFEQAMKETVDKFQ-GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS  180 (472)
Q Consensus       105 ~~~~~~~---~~~~~~~~~~~~~~~~~~~-~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~  180 (472)
                      .....--   ..+-..+..........-. ...+ ++.|+...+..-++.+|+.+|.+.. +-    ++.-+..-|+.|.
T Consensus       148 ~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~-~g~l~P~~s~~~~~~~~~~~~~~~~-~~----~~~~~hq~~~~~~  221 (549)
T KOG4660|consen  148 ARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQL-FGMLSPTRSSILLEHISSVDGSSPG-RE----TPLLNHQRFVEFA  221 (549)
T ss_pred             ccccchhcccchhhhhccchhhcCCCCCCcCCcc-eeeeccchhhhhhhcchhccCcccc-cc----ccchhhhhhhhhc
Confidence            1111100   0111111111111111000 1123 3338888888888888888887765 32    1222225678888


Q ss_pred             CHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          181 TPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       181 s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      +..++..+...+ |..+.++....++...
T Consensus       222 ~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  222 DNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             cccchhhcccCC-ceecCCCCceEEecCC
Confidence            888886666544 6667777666666554

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.61  E-value=5.6e-08  Score=98.87  Aligned_cols=80  Identities=33%  Similarity=0.565  Sum_probs=68.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++++++|+++|..||.|+...|.... .+++.+||||+|++.++++.||++ +-..|++++|.|+..
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEK  364 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEec
Confidence            345569999999999999999999999999998887753 455559999999999999999987 577789999999865


Q ss_pred             cc
Q 012034          105 QK  106 (472)
Q Consensus       105 ~~  106 (472)
                      ..
T Consensus       365 ~~  366 (419)
T KOG0116|consen  365 RP  366 (419)
T ss_pred             cc
Confidence            43

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.60  E-value=8.1e-08  Score=97.54  Aligned_cols=80  Identities=28%  Similarity=0.485  Sum_probs=71.9

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+.||||.+|...+-..||+.+|++||.|+-.+|+++. +--.++|+||++.+.++|.+||+.||..+++|+.|.|..++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            35689999999999999999999999999999998873 33358999999999999999999999999999999998764


Q ss_pred             c
Q 012034          209 R  209 (472)
Q Consensus       209 ~  209 (472)
                      .
T Consensus       484 N  484 (940)
T KOG4661|consen  484 N  484 (940)
T ss_pred             c
Confidence            3

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.58  E-value=2.8e-07  Score=89.79  Aligned_cols=165  Identities=18%  Similarity=0.206  Sum_probs=117.8

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      .+..+-|..++|||..++.+|..+|.-.-...--..++. ..|+.-|+|.|.|.|.|.-..|++. +.+.+.++.|.|-.
T Consensus        57 ~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYk  135 (508)
T KOG1365|consen   57 ADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYK  135 (508)
T ss_pred             cCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeec
Confidence            466777889999999999999999986543333233332 4577788999999999999999986 67778888888877


Q ss_pred             cccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhcc----CceEEEEEeeCCCCCcccEEEEEc
Q 012034          104 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEF----GTITSCKVMRDPSGISKGSGFVAF  179 (472)
Q Consensus       104 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~----G~I~~v~i~~~~~g~s~g~afV~f  179 (472)
                      +....--...  .-..........+..-.-+.+++||+++++.|+.++|...    |..+.+-+++..+|+..|-|||.|
T Consensus       136 a~ge~f~~ia--gg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlf  213 (508)
T KOG1365|consen  136 ATGEEFLKIA--GGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLF  213 (508)
T ss_pred             cCchhheEec--CCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEe
Confidence            6543211000  0000000111122223457789999999999999999632    355667777777999999999999


Q ss_pred             CCHHHHHHHHHHh
Q 012034          180 STPEEASRALAEM  192 (472)
Q Consensus       180 ~s~~~A~~Ai~~l  192 (472)
                      ..+++|..|+.+-
T Consensus       214 a~ee~aq~aL~kh  226 (508)
T KOG1365|consen  214 ACEEDAQFALRKH  226 (508)
T ss_pred             cCHHHHHHHHHHH
Confidence            9999999999643

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.54  E-value=2.3e-07  Score=87.58  Aligned_cols=80  Identities=30%  Similarity=0.503  Sum_probs=75.0

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .+.|+|.||+..|+++||+++|..||.++.+.|..++.|.|.|.|-|.|...++|..|++.+||..++|+.+.+.+....
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            36799999999999999999999999999999999999999999999999999999999999999999999988876544

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.48  E-value=3.3e-07  Score=88.42  Aligned_cols=79  Identities=24%  Similarity=0.363  Sum_probs=73.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEE--------EEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCee
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP  201 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~--------v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~  201 (472)
                      .+++|||.|||.++|.+++.++|+++|.|..        |++.++++|.-+|-|+|+|.-.++..-|+..|++..+.|+.
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            4567999999999999999999999998854        78999999999999999999999999999999999999999


Q ss_pred             EEEEEcc
Q 012034          202 LYVAVAQ  208 (472)
Q Consensus       202 l~V~~a~  208 (472)
                      |+|..|+
T Consensus       213 ~rVerAk  219 (382)
T KOG1548|consen  213 LRVERAK  219 (382)
T ss_pred             EEEehhh
Confidence            9999764

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.43  E-value=2.6e-07  Score=96.31  Aligned_cols=82  Identities=28%  Similarity=0.473  Sum_probs=74.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCC----CCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD----GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~----g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      +-..|||||+||+..++++.|...|..||+|.+++|++..+    .+.+-||||.|-+..||.+|++.|+|..+.+..+.
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            35689999999999999999999999999999999999743    45577999999999999999999999999999999


Q ss_pred             eecccc
Q 012034          101 VGKAQK  106 (472)
Q Consensus       101 V~~a~~  106 (472)
                      +.|+..
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999853

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.43  E-value=6.7e-07  Score=93.08  Aligned_cols=73  Identities=26%  Similarity=0.469  Sum_probs=66.5

Q ss_pred             eeeecCCCCccHHHHHHHHhccCce-EEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          134 LYIKNLGDSIDDEKLKELFSEFGTI-TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       134 l~V~nL~~~~t~e~L~~~F~~~G~I-~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      |-+.|+|++++-+||.++|..|-.+ .+|.+.++.+|...|-|.|.|++.++|..|...++++.|..+.|++.+
T Consensus       870 ~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  870 LSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            7899999999999999999999755 456777777899999999999999999999999999999999998875

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.33  E-value=1.1e-07  Score=93.64  Aligned_cols=153  Identities=24%  Similarity=0.420  Sum_probs=119.6

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcC--CCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCc-cCCcceeeeccc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEY--GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK-FDDREWYVGKAQ  105 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~f--G~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~-i~g~~l~V~~a~  105 (472)
                      +.+|++||...++-.+|+.+|...  +--..+ +++      .||+||.+.+...|.+|++.++|+. +.|+++.|..+-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~f-l~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQF-LVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcce-eee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            569999999999999999999864  221222 222      4799999999999999999999876 788898888765


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA  185 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A  185 (472)
                      .+..+.                    ..+-|.|++.....+.|..+...||.++.|........  .-..-|+|.+.+.+
T Consensus        75 ~kkqrs--------------------rk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e--tavvnvty~~~~~~  132 (584)
T KOG2193|consen   75 PKKQRS--------------------RKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE--TAVVNVTYSAQQQH  132 (584)
T ss_pred             hHHHHh--------------------hhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH--HHHHHHHHHHHHHH
Confidence            544332                    24778899999999999999999999999976332111  11234688999999


Q ss_pred             HHHHHHhCCcEecCeeEEEEEcccH
Q 012034          186 SRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       186 ~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ..||..++|..+....+.|.|-...
T Consensus       133 ~~ai~kl~g~Q~en~~~k~~YiPde  157 (584)
T KOG2193|consen  133 RQAIHKLNGPQLENQHLKVGYIPDE  157 (584)
T ss_pred             HHHHHhhcchHhhhhhhhcccCchh
Confidence            9999999999998888888875543

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.33  E-value=3.3e-06  Score=68.53  Aligned_cols=79  Identities=24%  Similarity=0.322  Sum_probs=67.8

Q ss_pred             ceeeeecCCCCccHHHHHHHHhcc--CceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEec----CeeEEE
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV----SKPLYV  204 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~--G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~----gk~l~V  204 (472)
                      ++|-|+|||...|.++|.+++...  |....+.+.-|- ++.+.|||||.|.+++.|.+..+.++|+.+.    .|.+.|
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            589999999999999999998754  677777777774 6778999999999999999999999999874    677788


Q ss_pred             EEcccH
Q 012034          205 AVAQRK  210 (472)
Q Consensus       205 ~~a~~k  210 (472)
                      .+|.-.
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            887654

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.31  E-value=2e-05  Score=76.18  Aligned_cols=84  Identities=21%  Similarity=0.249  Sum_probs=71.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCC--CeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYG--TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG--~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      +-+..++||+||-|.+|+++|.+.+...|  .|.++++..+ .+|.|||||.|...+..+.++.++-|-.+.|.|..-.|
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            34566799999999999999999998877  5777777777 57999999999999999999999999999999988777


Q ss_pred             eccccch
Q 012034          102 GKAQKKS  108 (472)
Q Consensus       102 ~~a~~~~  108 (472)
                      ...++..
T Consensus       157 ~~~NK~~  163 (498)
T KOG4849|consen  157 LSYNKTN  163 (498)
T ss_pred             eccchhh
Confidence            6665443

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.30  E-value=1e-06  Score=83.46  Aligned_cols=81  Identities=23%  Similarity=0.327  Sum_probs=74.4

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      +...+.+||+|+...+|.+++...|+.||.|..+.+.+|. .|.+|||+||+|.+.+.+..++. |++..|.++.+.|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            4678899999999999999999999999999999999995 56799999999999999999998 999999999999887


Q ss_pred             ccc
Q 012034          104 AQK  106 (472)
Q Consensus       104 a~~  106 (472)
                      ...
T Consensus       177 ~r~  179 (231)
T KOG4209|consen  177 KRT  179 (231)
T ss_pred             eee
Confidence            643

>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=98.22  E-value=4.6e-06  Score=64.67  Aligned_cols=72  Identities=18%  Similarity=0.270  Sum_probs=49.3

Q ss_pred             cceEEeCCCCCCCCHHHHH----HHHhcCC-CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           28 FNNVFVKNLDESTTDEDLK----KIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~----~~F~~fG-~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      ++.|||.|||.+.+-..|+    .++..+| .|.+|.         .+-|+|.|.+.+.|.+|.+.|+|..+.|++|.|.
T Consensus         2 ~s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~---------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    2 HSLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS---------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             SEEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             ccEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe---------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            5679999999999876555    5666775 666652         3689999999999999999999999999999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      +.....
T Consensus        73 ~~~~~r   78 (90)
T PF11608_consen   73 FSPKNR   78 (90)
T ss_dssp             SS--S-
T ss_pred             EcCCcc
Confidence            985443

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.21  E-value=7.7e-07  Score=80.83  Aligned_cols=78  Identities=18%  Similarity=0.204  Sum_probs=72.3

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .+|||.|+...++++-|.++|-..|.|..+.|..+.+++.+ ||||.|.++.+..-|++.+||..+.+..+.+++-...
T Consensus        10 rtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G~   87 (267)
T KOG4454|consen   10 RTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCGN   87 (267)
T ss_pred             hHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccCC
Confidence            48999999999999999999999999999999999888888 9999999999999999999999999999988875443

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.16  E-value=3.2e-06  Score=86.22  Aligned_cols=77  Identities=26%  Similarity=0.425  Sum_probs=66.1

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...|||+|||.+++.++|+++|..||.|+...|.... .+++.+||||+|.+.+++..||.+- -..+++++|.|+-.+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKR  365 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCeeEEEEecc
Confidence            4569999999999999999999999999998886643 4555699999999999999999765 667899999998543

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.15  E-value=3.2e-06  Score=80.03  Aligned_cols=82  Identities=22%  Similarity=0.349  Sum_probs=73.6

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ......+||+|++..+|.+++..+|+.||.|..+.|..|. .+.++||+||.|.+.+.+.+++. |++..|.++.+.|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            3445689999999999999999999999999999998887 55799999999999999999997 999999999999997


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      ..-.
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            5543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.08  E-value=5.7e-06  Score=86.60  Aligned_cols=80  Identities=33%  Similarity=0.543  Sum_probs=71.6

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC----CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP----SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~----~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      ..+||||+||+..++++.|...|..||.|.+++|+-.+    ....+-|+||.|-+..+|.+|++.|+|..+.+..+++.
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            34789999999999999999999999999999997653    34557799999999999999999999999999999998


Q ss_pred             Eccc
Q 012034          206 VAQR  209 (472)
Q Consensus       206 ~a~~  209 (472)
                      |.+.
T Consensus       253 Wgk~  256 (877)
T KOG0151|consen  253 WGKA  256 (877)
T ss_pred             cccc
Confidence            8753

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.08  E-value=4e-06  Score=87.48  Aligned_cols=180  Identities=14%  Similarity=0.041  Sum_probs=128.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCc-eeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS-KCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~s-kG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...+-+-+++.+.+.++.+++++|--. .|.++.|..+.-+.+ .|-++|.|....++.+|++. |...+-.|.+.|...
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~  386 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPP  386 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCC
Confidence            345567788999999999999998643 345566666643333 78999999999999999975 555666666666544


Q ss_pred             ccchhHHHHHHHHH---------------------HhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEE-EE
Q 012034          105 QKKSEREQELKGQF---------------------EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS-CK  162 (472)
Q Consensus       105 ~~~~~~~~~~~~~~---------------------~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~-v~  162 (472)
                      -.....-..-...+                     ............+.+|||..||..+++.++.+.|..--.|++ |.
T Consensus       387 g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~  466 (944)
T KOG4307|consen  387 GNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIE  466 (944)
T ss_pred             CccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeE
Confidence            22111000000000                     000011122334568999999999999999999998777776 77


Q ss_pred             EeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          163 VMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       163 i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      |.+.++++.++.|||.|..++++.+|...-+.+.++.+.|+|.-.
T Consensus       467 lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  467 LTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             eccCCcccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            777788999999999999999999999888888888888888744

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.07  E-value=2.3e-06  Score=87.67  Aligned_cols=69  Identities=28%  Similarity=0.442  Sum_probs=62.9

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEE
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY  203 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~  203 (472)
                      ..+|+|.|||..|++++|+++|+.||+|..|+.-..    .+|.+||+|-|..+|+.|+++|++.++.|+.|.
T Consensus        75 ~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   75 QGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            457999999999999999999999999999765443    578999999999999999999999999999887

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.04  E-value=3.9e-06  Score=77.72  Aligned_cols=71  Identities=28%  Similarity=0.560  Sum_probs=64.9

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .+||++|++.+.+.+|.++|..||.|..+.+.       .||+||.|.+..+|..|+..+|++++.+..+.|.++...
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK-------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee-------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            58999999999999999999999999998875       469999999999999999999999999998888876644

>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=98.04  E-value=1.8e-05  Score=61.49  Aligned_cols=70  Identities=26%  Similarity=0.438  Sum_probs=48.4

Q ss_pred             ceeeeecCCCCccHH----HHHHHHhccC-ceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          132 LNLYIKNLGDSIDDE----KLKELFSEFG-TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e----~L~~~F~~~G-~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      +.|||.|||.+.+..    .|+.++..+| .|.+|.         .+.|+|.|.+.+.|.+|.+.|+|..+.|.+|.|++
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~---------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS---------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe---------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            369999999988764    5667777886 565553         45799999999999999999999999999999998


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      ....
T Consensus        74 ~~~~   77 (90)
T PF11608_consen   74 SPKN   77 (90)
T ss_dssp             S--S
T ss_pred             cCCc
Confidence            8543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.04  E-value=1.4e-05  Score=73.05  Aligned_cols=83  Identities=18%  Similarity=0.343  Sum_probs=69.2

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEee-CC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEec---CeeEEEEE
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMR-DP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV---SKPLYVAV  206 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~-~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~---gk~l~V~~  206 (472)
                      ++|||.+||.++...+|..+|..|-..+.+.+-. ++ +...+-+|||+|.+..+|..|...|||..|+   +..|++.+
T Consensus        35 RTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiEl  114 (284)
T KOG1457|consen   35 RTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIEL  114 (284)
T ss_pred             ceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeee
Confidence            5899999999999999999999997777665533 22 2245679999999999999999999999985   78999999


Q ss_pred             cccHHHHH
Q 012034          207 AQRKEERR  214 (472)
Q Consensus       207 a~~k~~~~  214 (472)
                      ++....++
T Consensus       115 AKSNtK~k  122 (284)
T KOG1457|consen  115 AKSNTKRK  122 (284)
T ss_pred             hhcCcccc
Confidence            98775543

>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=97.90  E-value=2.7e-05  Score=64.65  Aligned_cols=78  Identities=33%  Similarity=0.546  Sum_probs=49.4

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCC-----cEecCeeEEEE
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG-----KMIVSKPLYVA  205 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g-----~~i~gk~l~V~  205 (472)
                      |+.|+|.++...++.++|++.|+.||.|..|.+.+.     -..|+|.|.+.++|.+|+..+..     ..+.+..+.+.
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-----~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-----DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-----CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            457899999999999999999999999999998765     33799999999999999987643     36778888888


Q ss_pred             EcccHHHH
Q 012034          206 VAQRKEER  213 (472)
Q Consensus       206 ~a~~k~~~  213 (472)
                      +-...++.
T Consensus        76 vLeGeeE~   83 (105)
T PF08777_consen   76 VLEGEEEE   83 (105)
T ss_dssp             ---HHHHH
T ss_pred             ECCCHHHH
Confidence            77666544

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.70  E-value=3.5e-05  Score=75.37  Aligned_cols=84  Identities=24%  Similarity=0.342  Sum_probs=74.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCee--------EEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTIT--------SAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDD   96 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~--------~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g   96 (472)
                      ....+|||-+|+..+++++|.++|..+|.|.        .|+|.+| +|++.||-|.|.|++..+|+.||.-++++.+.+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            4567899999999999999999999999875        3666667 689999999999999999999999999999999


Q ss_pred             cceeeeccccchh
Q 012034           97 REWYVGKAQKKSE  109 (472)
Q Consensus        97 ~~l~V~~a~~~~~  109 (472)
                      ..|.|..+..+..
T Consensus       144 n~ikvs~a~~r~~  156 (351)
T KOG1995|consen  144 NTIKVSLAERRTG  156 (351)
T ss_pred             CCchhhhhhhccC
Confidence            9999988876654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.67  E-value=1.8e-05  Score=77.66  Aligned_cols=162  Identities=16%  Similarity=0.178  Sum_probs=114.7

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC----CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG----DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~----~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ..-|-|.||..++|.+++..+|.-.|+|.++.++...    -....-.|||.|.|..++..|-. |.++.+-++.|.|-.
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEe
Confidence            3469999999999999999999999999999998752    13345689999999999998886 777887788777765


Q ss_pred             cccchhHHHH-H---HHH--------------------------------------HHhhhhhhccccccceeeeecCCC
Q 012034          104 AQKKSEREQE-L---KGQ--------------------------------------FEQAMKETVDKFQGLNLYIKNLGD  141 (472)
Q Consensus       104 a~~~~~~~~~-~---~~~--------------------------------------~~~~~~~~~~~~~~~~l~V~nL~~  141 (472)
                      .-........ +   ...                                      +.....   +.+ ..+++|.+|..
T Consensus        86 ~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kl---eei-rRt~~v~sl~~  161 (479)
T KOG4676|consen   86 YGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKL---EEI-RRTREVQSLIS  161 (479)
T ss_pred             cCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhh---HHH-Hhhhhhhcchh
Confidence            4332221111 0   000                                      000000   000 13689999999


Q ss_pred             CccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec
Q 012034          142 SIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV  198 (472)
Q Consensus       142 ~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~  198 (472)
                      .+...++.+.|..+|.|....+-...   ..-+|-|.|........|+ .++|..+.
T Consensus       162 ~~~l~e~~e~f~r~Gev~ya~~ask~---~s~~c~~sf~~qts~~hal-r~~gre~k  214 (479)
T KOG4676|consen  162 AAILPESGESFERKGEVSYAHTASKS---RSSSCSHSFRKQTSSKHAL-RSHGRERK  214 (479)
T ss_pred             hhcchhhhhhhhhcchhhhhhhhccC---CCcchhhhHhhhhhHHHHH-Hhcchhhh
Confidence            99999999999999998887765432   2346778888877777777 56666554

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.64  E-value=9.2e-05  Score=69.18  Aligned_cols=89  Identities=26%  Similarity=0.346  Sum_probs=79.2

Q ss_pred             HHHHHHHHCCCccCCcceeeeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEE
Q 012034           82 AAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC  161 (472)
Q Consensus        82 A~~Av~~lng~~i~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v  161 (472)
                      |..|-.+|++....++.|.|.++..+                         .|||.||...++.|.|.+.|+.||.|+..
T Consensus         7 ae~ak~eLd~~~~~~~~lr~rfa~~a-------------------------~l~V~nl~~~~sndll~~~f~~fg~~e~a   61 (275)
T KOG0115|consen    7 AEIAKRELDGRFPKGRSLRVRFAMHA-------------------------ELYVVNLMQGASNDLLEQAFRRFGPIERA   61 (275)
T ss_pred             HHHHHHhcCCCCCCCCceEEEeeccc-------------------------eEEEEecchhhhhHHHHHhhhhcCccchh
Confidence            55566678899999999999999762                         49999999999999999999999999999


Q ss_pred             EEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCc
Q 012034          162 KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK  195 (472)
Q Consensus       162 ~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~  195 (472)
                      .+..|..++..+-++|.|...-.|.+|...++-.
T Consensus        62 v~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~   95 (275)
T KOG0115|consen   62 VAKVDDRGKPTREGIVEFAKKPNARKAARRCREG   95 (275)
T ss_pred             eeeecccccccccchhhhhcchhHHHHHHHhccC
Confidence            9988888999999999999999999999877543

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.60  E-value=3.8e-05  Score=78.67  Aligned_cols=77  Identities=31%  Similarity=0.439  Sum_probs=62.2

Q ss_pred             CCcceEEeCCCCCCCC--HHH----HHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCc-c
Q 012034           26 TKFNNVFVKNLDESTT--DED----LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR-E   98 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~t--ee~----L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~-~   98 (472)
                      --.+.|+|.|+|.--.  -+.    |..+|+++|+|..+.+..++.|.++||.|++|.+..+|+.||++|||+.|+-+ .
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            3467799999984322  223    44689999999999999888888999999999999999999999999998755 4


Q ss_pred             eeee
Q 012034           99 WYVG  102 (472)
Q Consensus        99 l~V~  102 (472)
                      +.|.
T Consensus       136 f~v~  139 (698)
T KOG2314|consen  136 FFVR  139 (698)
T ss_pred             EEee
Confidence            4443

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.60  E-value=5.2e-06  Score=88.76  Aligned_cols=161  Identities=19%  Similarity=0.205  Sum_probs=118.0

Q ss_pred             ceEEeCCCCCCCCHH-HHHHHHhcCCCeeEEEEEECCC-CCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           29 NNVFVKNLDESTTDE-DLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        29 ~~l~V~nLp~~~tee-~L~~~F~~fG~I~~v~i~~d~~-g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      ...++.++.....+. ..+..|..+|.|+.|.+-.... -.+..++++.++.+.+++.|.. ..+..+.++.+.|..+.+
T Consensus       572 ~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~ad~  650 (881)
T KOG0128|consen  572 REKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGLADA  650 (881)
T ss_pred             hhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCCCCCc
Confidence            345566665555444 6788999999999998877422 2223389999999999999986 578889999998888876


Q ss_pred             chhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEe-eCCCCCcccEEEEEcCCHHHH
Q 012034          107 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVM-RDPSGISKGSGFVAFSTPEEA  185 (472)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~-~~~~g~s~g~afV~f~s~~~A  185 (472)
                      +.......        ....+.-..+++||+||+..+.+++|...|+.+|.+..+.+. ....++-+|+|+|.|.+.+++
T Consensus       651 ~~~~~~~k--------vs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~  722 (881)
T KOG0128|consen  651 EEKEENFK--------VSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHA  722 (881)
T ss_pred             hhhhhccC--------cCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCch
Confidence            65221110        000111123478999999999999999999999998887664 334678899999999999999


Q ss_pred             HHHHHHhCCcEec
Q 012034          186 SRALAEMNGKMIV  198 (472)
Q Consensus       186 ~~Ai~~l~g~~i~  198 (472)
                      .+||....+..++
T Consensus       723 ~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  723 GAAVAFRDSCFFG  735 (881)
T ss_pred             hhhhhhhhhhhhh
Confidence            9999655554444

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.59  E-value=0.00012  Score=70.64  Aligned_cols=80  Identities=25%  Similarity=0.490  Sum_probs=63.5

Q ss_pred             cceEEeCCCCCCCCHHH----H--HHHHhcCCCeeEEEEEECC-C-CCceeEE--EEEeCCHHHHHHHHHHHCCCccCCc
Q 012034           28 FNNVFVKNLDESTTDED----L--KKIFGEYGTITSAVVMRDG-D-GKSKCFG--FVNFENADDAAKAVEALNGKKFDDR   97 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~----L--~~~F~~fG~I~~v~i~~d~-~-g~skG~a--FV~F~~~e~A~~Av~~lng~~i~g~   97 (472)
                      .+-+||-+|+..+-+|+    |  .++|.+||.|..|.|-+.. . ....+.+  ||+|.+.|||.+||.+.+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            45578999998777766    3  3799999999999887653 1 1222334  9999999999999999999999999


Q ss_pred             ceeeeccccc
Q 012034           98 EWYVGKAQKK  107 (472)
Q Consensus        98 ~l~V~~a~~~  107 (472)
                      .|+..+...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999887544

>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=97.59  E-value=0.00026  Score=58.79  Aligned_cols=71  Identities=27%  Similarity=0.413  Sum_probs=43.5

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCC-----ccCCcceeeec
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK-----KFDDREWYVGK  103 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~-----~i~g~~l~V~~  103 (472)
                      +.|+|.++...++-++|++.|+.||.|.-|.+....     .-|||-|.+.++|+.|++++...     .|.+..+.+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-----~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-----TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-----CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            358899999999999999999999998877776542     27899999999999999987544     45555555544


Q ss_pred             c
Q 012034          104 A  104 (472)
Q Consensus       104 a  104 (472)
                      -
T Consensus        77 L   77 (105)
T PF08777_consen   77 L   77 (105)
T ss_dssp             -
T ss_pred             C
Confidence            3

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.54  E-value=7.1e-05  Score=73.23  Aligned_cols=83  Identities=23%  Similarity=0.422  Sum_probs=72.9

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEE--------EEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCe
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSK  200 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~--------v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk  200 (472)
                      ...+|||.+|++.+++++|.++|..+|.|..        |.|.++. ++.+||-|.|.|.|...|+.||..++++.+.+.
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            4458999999999999999999999998853        4555553 788999999999999999999999999999999


Q ss_pred             eEEEEEcccHHH
Q 012034          201 PLYVAVAQRKEE  212 (472)
Q Consensus       201 ~l~V~~a~~k~~  212 (472)
                      .|.|.+++.+..
T Consensus       145 ~ikvs~a~~r~~  156 (351)
T KOG1995|consen  145 TIKVSLAERRTG  156 (351)
T ss_pred             CchhhhhhhccC
Confidence            999998887753

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=97.44  E-value=0.0008  Score=71.70  Aligned_cols=12  Identities=8%  Similarity=-0.028  Sum_probs=4.8

Q ss_pred             HHHHhhhhhhhh
Q 012034          390 QRTLLGESLYPL  401 (472)
Q Consensus       390 q~~~~g~~l~~~  401 (472)
                      +|...|-.+=..
T Consensus       673 ~k~~e~~eekkt  684 (1102)
T KOG1924|consen  673 KKEQEGGEEKKT  684 (1102)
T ss_pred             cccccccccccc
Confidence            444444333333

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.42  E-value=9.5e-05  Score=72.41  Aligned_cols=82  Identities=28%  Similarity=0.397  Sum_probs=72.3

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..+-.+|++|+.++++++|+..|..+|.|+.+.+..+ .++.++|||||.|.+..++..++.. ....+.++.+.+.+..
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCC
Confidence            3444459999999999999999999999999999888 5899999999999999999999987 7888999999998876


Q ss_pred             cchh
Q 012034          106 KKSE  109 (472)
Q Consensus       106 ~~~~  109 (472)
                      ....
T Consensus       263 ~~~~  266 (285)
T KOG4210|consen  263 PRPK  266 (285)
T ss_pred             CCcc
Confidence            5543

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.30  E-value=0.00017  Score=71.90  Aligned_cols=96  Identities=27%  Similarity=0.272  Sum_probs=69.4

Q ss_pred             eeEEEcCcccchhhhh---hhc--cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC---C-C--CC-------
Q 012034            6 KQVFVGHFLRKQERET---VAI--KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---G-D--GK-------   67 (472)
Q Consensus         6 k~v~v~~~~~~~~r~~---~~~--~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d---~-~--g~-------   67 (472)
                      .+++|...-++-.|..   ...  +-..++|.+.|||.+-.-+.|.++|+.||.|.+|+|...   . +  +.       
T Consensus       204 ~kL~vseDgkKVrRisPlp~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~  283 (484)
T KOG1855|consen  204 SKLEVSEDGKKVRRISPLPEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFEL  283 (484)
T ss_pred             ceEEEccCCceeeecCCCCCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhh
Confidence            3566554444443322   222  247899999999999999999999999999999999876   1 1  21       


Q ss_pred             -ceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           68 -SKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        68 -skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                       .+-||||+|++.+.|.+|.+.|+.....-..|.|
T Consensus       284 ~tk~~AlvEye~~~~A~KA~e~~~~e~~wr~glkv  318 (484)
T KOG1855|consen  284 QTKECALVEYEEVEAARKARELLNPEQNWRMGLKV  318 (484)
T ss_pred             hhhhhhhhhhhhhHHHHHHHHhhchhhhhhhcchh
Confidence             2568999999999999999987655443333433

>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]

Probab=97.24  E-value=0.00017  Score=79.34  Aligned_cols=65  Identities=26%  Similarity=0.351  Sum_probs=60.9

Q ss_pred             HHHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHH--HHHHHHHHhh
Q 012034          389 QQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAM--EVLRSVAQQQ  453 (472)
Q Consensus       389 ~q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~--~~l~~~~~~~  453 (472)
                      --+|-|||+||+.++.+.|..|.||||||||.....+|..|..++.|+..|++|+  +++..|-++.
T Consensus      2606 Ae~Q~la~l~wgqhe~~l~a~~s~~sGfL~dek~~g~llgi~ce~p~eafVdaa~ndd~i~~H~qei 2672 (3015)
T KOG0943|consen 2606 AERQALAELLWGQHEAMLPAFASKISGFLLDEKPAGLLLGIACEDPLEAFVDAAMNDDLIIAHGQEI 2672 (3015)
T ss_pred             hhhccchhhcchhhhhHHHHHHHhhhhhhhccchHHHHHHHhhcCcHHHHHHHhcchHHHHHHHHHh
Confidence            3678899999999999999999999999999999999999999999999999999  8999887654

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.21  E-value=0.00027  Score=66.06  Aligned_cols=72  Identities=21%  Similarity=0.357  Sum_probs=62.0

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-C--------CCcee----EEEEEeCCHHHHHHHHHHHCCCc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-D--------GKSKC----FGFVNFENADDAAKAVEALNGKK   93 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~--------g~skG----~aFV~F~~~e~A~~Av~~lng~~   93 (472)
                      +.--||+++||+.++-..|+++|+.||.|-.|++.... .        |.+++    -|+|+|.+...|+++.+.||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            56779999999999999999999999999999998763 2        23333    35699999999999999999999


Q ss_pred             cCCcc
Q 012034           94 FDDRE   98 (472)
Q Consensus        94 i~g~~   98 (472)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99874

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.21  E-value=0.00079  Score=65.16  Aligned_cols=81  Identities=27%  Similarity=0.468  Sum_probs=63.7

Q ss_pred             ccceeeeecCCCCccHHH----H--HHHHhccCceEEEEEeeCC-CC--C-cccEEEEEcCCHHHHHHHHHHhCCcEecC
Q 012034          130 QGLNLYIKNLGDSIDDEK----L--KELFSEFGTITSCKVMRDP-SG--I-SKGSGFVAFSTPEEASRALAEMNGKMIVS  199 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~----L--~~~F~~~G~I~~v~i~~~~-~g--~-s~g~afV~f~s~~~A~~Ai~~l~g~~i~g  199 (472)
                      +..-+||-+|+..+-+|+    |  .++|.+||.|..|.|-+.. ..  . +.--.+|+|.+.++|.+||.+.+|..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            334589999998887776    2  3799999999999886653 11  1 11223999999999999999999999999


Q ss_pred             eeEEEEEcccH
Q 012034          200 KPLYVAVAQRK  210 (472)
Q Consensus       200 k~l~V~~a~~k  210 (472)
                      +.|+..|...|
T Consensus       193 r~lkatYGTTK  203 (480)
T COG5175         193 RVLKATYGTTK  203 (480)
T ss_pred             ceEeeecCchH
Confidence            99999987554

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.14  E-value=0.00079  Score=48.48  Aligned_cols=52  Identities=19%  Similarity=0.379  Sum_probs=41.5

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHH
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV   86 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av   86 (472)
                      +.|-|.+++.+..+ ++.+.|..||+|..+.+-.     .+-+.||+|++..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~-----~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPE-----STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCC-----CCcEEEEEECCHHHHHhhC
Confidence            56889999877665 4555899999999877652     2449999999999999985

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.00  E-value=0.00041  Score=65.08  Aligned_cols=64  Identities=23%  Similarity=0.294  Sum_probs=53.4

Q ss_pred             HHHHHHHh-cCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           43 EDLKKIFG-EYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        43 e~L~~~F~-~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      ++|...|+ +||+|++++|..+-.-.-+|-+||.|...|+|.+|++.||+..+.|+.|...+..-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            44445556 89999999887765445678999999999999999999999999999998887643

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.97  E-value=0.0013  Score=67.83  Aligned_cols=76  Identities=22%  Similarity=0.311  Sum_probs=62.2

Q ss_pred             cceeeeecCCCCc------cHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec-CeeEE
Q 012034          131 GLNLYIKNLGDSI------DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPLY  203 (472)
Q Consensus       131 ~~~l~V~nL~~~~------t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~-gk~l~  203 (472)
                      .+.++|.|+|---      -...|.++|+++|.|....+..++.|.++||.|++|.+..+|..|++.+||+.++ .+...
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            3578899988421      2245668999999999999998888889999999999999999999999999986 45555


Q ss_pred             EEE
Q 012034          204 VAV  206 (472)
Q Consensus       204 V~~  206 (472)
                      |..
T Consensus       138 v~~  140 (698)
T KOG2314|consen  138 VRL  140 (698)
T ss_pred             eeh
Confidence            553

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.93  E-value=0.00041  Score=65.06  Aligned_cols=68  Identities=21%  Similarity=0.363  Sum_probs=56.9

Q ss_pred             HHHHHHHh-ccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHHHH
Q 012034          146 EKLKELFS-EFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEER  213 (472)
Q Consensus       146 e~L~~~F~-~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~  213 (472)
                      ++|...|+ +||.|+++.|-.+-.-.-+|-++|.|...++|.+|++.||+..+.|++|+..+..-..-+
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~r  151 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDFR  151 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCchh
Confidence            56666666 899999998876654566889999999999999999999999999999999987654433

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.79  E-value=0.0044  Score=59.11  Aligned_cols=70  Identities=19%  Similarity=0.290  Sum_probs=56.9

Q ss_pred             HHHHHHHHhccCceEEEEEeeCCCC--CcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHHHHH
Q 012034          145 DEKLKELFSEFGTITSCKVMRDPSG--ISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR  214 (472)
Q Consensus       145 ~e~L~~~F~~~G~I~~v~i~~~~~g--~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~~  214 (472)
                      ++++.+.+++||.|..|.|+..++.  .----.||+|+..++|.+|+-.|||+.|+|+.+...|..-.+-+.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~ekfs~  371 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLEKFSN  371 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHHhhhh
Confidence            4678899999999999999887521  112247999999999999999999999999999988876654443

>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=96.73  E-value=0.0039  Score=51.04  Aligned_cols=76  Identities=21%  Similarity=0.271  Sum_probs=51.0

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEE-EEEC-------CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAV-VMRD-------GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDRE   98 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~-i~~d-------~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~   98 (472)
                      ..+-|.|-++|.. ....|.+.|++||+|.+.. +.++       .......+-.|.|.++.+|.+||.+ ||..+.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcE
Confidence            3556999999987 5667888999999998775 1111       0011245899999999999999985 999998875


Q ss_pred             ee-eecc
Q 012034           99 WY-VGKA  104 (472)
Q Consensus        99 l~-V~~a  104 (472)
                      +. |.++
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            54 4444

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.

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=96.70  E-value=0.0085  Score=64.22  Aligned_cols=10  Identities=20%  Similarity=0.704  Sum_probs=4.4

Q ss_pred             hhHhhcCCCh
Q 012034          413 VTGMLLEMDQ  422 (472)
Q Consensus       413 itgmll~~~~  422 (472)
                      |--|+||.|.
T Consensus       718 ik~~ILevne  727 (1102)
T KOG1924|consen  718 IKNVILEVNE  727 (1102)
T ss_pred             HHHHHhhccH
Confidence            3344455443

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.68  E-value=0.0012  Score=65.91  Aligned_cols=68  Identities=24%  Similarity=0.389  Sum_probs=56.7

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC---C---CCCc--------ccEEEEEcCCHHHHHHHHHHhCC
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD---P---SGIS--------KGSGFVAFSTPEEASRALAEMNG  194 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~---~---~g~s--------~g~afV~f~s~~~A~~Ai~~l~g  194 (472)
                      .++.+|.+-|||.+-.-+.|.++|+.+|.|..|+|..-   +   .+.+        +-+|||+|...+.|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            46678999999999888999999999999999999765   1   2222        45799999999999999988865


Q ss_pred             cE
Q 012034          195 KM  196 (472)
Q Consensus       195 ~~  196 (472)
                      ..
T Consensus       309 e~  310 (484)
T KOG1855|consen  309 EQ  310 (484)
T ss_pred             hh
Confidence            43

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.64  E-value=0.0046  Score=44.46  Aligned_cols=51  Identities=20%  Similarity=0.370  Sum_probs=40.1

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHH
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL  189 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai  189 (472)
                      .|-|.+.+.+.. +.+++.|..||.|+.+.+...     .-+.+|+|.+..+|.+|+
T Consensus         3 wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~-----~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    3 WISVSGFPPDLA-EEVLEHFASFGEIVDIYVPES-----TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             EEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCC-----CcEEEEEECCHHHHHhhC
Confidence            466777776555 456669999999999888632     458999999999999985

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.54  E-value=0.0063  Score=58.05  Aligned_cols=63  Identities=25%  Similarity=0.348  Sum_probs=52.5

Q ss_pred             HHHHHHHhcCCCeeEEEEEECCCC--CceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           43 EDLKKIFGEYGTITSAVVMRDGDG--KSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        43 e~L~~~F~~fG~I~~v~i~~d~~g--~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      +++++.+++||.|..|.|..+.+-  ...---||+|+..++|.+|+-.|||..|+|+.+..++.+
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            578889999999999999887421  112247999999999999999999999999998887764

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.51  E-value=0.0026  Score=59.66  Aligned_cols=65  Identities=28%  Similarity=0.422  Sum_probs=60.0

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK   93 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~   93 (472)
                      ..|||.||..-++.|.|.+.|+.||+|...+++.|..++..+-++|.|...-.|.+|...++..-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g   96 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGG   96 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCc
Confidence            67999999999999999999999999999999999889999999999999999999999875443

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.34  E-value=0.0022  Score=60.19  Aligned_cols=71  Identities=23%  Similarity=0.354  Sum_probs=59.5

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCC---------CCccc----EEEEEcCCHHHHHHHHHHhCCcEec
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS---------GISKG----SGFVAFSTPEEASRALAEMNGKMIV  198 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~---------g~s~g----~afV~f~s~~~A~~Ai~~l~g~~i~  198 (472)
                      -.||+++||...+...||++|+.||.|-.|.+-....         |.++.    -|+|+|.+...|..+...||+..|+
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Ig  154 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIG  154 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccC
Confidence            3699999999999999999999999999988865431         22222    3789999999999999999999999


Q ss_pred             CeeE
Q 012034          199 SKPL  202 (472)
Q Consensus       199 gk~l  202 (472)
                      |++-
T Consensus       155 gkk~  158 (278)
T KOG3152|consen  155 GKKK  158 (278)
T ss_pred             CCCC
Confidence            8643

>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=96.32  E-value=0.022  Score=46.71  Aligned_cols=74  Identities=23%  Similarity=0.275  Sum_probs=49.2

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEE-EeeCC-------CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeE-
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCK-VMRDP-------SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL-  202 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~-i~~~~-------~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l-  202 (472)
                      +-|.|-+.|.. ....+.+.|++||+|.+.. +.++.       .-.......|+|++..+|.+|+ .-||..+.|..+ 
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL-~~NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL-QKNGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHH-TTTTEEETTCEEE
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH-HhCCeEEcCcEEE
Confidence            45778888877 5567788999999998875 22210       0112457889999999999999 789999988644 


Q ss_pred             EEEEc
Q 012034          203 YVAVA  207 (472)
Q Consensus       203 ~V~~a  207 (472)
                      -|.+.
T Consensus        85 GV~~~   89 (100)
T PF05172_consen   85 GVKPC   89 (100)
T ss_dssp             EEEE-
T ss_pred             EEEEc
Confidence            45555

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.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=95.89  E-value=0.021  Score=58.77  Aligned_cols=63  Identities=29%  Similarity=0.295  Sum_probs=57.5

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHh-cCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHH
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFG-EYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA   88 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~-~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~   88 (472)
                      +..+||||++||.-++-++|-.+|+ -||-|.-+-|=.| +-+=.||-|-|+|++..+-.+||++
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            6788999999999999999999999 7999999999888 4466889999999999999999985

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.87  E-value=0.026  Score=44.07  Aligned_cols=55  Identities=20%  Similarity=0.347  Sum_probs=40.8

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHC
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN   90 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~ln   90 (472)
                      ..-.+|. +|++|...||.++|+.||.|. |..+.|      .-|||...+.+.|..++..++
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT------TEEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC------CcEEEEeecHHHHHHHHHHhc
Confidence            3334455 999999999999999999986 444444      269999999999999998875

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.79  E-value=0.014  Score=58.43  Aligned_cols=81  Identities=25%  Similarity=0.377  Sum_probs=64.4

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCc-EecCeeEEEEEcccHH
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK-MIVSKPLYVAVAQRKE  211 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~-~i~gk~l~V~~a~~k~  211 (472)
                      .+|++||...++.+||+.+|...-.-.+-.++.     ..||+||.+.+..-|.+|++.++|+ ++.|+++.|...-.+.
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~-----k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kk   77 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-----KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKK   77 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee-----ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHH
Confidence            589999999999999999998752111112222     2679999999999999999999997 5889999999888887


Q ss_pred             HHHHHHH
Q 012034          212 ERRARLQ  218 (472)
Q Consensus       212 ~~~~~~~  218 (472)
                      .+..+.+
T Consensus        78 qrsrk~Q   84 (584)
T KOG2193|consen   78 QRSRKIQ   84 (584)
T ss_pred             HHhhhhh
Confidence            7665543

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.75  E-value=0.00058  Score=71.76  Aligned_cols=71  Identities=24%  Similarity=0.286  Sum_probs=63.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ..-.+|||+|+-..+..+-++.+...+|.|.++....        |||+.|..+....+|+..++...++|..+.+...
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            4567899999999999999999999999998876543        9999999999999999999999999988877653

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.71  E-value=0.052  Score=47.29  Aligned_cols=56  Identities=20%  Similarity=0.419  Sum_probs=45.4

Q ss_pred             HHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          147 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       147 ~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +|.+.|..||.+.=+++..+       .-+|+|.+-+.|-+|+ .++|..++|+.|.|++..+.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaal-s~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAAL-SLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHH-HGCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHH-ccCCcEECCEEEEEEeCCcc
Confidence            66788999999888887754       5799999999999999 79999999999999987655

; PDB: 1UFW_A 2DNR_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.66  E-value=0.052  Score=40.20  Aligned_cols=55  Identities=29%  Similarity=0.436  Sum_probs=45.0

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcC----CCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHH
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEY----GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL   89 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~f----G~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~l   89 (472)
                      ....|+|+++. +++.++|+.+|..|    + ...|..+.|.      -|=|.|.+.+.|.+|+.+|
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            35679999995 68999999999999    4 3567777773      4668999999999999764

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=95.64  E-value=0.01  Score=61.70  Aligned_cols=81  Identities=25%  Similarity=0.266  Sum_probs=66.1

Q ss_pred             cceeeeecCCCCccHHHHHHHHhc-cCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEe---cCeeEEEEE
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI---VSKPLYVAV  206 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~-~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i---~gk~l~V~~  206 (472)
                      +..|||.||-..+|.-.|++++.+ .|.|++. .|..    -+..|||.|.+.++|...+.+|||..+   +++.|.+.|
T Consensus       444 SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf  518 (718)
T KOG2416|consen  444 SNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADF  518 (718)
T ss_pred             cceEeeecccccchHHHHHHHHhhccCchHHH-HHHH----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeee
Confidence            346999999999999999999994 5566666 3221    255799999999999999999999876   689999999


Q ss_pred             cccHHHHHHH
Q 012034          207 AQRKEERRAR  216 (472)
Q Consensus       207 a~~k~~~~~~  216 (472)
                      ....+..+.+
T Consensus       519 ~~~deld~hr  528 (718)
T KOG2416|consen  519 VRADELDKHR  528 (718)
T ss_pred             cchhHHHHHh
Confidence            9887766544

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=95.61  E-value=0.0077  Score=62.66  Aligned_cols=74  Identities=20%  Similarity=0.302  Sum_probs=59.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHh-cCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCcc---CCcceee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFG-EYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF---DDREWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~-~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i---~g~~l~V  101 (472)
                      ...+.|+|.||-.-+|...|++++. ..|.|+++||=+     -|..|||.|.+.++|.....+|||..+   +++.|.+
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk-----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK-----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHHHH-----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            5578899999999999999999999 567788875422     255899999999999999999999775   3455655


Q ss_pred             ecc
Q 012034          102 GKA  104 (472)
Q Consensus       102 ~~a  104 (472)
                      .|.
T Consensus       517 df~  519 (718)
T KOG2416|consen  517 DFV  519 (718)
T ss_pred             eec
Confidence            554

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.40  E-value=0.033  Score=48.48  Aligned_cols=73  Identities=22%  Similarity=0.341  Sum_probs=51.1

Q ss_pred             CcceEEeCCCC-----CCCCHH----HHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCc
Q 012034           27 KFNNVFVKNLD-----ESTTDE----DLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR   97 (472)
Q Consensus        27 ~~~~l~V~nLp-----~~~tee----~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~   97 (472)
                      ..-||.|.=+.     .+.-++    +|.+.|+.||++.-+++..+       .-+|+|.+-++|-+|+. ++|..++|+
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaals-~dg~~v~g~   97 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAALS-LDGIQVNGR   97 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHHH-GCCSEETTE
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHHc-cCCcEECCE
Confidence            45556665544     223333    66778899999887777654       57999999999999996 899999999


Q ss_pred             ceeeeccccc
Q 012034           98 EWYVGKAQKK  107 (472)
Q Consensus        98 ~l~V~~a~~~  107 (472)
                      .|.|....+.
T Consensus        98 ~l~i~LKtpd  107 (146)
T PF08952_consen   98 TLKIRLKTPD  107 (146)
T ss_dssp             EEEEEE----
T ss_pred             EEEEEeCCcc
Confidence            9999876543

; PDB: 1UFW_A 2DNR_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.09  E-value=0.054  Score=46.61  Aligned_cols=75  Identities=23%  Similarity=0.341  Sum_probs=58.5

Q ss_pred             cCCcceEEeCCCCCCCCH-HHHH---HHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           25 KTKFNNVFVKNLDESTTD-EDLK---KIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~te-e~L~---~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      +....+|.|+=|.+++.- +||+   ..++.||+|.+|...-      +--|.|.|+|..+|-+||.++.. ...|..++
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~q  155 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQ  155 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcC-CCCCceEE
Confidence            456788999888777643 4454   5678899999998753      34799999999999999999865 67788888


Q ss_pred             eecccc
Q 012034          101 VGKAQK  106 (472)
Q Consensus       101 V~~a~~  106 (472)
                      +.|-++
T Consensus       156 CsWqqr  161 (166)
T PF15023_consen  156 CSWQQR  161 (166)
T ss_pred             eecccc
Confidence            887653

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.74  E-value=0.016  Score=56.68  Aligned_cols=79  Identities=27%  Similarity=0.473  Sum_probs=61.4

Q ss_pred             ceEEeCCCCCCCCHHHHH---HHHhcCCCeeEEEEEECCC--C--CceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           29 NNVFVKNLDESTTDEDLK---KIFGEYGTITSAVVMRDGD--G--KSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~---~~F~~fG~I~~v~i~~d~~--g--~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      +-+||-+|+.++.++.+-   +.|..||.|.+|.+.++..  .  ....-+||+|+..|+|..||...+|..++|+.|..
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            557888888776665544   4899999999999888752  1  11234899999999999999999999999998777


Q ss_pred             eccccc
Q 012034          102 GKAQKK  107 (472)
Q Consensus       102 ~~a~~~  107 (472)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            666544

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=94.57  E-value=1.2  Score=43.06  Aligned_cols=183  Identities=14%  Similarity=0.222  Sum_probs=110.4

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC--------CCCceeEEEEEeCCHHHHHHHH----HHHCC--C
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG--------DGKSKCFGFVNFENADDAAKAV----EALNG--K   92 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~--------~g~skG~aFV~F~~~e~A~~Av----~~lng--~   92 (472)
                      ..|.|.+.|+..+++--.+...|-+||.|++|.++.+.        +.+......+.|-+.+.+-..-    +.|+.  +
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~   93 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKT   93 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHH
Confidence            46678999999999999999999999999999999875        2334567889999998765433    33332  3


Q ss_pred             ccCCcceeeeccccchhH----H---HHHHHH-HHhhhhhhccccccceeeeecCCCCccHHHHH-HHH---hccC----
Q 012034           93 KFDDREWYVGKAQKKSER----E---QELKGQ-FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK-ELF---SEFG----  156 (472)
Q Consensus        93 ~i~g~~l~V~~a~~~~~~----~---~~~~~~-~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~-~~F---~~~G----  156 (472)
                      .+....|.+.+-.-+-..    +   ...... ......+.......++|.|.- ...++++++. +.+   ..-+    
T Consensus        94 ~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF-~~~~~~~dl~~~kL~fL~~~~n~RY  172 (309)
T PF10567_consen   94 KLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEF-KDPVDKDDLIEKKLPFLKNSNNKRY  172 (309)
T ss_pred             hcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEe-cCccchhHHHHHhhhhhccCCCceE
Confidence            356666766654311100    0   001000 011111223333445666653 3445444333 222   2212    


Q ss_pred             ceEEEEEeeCC---CCCcccEEEEEcCCHHHHHHHHHHhC--CcEe-cCeeEEEEEcccH
Q 012034          157 TITSCKVMRDP---SGISKGSGFVAFSTPEEASRALAEMN--GKMI-VSKPLYVAVAQRK  210 (472)
Q Consensus       157 ~I~~v~i~~~~---~g~s~g~afV~f~s~~~A~~Ai~~l~--g~~i-~gk~l~V~~a~~k  210 (472)
                      .+++|.++...   +.-.+.||.++|-+..-|...++-+.  +... -.+..+|.+....
T Consensus       173 VlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~~~~~~~Iskc~fVs~~~~~  232 (309)
T PF10567_consen  173 VLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKSNSKKLGISKCFFVSVQPHA  232 (309)
T ss_pred             EEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHhcccccCcceEEEEeccCcc
Confidence            46778776542   34467899999999999888877655  3333 3577778766544

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.22  E-value=0.21  Score=36.98  Aligned_cols=53  Identities=26%  Similarity=0.408  Sum_probs=42.7

Q ss_pred             eeeeecCCCCccHHHHHHHHhcc---CceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHh
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEF---GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM  192 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~---G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l  192 (472)
                      .|+|.+++ +++-++++.+|..|   .....|..+.|.      -|-|.|.|.+.|.+|+..|
T Consensus         7 avhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    7 AVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            69999986 48889999999999   134567777663      3789999999999999754

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=94.14  E-value=0.11  Score=51.65  Aligned_cols=72  Identities=17%  Similarity=0.367  Sum_probs=57.6

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCC----CCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS----GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~----g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      .|.|.||....|.+.++.+|...|.|.++.++...+    ......|||.|.+...+..|.. |.++.|-++.|.|.
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~   84 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVR   84 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEE
Confidence            689999999999999999999999999999987532    2345689999999998888874 55555555555554

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.14  E-value=0.062  Score=58.80  Aligned_cols=76  Identities=17%  Similarity=0.269  Sum_probs=65.4

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC--cceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD--REWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g--~~l~V~  102 (472)
                      ....+.+|+++|..++....|...|..||.|..|.+-..     .-||||.|++.+.|..|++.|.|..|++  +.|.|.
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCccchhhHHHHhcCcCCCCCcccccc
Confidence            466889999999999999999999999999998655432     3499999999999999999999999976  567777


Q ss_pred             ccc
Q 012034          103 KAQ  105 (472)
Q Consensus       103 ~a~  105 (472)
                      ++.
T Consensus       527 la~  529 (975)
T KOG0112|consen  527 LAS  529 (975)
T ss_pred             ccc
Confidence            664

>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=94.01  E-value=0.067  Score=48.70  Aligned_cols=72  Identities=15%  Similarity=0.175  Sum_probs=47.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhc-CCCe---eEEEEEECC--CC-CceeEEEEEeCCHHHHHHHHHHHCCCccCCc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGE-YGTI---TSAVVMRDG--DG-KSKCFGFVNFENADDAAKAVEALNGKKFDDR   97 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~-fG~I---~~v~i~~d~--~g-~skG~aFV~F~~~e~A~~Av~~lng~~i~g~   97 (472)
                      ...++|.|++||.++|++++.+.++. ++..   ..+.-..+.  .. ..-.-|||.|.+.+++....+.++|+.+.+.
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            34568999999999999999998887 6765   333322331  11 1234689999999999999999999887543

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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.55  E-value=0.18  Score=43.44  Aligned_cols=72  Identities=22%  Similarity=0.303  Sum_probs=53.4

Q ss_pred             cceeeeecCCCCcc-HHHHH---HHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          131 GLNLYIKNLGDSID-DEKLK---ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       131 ~~~l~V~nL~~~~t-~e~L~---~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      -.+|.|.=|..++. .+||+   ..++.||.|.+|...-      +.-|.|.|.|..+|-+|+.+++. ..-|..++++|
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            34677766555443 24444   5678899999999864      45799999999999999999987 45677788887


Q ss_pred             ccc
Q 012034          207 AQR  209 (472)
Q Consensus       207 a~~  209 (472)
                      -++
T Consensus       159 qqr  161 (166)
T PF15023_consen  159 QQR  161 (166)
T ss_pred             ccc
Confidence            543

>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=93.38  E-value=0.62  Score=38.90  Aligned_cols=69  Identities=19%  Similarity=0.280  Sum_probs=51.3

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcC-CCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEY-GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD   96 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~f-G~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g   96 (472)
                      ..+.+.+...|..++-++|..+.+.+ ..|..++|++|... ++--+.+.|.+.++|....+.+||+.+..
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p-nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP-NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC-ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            33444444455556666777666666 46788999998553 56788999999999999999999998764

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=93.29  E-value=0.039  Score=54.09  Aligned_cols=79  Identities=24%  Similarity=0.420  Sum_probs=60.3

Q ss_pred             ceeeeecCCCCccHHHHH---HHHhccCceEEEEEeeCCC--CCc--ccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEE
Q 012034          132 LNLYIKNLGDSIDDEKLK---ELFSEFGTITSCKVMRDPS--GIS--KGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  204 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~---~~F~~~G~I~~v~i~~~~~--g~s--~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V  204 (472)
                      .-+||-+|+..+.++.+.   +.|..||.|.+|.+.++..  ..+  -.-++|+|...++|..||...+|...+|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            347888888777766655   5788999999999988652  111  122799999999999999999999999988766


Q ss_pred             EEcccH
Q 012034          205 AVAQRK  210 (472)
Q Consensus       205 ~~a~~k  210 (472)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            655443

>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=93.20  E-value=0.23  Score=45.52  Aligned_cols=61  Identities=28%  Similarity=0.330  Sum_probs=46.6

Q ss_pred             cHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhC--CcEecCeeEEEEEccc
Q 012034          144 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN--GKMIVSKPLYVAVAQR  209 (472)
Q Consensus       144 t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~--g~~i~gk~l~V~~a~~  209 (472)
                      ..+.|+++|..|+.+.++.+++.     -+-..|.|.+.++|.+|...++  +..+.|+.++|.+++.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            45789999999999998888764     4468999999999999999999  9999999999998843

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.

>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=92.61  E-value=0.44  Score=35.81  Aligned_cols=56  Identities=25%  Similarity=0.392  Sum_probs=45.2

Q ss_pred             CCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           38 ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        38 ~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      ..++-++++..+.+|+-.   .|..|.+|    | ||.|.+.++|++|....++..+..-.+.+
T Consensus        10 ~~~~v~d~K~~Lr~y~~~---~I~~d~tG----f-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRWD---RIRDDRTG----F-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCCcc---eEEecCCE----E-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            357888999999999864   46666544    5 89999999999999999998887766554

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>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=92.58  E-value=0.43  Score=35.89  Aligned_cols=56  Identities=16%  Similarity=0.408  Sum_probs=44.2

Q ss_pred             CCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEE
Q 012034          141 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  204 (472)
Q Consensus       141 ~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V  204 (472)
                      ..++-++++..+..|+- .  +|..|.+    || ||.|.+.++|.++....+|..+.+..+.+
T Consensus        10 ~~~~v~d~K~~Lr~y~~-~--~I~~d~t----Gf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRW-D--RIRDDRT----GF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCCc-c--eEEecCC----EE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            35788999999999963 2  3444433    34 89999999999999999999988877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>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=92.44  E-value=0.81  Score=38.19  Aligned_cols=64  Identities=19%  Similarity=0.178  Sum_probs=49.1

Q ss_pred             eeeecCCCCccHHHHHHHHhccC-ceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec
Q 012034          134 LYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV  198 (472)
Q Consensus       134 l~V~nL~~~~t~e~L~~~F~~~G-~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~  198 (472)
                      +.+...++.++.++|..+.+.+- .|..++|++|.. .++-.+++.|.+.++|..-....||+.+.
T Consensus        16 ~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~-pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   16 CCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT-PNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             EEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC-CceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            44455566677777876666653 677889998743 25667899999999999999999999874

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2893 consensus Zn finger protein [General function prediction only]

Probab=92.00  E-value=8.6  Score=36.10  Aligned_cols=11  Identities=36%  Similarity=0.507  Sum_probs=6.1

Q ss_pred             CCCCccHHHHH
Q 012034          139 LGDSIDDEKLK  149 (472)
Q Consensus       139 L~~~~t~e~L~  149 (472)
                      ...++++|.|.
T Consensus        16 cnrefddekil   26 (341)
T KOG2893|consen   16 CNREFDDEKIL   26 (341)
T ss_pred             cccccchhhhh
Confidence            34556666554

>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=91.87  E-value=0.24  Score=45.37  Aligned_cols=62  Identities=21%  Similarity=0.262  Sum_probs=46.5

Q ss_pred             CHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHC--CCccCCcceeeeccccc
Q 012034           41 TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN--GKKFDDREWYVGKAQKK  107 (472)
Q Consensus        41 tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~ln--g~~i~g~~l~V~~a~~~  107 (472)
                      ..+.|+++|..|+.+.++..++.     -+-..|.|.+.++|.+|...|+  +..+.|..+.|.+++..
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            45789999999999998887764     4467899999999999999999  89999999999888543

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=90.88  E-value=0.63  Score=47.45  Aligned_cols=82  Identities=20%  Similarity=0.361  Sum_probs=65.8

Q ss_pred             ccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCC-CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCC
Q 012034           14 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK   92 (472)
Q Consensus        14 ~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG-~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~   92 (472)
                      .+.........+...+.|+|-.+|..+|--||..|...|- .|.+++|++|.... +=-..|.|.+.++|....+.+||+
T Consensus        60 yk~n~~~s~~~~~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pn-rymvLIkFr~q~da~~Fy~efNGk  138 (493)
T KOG0804|consen   60 YKKNSHSSLKNASSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPN-RYMVLIKFRDQADADTFYEEFNGK  138 (493)
T ss_pred             EecCcccccccCCCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCc-eEEEEEEeccchhHHHHHHHcCCC
Confidence            3344443333345589999999999999999999998774 78999999985443 446789999999999999999999


Q ss_pred             ccCC
Q 012034           93 KFDD   96 (472)
Q Consensus        93 ~i~g   96 (472)
                      .|..
T Consensus       139 ~Fn~  142 (493)
T KOG0804|consen  139 QFNS  142 (493)
T ss_pred             cCCC
Confidence            9865

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=90.79  E-value=0.54  Score=49.07  Aligned_cols=69  Identities=17%  Similarity=0.357  Sum_probs=53.4

Q ss_pred             cceeeeecCCCCccHHHHHHHHhc--cCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCC--cEecCeeEEEE
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSE--FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG--KMIVSKPLYVA  205 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~--~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g--~~i~gk~l~V~  205 (472)
                      .|-+.++.|++.+-.|+++.+|+.  +-.+.+|.+-.+.      -=||+|++..||+.|.+-|..  ++|-||+|...
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            356788999999999999999974  6678888876542      138999999999999887654  45666666444

>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=90.01  E-value=1  Score=34.58  Aligned_cols=59  Identities=29%  Similarity=0.415  Sum_probs=37.2

Q ss_pred             CCCCHHHHHHHHhcCC-----CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           38 ESTTDEDLKKIFGEYG-----TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        38 ~~~tee~L~~~F~~fG-----~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ..++..+|..++...+     .|-.|.|..+       |.||+-.. +.|..+++.|++..+.|++|.|+.|
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 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3577888999888764     4667777765       89998755 5899999999999999999999865

; PDB: 2G0C_A 3MOJ_B.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=89.72  E-value=0.61  Score=48.66  Aligned_cols=68  Identities=24%  Similarity=0.317  Sum_probs=53.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhc--CCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCC--CccCCcce
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGE--YGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG--KKFDDREW   99 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~--fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng--~~i~g~~l   99 (472)
                      .+-+.|.++-||..+..|+++.+|+.  +-.+.+|.+-.+.      -=||+|++..||+.|.+.|..  +.|-|+.|
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            45677899999999999999999974  6788888876652      248999999999999988743  33555554

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=89.28  E-value=0.92  Score=43.95  Aligned_cols=73  Identities=19%  Similarity=0.232  Sum_probs=53.0

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcc-eeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDRE-WYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~-l~V~~a~~  106 (472)
                      .+=|-|-++|..-. .-|-.+|++||+|.+...-  .+|   .|-+|.|.+.-+|++||.+ ||+.|+|.. |-|..+..
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~--~ng---NwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP--SNG---NWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecC--CCC---ceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCC
Confidence            44477778886543 4577889999999876543  333   3999999999999999986 899888764 34444444


Q ss_pred             c
Q 012034          107 K  107 (472)
Q Consensus       107 ~  107 (472)
                      +
T Consensus       270 k  270 (350)
T KOG4285|consen  270 K  270 (350)
T ss_pred             H
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=89.14  E-value=1.6  Score=34.26  Aligned_cols=55  Identities=22%  Similarity=0.403  Sum_probs=40.1

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCC
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG  194 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g  194 (472)
                      .+|--..|.++...||.++|+.||.|. |..+.|      .-|||...+.+.|..++..+.-
T Consensus        10 HVFhltFPkeWK~~DI~qlFspfG~I~-VsWi~d------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLTFPKEWKTSDIYQLFSPFGQIY-VSWIND------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE--TT--HHHHHHHCCCCCCEE-EEEECT------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEeCchHhhhhhHHHHhccCCcEE-EEEEcC------CcEEEEeecHHHHHHHHHHhcc
Confidence            344444999999999999999999875 444443      2699999999999999888764

; 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.

>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=88.49  E-value=0.68  Score=42.16  Aligned_cols=78  Identities=18%  Similarity=0.254  Sum_probs=49.3

Q ss_pred             cceeeeecCCCCccHHHHHHHHhc-cCce---EEEEEeeCC--C-CCcccEEEEEcCCHHHHHHHHHHhCCcEecC----
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSE-FGTI---TSCKVMRDP--S-GISKGSGFVAFSTPEEASRALAEMNGKMIVS----  199 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~-~G~I---~~v~i~~~~--~-g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g----  199 (472)
                      ++.|.|++||..+|++++.+.++. ++..   ..+.-....  . -..-.-|+|.|.+.+++......++|..+.+    
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            457999999999999999997776 5554   333311211  1 1123458999999999999999999988743    


Q ss_pred             -eeEEEEEcc
Q 012034          200 -KPLYVAVAQ  208 (472)
Q Consensus       200 -k~l~V~~a~  208 (472)
                       .+..|.+|-
T Consensus        87 ~~~~~VE~Ap   96 (176)
T PF03467_consen   87 EYPAVVEFAP   96 (176)
T ss_dssp             EEEEEEEE-S
T ss_pred             CcceeEEEcc
Confidence             244555543

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.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=87.87  E-value=0.32  Score=53.12  Aligned_cols=72  Identities=26%  Similarity=0.361  Sum_probs=61.1

Q ss_pred             EEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCcc--CCcceeeeccccc
Q 012034           31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF--DDREWYVGKAQKK  107 (472)
Q Consensus        31 l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i--~g~~l~V~~a~~~  107 (472)
                      .++.|.+-+.+...|.-+|++||.|.+++..+|-     ..|.|+|.+.|.|..|+++|+|+++  .|-..+|.+++.-
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~-----N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL-----NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheecccc-----cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            4567778888999999999999999999998883     3799999999999999999999985  4667777776543

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=87.04  E-value=0.28  Score=50.22  Aligned_cols=78  Identities=17%  Similarity=0.177  Sum_probs=64.1

Q ss_pred             cCCcceEEeCCCCCCC-CHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDEST-TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~-tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....+.|-+.-.+... |.++|...|.+||+|..|.|-+.     --.|.|+|.+..+|-+|-. .++..|+++.|+|.|
T Consensus       369 ~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~w  442 (526)
T KOG2135|consen  369 VVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFW  442 (526)
T ss_pred             hcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhc-cccceecCceeEEEE
Confidence            4667777788778766 45799999999999999988765     2268999999999977775 589999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      .+...
T Consensus       443 hnps~  447 (526)
T KOG2135|consen  443 HNPSP  447 (526)
T ss_pred             ecCCc
Confidence            87644

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=86.72  E-value=1.5  Score=44.83  Aligned_cols=67  Identities=19%  Similarity=0.271  Sum_probs=57.0

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccC-ceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV  198 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G-~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~  198 (472)
                      ++.|+|-.+|..+|-.||-.++..|- .|..++|++|... .+-..+|.|.+.++|....+.+||+.|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p-nrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP-NRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC-ceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            56799999999999999999998764 6889999996322 2446789999999999999999999875

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=86.51  E-value=0.4  Score=49.11  Aligned_cols=61  Identities=21%  Similarity=0.272  Sum_probs=52.1

Q ss_pred             cHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          144 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       144 t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      |-++|...|..||.|..|.|-..     --.|.|+|.+..+|-+|. ..++-.|+++.|+|.|-...
T Consensus       386 t~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  386 TIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             hHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchh-ccccceecCceeEEEEecCC
Confidence            45899999999999999988553     336899999999998887 68999999999999987653

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=86.23  E-value=0.5  Score=51.65  Aligned_cols=72  Identities=28%  Similarity=0.412  Sum_probs=61.3

Q ss_pred             eeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEe--cCeeEEEEEcccH
Q 012034          134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVAVAQRK  210 (472)
Q Consensus       134 l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i--~gk~l~V~~a~~k  210 (472)
                      .++.|..-..+..-|..+|++||.|.++...++     -..|.|.|.+.+.|..|.++++|+++  .|-+.+|.+++.-
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~-----~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-----LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccc-----ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            466777778888999999999999999998877     34799999999999999999999986  5778888877643

>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=86.03  E-value=2.8  Score=32.18  Aligned_cols=59  Identities=24%  Similarity=0.330  Sum_probs=36.6

Q ss_pred             CCccHHHHHHHHhccC-----ceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          141 DSIDDEKLKELFSEFG-----TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       141 ~~~t~e~L~~~F~~~G-----~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      +.++..+|..++...+     .|-.|.|..+       |+||.-.. +.|..+++.|++..+.|+++.|+.|
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 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            5678888888887664     4567777765       88988765 4689999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=85.22  E-value=0.68  Score=36.90  Aligned_cols=71  Identities=13%  Similarity=0.215  Sum_probs=44.0

Q ss_pred             EEEEeCCHHHHHHHHHHHCCCc--cCCcceeeeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHH
Q 012034           72 GFVNFENADDAAKAVEALNGKK--FDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK  149 (472)
Q Consensus        72 aFV~F~~~e~A~~Av~~lng~~--i~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~  149 (472)
                      |.|+|++.+-|.+.++. ..+.  ++++.+.|.-..-....         ..+-+........+|.|.|||+..++|+|+
T Consensus         1 AlITF~e~~VA~~i~~~-~~~~v~l~~~~~~V~v~P~~~~~---------~~k~qv~~~vs~rtVlvsgip~~l~ee~l~   70 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKK-KKHPVPLEDCCVRVKVSPVTLGH---------LQKFQVFSGVSKRTVLVSGIPDVLDEEELR   70 (88)
T ss_pred             CEEEeCcHHHHHHHHhC-CEEEEEECCEEEEEEEEeEecCC---------ceEEEEEEcccCCEEEEeCCCCCCChhhhe
Confidence            68999999999999973 2222  45555555432211100         001112233445689999999999999998


Q ss_pred             HHH
Q 012034          150 ELF  152 (472)
Q Consensus       150 ~~F  152 (472)
                      +.+
T Consensus        71 D~L   73 (88)
T PF07292_consen   71 DKL   73 (88)
T ss_pred             eeE
Confidence            754

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=83.91  E-value=2.3  Score=41.37  Aligned_cols=58  Identities=21%  Similarity=0.280  Sum_probs=43.1

Q ss_pred             eecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCe
Q 012034          136 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK  200 (472)
Q Consensus       136 V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk  200 (472)
                      |-+++.. ...-|..+|++||.|.+..-.  .+|.   +-+|.|.+.-+|.+|| .-||+.|+|.
T Consensus       202 VfGFppg-~~s~vL~~F~~cG~Vvkhv~~--~ngN---wMhirYssr~~A~KAL-skng~ii~g~  259 (350)
T KOG4285|consen  202 VFGFPPG-QVSIVLNLFSRCGEVVKHVTP--SNGN---WMHIRYSSRTHAQKAL-SKNGTIIDGD  259 (350)
T ss_pred             EeccCcc-chhHHHHHHHhhCeeeeeecC--CCCc---eEEEEecchhHHHHhh-hhcCeeeccc
Confidence            3344432 335678899999999876544  2333   7899999999999999 6788888775

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=81.78  E-value=0.69  Score=49.38  Aligned_cols=69  Identities=20%  Similarity=0.211  Sum_probs=62.1

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..++||+|+...+..+-++.+...+|.|.+++...        |||+.|.....+.+|+..++-..++|..+.+...
T Consensus        40 ~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   40 RDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            35799999999999999999999999999988654        8999999999999999999999999988877764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	472
2dyd_A	85	Solution Structure Of The Pabc Domain From Triticum		8e-29
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		5e-27
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		4e-19
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-18
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-17
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-07
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		7e-17
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-16
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		6e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		9e-16
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		7e-07
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		9e-16
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		7e-07
1nmr_A	85	Solution Structure Of C-Terminal Domain From Trypan		1e-15
1g9l_A	144	Solution Structure Of The Pabc Domain Of Human Poly		2e-15
1jgn_A	98	Solution Structure Of The C-Terminal Pabc Domain Of		3e-15
3kur_A	79	Crystal Structure Of The Mlle Domain Of Poly(A)-Bin		3e-15
3kus_A	88	Crystal Structure Of The Mlle Domain Of Poly(A)-Bin		3e-15
3pth_A	82	The Pabc1 Mlle Domain Bound To The Variant Pam2 Mot		4e-15
2rqg_B	83	Structure Of Gspt1ERF3A-Pabc Length = 83		4e-15
2x04_A	80	Crystal Structure Of The Pabc-Tnrc6c Complex Length		7e-15
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		8e-15
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-14
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		5e-07
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		5e-14
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		7e-14
4ive_A	98	Crystal Structure Of A Polyadenylate-binding Protei		2e-12
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		3e-12
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-11
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		9e-11
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		1e-10
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-10
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		5e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		3e-10
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-10
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		6e-10
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-09
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		6e-09
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		6e-09
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-05
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		9e-09
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-08
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-08
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		1e-08
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-08
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-08
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		1e-08
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		2e-08
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		4e-08
2khc_A	118	Bruno Rrm3+ Length = 118		4e-08
2khc_A	118	Bruno Rrm3+ Length = 118		2e-06
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		9e-08
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-07
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		1e-07
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		2e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		2e-07
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		8e-04
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		3e-07
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		3e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		3e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		4e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-06
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		8e-07
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-05
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		8e-07
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		1e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		1e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		1e-06
1sxl_A	97	Resonance Assignments And Solution Structure Of The		1e-06
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-06
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-06
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-06
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		2e-06
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		2e-06
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		3e-06
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		1e-05
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		3e-06
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		3e-06
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		4e-06
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		5e-06
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		5e-06
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		1e-04
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		6e-06
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		8e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		7e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		2e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		8e-06
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		4e-04
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		9e-06
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		9e-06
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		7e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		1e-05
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		1e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		1e-05
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		1e-05
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		1e-05
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		2e-05
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		3e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-05
3ntw_A	65	Structure Of The Mlle Domain Of Edd In Complex With		2e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		2e-05
1i2t_A	61	X-Ray Structure Of The Human Hyperplastic Discs Pro		2e-05
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		3e-05
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		9e-05
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		3e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-05
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		5e-05
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		5e-05
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		8e-05
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		1e-04
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		8e-05
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		7e-04
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		9e-05
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		1e-04
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		1e-04
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		1e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		1e-04
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		3e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		4e-04
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		4e-04
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		4e-04
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		4e-04
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		4e-04
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		4e-04
2dk2_A	97	Solution Structure Of Rrm Domain In Heterogeneous N		4e-04
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		5e-04
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		5e-04
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		6e-04
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		6e-04
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		6e-04
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		7e-04
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		7e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		7e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		8e-04
2ghp_A	292	Crystal Structure Of The N-Terminal 3 Rna Binding D		8e-04
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		8e-04

>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum Aevestium Poly(A)-Binding Protein Length = 85

Iteration: 1
 Score =  124 bits (312), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 63/79 (79%), Positives = 70/79 (88%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
           PI AL++ALAN+ PE QR +LGE+LYPLV+QLE D AAKVTGMLLEMDQTEVLHLLESP+
Sbjct: 6   PIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPD 65
Query: 434 ALKAKVAEAMEVLRSVAQQ 452
           ALKAKVAEAMEVLRS  Q 
Sbjct: 66  ALKAKVAEAMEVLRSAQQH 84

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score =  118 bits (296), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 55/90 (61%), Positives = 75/90 (83%), Gaps = 1/90 (1%)
Query: 126 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 185
           + ++Q +NLY+KNL D IDDE+L++ FS FGTITS KVM +  G SKG GFV FS+PEEA
Sbjct: 10  ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEA 68
Query: 186 SRALAEMNGKMIVSKPLYVAVAQRKEERRA 215
           ++A+ EMNG+++ +KPLYVA+AQRKEER++
Sbjct: 69  TKAVTEMNGRIVATKPLYVALAQRKEERQS 98

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 92.4 bits (228), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 70/200 (35%), Positives = 108/200 (54%), Gaps = 22/200 (11%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           +++V +L    T+  L + F   G I S  V RD    +S  + +VNF+   DA +A++ 
Sbjct: 17  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 89  LNGKKFDDREWYVGKAQK--KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 146
           +N   FD  +   GK  +   S+R+  L+       K  V      N++IKNL  SID++
Sbjct: 77  MN---FDVIK---GKPVRIMWSQRDPSLR-------KSGVG-----NIFIKNLDKSIDNK 118
Query: 147 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV 206
            L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++  + ++V  
Sbjct: 119 ALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Query: 207 AQRKEERRARLQAQFSQMRP 226
            + ++ER A L A+  +  P
Sbjct: 178 FKSRKEREAELGARAKEFYP 197

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 90.5 bits (223), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/194 (35%), Positives = 106/194 (54%), Gaps = 22/194 (11%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           +++V +L    T+  L + F   G I S  V RD    +S  + +VNF+   DA +A++ 
Sbjct: 12  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 89  LNGKKFDDREWYVGKAQK--KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 146
           +N   FD  +   GK  +   S+R+  L+       K  V      N++IKNL  SID++
Sbjct: 72  MN---FDVIK---GKPVRIMWSQRDPSLR-------KSGVG-----NIFIKNLDKSIDNK 113
Query: 147 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV 206
            L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++  + ++V  
Sbjct: 114 ALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 172
Query: 207 AQRKEERRARLQAQ 220
            + ++ER A L A+
Sbjct: 173 FKSRKEREAELGAR 186

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 85.5 bits (210), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 54/178 (30%), Positives = 92/178 (51%), Gaps = 24/178 (13%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L ++ T ++ K +FG  G I S  ++RD   G+S  +GFVN+ + +DA KA+  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
           LNG K   +   V  A+  S                     +  NLY+  L  ++  +++
Sbjct: 66  LNGLKLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMSQKEM 107
Query: 149 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA 205
           ++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  +NG+    KPL  A
Sbjct: 108 EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ----KPLGAA 161

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  ++ K LF   G I SCK++RD  +G S G GFV +S P +A +A+  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K + V+ A+
Sbjct: 66  LNGLKLQTKTIKVSYAR 82

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 85.1 bits (209), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 96/180 (53%), Gaps = 17/180 (9%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           ++V NLD++ T++ LK+ F   G I +  +M D + K+  + FV +  + DA  A++ LN
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 91  GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 150
           GK+ ++    +  A             F+     + D F   NL++ +L  ++DDE L+ 
Sbjct: 63  GKQIENNIVKINWA-------------FQSQQSSSDDTF---NLFVGDLNVNVDDETLRN 106
Query: 151 LFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR 209
            F +F +  S  VM D  +G S+G GFV+F++ ++A  A+  M G+ +  +PL +  A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 83.2 bits (204), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 50/169 (29%), Positives = 87/169 (51%), Gaps = 20/169 (11%)
Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 87
            N+ V  L ++ T E+ + +FG  G I S  ++RD   G+S  +GFVN+ +  DA KA+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEK 147
            LNG +   +   V  A+  S                     +  NLY+  L  ++  ++
Sbjct: 63  TLNGLRLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMTQKE 104
Query: 148 LKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGK 195
           L++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  +NG+
Sbjct: 105 LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  E+ + LF   G I SCK++RD  +G S G GFV +  P++A +A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K + V+ A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 81.6 bits (200), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 85/167 (50%), Gaps = 20/167 (11%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L ++ T ++L+ +F   G + SA ++RD   G S  +GFVN+  A DA +A+  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
           LNG +   +   V  A+  SE            +K+        NLYI  L  ++  + +
Sbjct: 64  LNGLRLQSKTIKVSYARPSSE-----------VIKDA-------NLYISGLPRTMTQKDV 105
Query: 149 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNG 194
           +++FS FG I + +V+ D  +G+S+G  F+ F    EA  A+   NG
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  ++L+ LFS  G + S K++RD  +G S G GFV + T ++A RA+  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 192 MNGKMIVSKPLYVAVAQRKEE 212
           +NG  + SK + V+ A+   E
Sbjct: 64  LNGLRLQSKTIKVSYARPSSE 84

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 81.6 bits (200), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 85/167 (50%), Gaps = 20/167 (11%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L ++ T ++L+ +F   G + SA ++RD   G S  +GFVN+  A DA +A+  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
           LNG +   +   V  A+  SE            +K+        NLYI  L  ++  + +
Sbjct: 64  LNGLRLQSKTIKVSYARPSSE-----------VIKDA-------NLYISGLPRTMTQKDV 105
Query: 149 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNG 194
           +++FS FG I + +V+ D  +G+S+G  F+ F    EA  A+   NG
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  ++L+ LFS  G + S K++RD  +G S G GFV + T ++A RA+  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 192 MNGKMIVSKPLYVAVAQRKEE 212
           +NG  + SK + V+ A+   E
Sbjct: 64  LNGLRLQSKTIKVSYARPSSE 84

>pdb|1NMR|A Chain A, Solution Structure Of C-Terminal Domain From Trypanosoma Cruzi Poly(A)-Binding Protein Length = 85

Iteration: 1
 Score = 81.3 bits (199), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 42/70 (60%), Positives = 52/70 (74%)
Query: 378 LSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKA 437
           LST LAN +PEQQ+ +LGE LY  +  +   AAAKVTGMLLEMD  E+L+LL++P  L A
Sbjct: 11  LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDA 70
Query: 438 KVAEAMEVLR 447
           KV EA+EVL 
Sbjct: 71  KVQEALEVLN 80

>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A) Binding Protein Length = 144

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 52  PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 109
Query: 434 ALKAKVAEAMEVLRS 448
           +L++KV EA+ VL++
Sbjct: 110 SLRSKVDEAVAVLQA 124

>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human Poly(A)-Binding Protein In Complex With The Peptide From Paip2 Length = 98

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6   PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 434 ALKAKVAEAMEVLRS 448
           +L++KV EA+ VL++
Sbjct: 64  SLRSKVDEAVAVLQA 78

>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding Protein Length = 79

Iteration: 1
 Score = 79.7 bits (195), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6   PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 434 ALKAKVAEAMEVLRS 448
           +L++KV EA+ VL++
Sbjct: 64  SLRSKVDEAVAVLQA 78

>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding Protein In Complex With The Binding Region Of Paip2 Length = 88

Iteration: 1
 Score = 79.7 bits (195), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6   PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 434 ALKAKVAEAMEVLRS 448
           +L++KV EA+ VL++
Sbjct: 64  SLRSKVDEAVAVLQA 78

>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of Larp4b Length = 82

Iteration: 1
 Score = 79.3 bits (194), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 5   PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 62
Query: 434 ALKAKVAEAMEVLRS 448
           +L++KV EA+ VL++
Sbjct: 63  SLRSKVDEAVAVLQA 77

>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc Length = 83

Iteration: 1
 Score = 79.3 bits (194), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
           P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE
Sbjct: 4   PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 61
Query: 434 ALKAKVAEAMEVLRS 448
           +L++KV EA+ VL++
Sbjct: 62  SLRSKVDEAVAVLQA 76

>pdb|2X04|A Chain A, Crystal Structure Of The Pabc-Tnrc6c Complex Length = 80

Iteration: 1
 Score = 78.6 bits (192), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 37/76 (48%), Positives = 61/76 (80%), Gaps = 1/76 (1%)
Query: 374 PITALSTA-LANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESP 432
           P+ +L+ + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESP
Sbjct: 2   PLGSLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 61
Query: 433 EALKAKVAEAMEVLRS 448
           E+L++KV EA+ VL++
Sbjct: 62  ESLRSKVDEAVAVLQA 77

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 78.6 bits (192), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 42/95 (44%), Positives = 61/95 (64%), Gaps = 1/95 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           N++IKNL  SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 193 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPV 227
           NG ++  + ++V   + ++ER A L A+  +   V
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNV 100

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 54/182 (29%), Positives = 93/182 (51%), Gaps = 22/182 (12%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L +  TD +L  +F   G I +  +MRD   G S  + FV+F +  D+ +A++ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
           LNG    ++   V  A+   E           ++K+T       NLY+ NL  +I D++L
Sbjct: 65  LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 106
Query: 149 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVA 205
             +F ++G+I    ++RD  +G  +G  FV ++  EEA  A++ +N  +    S+PL V 
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166
Query: 206 VA 207
           +A
Sbjct: 167 LA 168

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 52.4 bits (124), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           NL +  L   + D +L  LF   G I +C++MRD  +G S G  FV F++  ++ RA+  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K L V+ A+
Sbjct: 65  LNGITVRNKRLKVSYAR 81

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 75.9 bits (185), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 39/83 (46%), Positives = 56/83 (67%), Gaps = 1/83 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           N++IKNL  SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 13  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
           NG ++  + ++V   + ++ER A
Sbjct: 72  NGMLLNDRKVFVGRFKSRKEREA 94

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 75.5 bits (184), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 53/183 (28%), Positives = 93/183 (50%), Gaps = 22/183 (12%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L +  TD +L  +F   G I +  + RD   G S  + FV+F +  D+ +A++ 
Sbjct: 16  NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
           LNG    ++   V  A+   E           ++K+T       NLY+ NL  +I D++L
Sbjct: 76  LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 117
Query: 149 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVA 205
             +F ++G+I    ++RD  +G  +G  FV ++  EEA  A++ +N  +    S+PL V 
Sbjct: 118 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 177
Query: 206 VAQ 208
           +A+
Sbjct: 178 LAE 180

>pdb|4IVE|A Chain A, Crystal Structure Of A Polyadenylate-binding Protein 3 (pabpc3) From Homo Sapiens At 2.30 A Resolution Length = 98

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/83 (43%), Positives = 58/83 (69%)
Query: 376 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEAL 435
           T  ++ LA+A P++Q+  LGE L+PL++      A K+TG LLE+D +E+L+ LESPE+L
Sbjct: 6   TLTASRLASAPPQKQKQXLGERLFPLIQAXHPTLAGKITGXLLEIDNSELLYXLESPESL 65
Query: 436 KAKVAEAMEVLRSVAQQQANNPA 458
           ++KV EA+ VL++   ++A   A
Sbjct: 66  RSKVDEAVAVLQAHQAKEATQKA 88

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 45/164 (27%), Positives = 87/164 (53%), Gaps = 28/164 (17%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFE---NADDAAKAV 86
           +F+  L+  TT+++L++ FG+YGT+T   +M+D   G+S+ FGF++FE   + D+  K  
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 87  EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 146
             L+GK  D +     +A  + E+++  K                  +++  +G  +  +
Sbjct: 66  HILDGKVIDPK-----RAIPRDEQDKTGK------------------IFVGGIGPDVRPK 102
Query: 147 KLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           + +E FS++GTI   ++M D  +G S+G GFV + + +   R  
Sbjct: 103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP---EEA 185
           +   ++I  L     ++ L+E F ++GT+T  K+M+DP +G S+G GF++F  P   +E 
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 186 SRALAEMNGKMI 197
            +    ++GK+I
Sbjct: 62  VKTQHILDGKVI 73

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 66.2 bits (160), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 17  QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 75
           Q +  +AI  +   V+V ++     ++ +++ F  +G I S  +  D    K K F FV 
Sbjct: 5   QRQRALAIMCR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 61
Query: 76  FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 134
           +E  + A  A+E +N      R   VG+            GQ +  + +  ++ +  N +
Sbjct: 62  YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 113
Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 193
           Y+ ++   + D+ +K +F  FG I SC + RDP +G  KG GF+ +   + +  A++ MN
Sbjct: 114 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 64.7 bits (156), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 49/188 (26%), Positives = 82/188 (43%), Gaps = 30/188 (15%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG---KSKCFGFVNFENADDAAKAVE 87
           +FV  +  + +++DL+++F +YG +    V+RD      +SK   FV F     A +A  
Sbjct: 18  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDS 142
           AL+  K                    L G     Q + A  E  +  +   L+I  +   
Sbjct: 78  ALHNMKV-------------------LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKK 118
Query: 143 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI---VS 199
             +  ++ +FS FG I  C+++R P G+S+G  FV F+T   A  A+  M+        S
Sbjct: 119 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 178
Query: 200 KPLYVAVA 207
            P+ V  A
Sbjct: 179 SPMVVKFA 186

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 49/188 (26%), Positives = 82/188 (43%), Gaps = 30/188 (15%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG---KSKCFGFVNFENADDAAKAVE 87
           +FV  +  + +++DL+++F +YG +    V+RD      +SK   FV F     A +A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDS 142
           AL+  K                    L G     Q + A  E  +  +   L+I  +   
Sbjct: 66  ALHNMKV-------------------LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKK 106
Query: 143 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI---VS 199
             +  ++ +FS FG I  C+++R P G+S+G  FV F+T   A  A+  M+        S
Sbjct: 107 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 166
Query: 200 KPLYVAVA 207
            P+ V  A
Sbjct: 167 SPMVVKFA 174

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/80 (42%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 89
           +FV  L   T ++ L+++F +YG I+  VV++D +  +S+ FGFV FEN DDA  A+ A+
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 90  NGKKFDDREWYVGKAQKKSE 109
           NGK  D R+  V +A K S+
Sbjct: 75  NGKSVDGRQIRVDQAGKSSD 94

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
           L++  L    +++ L+++FS++G I+   V++D  +  S+G GFV F   ++A  A+  M
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
           NGK +  + + V  A +  + R+
Sbjct: 75  NGKSVDGRQIRVDQAGKSSDNRS 97

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 63.2 bits (152), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 46/164 (28%), Positives = 69/164 (42%), Gaps = 29/164 (17%)
Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
           T+   +FV NL    T+ED K++F  YG  +   + RD     + FGF+  E+   A  A
Sbjct: 20  TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIA 74
Query: 86  VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
              L+G     R   +  A                          G  L +KNL   + +
Sbjct: 75  KAELDGTILKSRPLRIRFAT------------------------HGAALTVKNLSPVVSN 110
Query: 146 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           E L++ FS+FG +    V+ D  G + G GFV F+    A +AL
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKAL 154

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           Q   L++ NL   I +E  K LF  +G  +   + RD     +G GF+   +   A  A 
Sbjct: 21  QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAK 75
Query: 190 AEMNGKMIVSKPLYVAVA 207
           AE++G ++ S+PL +  A
Sbjct: 76  AELDGTILKSRPLRIRFA 93

>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 = 62.8 bits (151), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 83/180 (46%), Gaps = 14/180 (7%)
Query: 17  QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 75
           Q +  +AI  +   V+V ++     ++ +++ F  +G I S     D    K K F FV 
Sbjct: 4   QRQRALAIXCR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVE 60
Query: 76  FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 134
           +E  + A  A+E  N      R   VG+            GQ +  + +  ++ +  N +
Sbjct: 61  YEVPEAAQLALEQXNSVXLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 112
Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 193
           Y+ ++   + D+ +K +F  FG I SC + RDP +G  KG GF+ +   + +  A++  N
Sbjct: 113 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172

>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 = 62.4 bits (150), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 17  QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 75
           Q +  +AI ++   V+V ++     ++ +++ F  +G I S  +  D    K K F FV 
Sbjct: 20  QRQGALAIMSR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76
Query: 76  FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 134
           +E  + A  A+E +N      R   VG+            GQ +  + +  ++ +  N +
Sbjct: 77  YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 128
Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 193
           Y+ ++   + D+ +K +F  FG I S  + RDP +G  KG GF+ +   + +  A++ MN
Sbjct: 129 YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 73/166 (43%), Gaps = 27/166 (16%)
Query: 32  FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG---KSKCFGFVNFENADDAAKAVEA 88
           FV  +  + +++DL+++F +YG +    V+RD      +SK   FV F     A +A  A
Sbjct: 7   FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDSI 143
           L+  K                    L G     Q + A  E  +  +   L+I  +    
Sbjct: 67  LHNXKV-------------------LPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKC 107
Query: 144 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
            +  ++  FS FG I  C+++R P G+S+G  FV F+T   A  A+
Sbjct: 108 TENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 41/69 (59%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           NLYI NL  S+D+++L+ +   FG + S +++RD SG S+G GF    + E+    +   
Sbjct: 27  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 193 NGKMIVSKP 201
           NGK I + P
Sbjct: 87  NGKFIKTPP 95

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 47/78 (60%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           +F+  L+  T ++ LK +FG++G I+  ++++D   KS+ F F+ FEN  DA  A + +N
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 91  GKKFDDREWYVGKAQKKS 108
           GK    +   V +A+K S
Sbjct: 70  GKSLHGKAIKVEQAKKPS 87

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L+I  L    +++ LK +F + G I+   +++D +  S+G  F+ F  P +A  A  +MN
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 194 GKMIVSKPLYVAVAQR 209
           GK +  K + V  A++
Sbjct: 70  GKSLHGKAIKVEQAKK 85

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 58.5 bits (140), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 190
            NL++ +L  ++DDE L+  F +F +  S  VM D  +G S+G GFV+F++ ++A  A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 191 EMNGKMIVSKPLYVAVAQRKEE 212
            M G+ +  +PL +  A + E 
Sbjct: 62  SMQGQDLNGRPLRINWAAKLEH 83

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 12  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 86  VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 72  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 118
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 179
             L++ F ++G I   ++M D  SG  +G  FV F
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 80/167 (47%), Gaps = 15/167 (8%)
Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 12  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 86  VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 72  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 118
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
             L++ F ++G I   ++M D  SG  +G  FV F   +   + + +
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165

>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 = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 11  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 86  VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 71  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 117
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 179
             L++ F ++G I   ++M D  SG  +G  FV F
Sbjct: 118 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 80/167 (47%), Gaps = 15/167 (8%)
Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 10  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 86  VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 70  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 116
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
             L++ F ++G I   ++M D  SG  +G  FV F   +   + + +
Sbjct: 117 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 43/165 (26%), Positives = 79/165 (47%), Gaps = 15/165 (9%)
Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 86  VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 65  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 111
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
             L++ F ++G I   ++M D  SG  +G  FV F   +   + +
Sbjct: 112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156

>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 = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
           +   +F+  L   TTDE L+  F ++GT+T  VVMRD + K S+ FGFV +   ++   A
Sbjct: 13  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 86  VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
           + A    K D R   V + ++   RE   +      +K+         +++  + +  ++
Sbjct: 73  MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 119
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 179
             L++ F ++G I   ++M D  SG  +G  FV F
Sbjct: 120 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/82 (36%), Positives = 53/82 (64%), Gaps = 2/82 (2%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTI-TSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           ++I NL   ID++ L + FS FG I  + K+MRDP +G SKG  F+ F++ + +  A+  
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 192 MNGKMIVSKPLYVAVAQRKEER 213
           MNG+ + ++P+ V+ A +K+ +
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSK 89

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 187
           FQG NL +  L  +   ++L+ LFS  G + S K++RD  +G S G GFV + T ++A R
Sbjct: 17  FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 188 ALAEMNGKMIVSKPLYVAVAQ 208
           A+  +NG  + SK + V+ A+
Sbjct: 77  AINTLNGLRLQSKTIKVSYAR 97

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/63 (44%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 88
           N+F+ +L +  TD DL   F  +G + SA V  D     SKCFGFV+F+N D A  A++A
Sbjct: 42  NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 89  LNG 91
           +NG
Sbjct: 102 MNG 104

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           +G NL+I +L     D  L   F  FG + S KV  D  + +SK  GFV+F  P+ A  A
Sbjct: 39  EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 189 LAEMNGKMIVSKPLYV 204
           +  MNG  + +K L V
Sbjct: 99  IKAMNGFQVGTKRLKV 114

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 55.1 bits (131), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 43/82 (52%), Gaps = 3/82 (3%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++  LG    DE ++++F  FGTI  C V+R P G SKG  FV F T  EA  A+  ++
Sbjct: 15  LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 194 GKMIV---SKPLYVAVAQRKEE 212
               +   S  L V  A  ++E
Sbjct: 75  SSRTLPGASSSLVVKFADTEKE 96

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 50/82 (60%), Gaps = 2/82 (2%)
Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
           + LY+ +L  +I ++ L+ +F  FG I S ++M D  +G SKG GF+ FS  E A +AL 
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 191 EMNGKMIVSKPLYVA-VAQRKE 211
           ++NG  +  +P+ V  V +R +
Sbjct: 87  QLNGFELAGRPMKVGHVTERTD 108

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 41/73 (56%)
Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           + VFV NLD     + LK++F   G +  A ++ D DGKS+  G V FE + +A +A+  
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 89  LNGKKFDDREWYV 101
            NG+   DR  +V
Sbjct: 76  FNGQLLFDRPMHV 88

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 46/79 (58%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           G  +++ NL   +  +KLKE+FS  G +    ++ D  G S+G G V F    EA +A++
Sbjct: 15  GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 191 EMNGKMIVSKPLYVAVAQR 209
             NG+++  +P++V + +R
Sbjct: 75  MFNGQLLFDRPMHVKMDER 93

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           NL +  +  ++D+ +L++LF  +G I S K++ D  +  S+G GFV F +   A +A+A 
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 192 MNGKMIVSKPLYVAVAQRKEER 213
           +NG  I++K L VA+A    +R
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/164 (26%), Positives = 70/164 (42%), Gaps = 29/164 (17%)
Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
           T+ + +FV NL    T+E+++K+F +YG      + +D     K FGF+  E    A  A
Sbjct: 20  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIA 74
Query: 86  VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
              L+                   R ++L+ +F              +L ++NL   + +
Sbjct: 75  KVELDNMPL---------------RGKQLRVRF---------ACHSASLTVRNLPQYVSN 110
Query: 146 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           E L+E FS FG +    V+ D  G   G G V FS    A +AL
Sbjct: 111 ELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154

>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 = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 1/91 (1%)
Query: 23  AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADD 81
           A+     +VFV N+    T+E LK IF E G + S  ++ D + GK K +GF  +++ + 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 82  AAKAVEALNGKKFDDREWYVGKAQKKSEREQ 112
           A  A+  LNG++F  R   V  A  +  +E+
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNKEE 93

>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 = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 26/87 (29%), Positives = 48/87 (55%), Gaps = 4/87 (4%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           ++++ N+     +E+LK++FSE G + S +++ D  +G  KG GF  +   E A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 192 MNGKMIVSKPLYV---AVAQRKEERRA 215
           +NG+    + L V   A  + KEE ++
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKS 96

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  ++ K LF   G I SCK++RD  +G S G GFV +S P +A +A+  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K + V+ A+
Sbjct: 66  LNGLKLQTKTIKVSYAR 82

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG----ISKGSGFVAFSTPEEASRAL 189
           L+IKNL  S  +E LK +FS+ G I SC + +  +     +S G GFV +  PE+A +AL
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 190 AEMNGKMIVSKPLYVAVAQR 209
            ++ G  +    L V +++R
Sbjct: 68  KQLQGHTVDGHKLEVRISER 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 = 53.1 bits (126), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 28/73 (38%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           LY+ +L  +I ++ L+ +F  FG I +  +M+D  +G SKG GF+ FS  E A RAL ++
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 193 NGKMIVSKPLYVA 205
           NG  +  +P+ V 
Sbjct: 68  NGFELAGRPMRVG 80

>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 = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
          +VFV +L    T ED+K  F  +G I+ A V++D   GKSK +GFV+F N  DA  A++ 
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 89 LNGKKFDDRE 98
          + G+    R+
Sbjct: 77 MGGQWLGGRQ 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 = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 49/89 (55%), Gaps = 4/89 (4%)
Query: 123 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST 181
           K+T + F    +++ +L   I  E +K  F+ FG I+  +V++D  +G SKG GFV+F  
Sbjct: 10  KDTSNHFH---VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 182 PEEASRALAEMNGKMIVSKPLYVAVAQRK 210
             +A  A+ +M G+ +  + +    A RK
Sbjct: 67  KWDAENAIQQMGGQWLGGRQIRTNWATRK 95

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 30/79 (37%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
           +VFV +L    T ED+K  F  +G I+ A V++D   GKSK +GFV+F N  DA  A+  
Sbjct: 17  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 89  LNGKKFDDREWYVGKAQKK 107
           + G+    R+     A +K
Sbjct: 77  MGGQWLGGRQIRTNWATRK 95

>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 = 28/89 (31%), Positives = 49/89 (55%), Gaps = 4/89 (4%)
Query: 123 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST 181
           K+T + F   ++++ +L   I  E +K  F+ FG I+  +V++D  +G SKG GFV+F  
Sbjct: 10  KDTSNHF---HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYN 66
Query: 182 PEEASRALAEMNGKMIVSKPLYVAVAQRK 210
             +A  A+  M G+ +  + +    A RK
Sbjct: 67  KLDAENAIVHMGGQWLGGRQIRTNWATRK 95

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 1/87 (1%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           +G NL+I +L     D+ L ++F  FG + S KV  D  + +SK  GFV++  P  A  A
Sbjct: 24  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRA 215
           +  MNG  I  K L V + + K + ++
Sbjct: 84  IQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           NL +  L   + D +L  LF   G I +C++MRD  +G S G  FV F++  ++ RA+  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K L V+ A+
Sbjct: 65  LNGITVRNKRLKVSYAR 81

>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 = 51.2 bits (121), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 40 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 97
          TT+ DL+++F +YG I    ++ D   + S+ F FV FEN DDA +A E  NG + D R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 85

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 40 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 97
          TT+ DL+++F +YG I    ++ D   + S+ F FV FEN DDA +A E  NG + D R
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 82

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 85
          K  N++V NL  + TD+ L  IFG+YG+I    ++RD   G+ +   FV +   ++A +A
Sbjct: 12 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 86 VEALN 90
          + ALN
Sbjct: 72 ISALN 76

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 48/79 (60%), Gaps = 3/79 (3%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NLY+ NL  +I D++L  +F ++G+I    ++RD  +G  +G  FV ++  EEA  A++ 
Sbjct: 15  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 192 MNGKMIV--SKPLYVAVAQ 208
           +N  +    S+PL V +A+
Sbjct: 75  LNNVIPEGGSQPLSVRLAE 93

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 40 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 97
          TT+ DL+++F +YG I    ++ D   + S+ F FV FEN DDA +A E  NG + D R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 85

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 46/187 (24%), Positives = 85/187 (45%), Gaps = 18/187 (9%)
Query: 31  VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 84
           ++V N+    T+E +   F      G +T A    V+     + K F F+ F + D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ------AMKETVDKFQGLNLYIKN 138
           A+ A +G  F  +   +    ++    Q L G  E        +  TV       L+I  
Sbjct: 67  AM-AFDGIIFQGQSLKI----RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121
Query: 139 LGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMI 197
           L + ++D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +NG  +
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
Query: 198 VSKPLYV 204
             K L V
Sbjct: 182 GDKKLLV 188

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  ++L+ LFS  G + S K++RD  +G S G GFV + T ++A RA+  
Sbjct: 6   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + SK + V+ A+
Sbjct: 66  LNGLRLQSKTIKVSYAR 82

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 46/74 (62%), Gaps = 5/74 (6%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           NLY+  L  ++  +++++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 192 MNGKMIVSKPLYVA 205
           +NG+    KPL  A
Sbjct: 63  LNGQ----KPLGAA 72

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 33  VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 91
           V  L   TT+ DL+++F +YG I    ++ D   + S+ F FV FEN DDA +A E  NG
Sbjct: 51  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 92  KKFDDREWYV 101
            + D R   V
Sbjct: 111 MELDGRRIRV 120

>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 = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVE 87
          + V+V NL  S T+ DL +IF +YG +    +M+D D  KSK   F+ F + D A     
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 88 ALNGKKFDDR 97
          A+N K+   R
Sbjct: 77 AINNKQLFGR 86

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 38/67 (56%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++  N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 91 GKKFDDR 97
          G   D R
Sbjct: 91 GVPLDGR 97

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A+ + N
Sbjct: 31  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 194 GKMIVSKPLYV 204
           G  +  +P+ +
Sbjct: 91  GVPLDGRPMNI 101

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 54/90 (60%), Gaps = 11/90 (12%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L+++NL +++ +E L++ FS+FG +   K ++D +       F+ F   + A +A+ EMN
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYA-------FIHFDERDGAVKAMEEMN 66
Query: 194 GKMIVSKPLYVAVA----QRKEERRARLQA 219
           GK +  + + +  A    Q+++ER+A+ QA
Sbjct: 67  GKDLEGENIEIVFAKPPDQKRKERKAQRQA 96

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++  L     +E +  LF  FG I  C V+R P G SKG  FV FS+  EA  A+  ++
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 194 GKMIV---SKPLYVAVAQRKEE 212
           G   +   S  L V  A   +E
Sbjct: 78  GSQTMPGASSSLVVKFADTDKE 99

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 48/85 (56%), Gaps = 6/85 (7%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSC---KVMRDPSGISKGSGFVAFSTPEEASRAL 189
           +L++ +L   +DD  L E F +     SC   KV+ D +G+SKG GFV F+   E  RAL
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVK--VYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL 68
Query: 190 AEMNGKM-IVSKPLYVAVAQRKEER 213
            E  G + + SKP+ ++VA  K  R
Sbjct: 69  TECQGAVGLGSKPVRLSVAIPKASR 93

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +++ NL   + +E L ELF + G +T   + +D  G  K  GFV F  PE  S A+A +N
Sbjct: 19  VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 194 GKMIVSKPLYVA 205
           G  +  +P+ V+
Sbjct: 79  GIRLYGRPINVS 90

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 33  VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
           V N+     D DL+++FG++G I    ++ +  G SK FGFV FEN+ DA +A E L+G 
Sbjct: 34  VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 92
Query: 93  KFDDREWYVGKAQKK 107
             + R+  V  A  +
Sbjct: 93  VVEGRKIEVNNATAR 107

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 125 TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE 184
           T +K Q   L++ N+     D  L+++F +FG I   +++ +  G SKG GFV F    +
Sbjct: 23  TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSAD 81
Query: 185 ASRALAEMNGKMIVSKPLYVAVA 207
           A RA  +++G ++  + + V  A
Sbjct: 82  ADRAREKLHGTVVEGRKIEVNNA 104

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 37/67 (55%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA +  N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 91 GKKFDDR 97
          G   D R
Sbjct: 92 GVPLDGR 98

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 36/68 (52%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A  + N
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 194 GKMIVSKP 201
           G  +  +P
Sbjct: 92  GVPLDGRP 99

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 23/64 (35%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNG 91
          V NL E T + DL+++F  +G+I+   + +D   G+SK F F++F   +DAA+A+  ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 92 KKFD 95
            +D
Sbjct: 80 FGYD 83

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/60 (36%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 136 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEMNG 194
           + NL +   +  L+ELF  FG+I+   + +D + G SKG  F++F   E+A+RA+A ++G
Sbjct: 20  VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 33  VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
           V N+     D DL+++FG++G I    ++ +  G SK FGFV FEN+ DA +A E L+G 
Sbjct: 20  VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 78
Query: 93  KFDDREWYVGKAQKK 107
             + R+  V  A  +
Sbjct: 79  VVEGRKIEVNNATAR 93

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ N+     D  L+++F +FG I   +++ +  G SKG GFV F    +A RA  +++
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 194 GKMIVSKPLYVAVA 207
           G ++  + + V  A
Sbjct: 77  GTVVEGRKIEVNNA 90

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 48.1 bits (113), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 31/175 (17%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           + ++ L    T++++  +  +Y      V       K K   FV   N + A  A+ A +
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 91  GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 150
             +                RE+EL  Q +       D      L + NL  S+  ++ +E
Sbjct: 79  QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 114
Query: 151 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 204
           L   FG++  C  V  + +G SKG GF  +   + A+RA +++ GK +  + LYV
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 48.1 bits (113), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
           +FV+NL  ++++EDL+K+F  YG ++      D    K K F FV F   + A KA   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 90  NGKKFDDREWYVGKAQKKSEREQ 112
           +G+ F  R  +V  +  K E  Q
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEASQ 93

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L+++NL  +  +E L++LFS +G ++      D  +   KG  FV F  PE A +A AE+
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 193 NGKMIVSKPLYVAVAQRKEE 212
           +G++   + L+V  +  K+E
Sbjct: 71  DGQVFQGRMLHVLPSTIKKE 90

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 31/175 (17%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           + ++ L    T++++  +  +Y      V       K K   FV   N + A  A+ A +
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 91  GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 150
             +                RE+EL  Q +       D      L + NL  S+  ++ +E
Sbjct: 79  QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 114
Query: 151 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 204
           L   FG++  C  V  + +G SKG GF  +   + A+RA +++ GK +  + LYV
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 43/181 (23%), Positives = 82/181 (45%), Gaps = 26/181 (14%)
Query: 31  VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 84
           ++V N+    T+E +   F      G +T A    V+     + K F F+ F + D+  +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 144
           A+ A +G  F  +   +    ++    Q L G  +              L+I  L + ++
Sbjct: 69  AM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHK--------------LFIGGLPNYLN 109
Query: 145 DEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 203
           D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +NG  +  K L 
Sbjct: 110 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 169
Query: 204 V 204
           V
Sbjct: 170 V 170

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 31/175 (17%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           + ++ L    T++++  +  +Y      V       K K   FV   N + A  A+ A +
Sbjct: 23  ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 76
Query: 91  GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 150
             +                RE+EL  Q +       D      L + NL  S+  ++ +E
Sbjct: 77  QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 112
Query: 151 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 204
           L   FG++  C  V  + +G SKG GF  +   + A+RA +++ GK +  + LYV
Sbjct: 113 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++  L     ++ ++ LF  FG I  C ++R P G SKG  FV +S+  EA  A+  ++
Sbjct: 18  LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 194 GKMIV---SKPLYVAVAQRKEE 212
           G   +   S  L V  A   +E
Sbjct: 78  GSQTMPGASSSLVVKFADTDKE 99

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 43/181 (23%), Positives = 82/181 (45%), Gaps = 26/181 (14%)
Query: 31  VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 84
           ++V N+    T+E +   F      G +T A    V+     + K F F+ F + D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 144
           A+ A +G  F  +   +    ++    Q L G  +              L+I  L + ++
Sbjct: 67  AM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHK--------------LFIGGLPNYLN 107
Query: 145 DEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 203
           D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +NG  +  K L 
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Query: 204 V 204
           V
Sbjct: 168 V 168

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 14 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFG 72
          L +++RE    K +F  +F+  L   TT+E L+  + ++G +T  VVMRD    +S+ FG
Sbjct: 17 LERKKRE----KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72
Query: 73 FVNFENADDAAKAVEA 88
          FV F +  +   A+ A
Sbjct: 73 FVTFSSMAEVDAAMAA 88

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 185
           +K Q   L+I  L     +E L+  + ++G +T C VMRDP S  S+G GFV FS+  E 
Sbjct: 23  EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 186 SRALA----EMNGKMI 197
             A+A     ++G+++
Sbjct: 83  DAAMAARPHSIDGRVV 98

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 33  VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 91
           V NL   T+ + L+++F +YG +    + RD   K S+ F FV F +  DA  A++A++G
Sbjct: 52  VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 92  KKFDDREWYVGKAQ 105
              D RE  V  A+
Sbjct: 112 AVLDGRELRVQMAR 125

>pdb|3NTW|A Chain A, Structure Of The Mlle Domain Of Edd In Complex With A Pam2 Peptide From Paip1 Length = 65

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 390 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 446
            R  LGE LYP V+ ++   A+K+TGMLLE+   ++L LL S ++L+A+V EAME++
Sbjct: 6   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEEAMELI 62

>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 = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/125 (27%), Positives = 57/125 (45%), Gaps = 6/125 (4%)
Query: 12  HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC- 70
           HF    E +   +K K   ++V NL   TT+E + ++F + G I   ++  D   K+ C 
Sbjct: 24  HFRGDNEEQEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 71  FGFVNFENADDAAKAVEALNGKKFDDR----EWYVGKAQKKSEREQELKGQFEQAMKETV 126
           F FV + +  DA  A+  +NG + DDR    +W  G  + +        GQ     ++  
Sbjct: 83  FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDY 142
Query: 127 DKFQG 131
           D  +G
Sbjct: 143 DAGRG 147

>pdb|1I2T|A Chain A, X-Ray Structure Of The Human Hyperplastic Discs Protein: An Ortholog Of The C-Terminal Domain Of Poly(A)-Binding Protein Length = 61

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 390 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 446
            R  LGE LYP V+ ++   A+K+TGMLLE+   ++L LL S ++L+A+V EAME++
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELI 57

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++   
Sbjct: 91  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 91  GKKFDDR 97
           G   D R
Sbjct: 151 GVPLDGR 157

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           G  L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A+ 
Sbjct: 88  GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 147
Query: 191 EMNGKMIVSKPLYV 204
           +  G  +  +P+ +
Sbjct: 148 QYKGVPLDGRPMDI 161

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          N VFV  +D    + +++  F  YG++    ++ D  G SK +GFV+F N  D  K VE+
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 89 ---LNGKKF 94
              +GKK 
Sbjct: 71 QINFHGKKL 79

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          N VFV  +D    + +++  F  YG++    ++ D  G SK +GFV+F N  D  K VE+
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 89 ---LNGKKF 94
              +GKK 
Sbjct: 70 QINFHGKKL 78

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
          N VFV  +D    + +++  F  YG++    ++ D  G SK +GFV+F N  D  K VE+
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 89 ---LNGKKF 94
              +GKK 
Sbjct: 70 QINFHGKKL 78

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 30/85 (35%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           G  ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + L
Sbjct: 25  GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 190 A----EMNGKMIVSKPLYVAVAQRK 210
           A    E++ K I  K  +   AQ K
Sbjct: 85  AQSRHELDSKTIDPKVAFPRRAQPK 109

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          +FVK L E TT+E LK+ F   G++ + +V     G SK FGFV+F + +DA  A EA+ 
Sbjct: 18 LFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 91 GKKFD 95
            + D
Sbjct: 76 DGEID 80

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++   
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 91  GKKFDDR 97
           G   D R
Sbjct: 98  GVPLDGR 104

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           G  L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A+ 
Sbjct: 35  GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 191 EMNGKMIVSKPLYV 204
           +  G  +  +P+ +
Sbjct: 95  QYKGVPLDGRPMDI 108

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           V+V NL  +    +L++ FG YG + S  V R+  G    F FV FE+  DAA AV  L+
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 131
Query: 91  GK 92
           G+
Sbjct: 132 GR 133

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +Y+ NLG++ +  +L+  F  +G + S  V R+P G +    FV F  P +A+ A+ E++
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRELD 131
Query: 194 GKMI 197
           G+ +
Sbjct: 132 GRTL 135

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++   
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 91  GKKFDDR 97
           G   D R
Sbjct: 98  GVPLDGR 104

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           G  L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A+ 
Sbjct: 35  GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 191 EMNGKMIVSKPLYV 204
           +  G  +  +P+ +
Sbjct: 95  QYKGVPLDGRPMDI 108

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           V+V NL  +    +L++ FG YG + S  V R+  G    F FV FE+  DAA AV  L+
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRDLD 131
Query: 91  GK 92
           G+
Sbjct: 132 GR 133

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 133 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 188
            +YI NL + I  ++LK+    +FS+FG I    V R  S   +G  FV F     A+ A
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 68
Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 221
           L  M G     KP+ +  A+   +  A+++  F
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 85
          +   +FV  LD STT E L+  F +YG +   V+M+D    +S+ FGFV F++ +     
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
Query: 86 VEA----LNGKKFDDR 97
          + +    L+G+  D +
Sbjct: 75 LASRPHTLDGRNIDPK 90

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 5/82 (6%)
Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAK 84
           T F  +FV  L   TTD  L+K F  +G I  AVV+ D   GKS+ +GFV   +   A +
Sbjct: 15  TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74
Query: 85  AVE----ALNGKKFDDREWYVG 102
           A +     ++G+K +    Y+G
Sbjct: 75  ACKDPNPIIDGRKANVNLAYLG 96

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 5/95 (5%)
Query: 12  HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 71
           HF    E +   +K K   ++V NL   TT+E + ++F + G I   ++  D    +  F
Sbjct: 3   HFRGDNEEQEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGF 61
Query: 72  GFVNFENADDAAKAVEALNGKKFDDR----EWYVG 102
            FV + +  DA  A+  +NG + DDR    +W  G
Sbjct: 62  CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG 96

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 33  VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 91
           V NL   T+ + L+++F +YG +    + RD   K S+ F FV F +  DA  A++A++G
Sbjct: 75  VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 92  KKFDDREWYVGKAQ 105
              D RE  V  A+
Sbjct: 135 AVLDGRELRVQMAR 148

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 44/92 (47%), Gaps = 6/92 (6%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           +YI NL + I  ++LK+    +FS FG I    V R  S   +G  FV F     A+ AL
Sbjct: 11  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 221
             M G     KP+ +  A+   +  A+++  F
Sbjct: 69  RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           +YI NL + I  ++LK+    +FS+FG I    V R  S   +G  FV F     A+ AL
Sbjct: 11  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 221
             M G     KP+ +  A+   +  A+++  F
Sbjct: 69  RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 12/86 (13%)
Query: 12 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 71
          H   +QE E    +     +FV+       + +L +IFG +G +    ++         F
Sbjct: 20 HMHHRQEGELSNTR-----LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------F 67
Query: 72 GFVNFENADDAAKAVEALNGKKFDDR 97
           FV FE A+ AAKA+E ++GK F ++
Sbjct: 68 AFVEFEEAESAAKAIEEVHGKSFANQ 93

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
             ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + LA
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 191 ----EMNGKMI 197
               E++ K I
Sbjct: 61  QSRHELDSKTI 71

>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleoprotein R (Hnrnp R) Length = 97

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 7/69 (10%)
Query: 24 IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 83
          +  K   +FV+NL  + T+E L+K F E+G +     ++D       + FV+FE+   A 
Sbjct: 11 VMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAV 63
Query: 84 KAVEALNGK 92
          KA++ +NGK
Sbjct: 64 KAMDEMNGK 72

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 28  FNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAV 86
           F  +FV  ++  TT+  L++ F  YG I    +V     GK + + F+ +E+  D   A 
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 87  EALNGKKFDDR 97
           +  +GKK D R
Sbjct: 162 KHADGKKIDGR 172

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 46/174 (26%), Positives = 79/174 (45%), Gaps = 23/174 (13%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           N+FV NL+ + +  +LK    +        V+    G ++ FG+V+FE+A+D  KA+E L
Sbjct: 9   NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALE-L 67
Query: 90  NGKKFDDREWYVGKAQ-KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
            G K    E  + K + K S++E++ +                  L  KNL   +  ++L
Sbjct: 68  TGLKVFGNEIKLEKPKGKDSKKERDAR-----------------TLLAKNLPYKVTQDEL 110
Query: 149 KELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL 202
           KE+F +   I     +    G SKG  ++ F T  +A +   E  G  I  + +
Sbjct: 111 KEVFEDAAEIR----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSI 160

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L+I  L + ++D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 193 NGKMIVSKPLYVAVA 207
           NG  +  K L V  A
Sbjct: 64  NGMQLGDKKLLVQRA 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 = 22/58 (37%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 87
          +FV  L  +TT ED+K  F ++G +  A++M D    + + FGFV FE+ D   K  E
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 46/168 (27%), Positives = 77/168 (45%), Gaps = 21/168 (12%)
Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           N+F+ NL+ + +  +LK    E        V+    G ++ FG+V+FE+A+D  KA+E L
Sbjct: 15  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 90  NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 149
            G K    E  + K           KG+  + ++          L  KNL  +I +++LK
Sbjct: 74  TGLKVFGNEIKLEKP----------KGRDSKKVR------AARTLLAKNLSFNITEDELK 117
Query: 150 ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI 197
           E+F +   I     +    G SKG  ++ F +  +A + L E  G  I
Sbjct: 118 EVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           + V N+  + T+++L+  F EYG +    +++D       + FV+ E A+DA +A+  L+
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD 65
Query: 91  GKKFDDREWYV 101
             +F  +  +V
Sbjct: 66  NTEFQGKRMHV 76

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 191
           ++I  L      + LK+ FS+FG +  C +  DP +G S+G GFV F   E   + + + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 192 ---MNGKMIVSK 200
              +NGK+I  K
Sbjct: 62  EHKLNGKVIDPK 73

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 33  VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS-KCFGFVNFENADDAAKAVEALNG 91
           V NL   T+ + L+++F +YG +    + R+   K+ + F FV F +  DA  A  A++G
Sbjct: 18  VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 92  KKFDDREWYV 101
            + D RE  V
Sbjct: 78  AELDGRELRV 87

>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 = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
           N+Y+ NL  S   E++KELFS+FG + + K++ D  +   KG GFV     E  S A+A+
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 192 MNGKMIVSKPLYVAVAQRKE 211
           ++    + + + V  A  K+
Sbjct: 62  LDNTDFMGRTIRVTEANPKK 81

>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains Of The Yeast Splicing Factor Prp24 Length = 292

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 37/149 (24%), Positives = 67/149 (44%), Gaps = 21/149 (14%)
Query: 68  SKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVD 127
           S+ F +++  + +DA   VE LNG K    E Y    +        +    E++ +    
Sbjct: 158 SRRFAYIDVTSKEDARYCVEKLNGLKI---EGYTLVTK--------VSNPLEKSKRTDSA 206
Query: 128 KFQGLNLYIKNLGDSIDDEK-LKELFSEFGTITSCKVMRDPSG-----ISKGSGFVAFST 181
             +G  + I+NL   + DE  L+E F  FG+I    +   P+G      +    F  F  
Sbjct: 207 TLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINI---PAGQKEHSFNNCCAFXVFEN 263
Query: 182 PEEASRALAEMNGKMIVSKPLYVAVAQRK 210
            + A RAL + N  ++ ++ + V++A +K
Sbjct: 264 KDSAERAL-QXNRSLLGNREISVSLADKK 291

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 87
          + ++++ L   TTD+DL K+   YG I S   + D    K K +GFV+F++   A KAV 
Sbjct: 6  SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 88 AL 89
          AL
Sbjct: 66 AL 67

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	472
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-88
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-56
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-78
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-32
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-78
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-53
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-75
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-29
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-25
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	9e-74
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-29
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-28
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-73
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-42
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-28
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-70
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-33
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-28
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-66
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-26
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-65
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-26
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-25
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-64
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-27
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-62
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-32
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-23
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-50
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-32
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-50
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-26
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-15
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-48
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-37
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-44
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	7e-32
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-44
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-35
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-44
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-31
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-44
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-19
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-15
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-43
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-27
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	8e-43
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	9e-28
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-41
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-21
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-18
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-41
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-28
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-41
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-28
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-41
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-30
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-40
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-18
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-39
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-36
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-39
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-17
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-39
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-35
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-39
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-31
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-38
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-17
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-14
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-36
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-32
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-36
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-28
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-35
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-33
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-35
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-29
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-33
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-22
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-19
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-33
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	4e-32
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-32
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-23
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-32
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-32
1ifw_A	92	Polyadenylate-binding protein, cytoplasmic and nuc	9e-32
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-31
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-28
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-31
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-30
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	9e-30
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-28
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	9e-30
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-25
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-29
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-29
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-29
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	7e-25
2dyd_A	85	Poly(A)-binding protein; alpha helical protein, RN	3e-28
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-28
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	8e-28
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-28
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-22
1nmr_A	85	Poly(A)-binding protein; all helical domain, pepti	9e-28
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-27
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-25
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-27
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-25
3kuj_A	88	Polyadenylate-binding protein 1; protein-protein c	4e-27
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-27
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-23
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-26
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-22
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-26
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-21
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-26
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-25
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	5e-26
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-24
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-26
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	8e-25
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-25
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-22
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-25
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-22
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-25
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-21
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-25
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-21
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-25
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	6e-23
1i2t_A	61	HYD protein; four alpha-helical domain, ligase; 1.	6e-25
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-25
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-21
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	8e-25
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	8e-23
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-24
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-20
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-24
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	7e-19
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-24
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-22
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-24
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-20
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-24
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-19
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-24
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-19
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-23
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-23
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-20
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-23
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	9e-20
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-23
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-23
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-23
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-19
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-23
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-17
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-23
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	6e-20
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	8e-23
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-19
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-23
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-22
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-20
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-22
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-18
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-22
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-21
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-22
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	9e-18
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-22
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-20
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-22
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-19
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-22
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-21
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-22
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-17
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-22
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	7e-17
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-22
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	8e-20
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	5e-22
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-21
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-21
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-21
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-18
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-21
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-17
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-21
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-20
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-21
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-16
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-21
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-19
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-21
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-17
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-21
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-19
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-21
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	8e-17
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	8e-21
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-19
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-20
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-18
1g9l_A	144	Polyadenylate-binding protein 1; all-helical domai	1e-20
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-20
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	9e-17
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-20
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	7e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-20
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	9e-19
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-20
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-17
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-20
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-15
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-20
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-16
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-20
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-14
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-20
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-18
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-19
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-19
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	9e-18
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-19
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-16
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-19
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-18
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-19
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-15
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	6e-19
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-12
2div_A	99	TRNA selenocysteine associated protein; structural	7e-19
2div_A	99	TRNA selenocysteine associated protein; structural	5e-17
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	8e-19
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-16
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-18
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-18
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	6e-16
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-18
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-12
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-18
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	9e-17
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-18
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-14
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-18
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-18
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-17
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	6e-18
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-17
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	7e-18
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-13
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	8e-18
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-14
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-17
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-15
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	3e-17
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-16
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-17
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-15
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-17
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-15
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-17
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-14
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-17
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	8e-17
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	8e-15
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	8e-17
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-13
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-17
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-13
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-16
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-14
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-16
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-16
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	9e-13
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-16
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	8e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-16
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-13
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-16
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-16
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-15
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-14
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-15
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-15
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-10
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-15
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-15
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	8e-15
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-12
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-14
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	6e-11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-14
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	5e-14
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	7e-14
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-11
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-13
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	6e-12
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-13
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-13
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-12
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-13
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-13
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-13
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-11
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	5e-13
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-12
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	5e-13
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-12
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-12
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-10
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	6e-12
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-11
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-10
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-10
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-10
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	7e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	8e-10
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-09
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	4e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	3e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	8e-09
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-09
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	1e-07
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	8e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-08
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-08
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	2e-08
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	1e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-07
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	9e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	7e-07
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	4e-04
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	8e-07
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	1e-06
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	7e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	9e-06
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	2e-06
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	4e-06
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	6e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	6e-06
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	1e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-04
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	2e-04
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	2e-04
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	5e-04
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-04

>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 =  269 bits (689), Expect = 9e-88
 Identities = 43/227 (18%), Positives = 79/227 (34%), Gaps = 29/227 (12%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
             + ++++ V             ++     + V NL  S T +  +++   +G++    +
Sbjct: 80  SRLRERELSV------------QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFL 127

Query: 61  MRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFE 119
           +     G+SK +GF  +   D AA+A   L GK    R  YV            L  +  
Sbjct: 128 VYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR-- 185

Query: 120 QAMKETVDKFQGLNLYIKNLGDSIDD-EKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
                         L +  L    +D + L    S   + T C++     G  KG   + 
Sbjct: 186 -------------CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLE 232

Query: 179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMR 225
           + T E A  A  + +G  +    L V+        R+ L A  +   
Sbjct: 233 YETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQA 279

>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 =  186 bits (475), Expect = 7e-56
 Identities = 44/215 (20%), Positives = 82/215 (38%), Gaps = 36/215 (16%)

Query: 12  HFLRKQER-----ETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG 66
           H L  +E       T         + ++ L    T++++  +  +Y  +    V      
Sbjct: 1   HMLDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----D 54

Query: 67  KSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETV 126
           K K   FV   N + A  A+ A +  +  +RE  V      +                  
Sbjct: 55  KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDA------------------ 96

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 185
                  L + NL  S+  ++ +EL   FG++  C ++    +G SKG GF  +   + A
Sbjct: 97  ------LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA 150

Query: 186 SRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQ 220
           +RA +++ GK +  + LYV      +   A L ++
Sbjct: 151 ARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSR 185

>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 =  243 bits (622), Expect = 5e-78
 Identities = 54/250 (21%), Positives = 93/250 (37%), Gaps = 37/250 (14%)

Query: 6   KQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD 65
             + +  FL+  E+      T+   +FV NL    T+ED K++F  YG  +   + RD  
Sbjct: 4   FTIDIKSFLKPGEKT----YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-- 57

Query: 66  GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKET 125
              + FGF+  E+   A  A   L+G     R   +  A                     
Sbjct: 58  ---RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT-------------------- 94

Query: 126 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 185
                G  L +KNL   + +E L++ FS+FG +    V+ D  G + G GFV F+    A
Sbjct: 95  ----HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPA 150

Query: 186 SRALAEMNGKMIV----SKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYP 241
            +AL        +     +P+ V   ++ ++     +    + +        PPR     
Sbjct: 151 RKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPG 210

Query: 242 PGPSGLGQQF 251
                   ++
Sbjct: 211 TFEFEYASRW 220

>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 =  123 bits (311), Expect = 2e-32
 Identities = 28/145 (19%), Positives = 55/145 (37%), Gaps = 23/145 (15%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             + VKNL    ++E L++ F ++G +  AVV+ D  G++   GFV F     A KA+E 
Sbjct: 97  AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156

Query: 89  LNGKKF----DDREWYVGKAQKKSEREQELKGQFEQAMK-------------------ET 125
                F      R   V   ++  + +   +   ++  +                   E 
Sbjct: 157 CGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEY 216

Query: 126 VDKFQGLNLYIKNLGDSIDDEKLKE 150
             +++ L+   K   + +D    + 
Sbjct: 217 ASRWKALDEMEKQQREQVDRNIREA 241

>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 = 2e-09
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 71  FGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAM 122
            G   FE A    KA++ +  ++ +  +  + +A++K E E E      Q M
Sbjct: 209 PGTFEFEYAS-RWKALDEMEKQQREQVDRNIREAKEKLEAEMEAARHEHQLM 259

>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 =  243 bits (623), Expect = 9e-78
 Identities = 38/214 (17%), Positives = 84/214 (39%), Gaps = 29/214 (13%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
            ++   ++ V H                  +++ N   S T  +++ +  +   +  ++ 
Sbjct: 103 KVVGQNEIIVSHL-------------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIR 149

Query: 61  M-RDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFE 119
           +       S+ F +++  + +DA   VE LNG K +        +    + ++       
Sbjct: 150 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKR------- 202

Query: 120 QAMKETVDKFQGLNLYIKNLGDSIDDEK-LKELFSEFGTITSCKVMRD--PSGISKGSGF 176
                     +G  + I+NL   + DE  L+E F  FG+I    +         +    F
Sbjct: 203 ----TDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAF 258

Query: 177 VAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK 210
           + F   + A RAL +MN  ++ ++ + V++A +K
Sbjct: 259 MVFENKDSAERAL-QMNRSLLGNREISVSLADKK 291

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  180 bits (458), Expect = 2e-53
 Identities = 36/209 (17%), Positives = 68/209 (32%), Gaps = 29/209 (13%)

Query: 16  KQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVN 75
           K+  E +    +   V VKNL +S     + K F   G I    V      K+  F  + 
Sbjct: 29  KKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS-LKKNFRFARIE 87

Query: 76  FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLY 135
           F   D A  A+   +       E  V    +                           L+
Sbjct: 88  FARYDGALAAITKTHKV-VGQNEIIVSHLTEC-------------------------TLW 121

Query: 136 IKNLGDSIDDEKLKELFSEFGTIT-SCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 194
           + N   S     +++L  +   +  S ++       S+   ++  ++ E+A   + ++NG
Sbjct: 122 MTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNG 181

Query: 195 KMIVSKPLYVAVAQRKEERRARLQAQFSQ 223
             I    L   V+    E+  R  +   +
Sbjct: 182 LKIEGYTLVTKVS-NPLEKSKRTDSATLE 209

>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 =  233 bits (596), Expect = 2e-75
 Identities = 45/184 (24%), Positives = 81/184 (44%), Gaps = 20/184 (10%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAV 86
            +FV  +  + +++DL+++F +YG +    V+RD      +SK   FV F     A +A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 87  EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 146
            AL+  K      +  + +                  E  +  +   L+I  +     + 
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADS--------------EKNNAVEDRKLFIGMISKKCTEN 110

Query: 147 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV---SKPLY 203
            ++ +FS FG I  C+++R P G+S+G  FV F+T   A  A+  M+    +   S P+ 
Sbjct: 111 DIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170

Query: 204 VAVA 207
           V  A
Sbjct: 171 VKFA 174

>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 =  110 bits (278), Expect = 9e-29
 Identities = 20/94 (21%), Positives = 43/94 (45%), Gaps = 3/94 (3%)

Query: 4   NDKQVFVGHFLRKQERETVAIK---TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           ++ +V  G     Q +   + K    +   +F+  + +  T+ D++ +F  +G I    +
Sbjct: 68  HNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRI 127

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF 94
           +R  DG S+   FV F     A  A++A++  + 
Sbjct: 128 LRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQT 161

>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 =  101 bits (253), Expect = 2e-25
 Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG---ISKGSGFVAFSTPEEASRAL 189
            +++  +  +  ++ L+ELF ++G +    V+RD S     SKG  FV F T + A  A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRAR 216
             ++   ++    +    +  +  +  
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEKNN 91

>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 =  228 bits (584), Expect = 9e-74
 Identities = 52/182 (28%), Positives = 90/182 (49%), Gaps = 22/182 (12%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L +  TD +L  +F   G I +  +MRD   G S  + FV+F +  D+ +A++ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
           LNG    ++   V  A+   E  ++                   NLY+ NL  +I D++L
Sbjct: 65  LNGITVRNKRLKVSYARPGGESIKD------------------TNLYVTNLPRTITDDQL 106

Query: 149 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVA 205
             +F ++G+I    ++RD  +G  +G  FV ++  EEA  A++ +N  +    S+PL V 
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166

Query: 206 VA 207
           +A
Sbjct: 167 LA 168

>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 =  111 bits (281), Expect = 2e-29
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 1/83 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L   + D +L  LF   G I +C++MRD  +G S G  FV F++  ++ RA+  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 192 MNGKMIVSKPLYVAVAQRKEERR 214
           +NG  + +K L V+ A+   E  
Sbjct: 65  LNGITVRNKRLKVSYARPGGESI 87

>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 =  108 bits (272), Expect = 5e-28
 Identities = 29/107 (27%), Positives = 52/107 (48%), Gaps = 9/107 (8%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           + + +K++ V +     E        K  N++V NL  + TD+ L  IFG+YG+I    +
Sbjct: 68  ITVRNKRLKVSYARPGGESI------KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121

Query: 61  MRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFD--DREWYVGKA 104
           +RD   G+ +   FV +   ++A +A+ ALN    +   +   V  A
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  230 bits (588), Expect = 1e-73
 Identities = 47/212 (22%), Positives = 90/212 (42%), Gaps = 14/212 (6%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
            +   +Q+  G   ++Q           + V+V ++     ++ +++ F  +G I S  +
Sbjct: 6   SMTGGQQMGRGSAAQRQGALA-----IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM 60

Query: 61  MRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFE 119
             D    K K F FV +E  + A  A+E +N      R   VG+     + +  +    E
Sbjct: 61  SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAE 120

Query: 120 QAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVA 178
           +A            +Y+ ++   + D+ +K +F  FG I S  + RDP +G  KG GF+ 
Sbjct: 121 EARAFN-------RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIE 173

Query: 179 FSTPEEASRALAEMNGKMIVSKPLYVAVAQRK 210
           +   + +  A++ MN   +  + L V  A   
Sbjct: 174 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  147 bits (373), Expect = 6e-42
 Identities = 29/118 (24%), Positives = 56/118 (47%), Gaps = 6/118 (5%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKT-----KFNNVFVKNLDESTTDEDLKKIFGEYGTI 55
           +++  + + VG      + + +  +       FN ++V ++ +  +D+D+K +F  +G I
Sbjct: 93  VMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI 152

Query: 56  TSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 112
            SA + RD   GK K +GF+ +E A  +  AV ++N      +   VGKA        
Sbjct: 153 KSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLL 210

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  109 bits (275), Expect = 7e-28
 Identities = 22/107 (20%), Positives = 45/107 (42%), Gaps = 1/107 (0%)

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 179
           A +          +Y+ ++   + ++ +++ F+ FG I S  +  D  +   KG  FV +
Sbjct: 18  AAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY 77

Query: 180 STPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRP 226
             PE A  AL +MN  M+  + + V       + +  +     + R 
Sbjct: 78  EVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124

>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 =  220 bits (563), Expect = 2e-70
 Identities = 46/186 (24%), Positives = 80/186 (43%), Gaps = 21/186 (11%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
            T   N+F+ NL+ + +  +LK    E        V+    G ++ FG+V+FE+A+D  K
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 144
           A+E L G K    E  + K + +  ++                      L  KNL  +I 
Sbjct: 70  ALE-LTGLKVFGNEIKLEKPKGRDSKKVR----------------AARTLLAKNLSFNIT 112

Query: 145 DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 204
           +++LKE+F +   I     +    G SKG  ++ F +  +A + L E  G  I  + + +
Sbjct: 113 EDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168

Query: 205 AVAQRK 210
                K
Sbjct: 169 YYTGEK 174

>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 =  121 bits (306), Expect = 8e-33
 Identities = 22/107 (20%), Positives = 47/107 (43%), Gaps = 8/107 (7%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           + +   ++ +     +  ++          +  KNL  + T+++LK++F +   I     
Sbjct: 76  LKVFGNEIKLEKPKGRDSKK----VRAARTLLAKNLSFNITEDELKEVFEDALEIR---- 127

Query: 61  MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 107
           +   DGKSK   ++ F++  DA K +E   G + D R   +    +K
Sbjct: 128 LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>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 =  108 bits (272), Expect = 6e-28
 Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 1/93 (1%)

Query: 124 ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPE 183
           E  +     NL+I NL  +    +LK   SE        V+   +G ++  G+V F + E
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65

Query: 184 EASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
           +  +AL E+ G  +    + +   + ++ ++ R
Sbjct: 66  DLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVR 97

>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 =  209 bits (534), Expect = 3e-66
 Identities = 53/182 (29%), Positives = 93/182 (51%), Gaps = 22/182 (12%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L ++ T E+ + +FG  G I S  ++RD   G+S  +GFVN+ +  DA KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
           LNG +   +   V  A+  S   +                    NLY+  L  ++  ++L
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIR------------------DANLYVSGLPKTMTQKEL 105

Query: 149 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVA 205
           ++LFS++G I + +++ D  +G+S+G GF+ F    EA  A+  +NG+     ++P+ V 
Sbjct: 106 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165

Query: 206 VA 207
            A
Sbjct: 166 FA 167

>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 =  103 bits (259), Expect = 3e-26
 Identities = 27/82 (32%), Positives = 46/82 (56%), Gaps = 1/82 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  E+ + LF   G I SCK++RD  +G S G GFV +  P++A +A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 192 MNGKMIVSKPLYVAVAQRKEER 213
           +NG  + +K + V+ A+     
Sbjct: 64  LNGLRLQTKTIKVSYARPSSAS 85

>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 = 96.1 bits (240), Expect = 1e-23
 Identities = 23/83 (27%), Positives = 46/83 (55%), Gaps = 3/83 (3%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAA 83
             +  N++V  L ++ T ++L+++F +YG I ++ ++ D   G S+  GF+ F+   +A 
Sbjct: 85  SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 144

Query: 84  KAVEALNGKKFD--DREWYVGKA 104
           +A++ LNG+K         V  A
Sbjct: 145 EAIKGLNGQKPSGATEPITVKFA 167

>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 =  207 bits (529), Expect = 2e-65
 Identities = 50/180 (27%), Positives = 94/180 (52%), Gaps = 17/180 (9%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           ++V NLD++ T++ LK+ F   G I +  +M D + K+  + FV +  + DA  A++ LN
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 91  GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 150
           GK+ ++    +  A +  +   +                   NL++ +L  ++DDE L+ 
Sbjct: 63  GKQIENNIVKINWAFQSQQSSSD----------------DTFNLFVGDLNVNVDDETLRN 106

Query: 151 LFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR 209
            F +F +  S  VM D  +G S+G GFV+F++ ++A  A+  M G+ +  +PL +  A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score =  103 bits (260), Expect = 2e-26
 Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           N+FV +L+ +  DE L+  F ++ +  S  VM D   G S+ +GFV+F + DDA  A+++
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 89  LNGKKFDDREWYVGKAQK 106
           + G+  + R   +  A K
Sbjct: 149 MQGQDLNGRPLRINWAAK 166

>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 =  101 bits (255), Expect = 1e-25
 Identities = 23/81 (28%), Positives = 42/81 (51%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY+ NL  +I ++ LK+ F   G I + K+M D +  +    FV +    +A+ AL  +N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 194 GKMIVSKPLYVAVAQRKEERR 214
           GK I +  + +  A + ++  
Sbjct: 63  GKQIENNIVKINWAFQSQQSS 83

>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 =  205 bits (523), Expect = 4e-64
 Identities = 41/191 (21%), Positives = 81/191 (42%), Gaps = 10/191 (5%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSA------VVMRDGDGKSKCFGFVNFENADDAAK 84
           ++V N+    T+E +   F     +          V+     + K F F+ F + D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 85  AVEALNGKKFDDREWYVGKAQKKSERE--QELKGQFEQAMKETVDKFQGLNLYIKNLGDS 142
           A+ A +G  F  +   + +           E    +   +  TV       L+I  L + 
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125

Query: 143 IDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP 201
           ++D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +NG  +  K 
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185

Query: 202 LYVAVAQRKEE 212
           L V  A    +
Sbjct: 186 LLVQRASVGAK 196

>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 =  106 bits (267), Expect = 4e-27
 Identities = 18/124 (14%), Positives = 51/124 (41%), Gaps = 15/124 (12%)

Query: 1   MLINDKQVFVGHFLRKQERETVA--------------IKTKFNNVFVKNLDESTTDEDLK 46
           ++   + + +      Q    ++              +    + +F+  L     D+ +K
Sbjct: 73  IIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVK 132

Query: 47  KIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ 105
           ++   +G + +  +++D   G SK + F  + + +   +A+  LNG +  D++  V +A 
Sbjct: 133 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 192

Query: 106 KKSE 109
             ++
Sbjct: 193 VGAK 196

>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 = 80.5 bits (199), Expect = 1e-17
 Identities = 19/108 (17%), Positives = 39/108 (36%), Gaps = 8/108 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCK------VMRDPSGISKGSGFVAFSTPEEASR 187
           LY+ N+   I +E + + F+    +          V+       K   F+ F + +E ++
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 188 ALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPP 235
           A+A  +G +   + L +      +          S   P  +   VP 
Sbjct: 67  AMA-FDGIIFQGQSLKIRRPHDYQPLPGM-SENPSVYVPGVVSTVVPD 112

>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 =  201 bits (514), Expect = 1e-62
 Identities = 63/201 (31%), Positives = 103/201 (51%), Gaps = 18/201 (8%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           +++V +L    T+  L + F   G I S  V RD    +S  + +VNF+   DA +A++ 
Sbjct: 17  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
           +N      +   +  +Q+                  ++ K    N++IKNL  SID++ L
Sbjct: 77  MNFDVIKGKPVRIMWSQRDP----------------SLRKSGVGNIFIKNLDKSIDNKAL 120

Query: 149 KELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 208
            + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++  + ++V   +
Sbjct: 121 YDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 179

Query: 209 RKEERRARLQAQFSQMRPVAM 229
            ++ER A L A+  +  P  +
Sbjct: 180 SRKEREAELGARAKEFYPYDV 200

>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 =  121 bits (306), Expect = 3e-32
 Identities = 38/109 (34%), Positives = 64/109 (58%), Gaps = 1/109 (0%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           K+   N+F+KNLD+S  ++ L   F  +G I S  V+ D +  SK +GFV+FE  + A +
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAER 158

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN 133
           A+E +NG   +DR+ +VG+ + + ERE EL  + ++     V  + G +
Sbjct: 159 AIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGSS 207

>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 = 96.6 bits (241), Expect = 3e-23
 Identities = 30/89 (33%), Positives = 44/89 (49%), Gaps = 1/89 (1%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 185
             +   +LY+ +L   + +  L E FS  G I S +V RD  +  S G  +V F  P +A
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70

Query: 186 SRALAEMNGKMIVSKPLYVAVAQRKEERR 214
            RAL  MN  +I  KP+ +  +QR    R
Sbjct: 71  ERALDTMNFDVIKGKPVRIMWSQRDPSLR 99

>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 =  166 bits (423), Expect = 1e-50
 Identities = 32/109 (29%), Positives = 51/109 (46%)

Query: 108 SEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP 167
           S     LK    QA      +    NLYI NL  S+D+++L+ +   FG + S +++RD 
Sbjct: 2   SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS 61

Query: 168 SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
           SG S+G GF    + E+    +   NGK I + P   A  +    + + 
Sbjct: 62  SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSG 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 =  119 bits (300), Expect = 1e-32
 Identities = 17/95 (17%), Positives = 39/95 (41%), Gaps = 3/95 (3%)

Query: 16  KQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVN 75
           +  ++    +    N+++ NL  S  +++L+ +   +G + S  ++RD  G S+  GF  
Sbjct: 16  QMAKQQ---EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFAR 72

Query: 76  FENADDAAKAVEALNGKKFDDREWYVGKAQKKSER 110
            E+ +     +   NGK            +    +
Sbjct: 73  MESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107

>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 =  168 bits (427), Expect = 3e-50
 Identities = 39/184 (21%), Positives = 76/184 (41%), Gaps = 26/184 (14%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSA------VVMRDGDGKSKCFGFVNFENADDAAK 84
           ++V N+    T+E +   F     +          V+     + K F F+ F + D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 144
           A+ A +G  F  +   + +           K                  L+I  L + ++
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPGAHK------------------LFIGGLPNYLN 107

Query: 145 DEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 203
           D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +NG  +  K L 
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167

Query: 204 VAVA 207
           V  A
Sbjct: 168 VQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  103 bits (260), Expect = 2e-26
 Identities = 18/105 (17%), Positives = 46/105 (43%), Gaps = 7/105 (6%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV 60
           ++   + + +      Q           + +F+  L     D+ +K++   +G + +  +
Sbjct: 73  IIFQGQSLKIRRPHDYQPLP------GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 126

Query: 61  MRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA 104
           ++D   G SK + F  + + +   +A+  LNG +  D++  V +A
Sbjct: 127 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 73.0 bits (180), Expect = 2e-15
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 7/87 (8%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCK------VMRDPSGISKGSGFVAFSTPEEASR 187
           LY+ N+   I +E + + F+    +          V+       K   F+ F + +E ++
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 188 ALAEMNGKMIVSKPLYVAVAQRKEERR 214
           A+A  +G +   + L +      +   
Sbjct: 67  AMA-FDGIIFQGQSLKIRRPHDYQPLP 92

>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 =  159 bits (405), Expect = 4e-48
 Identities = 55/97 (56%), Positives = 77/97 (79%), Gaps = 1/97 (1%)

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS 180
           +  + + ++Q +NLY+KNL D IDDE+L++ FS FGTITS KVM +  G SKG GFV FS
Sbjct: 5   SSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFS 63

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARL 217
           +PEEA++A+ EMNG+++ +KPLYVA+AQRKEER++  
Sbjct: 64  SPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGP 100

>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 =  131 bits (333), Expect = 1e-37
 Identities = 43/104 (41%), Positives = 61/104 (58%), Gaps = 4/104 (3%)

Query: 11  GHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC 70
           G      +R T   + +  N++VKNLD+   DE L+K F  +GTITSA VM +  G+SK 
Sbjct: 1   GSSGSSGDRIT---RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKG 56

Query: 71  FGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQEL 114
           FGFV F + ++A KAV  +NG+    +  YV  AQ+K ER+   
Sbjct: 57  FGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGP 100

>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 =  151 bits (383), Expect = 1e-44
 Identities = 33/107 (30%), Positives = 52/107 (48%), Gaps = 1/107 (0%)

Query: 114 LKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISK 172
           L  Q   A     +  +G NL+I +L     D+ L ++F  FG + S KV  D  + +SK
Sbjct: 8   LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67

Query: 173 GSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQA 219
             GFV++  P  A  A+  MNG  I  K L V + + K + ++   +
Sbjct: 68  CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSS 114

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score =  117 bits (294), Expect = 7e-32
 Identities = 26/87 (29%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
            N+F+ +L +   D+DL ++F  +G + SA V  D     SKCFGFV+++N   A  A++
Sbjct: 26  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQEL 114
           ++NG +   +   V   + K++ +   
Sbjct: 86  SMNGFQIGMKRLKVQLKRSKNDSKSGP 112

>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 =  150 bits (380), Expect = 3e-44
 Identities = 30/103 (29%), Positives = 53/103 (51%), Gaps = 4/103 (3%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
            G  +++ NL   +  +KLKE+FS  G +    ++ D  G S+G G V F    EA +A+
Sbjct: 14  LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73

Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPS 232
           +  NG+++  +P++V + +R   +      +    RP   GPS
Sbjct: 74  SMFNGQLLFDRPMHVKMDERALPKGDFFPPE----RPQQSGPS 112

>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 =  125 bits (317), Expect = 4e-35
 Identities = 28/94 (29%), Positives = 46/94 (48%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           + VFV NLD     + LK++F   G +  A ++ D DGKS+  G V FE + +A +A+  
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAM 122
            NG+   DR  +V   ++   +      +  Q  
Sbjct: 76  FNGQLLFDRPMHVKMDERALPKGDFFPPERPQQS 109

>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 =  150 bits (380), Expect = 4e-44
 Identities = 27/119 (22%), Positives = 49/119 (41%)

Query: 102 GKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC 161
           G  Q   + ++     F+           G  L + NL   + D  ++ELF+EFGT+   
Sbjct: 6   GGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA 65

Query: 162 KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQ 220
            V  D SG S G+  V F    +A +A+ +  G  +  +P+ + +   + +        
Sbjct: 66  AVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>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 =  115 bits (290), Expect = 3e-31
 Identities = 26/89 (29%), Positives = 41/89 (46%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++ 
Sbjct: 36  AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQ 117
             G   D R   +     + + E      
Sbjct: 96  YKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>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 =  152 bits (386), Expect = 4e-44
 Identities = 39/200 (19%), Positives = 77/200 (38%), Gaps = 26/200 (13%)

Query: 30  NVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
            + V NL+ E  T + L  +FG YG +    ++ +     K    V   + + A  A+  
Sbjct: 5   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSH 60

Query: 89  LNGKKFDDREWYVGKA-------QKKSEREQELKGQFEQAMKETVDKFQGLN-------- 133
           LNG K   +   +  +        ++ + +Q L   +  +      K    N        
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 134 --LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
             L++ N+  S+ +E LK LFS  G +             +    +   + EEA +AL +
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---DRKMALIQMGSVEEAVQALID 177

Query: 192 MNGKMIV-SKPLYVAVAQRK 210
           ++   +  +  L V+ ++  
Sbjct: 178 LHNHDLGENHHLRVSFSKST 197

>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 = 84.2 bits (208), Expect = 5e-19
 Identities = 21/120 (17%), Positives = 48/120 (40%), Gaps = 8/120 (6%)

Query: 133 NLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
            L + NL  + +  + L  LF  +G +   K++ +     K +  V  +   +A  A++ 
Sbjct: 5   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSH 60

Query: 192 MNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQF 251
           +NG  +  KP+ + +++ +  +  R   +  + + +       P      PG       F
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPR---EGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 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 = 74.2 bits (182), Expect = 1e-15
 Identities = 12/68 (17%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             + + N+  S ++EDLK +F   G +           K +    +   + ++A +A+  
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALID 177

Query: 89  LNGKKFDD 96
           L+     +
Sbjct: 178 LHNHDLGE 185

>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 =  149 bits (378), Expect = 1e-43
 Identities = 28/146 (19%), Positives = 58/146 (39%), Gaps = 13/146 (8%)

Query: 82  AAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGD 141
                + +  +    RE   G+  ++      +   +E              +Y+KNL  
Sbjct: 3   LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNC-------RIYVKNLAK 55

Query: 142 SIDDEKLKELFSEFGTITS--CKVMRD----PSGISKGSGFVAFSTPEEASRALAEMNGK 195
            + ++ LK +F  +   +S   ++M D      G  KG  F+     + A++AL E NG 
Sbjct: 56  HVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGY 115

Query: 196 MIVSKPLYVAVAQRKEERRARLQAQF 221
           ++  KP+ V  A+    ++   + + 
Sbjct: 116 VLFGKPMVVQFARSARPKQDPKEGKR 141

>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 =  105 bits (264), Expect = 3e-27
 Identities = 28/128 (21%), Positives = 54/128 (42%), Gaps = 11/128 (8%)

Query: 3   INDKQVFVGHFLRKQERETVAIK-----TKFNNVFVKNLDESTTDEDLKKIFGEYGTITS 57
           I+ +++  G   R++       +          ++VKNL +   ++DLK IFG Y   +S
Sbjct: 15  ISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSS 74

Query: 58  AV------VMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSERE 111
                   +    +G+ K   F+   N   AAKA++  NG     +   V  A+    ++
Sbjct: 75  ETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQ 134

Query: 112 QELKGQFE 119
              +G+ +
Sbjct: 135 DPKEGKRK 142

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score =  148 bits (375), Expect = 8e-43
 Identities = 27/126 (21%), Positives = 50/126 (39%)

Query: 95  DDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSE 154
             R      ++ K   ++     F+           G  L + NL   + D  ++ELF+E
Sbjct: 52  GGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAE 111

Query: 155 FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR 214
           FGT+    V  D SG S G+  V F    +A +A+ +  G  +  +P+ + +   + +  
Sbjct: 112 FGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLE 171

Query: 215 ARLQAQ 220
                 
Sbjct: 172 HHHHHH 177

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score =  108 bits (270), Expect = 9e-28
 Identities = 28/106 (26%), Positives = 43/106 (40%)

Query: 12  HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 71
           H L                + V NLD   +D D++++F E+GT+  A V  D  G+S   
Sbjct: 72  HDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGT 131

Query: 72  GFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQ 117
             V+FE   DA KA++   G   D R   +     + + E      
Sbjct: 132 ADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 177

>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 =  145 bits (368), Expect = 1e-41
 Identities = 42/182 (23%), Positives = 90/182 (49%), Gaps = 23/182 (12%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +F+  L+  TT+++L++ FG+YGT+T   +M+D   G+S+ FGF++FE      + V+  
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 90  NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 149
           +    D +     +A  + E+++  K                  +++  +G  +  ++ +
Sbjct: 66  H--ILDGKVIDPKRAIPRDEQDKTGK------------------IFVGGIGPDVRPKEFE 105

Query: 150 ELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 208
           E FS++GTI   ++M D  +G S+G GFV + + +   R   +        + + +  A+
Sbjct: 106 EFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAE 164

Query: 209 RK 210
            +
Sbjct: 165 PR 166

>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 = 89.1 bits (222), Expect = 4e-21
 Identities = 24/106 (22%), Positives = 52/106 (49%), Gaps = 8/106 (7%)

Query: 3   INDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMR 62
           ++ K +     + + E++          +FV  +      ++ ++ F ++GTI  A +M 
Sbjct: 68  LDGKVIDPKRAIPRDEQDKT------GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLML 121

Query: 63  DGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 107
           D D G+S+ FGFV +++AD   +  +      F DR+  + +A+ +
Sbjct: 122 DKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR 166

>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 = 82.2 bits (204), Expect = 1e-18
 Identities = 24/92 (26%), Positives = 50/92 (54%), Gaps = 7/92 (7%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           +   ++I  L     ++ L+E F ++GT+T  K+M+DP +G S+G GF++F  P      
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 189 LAEM---NGKMIVSKPLYVAVAQRKEERRARL 217
           +      +GK+I  K    A+ + ++++  ++
Sbjct: 62  VKTQHILDGKVIDPKR---AIPRDEQDKTGKI 90

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score =  141 bits (357), Expect = 6e-41
 Identities = 32/102 (31%), Positives = 53/102 (51%), Gaps = 2/102 (1%)

Query: 124 ETVDKFQGLNLYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTP 182
            +       +L++ +L   +DD  L E F + + +    KV+ D +G+SKG GFV F+  
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDE 61

Query: 183 EEASRALAEMNGKMIV-SKPLYVAVAQRKEERRARLQAQFSQ 223
            E  RAL E  G + + SKP+ ++VA  K  R   +++  S 
Sbjct: 62  LEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score =  105 bits (265), Expect = 6e-28
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 2/90 (2%)

Query: 30  NVFVKNLDESTTDEDLKKIFGE-YGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           ++FV +L     D  L + F + Y +     V+ D  G SK +GFV F +  +  +A+  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 89  LNGKKF-DDREWYVGKAQKKSEREQELKGQ 117
             G      +   +  A  K+ R + ++  
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPVESG 100

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  141 bits (357), Expect = 6e-41
 Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 1/98 (1%)

Query: 112 QELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGI 170
             L      A  + ++  +G NL+I +L     D  L   F  FG + S KV  D  + +
Sbjct: 21  VALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSL 80

Query: 171 SKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 208
           SK  GFV+F  P+ A  A+  MNG  + +K L V + +
Sbjct: 81  SKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  106 bits (267), Expect = 4e-28
 Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           N+F+ +L +  TD DL   F  +G + SA V  D     SKCFGFV+F+N D A  A++A
Sbjct: 42  NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101

Query: 89  LNGKKFDDREWYVGKAQ 105
           +NG +   +   V   +
Sbjct: 102 MNGFQVGTKRLKVQLKK 118

>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 =  140 bits (356), Expect = 6e-41
 Identities = 28/105 (26%), Positives = 48/105 (45%), Gaps = 5/105 (4%)

Query: 109 EREQELKGQ-----FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKV 163
            R ++L  +     F+           G  L + NL   + D  ++ELF+EFGT+    V
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

Query: 164 MRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 208
             D SG S G+  V F    +A +A+ + NG  +  +P+ + +  
Sbjct: 62  HYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>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 =  111 bits (281), Expect = 5e-30
 Identities = 29/94 (30%), Positives = 42/94 (44%)

Query: 12  HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 71
           H L        A       + V NLD   +D D++++F E+GT+  A V  D  G+S   
Sbjct: 13  HDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGT 72

Query: 72  GFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ 105
             V+FE   DA KA++  NG   D R   +    
Sbjct: 73  ADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score =  142 bits (361), Expect = 2e-40
 Identities = 47/195 (24%), Positives = 87/195 (44%), Gaps = 16/195 (8%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +F+  L   TTDE L+  F ++GT+T  VVMRD +  +S+ FGFV +   ++   A+ A 
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 74

Query: 90  NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 149
              K D R     +A  + + ++            TV K     +++  + +  ++  L+
Sbjct: 75  RPHKVDGRVVEPKRAVSREDSQR-------PGAHLTVKK-----IFVGGIKEDTEEHHLR 122

Query: 150 ELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 208
           + F ++G I   ++M D  SG  +G  FV F   +   + +       +      V  A 
Sbjct: 123 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKAL 181

Query: 209 RKEERRARLQAQFSQ 223
            K+E  +   +Q  +
Sbjct: 182 SKQEMASASSSQRGR 196

>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 = 82.7 bits (205), Expect = 1e-18
 Identities = 27/119 (22%), Positives = 46/119 (38%), Gaps = 2/119 (1%)

Query: 3   INDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMR 62
           ++ + V     + +++ +          +FV  + E T +  L+  F +YG I    +M 
Sbjct: 79  VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMT 138

Query: 63  DGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           D   GK + F FV F++ D   K V        +     V KA  K E       Q  +
Sbjct: 139 DRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMASASSSQRGR 196

>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 =  137 bits (347), Expect = 2e-39
 Identities = 41/118 (34%), Positives = 65/118 (55%), Gaps = 11/118 (9%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
            N+F+KNLD+S  ++ L   F  +G I S  V+ D +  SK +GFV+FE  + A +A+E 
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEK 64

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 146
           +NG   +DR+ +VG+ + + ERE EL  + ++            N+YIKN G      
Sbjct: 65  MNGMLLNDRKVFVGRFKSRKEREAELGARAKEFT----------NVYIKNFGPGSTRA 112

>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 =  128 bits (325), Expect = 2e-36
 Identities = 42/98 (42%), Positives = 62/98 (63%), Gaps = 1/98 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           N++IKNL  SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65

Query: 193 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMG 230
           NG ++  + ++V   + ++ER A L A+  +   V + 
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIK 103

>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 = 54.2 bits (131), Expect = 2e-09
 Identities = 19/45 (42%), Positives = 28/45 (62%), Gaps = 2/45 (4%)

Query: 1   MLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTTDE 43
           ML+ND++VFVG F  ++ERE    A   +F NV++KN    +T  
Sbjct: 68  MLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112

>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 =  140 bits (354), Expect = 2e-39
 Identities = 28/204 (13%), Positives = 59/204 (28%), Gaps = 29/204 (14%)

Query: 29  NNVFVKNLDESTTDED-LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
             + V  LD+S  + D +  +F  YG +     M+           V   +     +A+ 
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAIT 60

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKF------------------ 129
            LN      ++  V  +++ +    +  G  + +                          
Sbjct: 61  HLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ 120

Query: 130 -QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 187
                L+  N    + +E   E+  E G      V           SG + + +  +A  
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180

Query: 188 ALAEMNGKMI----VSKPLYVAVA 207
            L  +N   +       P  + + 
Sbjct: 181 TLGFLNHYQMKNPNGPYPYTLKLC 204

>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 = 80.1 bits (197), Expect = 2e-17
 Identities = 15/119 (12%), Positives = 37/119 (31%), Gaps = 5/119 (4%)

Query: 133 NLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
            L +  L    ++ +++  +F  +G +   K M+       G+  V  +      RA+  
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITH 61

Query: 192 MNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQ 250
           +N   +  + + V V+++      +                        P   +    Q
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ 120

>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 = 79.4 bits (195), Expect = 3e-17
 Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 1/88 (1%)

Query: 12  HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKC 70
            F   ++     I+   N +   N     T+E+  +I  E G      V +  G  +   
Sbjct: 107 RFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSS 166

Query: 71  FGFVNFENADDAAKAVEALNGKKFDDRE 98
            G + +++  DA + +  LN  +  +  
Sbjct: 167 SGLLEWDSKSDALETLGFLNHYQMKNPN 194

>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 =  136 bits (345), Expect = 3e-39
 Identities = 27/96 (28%), Positives = 50/96 (52%)

Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 86
               +F+  L+  T ++ LK +FG++G I+  ++++D   KS+ F F+ FEN  DA  A 
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65

Query: 87  EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAM 122
           + +NGK    +   V +A+K S +    +     + 
Sbjct: 66  KDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSR 101

>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 =  125 bits (315), Expect = 7e-35
 Identities = 26/112 (23%), Positives = 51/112 (45%)

Query: 126 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 185
           V+      L+I  L    +++ LK +F + G I+   +++D +  S+G  F+ F  P +A
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61

Query: 186 SRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRM 237
             A  +MNGK +  K + V  A++   +    +   +  R  +   S+    
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHHH 113

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score =  135 bits (343), Expect = 6e-39
 Identities = 23/114 (20%), Positives = 47/114 (41%), Gaps = 7/114 (6%)

Query: 101 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS 160
           +G +         L  +          +     L+++     + + +L E+F  FG +  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60

Query: 161 CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR 214
            K++        G  FV F   E A++A+ E++GK   ++PL V  ++   +R 
Sbjct: 61  VKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score =  116 bits (292), Expect = 1e-31
 Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 7/96 (7%)

Query: 17  QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNF 76
                   +     +FV+       + +L +IFG +G +    ++         F FV F
Sbjct: 20  HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEF 72

Query: 77  ENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 112
           E A+ AAKA+E ++GK F ++   V  ++  ++R +
Sbjct: 73  EEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108

>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 =  137 bits (346), Expect = 6e-38
 Identities = 36/201 (17%), Positives = 76/201 (37%), Gaps = 26/201 (12%)

Query: 29  NNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
           + + V NL+ E  T + L  +FG YG +    ++       K    V   + + A  A+ 
Sbjct: 35  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF----NKKENALVQMADGNQAQLAMS 90

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQ----------------- 130
            LNG K   +   +  ++ ++ +      + +   K+  +                    
Sbjct: 91  HLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 150

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
              L++ N+  S+ +E LK LFS  G +             +    +   + EEA +AL 
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---DRKMALIQMGSVEEAVQALI 207

Query: 191 EMNGKMIV-SKPLYVAVAQRK 210
           +++   +  +  L V+ ++  
Sbjct: 208 DLHNHDLGENHHLRVSFSKST 228

>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 = 79.3 bits (195), Expect = 4e-17
 Identities = 22/107 (20%), Positives = 46/107 (42%), Gaps = 6/107 (5%)

Query: 133 NLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
            L + NL  + +  + L  LF  +G +   K++ +     K +  V  +   +A  A++ 
Sbjct: 36  VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSH 91

Query: 192 MNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMP 238
           +NG  +  KP+ + +++ +  +  R + Q  Q      G S   R  
Sbjct: 92  LNGHKLHGKPIRITLSKHQNVQLPR-EGQEDQGLTKDYGNSPLHRFK 137

>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 = 72.3 bits (177), Expect = 1e-14
 Identities = 14/94 (14%), Positives = 34/94 (36%), Gaps = 7/94 (7%)

Query: 7   QVFVGHFLRKQERETVAIKTKF----NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMR 62
           + +    L + ++               + + N+  S ++EDLK +F   G +       
Sbjct: 126 KDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF 185

Query: 63  DGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD 96
             D K      +   + ++A +A+  L+     +
Sbjct: 186 QKDRK---MALIQMGSVEEAVQALIDLHNHDLGE 216

>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 =  128 bits (325), Expect = 2e-36
 Identities = 29/88 (32%), Positives = 48/88 (54%), Gaps = 4/88 (4%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG----ISKGSGFVAFSTPEEASRA 188
            L+IKNL  S  +E LK +FS+ G I SC + +  +     +S G GFV +  PE+A +A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRAR 216
           L ++ G  +    L V +++R  +  + 
Sbjct: 67  LKQLQGHTVDGHKLEVRISERATKPASG 94

>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 =  117 bits (296), Expect = 2e-32
 Identities = 26/90 (28%), Positives = 48/90 (53%), Gaps = 4/90 (4%)

Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK----SKCFGFVNFENADD 81
           +  + +F+KNL+ STT+E LK +F + G I S  + +  +      S  FGFV ++  + 
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 82  AAKAVEALNGKKFDDREWYVGKAQKKSERE 111
           A KA++ L G   D  +  V  +++ ++  
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISERATKPA 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 =  127 bits (321), Expect = 7e-36
 Identities = 29/93 (31%), Positives = 41/93 (44%), Gaps = 3/93 (3%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
              +   L++  L     +E +  LF  FG I  C V+R P G SKG  FV FS+  EA 
Sbjct: 11  RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQ 70

Query: 187 RALAEMNGKMIV---SKPLYVAVAQRKEERRAR 216
            A+  ++G   +   S  L V  A   +E    
Sbjct: 71  AAIHALHGSQTMPGASSSLVVKFADTDKESGPS 103

>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 =  106 bits (267), Expect = 4e-28
 Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 3/89 (3%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
             +   +FV  L++  ++ED+ ++F  +G I    V+R  DG SK   FV F +  +A  
Sbjct: 12  GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQA 71

Query: 85  AVEALNGKKFDD---REWYVGKAQKKSER 110
           A+ AL+G +          V  A    E 
Sbjct: 72  AIHALHGSQTMPGASSSLVVKFADTDKES 100

>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 =  126 bits (318), Expect = 2e-35
 Identities = 27/97 (27%), Positives = 50/97 (51%), Gaps = 7/97 (7%)

Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
            K   +FV+NL  + T+E L+K F ++G +     ++D       + F++F+  D A KA
Sbjct: 9   AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKA 61

Query: 86  VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAM 122
           +E +NGK  +     +  A+   ++ +E K Q + A 
Sbjct: 62  MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAAS 98

>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 =  120 bits (303), Expect = 3e-33
 Identities = 28/100 (28%), Positives = 54/100 (54%), Gaps = 11/100 (11%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L+++NL +++ +E L++ FS+FG +   K ++D         F+ F   + A +A+ EM
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEM 65

Query: 193 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPS 232
           NGK +  + + +  A+  +++R   +AQ       A GPS
Sbjct: 66  NGKDLEGENIEIVFAKPPDQKRKERKAQRQA----ASGPS 101

>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 =  125 bits (317), Expect = 3e-35
 Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 2/88 (2%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           K   N VFV  +D    + +++  F  YG++    ++ D  G SK +GFV+F N  D  K
Sbjct: 6   KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQ 112
            VE  +   F  ++  +G A +K     
Sbjct: 66  IVE--SQINFHGKKLKLGPAIRKQNLST 91

>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 =  110 bits (277), Expect = 1e-29
 Identities = 21/95 (22%), Positives = 46/95 (48%), Gaps = 6/95 (6%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            +++  +   +D+ +++  F+ +G++   K++ D +G+SKG GFV+F    +  + +   
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV--E 68

Query: 193 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPV 227
           +      K L +  A RK+           Q RP+
Sbjct: 69  SQINFHGKKLKLGPAIRKQNL----STYHVQPRPL 99

>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 =  127 bits (319), Expect = 1e-33
 Identities = 38/205 (18%), Positives = 62/205 (30%), Gaps = 7/205 (3%)

Query: 133 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 188
            +YI NL + I  ++LK+    +FS+FG I    V R      +G  FV F     A+ A
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATNA 68

Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGP-SVPPRMPMYPPGPSGL 247
           L  M G     KP+ +  A+   +  A+++  F +               P       G 
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 248 GQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGA 307
           G   + G     +          + +           P   +P          PG     
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188

Query: 308 GPVQQTQQPLPIMPHQMPPRGHAYR 332
             +     P   +    P       
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLT 213

>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 = 94.9 bits (235), Expect = 4e-22
 Identities = 26/104 (25%), Positives = 51/104 (49%), Gaps = 6/104 (5%)

Query: 29  NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           + +++ NL+E    ++LKK    IF ++G I   +V R    K +   FV F+    A  
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL--KMRGQAFVIFKEVSSATN 67

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDK 128
           A+ ++ G  F D+   +  A+  S+   ++KG F +  ++   +
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKR 111

>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 = 86.5 bits (213), Expect = 4e-19
 Identities = 26/212 (12%), Positives = 61/212 (28%), Gaps = 7/212 (3%)

Query: 1   MLINDKQVFVGHFLRKQER--ETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA 58
               DK + + +     +   +      + +    K   +S      KK     G     
Sbjct: 75  FPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVV 134

Query: 59  VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
             ++                     +                 G+    +   Q+L    
Sbjct: 135 GAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQ 194

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA 178
               +   +      L++ NL +  ++  L  LF++F      +++     I     FV 
Sbjct: 195 MPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDI----AFVE 250

Query: 179 FSTPEEASRALAEMNG-KMIVSKPLYVAVAQR 209
           F    +A  A   + G K+  +  + ++ A++
Sbjct: 251 FDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  121 bits (305), Expect = 1e-33
 Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 1/97 (1%)

Query: 11  GHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC 70
              + +        K++   + V N+     D DL+++FG++G I    ++ +  G SK 
Sbjct: 12  SGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKG 70

Query: 71  FGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK 107
           FGFV FEN+ DA +A E L+G   + R+  V  A  +
Sbjct: 71  FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  117 bits (295), Expect = 4e-32
 Identities = 27/110 (24%), Positives = 51/110 (46%), Gaps = 3/110 (2%)

Query: 101 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS 160
           +G +         L  +      E  +K Q   L++ N+     D  L+++F +FG I  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMNTE--NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD 58

Query: 161 CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK 210
            +++ +  G SKG GFV F    +A RA  +++G ++  + + V  A  +
Sbjct: 59  VEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>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 =  119 bits (299), Expect = 1e-32
 Identities = 26/105 (24%), Positives = 52/105 (49%), Gaps = 5/105 (4%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
            ++++NL    T E++  IFG+YG I    V      +++   +V +E+  DA  AV+ L
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNAVDHL 67

Query: 90  NGKKFDDREWYVGKAQ-KKSEREQELKGQFEQAMKETVDKFQGLN 133
           +G    +R   V      ++ ++ + K + EQ   + + +  G+N
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQ--LKLLKEKYGIN 110

>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 = 93.2 bits (232), Expect = 4e-23
 Identities = 20/94 (21%), Positives = 47/94 (50%), Gaps = 3/94 (3%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            LYI+NL   I  E++ ++F ++G I   +V   P   ++G+ +V +    +A  A+  +
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHL 67

Query: 193 NGKMIVSKPLYVAVAQ-RKEERRARLQAQFSQMR 225
           +G  + ++ L V      +  ++   + +  Q++
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLK 101

>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 =  117 bits (295), Expect = 3e-32
 Identities = 26/83 (31%), Positives = 42/83 (50%)

Query: 23  AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDA 82
           A +     VFV NL+    +E L ++F + G +T   + +D +GK K FGFV F++ +  
Sbjct: 11  AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESV 70

Query: 83  AKAVEALNGKKFDDREWYVGKAQ 105
           + A+  LNG +   R   V    
Sbjct: 71  SYAIALLNGIRLYGRPINVSGPS 93

>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 =  116 bits (294), Expect = 4e-32
 Identities = 25/82 (30%), Positives = 41/82 (50%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
            +     +++ NL   + +E L ELF + G +T   + +D  G  K  GFV F  PE  S
Sbjct: 12  QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVS 71

Query: 187 RALAEMNGKMIVSKPLYVAVAQ 208
            A+A +NG  +  +P+ V+   
Sbjct: 72  YAIALLNGIRLYGRPINVSGPS 93

>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.144.1.1 Length = 92

 Score =  116 bits (291), Expect = 9e-32
 Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 2/90 (2%)

Query: 372 PMPITALSTALANASPEQQRTLLGESLYPLVEQLERD--AAAKVTGMLLEMDQTEVLHLL 429
           P+     +        ++QR  LGE LY  V     +  AA K+TGM+L++   EV  LL
Sbjct: 2   PLGSPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLL 61

Query: 430 ESPEALKAKVAEAMEVLRSVAQQQANNPAD 459
           ES E  +    EA     S  ++Q      
Sbjct: 62  ESDELFEQHYKEASAAYESFKKEQEQQTEQ 91

>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 =  115 bits (290), Expect = 1e-31
 Identities = 30/88 (34%), Positives = 53/88 (60%), Gaps = 2/88 (2%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDP-SGISKGSGFVAFSTPEEASRALA 190
            ++I NL   ID++ L + FS FG I    K+MRDP +G SKG  F+ F++ + +  A+ 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 191 EMNGKMIVSKPLYVAVAQRKEERRARLQ 218
            MNG+ + ++P+ V+ A +K+ + +   
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>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 =  106 bits (266), Expect = 4e-28
 Identities = 29/84 (34%), Positives = 44/84 (52%), Gaps = 2/84 (2%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
            +F+ NLD    ++ L   F  +G I     +MRD D G SK + F+NF + D +  A+E
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 88  ALNGKKFDDREWYVGKAQKKSERE 111
           A+NG+   +R   V  A KK  + 
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKG 90

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  114 bits (287), Expect = 5e-31
 Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
               ++++NL      + LK+ F+E G +    +  + +G SKG G V F +PE A RA 
Sbjct: 7   GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERAC 65

Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRA 215
             MNG  +  + + V + +      +
Sbjct: 66  RMMNGMKLSGREIDVRIDRNASGPSS 91

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  111 bits (281), Expect = 3e-30
 Identities = 28/87 (32%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
            +    +FV+NL    T + LK  F E G +  A +  + +GKSK  G V FE+ + A +
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAER 63

Query: 85  AVEALNGKKFDDREWYVGKAQKKSERE 111
           A   +NG K   RE  V   +  S   
Sbjct: 64  ACRMMNGMKLSGREIDVRIDRNASGPS 90

>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 =  110 bits (278), Expect = 9e-30
 Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           N+F+ NL+ + +  +LK    E        V+    G ++ FG+V+FE+A+D  KA+E L
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 77

Query: 90  NGKKFDDREWYVGKAQKKSERE 111
            G K    E  + K + +    
Sbjct: 78  TGLKVFGNEIKLEKPKGRDGTR 99

>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 =  106 bits (266), Expect = 5e-28
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           NL+I NL  +    +LK   SE        V+   +G ++  G+V F + E+  +AL E+
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-EL 77

Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
            G  +    + +   + ++  R 
Sbjct: 78  TGLKVFGNEIKLEKPKGRDGTRG 100

>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 =  110 bits (278), Expect = 9e-30
 Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 6/90 (6%)

Query: 133 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 188
            +YI NL + I  ++LK+    +FS FG I    V R      +G  FV F     A+ A
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNA 67

Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRARLQ 218
           L  M G     KP+ +  A+   +  A+++
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97

>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 = 99.6 bits (249), Expect = 1e-25
 Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 6/91 (6%)

Query: 29  NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           + +++ NL+E    ++LKK    IF  +G I   +V R    K +   FV F+    A  
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATN 66

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELK 115
           A+ ++ G  F D+   +  A+  S+   ++K
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97

>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 =  109 bits (276), Expect = 1e-29
 Identities = 28/80 (35%), Positives = 49/80 (61%), Gaps = 1/80 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL++ +L  ++DDE L+  F +F +  S  VM D  +G S+G GFV+F++ ++A  A+  
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 192 MNGKMIVSKPLYVAVAQRKE 211
           M G+ +  +PL +  A + E
Sbjct: 63  MQGQDLNGRPLRINWAAKLE 82

>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 =  109 bits (274), Expect = 3e-29
 Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 1/80 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
            N+FV +L+ +  DE L+  F ++ +  S  VM D   G S+ +GFV+F + DDA  A++
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 88  ALNGKKFDDREWYVGKAQKK 107
           ++ G+  + R   +  A K 
Sbjct: 62  SMQGQDLNGRPLRINWAAKL 81

>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 =  108 bits (273), Expect = 5e-29
 Identities = 29/87 (33%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           K+    + V N+     D DL+++FG++G I    ++ +  G SK FGFV FEN+ DA +
Sbjct: 12  KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADR 70

Query: 85  AVEALNGKKFDDREWYVGKAQKKSERE 111
           A E L+G   + R+  V  A  +    
Sbjct: 71  AREKLHGTVVEGRKIEVNNATARVMTN 97

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 97.4 bits (243), Expect = 7e-25
 Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
            K     L++ N+     D  L+++F +FG I   +++ +  G SKG GFV F    +A 
Sbjct: 11  SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADAD 69

Query: 187 RALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
           RA  +++G ++  + + V  A  +    + 
Sbjct: 70  RAREKLHGTVVEGRKIEVNNATARVMTNSG 99

>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum} Length = 85

 Score =  106 bits (266), Expect = 3e-28
 Identities = 63/82 (76%), Positives = 70/82 (85%)

Query: 371 QPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLE 430
              PI AL++ALAN+ PE QR +LGE+LYPLV+QLE D AAKVTGMLLEMDQTEVLHLLE
Sbjct: 3   LGSPIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLE 62

Query: 431 SPEALKAKVAEAMEVLRSVAQQ 452
           SP+ALKAKVAEAMEVLRS  Q 
Sbjct: 63  SPDALKAKVAEAMEVLRSAQQH 84

>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 =  106 bits (267), Expect = 4e-28
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             +++KNL    T+ DL  +F  +       +      G+ +   F+ F N + A +A+ 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQ 112
            +NG K   +   +   + K +R  
Sbjct: 86  LVNGYKLYGKILVIEFGKNKKQRSS 110

>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 =  106 bits (266), Expect = 8e-28
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            LY+KNL   + +  L  LF+ F       +     +G  +G  F+ F   E A +AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 192 MNGKMIVSKPLYVAVAQRKEERRA 215
           +NG  +  K L +   + K++R +
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRSS 110

>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 =  105 bits (265), Expect = 5e-28
 Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENADDAAK 84
           K   V +  L  + T + + +IF  YG I    +  +      SK + +V FEN D+A K
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 85  AVEALNGKKFDDREWYVGKAQKKSER 110
           A++ ++G + D +E           R
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWPR 88

>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 = 89.9 bits (224), Expect = 2e-22
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALA 190
            ++I  L  ++  + + E+FS +G I    +  +     +SKG  +V F  P+EA +AL 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 191 EMNGKMIVSKPLYVAVAQRKEER 213
            M+G  I  + +          R
Sbjct: 66  HMDGGQIDGQEITATAVLAPWPR 88

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1 Length = 85

 Score =  104 bits (262), Expect = 9e-28
 Identities = 41/82 (50%), Positives = 54/82 (65%), Gaps = 2/82 (2%)

Query: 367 ASVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVL 426
           +S+       +  T LAN +PEQQ+ +LGE LY  +  +   AAAKVTGMLLEMD  E+L
Sbjct: 2   SSLASQGQNLS--TVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEIL 59

Query: 427 HLLESPEALKAKVAEAMEVLRS 448
           +LL++P  L AKV EA+EVL  
Sbjct: 60  NLLDTPGLLDAKVQEALEVLNR 81

>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 =  104 bits (261), Expect = 1e-27
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
            ++++ L   TTD+DL K+   YG I S   + D    K K +GFV+F++   A KAV A
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 89  LNGKKFDDREWYVGKAQ 105
           L       +        
Sbjct: 67  LKASGVQAQMAKQSGPS 83

>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 = 97.6 bits (244), Expect = 3e-25
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            LYI+ L     D+ L +L   +G I S K + D  +   KG GFV F +P  A +A+  
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 192 MNGKMIVSKPLYVA 205
           +    + ++    +
Sbjct: 67  LKASGVQAQMAKQS 80

>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 =  103 bits (259), Expect = 4e-27
 Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 5/89 (5%)

Query: 24  IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 83
             +    ++V+NL  ST++E ++K F          V      K + + FV+F N +DA 
Sbjct: 11  TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAV 65

Query: 84  KAVEALNGKKFDDREWYVGKAQKKSEREQ 112
           +A++ALNGK  D     V  A+   +   
Sbjct: 66  EAMKALNGKVLDGSPIEVTLAKPVDKDSS 94

>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 = 99.3 bits (248), Expect = 1e-25
 Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            LY++NL  S  +E +++ F+        +V +      +   FV FS  E+A  A+  +
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKAL 71

Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
           NGK++   P+ V +A+  ++  +
Sbjct: 72  NGKVLDGSPIEVTLAKPVDKDSS 94

>3kuj_A Polyadenylate-binding protein 1; protein-protein complex, methylation, mRNA processing, mRNA nucleus, phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A Length = 88

 Score =  103 bits (257), Expect = 4e-27
 Identities = 38/87 (43%), Positives = 63/87 (72%)

Query: 372 PMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLES 431
           P+     ++ LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LES
Sbjct: 2   PLGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLES 61

Query: 432 PEALKAKVAEAMEVLRSVAQQQANNPA 458
           PE+L++KV EA+ VL++   ++A   A
Sbjct: 62  PESLRSKVDEAVAVLQAHQAKEAAQKA 88

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score =  103 bits (258), Expect = 7e-27
 Identities = 14/108 (12%), Positives = 43/108 (39%), Gaps = 8/108 (7%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            +    L D++ +  LK++  ++G +   +++  P +    G   V F++   A   +  
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 192 MNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPM 239
           ++   ++   ++  +  + ++R    +        +  G   P  +P 
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRMKYYEL-------IVNGSYTPQTVPT 108

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 94.4 bits (235), Expect = 1e-23
 Identities = 14/88 (15%), Positives = 31/88 (35%), Gaps = 1/88 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             V    L+++  +  LK +  +YG +    ++      K      V F +   A + V+
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELK 115
            L+         +     K  +R +  +
Sbjct: 67  NLHLTSVMGNIIHAQLDIKGQQRMKYYE 94

>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 =  101 bits (254), Expect = 2e-26
 Identities = 25/83 (30%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             + V NL E T + DL+++F  +G+I+   + +D   G+SK F F++F   +DAA+A+ 
Sbjct: 16  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75

Query: 88  ALNGKKFDDREWYVGKAQKKSER 110
            ++G  +D     V  A+  +  
Sbjct: 76  GVSGFGYDHLILNVEWAKPSTNS 98

>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 = 90.7 bits (226), Expect = 2e-22
 Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 1/85 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            + + NL +   +  L+ELF  FG+I+   + +D  +G SKG  F++F   E+A+RA+A 
Sbjct: 17  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76

Query: 192 MNGKMIVSKPLYVAVAQRKEERRAR 216
           ++G       L V  A+        
Sbjct: 77  VSGFGYDHLILNVEWAKPSTNSGPS 101

>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 =  101 bits (254), Expect = 3e-26
 Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 8/108 (7%)

Query: 10  VGHFLRKQERETVAIKTKFN-------NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMR 62
           +GH          A+             ++V +L  + T++ L+ IF  +G I S  +M 
Sbjct: 1   MGHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMM 60

Query: 63  DGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSE 109
           D + G+SK +GF+ F +++ A KA+E LNG +   R   VG   ++++
Sbjct: 61  DSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 = 88.5 bits (220), Expect = 1e-21
 Identities = 30/113 (26%), Positives = 51/113 (45%), Gaps = 6/113 (5%)

Query: 101 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS 160
           +G                 Q           + LY+ +L  +I ++ L+ +F  FG I S
Sbjct: 1   MGHHHHHHSHMAAAMANNLQKGSAG-----PMRLYVGSLHFNITEDMLRGIFEPFGRIES 55

Query: 161 CKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEE 212
            ++M D  +G SKG GF+ FS  E A +AL ++NG  +  +P+ V     + +
Sbjct: 56  IQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 =  101 bits (253), Expect = 4e-26
 Identities = 29/113 (25%), Positives = 53/113 (46%), Gaps = 5/113 (4%)

Query: 121 AMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 179
           +  +  D     ++++ +L   I  E +K  F+ FG I+  +V++D  +G SKG GFV+F
Sbjct: 5   SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64

Query: 180 STPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPS 232
               +A  A+ +M G+ +  + +    A RK           ++      GPS
Sbjct: 65  FNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTK----QSGPS 113

>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 = 99.3 bits (248), Expect = 2e-25
 Identities = 30/84 (35%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           +VFV +L    T ED+K  F  +G I+ A V++D   GKSK +GFV+F N  DA  A++ 
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 89  LNGKKFDDREWYVGKAQKKSEREQ 112
           + G+    R+     A +K    +
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPK 100

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score =  100 bits (251), Expect = 5e-26
 Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 1/99 (1%)

Query: 19  RETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFEN 78
           R  +    K  +V++K      T +D+K+   + G + +  + R      K   FV F++
Sbjct: 2   RWILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDS 61

Query: 79  ADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQ 117
            + A K VE   G+K+ + +  +        ++ E + Q
Sbjct: 62  IESAKKFVE-TPGQKYKETDLLILFKDDYFAKKNEERKQ 99

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 96.3 bits (240), Expect = 2e-24
 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 6/95 (6%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
           +  +  ++YIK        + +KE   + G + + ++ R      KGS FV F + E A 
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66

Query: 187 RALAEMNGKMIVSKPLYVA-----VAQRKEERRAR 216
           + + E  G+      L +       A++ EER+  
Sbjct: 67  KFV-ETPGQKYKETDLLILFKDDYFAKKNEERKQN 100

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 99.6 bits (249), Expect = 7e-26
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           ++++ +L   I    +   F+ FG I+  +V++D  +G SKG GFV+F    +A  A+ +
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 192 MNGKMIVSKPLYVAVAQRK 210
           M G+ +  + +    A RK
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>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 = 96.9 bits (242), Expect = 8e-25
 Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           +VFV +L    T   +   F  +G I+ A V++D   GKSK +GFV+F N  DA  A++ 
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 89  LNGKKFDDREWYVGKAQKK 107
           + G+    R+     A +K
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>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 = 99.6 bits (249), Expect = 1e-25
 Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 1/85 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             ++V  L E   D+ L   F  +G IT   +  D +  K + F FV FE A+DAA A++
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQ 112
            +N  +   R   V  A+    +E 
Sbjct: 73  NMNESELFGRTIRVNLAKPMRIKES 97

>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 = 91.1 bits (227), Expect = 1e-22
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            LY+  L + +DD+ L   F  FG IT  ++  D  +   +G  FV F   E+A+ A+  
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73

Query: 192 MNGKMIVSKPLYVAVAQRKEERRAR 216
           MN   +  + + V +A+    + + 
Sbjct: 74  MNESELFGRTIRVNLAKPMRIKESG 98

>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 = 99.2 bits (248), Expect = 2e-25
 Identities = 34/83 (40%), Positives = 52/83 (62%), Gaps = 1/83 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             +FV  L   T ++ L+++F +YG I+  VV++D +  +S+ FGFV FEN DDA  A+ 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 88  ALNGKKFDDREWYVGKAQKKSER 110
           A+NGK  D R+  V +A K S+ 
Sbjct: 73  AMNGKSVDGRQIRVDQAGKSSDN 95

>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 = 90.8 bits (226), Expect = 2e-22
 Identities = 24/85 (28%), Positives = 48/85 (56%), Gaps = 1/85 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            L++  L    +++ L+++FS++G I+   V++D  +  S+G GFV F   ++A  A+  
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73

Query: 192 MNGKMIVSKPLYVAVAQRKEERRAR 216
           MNGK +  + + V  A +  + R+ 
Sbjct: 74  MNGKSVDGRQIRVDQAGKSSDNRSG 98

>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 = 98.8 bits (247), Expect = 2e-25
 Identities = 27/83 (32%), Positives = 51/83 (61%), Gaps = 1/83 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
           + ++V +L  + T++ L+ IF  +G I + V+M+D D G+SK +GF+ F +++ A +A+E
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 88  ALNGKKFDDREWYVGKAQKKSER 110
            LNG +   R   VG   ++ + 
Sbjct: 66  QLNGFELAGRPMRVGHVTERLDG 88

>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 = 87.6 bits (218), Expect = 2e-21
 Identities = 28/85 (32%), Positives = 48/85 (56%), Gaps = 1/85 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            LY+ +L  +I ++ L+ +F  FG I +  +M+D  +G SKG GF+ FS  E A RAL +
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 192 MNGKMIVSKPLYVAVAQRKEERRAR 216
           +NG  +  +P+ V     + +  + 
Sbjct: 67  LNGFELAGRPMRVGHVTERLDGGSG 91

>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 = 98.9 bits (247), Expect = 2e-25
 Identities = 23/92 (25%), Positives = 39/92 (42%), Gaps = 7/92 (7%)

Query: 124 ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPE 183
           E     +G  LY+      +    L+  FS FG I    +        +   FV +   E
Sbjct: 8   ERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKME 60

Query: 184 EASRALAEMNGKMIVSKPLYVAVAQRKEERRA 215
            A +A+AE+NG  + S  L V +A+++    +
Sbjct: 61  SADQAVAELNGTQVESVQLKVNIARKQPMLDS 92

>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 = 86.2 bits (214), Expect = 7e-21
 Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           N ++V   D   T   L+  F  +G I    +        +   FV +E  + A +AV  
Sbjct: 16  NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAE 68

Query: 89  LNGKKFDDREWYVGKAQKKSEREQ 112
           LNG + +  +  V  A+K+   + 
Sbjct: 69  LNGTQVESVQLKVNIARKQPMLDS 92

>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 = 98.5 bits (246), Expect = 3e-25
 Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 5/88 (5%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
            T+ + +FV NL    T+E+++K+F +YG      + +D     K FGF+  E    A  
Sbjct: 12  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEI 66

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQ 112
           A   L+      ++  V  A   +    
Sbjct: 67  AKVELDNMPLRGKQLRVRFACHSASLTS 94

>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 = 91.9 bits (229), Expect = 6e-23
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 5/84 (5%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L++ NL   I +E++++LF ++G      + +D     KG GF+   T   A  A  E+
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 71

Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
           +   +  K L V  A       + 
Sbjct: 72  DNMPLRGKQLRVRFACHSASLTSG 95

>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo sapiens} SCOP: a.144.1.1 PDB: 3ntw_A Length = 61

 Score = 96.3 bits (240), Expect = 6e-25
 Identities = 27/59 (45%), Positives = 42/59 (71%)

Query: 390 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRS 448
            R  LGE LYP V+ ++   A+K+TGMLLE+   ++L LL S ++L+A+V EAME++ +
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIA 59

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 97.7 bits (244), Expect = 6e-25
 Identities = 20/82 (24%), Positives = 39/82 (47%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           + +F+  L  S T E+L++I   +GT+    ++ +  GK K   +V +EN   A++AV  
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77

Query: 89  LNGKKFDDREWYVGKAQKKSER 110
           ++G    +    V  +      
Sbjct: 78  MDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 86.9 bits (216), Expect = 3e-21
 Identities = 21/81 (25%), Positives = 41/81 (50%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L+I  L  S   E+L+E+    GT+   +++ + +G  KG  +V +    +AS+A+ +M
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78

Query: 193 NGKMIVSKPLYVAVAQRKEER 213
           +G  I    + VA++      
Sbjct: 79  DGMTIKENIIKVAISNSGPSS 99

>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 = 98.7 bits (246), Expect = 8e-25
 Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
            N+ V  +  +  +  L+++F  YG I S  ++ D +  +S+ +GFV F++   A +A+ 
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 88  ALNGKKFDDREWYVGKAQKKSER 110
            LNG    ++   V  A    +R
Sbjct: 103 GLNGFNILNKRLKVALAASGHQR 125

>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 = 92.9 bits (231), Expect = 8e-23
 Identities = 29/85 (34%), Positives = 50/85 (58%), Gaps = 1/85 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  +  ++D+ +L++LF  +G I S K++ D  +  S+G GFV F +   A +A+A 
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 192 MNGKMIVSKPLYVAVAQRKEERRAR 216
           +NG  I++K L VA+A    +R   
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGI 128

>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 = 96.9 bits (242), Expect = 1e-24
 Identities = 28/79 (35%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 28  FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 86
              + V  L   TT+ DL+++F +YG I    ++ D    +S+ F FV FEN DDA +A 
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74

Query: 87  EALNGKKFDDREWYVGKAQ 105
           E  NG + D R   V    
Sbjct: 75  ERANGMELDGRRIRVSGPS 93

>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 = 85.3 bits (212), Expect = 1e-20
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            L +  L     +  L+E+FS++G I    ++ D  S  S+G  FV F   ++A  A   
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 192 MNGKMIVSKPLYVAVAQR 209
            NG  +  + + V+    
Sbjct: 77  ANGMELDGRRIRVSGPSS 94

>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 = 96.1 bits (240), Expect = 1e-24
 Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
           + V+V NL  S T+ DL +IF +YG +    +M+D D  KSK   F+ F + D A     
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 88  ALNGKKFDDREWYVGKA 104
           A+N K+   R      A
Sbjct: 77  AINNKQLFGRVIKASIA 93

>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 = 80.3 bits (199), Expect = 7e-19
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            +Y+ NL  S+ +  L  +FS++G +    +M+D  +  SKG  F+ F   + A      
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77

Query: 192 MNGKMIVSKPLYVAVA 207
           +N K +  + +  ++A
Sbjct: 78  INNKQLFGRVIKASIA 93

>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 = 98.4 bits (245), Expect = 2e-24
 Identities = 24/119 (20%), Positives = 47/119 (39%), Gaps = 6/119 (5%)

Query: 1   MLINDKQVFVGHFLRKQERETVAIKTK-----FNNVFVKNLDESTTDEDLKKIFGEYGTI 55
              N ++    +   + E +               +FV ++ E   ++++++ F +YG I
Sbjct: 40  SDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEI 99

Query: 56  TSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQE 113
            +  +  D   G SK +  V +E    A  A EALNG +   +   V     K  +  +
Sbjct: 100 KNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVK 158

>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 = 93.4 bits (232), Expect = 1e-22
 Identities = 29/147 (19%), Positives = 63/147 (42%), Gaps = 5/147 (3%)

Query: 75  NFENADDAAKAVEALN--GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDK--FQ 130
            FE  +D  + +  L    K    R +      +++    E     +    E   +   +
Sbjct: 12  EFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVE 71

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           G  L++ ++ +   +++++E F ++G I +  +  D  +G SKG   V + T ++A  A 
Sbjct: 72  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131

Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRAR 216
             +NG  I+ + + V     K  +R +
Sbjct: 132 EALNGAEIMGQTIQVDWCFVKGPKRVK 158

>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 = 95.7 bits (239), Expect = 3e-24
 Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +FV+NL  ++++EDL+K+F  YG ++      D    K K F FV F   + A KA   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 90  NGKKFDDREWYVGKAQKKSEREQ 112
           +G+ F  R  +V  +  K E  Q
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 26/84 (30%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L+++NL  +  +E L++LFS +G ++      D  +   KG  FV F  PE A +A AE+
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
           +G++   + L+V  +  K+E    
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEASQS 94

>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 = 99.0 bits (246), Expect = 6e-24
 Identities = 36/217 (16%), Positives = 64/217 (29%), Gaps = 12/217 (5%)

Query: 71  FGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQ 130
           +G  +  +  D   +  A NG   +DR+              +  G+            +
Sbjct: 12  YGGHDQIDLYDDVISPSANNGDAPEDRD----YMDTLPPTVGDDVGKGAAPNVVYTYTGK 67

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGT--ITSCKVMRDP-SGISKGSGFVAFSTPEEASR 187
            + LYI NL     DE L E     G   I   K   +  +G SKG   V   +   + +
Sbjct: 68  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 127

Query: 188 ALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF-----SQMRPVAMGPSVPPRMPMYPP 242
            +  +  + +  +   V    ++   +  +Q++              GP        +P 
Sbjct: 128 LMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQ 187

Query: 243 GPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRP 279
           G  G G+             P    G       G   
Sbjct: 188 GGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTH 224

>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 = 85.9 bits (212), Expect = 2e-19
 Identities = 21/101 (20%), Positives = 40/101 (39%), Gaps = 3/101 (2%)

Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGT--ITSAVVMRDGD-GKSKCFGFVNFENADDAA 83
           K   +++ NL   TTDEDL +     G   I       +   G+SK F  V   +   + 
Sbjct: 67  KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSK 126

Query: 84  KAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKE 124
           K ++ L  ++   +   V    K+   + E++ +      +
Sbjct: 127 KLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQ 167

>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 = 94.2 bits (235), Expect = 8e-24
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
            V++ ++    T+E +  +    G + +  +M D   G+SK + F+ F + + +A AV  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 89  LNGKKFDDREWYVGKAQKKSEREQE 113
           LNG +   R    G +         
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVS 88

>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 = 80.7 bits (200), Expect = 6e-19
 Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 1/87 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            +Y+ ++     +E++ +L S  G + + K+M DP +G SKG  F+ F   E ++ A+  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 192 MNGKMIVSKPLYVAVAQRKEERRARLQ 218
           +NG  + S+ L    +   +     L+
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLE 90

>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 = 93.4 bits (233), Expect = 2e-23
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
            + V NL   T+ + L+++F +YG +    + R+      + F FV F +  DA  A  A
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 89  LNGKKFDDREWYVGKAQKKSER 110
           ++G + D RE  V  A+     
Sbjct: 75  MDGAELDGRELRVQVARYGRRD 96

>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 = 85.0 bits (211), Expect = 2e-20
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            L + NL      + L+ +F ++G +    + R+P +   +G  FV F    +A  A A 
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 192 MNGKMIVSKPLYVAVAQRKEERRAR 216
           M+G  +  + L V VA+      + 
Sbjct: 75  MDGAELDGRELRVQVARYGRRDLSG 99

>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 = 93.0 bits (232), Expect = 2e-23
 Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             ++V  L E   D+ L   F  +G IT   +  D +  K + F FV FE A+DAA A++
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 88  ALNGKKFDDREWYVGKAQ 105
            +N  +   R   V  A+
Sbjct: 68  NMNESELFGRTIRVNLAK 85

>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 = 83.3 bits (207), Expect = 5e-20
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            LY+  L + +DD+ L   F  FG IT  ++  D  +   +G  FV F   E+A+ A+  
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 192 MNGKMIVSKPLYVAVAQ 208
           MN   +  + + V +A+
Sbjct: 69  MNESELFGRTIRVNLAK 85

>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 = 94.4 bits (235), Expect = 2e-23
 Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             + V  L   TT+ DL+++F +YG I    ++ D    +S+ F FV FEN DDA +A E
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 88  ALNGKKFDDREWYVGKAQKK 107
             NG + D R   V  +  K
Sbjct: 107 RANGMELDGRRIRVDFSITK 126

>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 = 84.0 bits (208), Expect = 9e-20
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            L +  L     +  L+E+FS++G I    ++ D  S  S+G  FV F   ++A  A   
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107

Query: 192 MNGKMIVSKPLYVAVAQRK 210
            NG  +  + + V  +  K
Sbjct: 108 ANGMELDGRRIRVDFSITK 126

>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 = 94.9 bits (236), Expect = 3e-23
 Identities = 31/149 (20%), Positives = 53/149 (35%), Gaps = 8/149 (5%)

Query: 71  FGFVNFENAD--DAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDK 128
            G    E  D   A K  +        D EW    A K     +           E    
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEG--- 69

Query: 129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 187
               +L + NL      + L+ +F ++G +    + RD  +  S+G  FV F    +A  
Sbjct: 70  --MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127

Query: 188 ALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
           A+  M+G ++  + L V +A+      + 
Sbjct: 128 AMDAMDGAVLDGRELRVQMARYGRPPDSH 156

>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 = 94.1 bits (234), Expect = 5e-23
 Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 1/86 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
            ++ V NL   T+ + L+++F +YG +    + RD    +S+ F FV F +  DA  A++
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQE 113
           A++G   D RE  V  A+     +  
Sbjct: 131 AMDGAVLDGRELRVQMARYGRPPDSH 156

>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 = 93.6 bits (233), Expect = 3e-23
 Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 1/89 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             +FV  + E  T+ED+   F EYG I +  +  D   G  K +  V +E   +A  A+E
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELKG 116
            LNG+    +   V     +   + + +G
Sbjct: 83  GLNGQDLMGQPISVDWCFVRGPPKGKRRG 111

>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 = 82.4 bits (204), Expect = 4e-19
 Identities = 21/96 (21%), Positives = 47/96 (48%), Gaps = 1/96 (1%)

Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
           G  L++  + +   +E + + F+E+G I +  +  D  +G  KG   V + T +EA  A+
Sbjct: 22  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81

Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMR 225
             +NG+ ++ +P+ V     +   + + +    + R
Sbjct: 82  EGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSR 117

>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 = 92.3 bits (230), Expect = 5e-23
 Identities = 29/85 (34%), Positives = 47/85 (55%), Gaps = 1/85 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
            +VFV N+    T+E LK IF E G + S  ++ D + GK K +GF  +++ + A  A+ 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQ 112
            LNG++F  R   V  A  +  +E+
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKEE 93

>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 = 77.3 bits (191), Expect = 1e-17
 Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           ++++ N+     +E+LK++FSE G + S +++ D  +G  KG GF  +   E A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 192 MNGKMIVSKPLYVAVAQRKEERRAR 216
           +NG+    + L V  A  ++ +   
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEEL 94

>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 = 92.0 bits (229), Expect = 7e-23
 Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD--GKSKCFGFVNFENADDA 82
           K   + + V+N+       +++++F  +G + +  + +     G  + FGFV+F    DA
Sbjct: 12  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71

Query: 83  AKAVEAL-NGKKFDDREWYVGKAQKKSERE 111
            KA  AL +      R   +  A  +   +
Sbjct: 72  KKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>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 = 83.9 bits (208), Expect = 6e-20
 Identities = 19/97 (19%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 123 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFS 180
            +   K     + ++N+    +  +++ELFS FG + + ++ +    +G  +G GFV F 
Sbjct: 7   GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66

Query: 181 TPEEASRALAEM-NGKMIVSKPLYVAVAQRKEERRAR 216
           T ++A +A   + +   +  + L +  A  +   ++ 
Sbjct: 67  TKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103

>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 = 91.6 bits (228), Expect = 8e-23
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 3/84 (3%)

Query: 28  FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
              + + NL  S T+E L+++F +   I    V ++ +GKSK + F+ F + +DA +A+ 
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALN 71

Query: 88  ALNGKKFDDREWYVGKAQKKSERE 111
           + N ++ + R   +     +    
Sbjct: 72  SCNKREIEGRAIRLELQGPRGSPN 95

>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 = 81.6 bits (202), Expect = 4e-19
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L + NL  S  +E L+E+F +   I   KV ++ +G SKG  F+ F++ E+A  AL   N
Sbjct: 18  LVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74

Query: 194 GKMIVSKPLYVAVAQRKEERRAR 216
            + I  + + + +   +    + 
Sbjct: 75  KREIEGRAIRLELQGPRGSPNSG 97

>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 = 92.0 bits (229), Expect = 9e-23
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +FV ++ E   ++++++ F +YG I +  +  D   G SK +  V +E    A  A EAL
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88

Query: 90  NGKKFDDREWYVGKAQKKSER 110
           NG +   +   V     K  +
Sbjct: 89  NGAEIMGQTIQVDWCFVKGPK 109

>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 = 79.6 bits (197), Expect = 2e-18
 Identities = 21/86 (24%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           +G  L++ ++ +   +++++E F ++G I +  +  D  +G SKG   V + T ++A  A
Sbjct: 25  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84

Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERR 214
              +NG  I+ + + V     K  +R
Sbjct: 85  KEALNGAEIMGQTIQVDWCFVKGPKR 110

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 92.5 bits (230), Expect = 1e-22
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 1/85 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
            ++ V NL   T+ + L+++F +YG +    + RD    +S+ F FV F +  DA  A++
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQ 112
           A++G   D RE  V  A+     + 
Sbjct: 108 AMDGAVLDGRELRVQMARYGRPPDS 132

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 85.2 bits (211), Expect = 4e-20
 Identities = 23/116 (19%), Positives = 46/116 (39%), Gaps = 1/116 (0%)

Query: 102 GKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC 161
           G         Q++        +   D     +L + NL      + L+ +F ++G +   
Sbjct: 18  GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 77

Query: 162 KVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
            + RD  +  S+G  FV F    +A  A+  M+G ++  + L V +A+      + 
Sbjct: 78  YIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 133

>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 = 91.1 bits (227), Expect = 1e-22
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           N++V NL  S T E +K++F ++G + +  ++ D +  K K FGFV  +  +  ++A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 89  LNGKKFDDREWYVGKAQKKSEREQE 113
           L+   F  R   V +A  K   E  
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHH 86

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 79.5 bits (197), Expect = 1e-18
 Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 2/85 (2%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           N+Y+ NL  S   E++KELFS+FG + + K++ D  +   KG GFV     E  S A+A+
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 192 MNGKMIVSKPLYVAVAQRKEERRAR 216
           ++    + + + V  A  K+     
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHH 86

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 91.2 bits (227), Expect = 1e-22
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
            ++V NL    T+  + ++F + G   S  ++ +       + FV F    DAA A+ A+
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAM 75

Query: 90  NGKKFDDREWYVGKAQKKSERE 111
           NG+K   +E  V  A   S ++
Sbjct: 76  NGRKILGKEVKVNWATTPSSQK 97

>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 = 87.7 bits (218), Expect = 3e-21
 Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
           D  Q   LY+ NL   + +  + +LFS+ G   SCK++ + +  +    FV F    +A+
Sbjct: 11  DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAA 69

Query: 187 RALAEMNGKMIVSKPLYVAVAQRKEERR 214
            ALA MNG+ I+ K + V  A     ++
Sbjct: 70  AALAAMNGRKILGKEVKVNWATTPSSQK 97

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 91.2 bits (227), Expect = 1e-22
 Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             +FV  + E  T+ED+   F EYG I +  +  D   G  K +  V +E   +A  A+E
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 88  ALNGKKFDDREWYVGKAQKK 107
            LNG+    +   V     +
Sbjct: 84  GLNGQDLMGQPISVDWCFVR 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 77.7 bits (192), Expect = 9e-18
 Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           +G  L++  + +   +E + + F+E+G I +  +  D  +G  KG   V + T +EA  A
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 189 LAEMNGKMIVSKPLYVAVAQRK 210
           +  +NG+ ++ +P+ V     +
Sbjct: 82  MEGLNGQDLMGQPISVDWCFVR 103

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 91.9 bits (228), Expect = 1e-22
 Identities = 19/117 (16%), Positives = 37/117 (31%), Gaps = 6/117 (5%)

Query: 104 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE----LFSEFGTIT 159
            +  + + +                     + I N+   +  EKL+     L S  G I 
Sbjct: 2   KETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL 61

Query: 160 SCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
              V       + G  ++ F+T E A   +    G      PL +  ++  + + A 
Sbjct: 62  DIVVDLSDD--NSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAE 116

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 85.0 bits (210), Expect = 4e-20
 Identities = 18/100 (18%), Positives = 31/100 (31%), Gaps = 7/100 (7%)

Query: 29  NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
             V + N++     E L+     +    G I   VV       +    ++ F   + A  
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD--DNSGKAYIVFATQESAQA 87

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKE 124
            VEA  G  F      +  ++    +  E  G  E     
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETPQSQVAE-DGSLEHHHHH 126

>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 = 90.7 bits (226), Expect = 1e-22
 Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 3/84 (3%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGT--ITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 86
            +++ NL   TTDEDL +     G   I       +   G+SK F  V   +   + K +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 87  EALNGKKFDDREWYVGKAQKKSER 110
           + L  ++   +   V  + K    
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLEHH 86

>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 = 82.2 bits (204), Expect = 1e-19
 Identities = 19/88 (21%), Positives = 32/88 (36%), Gaps = 3/88 (3%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGT--ITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
           + LYI NL     DE L E     G   I   K   +  +G SKG   V   +   + + 
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRAR 216
           +  +  + +  +   V  + + E     
Sbjct: 62  MDLLPKRELHGQNPVVTPSNKLEHHHHH 89

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 91.3 bits (227), Expect = 2e-22
 Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 7/90 (7%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
            VF++NL   + +E L ++  ++G +    V+   D   SK   F  F   + A K + A
Sbjct: 17  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76

Query: 89  LN------GKKFDDREWYVGKAQKKSEREQ 112
            +      G K D R+  V  A  + E   
Sbjct: 77  ASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106

>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 = 86.6 bits (215), Expect = 7e-21
 Identities = 27/97 (27%), Positives = 47/97 (48%), Gaps = 7/97 (7%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 185
           D  +G  ++I+NL    ++E L E+  +FG +   +V+  P +  SKG  F  F T E A
Sbjct: 11  DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70

Query: 186 SRALAEMN------GKMIVSKPLYVAVAQRKEERRAR 216
            + LA  +      G  +  + L V +A  ++E  + 
Sbjct: 71  QKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107

>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 = 90.8 bits (226), Expect = 2e-22
 Identities = 30/84 (35%), Positives = 44/84 (52%), Gaps = 4/84 (4%)

Query: 28  FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 86
              +FVK L E TT+E LK+ F        A ++ D + G SK FGFV+F + +DA  A 
Sbjct: 15  SKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71

Query: 87  EALNGKKFDDREWYVGKAQKKSER 110
           EA+   + D  +  +  A+ K E 
Sbjct: 72  EAMEDGEIDGNKVTLDWAKPKGEG 95

>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 = 76.9 bits (190), Expect = 2e-17
 Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 4/85 (4%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            L++K L +   +E LKE F         +++ D  +G SKG GFV F++ E+A  A   
Sbjct: 17  TLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 192 MNGKMIVSKPLYVAVAQRKEERRAR 216
           M    I    + +  A+ K E  + 
Sbjct: 74  MEDGEIDGNKVTLDWAKPKGEGGSG 98

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 90.1 bits (224), Expect = 2e-22
 Identities = 15/85 (17%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGT--ITSAVVMRDGD-GKSKCFGFVNFENADDAAKA 85
           + + ++N+   T  + +      Y +  + +  +++D    +++ F FV   +A DA++ 
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 86  VEALNGK----KFDDREWYVGKAQK 106
           ++ L       K D +   V  A+ 
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 74.7 bits (184), Expect = 7e-17
 Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 7/84 (8%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGT--ITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
            + ++N+      + +    S + +  + + ++++D  +  ++G  FV  S+  +AS+ L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 190 AEMNGK----MIVSKPLYVAVAQR 209
             +        I  K + V  A+ 
Sbjct: 71  QILQSLHPPLKIDGKTIGVDFAKS 94

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 91.8 bits (228), Expect = 3e-22
 Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             ++V  L E   D+ L   F  +G IT   +  D +  K + F FV FE A+DAA A++
Sbjct: 64  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123

Query: 88  ALNGKKFDDREWYVGKA 104
            +N  +   R   V  A
Sbjct: 124 NMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 84.4 bits (209), Expect = 8e-20
 Identities = 25/102 (24%), Positives = 44/102 (43%), Gaps = 1/102 (0%)

Query: 107 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD 166
            +  E+ + G    +            LY+  L + +DD+ L   F  FG IT  ++  D
Sbjct: 39  VNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLD 98

Query: 167 P-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA 207
             +   +G  FV F   E+A+ A+  MN   +  + + V +A
Sbjct: 99  YETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 = 89.6 bits (223), Expect = 5e-22
 Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           V+V  LDE  ++  L ++F + G + +  + +D   G+ + +GFV F + +DA  A++ +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77

Query: 90  NGKKFDDREWYVGKAQKKSERE 111
           +  K   +   V KA   ++  
Sbjct: 78  DMIKLYGKPIRVNKASAHNKNL 99

>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 = 86.9 bits (216), Expect = 4e-21
 Identities = 23/91 (25%), Positives = 45/91 (49%), Gaps = 1/91 (1%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 185
           ++ Q   +Y+  L + + +  L ELF + G + +  + +D  +G  +G GFV F + E+A
Sbjct: 11  ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70

Query: 186 SRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
             A+  M+   +  KP+ V  A    +  + 
Sbjct: 71  DYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101

>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 = 88.1 bits (219), Expect = 1e-21
 Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 7/83 (8%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             + V N+  + T+++L+  F EYG +    +++D       + FV+ E A+DA +A+  
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRG 63

Query: 89  LNGKKFDDREWYVGKAQKKSERE 111
           L+  +F  +  +V  +  +    
Sbjct: 64  LDNTEFQGKRMHVQLSTSRLRTA 86

>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 = 76.5 bits (189), Expect = 1e-17
 Identities = 15/84 (17%), Positives = 38/84 (45%), Gaps = 7/84 (8%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L++ N+  +  +++L+  F E+G +  C +++D         FV     E+A  A+  +
Sbjct: 12  KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY-------AFVHMERAEDAVEAIRGL 64

Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
           +      K ++V ++  +    + 
Sbjct: 65  DNTEFQGKRMHVQLSTSRLRTASG 88

>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 = 88.1 bits (219), Expect = 1e-21
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             +  KNL  + T+++LK++F +   I    ++   DGKSK   ++ F++  DA K +E 
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEI---RLVSQ-DGKSKGIAYIEFKSEADAEKNLEE 72

Query: 89  LNGKKFDDREWYVGKAQKKSER 110
             G + D R   +    +K   
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGT 94

>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 = 78.5 bits (194), Expect = 3e-18
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L  KNL  +I +++LKE+F +   I   +++    G SKG  ++ F +  +A + L E 
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEI---RLVSQ-DGKSKGIAYIEFKSEADAEKNLEEK 73

Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
            G  I  + + +     K   R 
Sbjct: 74  QGAEIDGRSVSLYYTGEKGGTRG 96

>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 = 87.3 bits (217), Expect = 2e-21
 Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 7/81 (8%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
            +F+ NL    T+++++ +F +YG +    ++++       +GFV+ E+   A  A+  L
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN-------YGFVHIEDKTAAEDAIRNL 62

Query: 90  NGKKFDDREWYVGKAQKKSER 110
           +  K       V  ++ KS+ 
Sbjct: 63  HHYKLHGVNINVEASKNKSKA 83

>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 = 75.7 bits (187), Expect = 3e-17
 Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L+I NL     +++++ LF ++G +  C ++       K  GFV       A  A+  +
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNL 62

Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
           +   +    + V  ++ K +  + 
Sbjct: 63  HHYKLHGVNINVEASKNKSKASSG 86

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 87.1 bits (216), Expect = 3e-21
 Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           +   L I+N+   +  E L  L  ++G + SC+ +   S        V +S+ ++A +AL
Sbjct: 14  RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS--ETAVVNVTYSSKDQARQAL 71

Query: 190 AEMNGKMIVSKPLYVAVAQRKEERR 214
            ++NG  + +  L VA    +   +
Sbjct: 72  DKLNGFQLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 84.4 bits (209), Expect = 3e-20
 Identities = 14/87 (16%), Positives = 34/87 (39%), Gaps = 2/87 (2%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           + +   + ++N+      E L  +  +YG + S   +            V + + D A +
Sbjct: 12  RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVN--TDSETAVVNVTYSSKDQARQ 69

Query: 85  AVEALNGKKFDDREWYVGKAQKKSERE 111
           A++ LNG + ++    V     +   +
Sbjct: 70  ALDKLNGFQLENFTLKVAYIPDEMAAQ 96

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 87.4 bits (217), Expect = 3e-21
 Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
            V+V NL       +L++ F  YG + +  + R+       F FV FE+  DA  AV  L
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 90  NGKKFDDREWYVGKAQKKSER 110
           +GK        V  +     R
Sbjct: 58  DGKVICGSRVRVELSTGMPRR 78

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 72.7 bits (179), Expect = 5e-16
 Identities = 26/102 (25%), Positives = 48/102 (47%), Gaps = 6/102 (5%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
           + +Y+ NLG      +L+  FS +G + +  + R+P G      FV F  P +A  A+  
Sbjct: 1   MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGF----AFVEFEDPRDAEDAVRG 56

Query: 192 MNGKMIVSKPLYVAVAQ--RKEERRARLQAQFSQMRPVAMGP 231
           ++GK+I    + V ++    +  R  R  A+   +  +  GP
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNGP 98

>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 = 89.1 bits (221), Expect = 3e-21
 Identities = 27/108 (25%), Positives = 45/108 (41%), Gaps = 5/108 (4%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             ++V NL   TT+E + ++F + G I   ++  D     +  F FV + +  DA  A+ 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQ----ELKGQFEQAMKETVDKFQG 131
            +NG + DDR           E  Q       GQ     ++  D  +G
Sbjct: 100 YINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRG 147

>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 = 83.3 bits (206), Expect = 3e-19
 Identities = 33/154 (21%), Positives = 62/154 (40%), Gaps = 14/154 (9%)

Query: 98  EWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGT 157
           + YV  +Q + +  +    + E+ +K++        LY+ NL     +E++ ELFS+ G 
Sbjct: 12  DSYVELSQYRDQHFRGDNEEQEKLLKKSC------TLYVGNLSFYTTEEQIYELFSKSGD 65

Query: 158 ITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
           I    +  D     + G  FV + +  +A  A+  +NG  +  + +        +E R  
Sbjct: 66  IKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR-- 123

Query: 217 LQAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQ 250
              Q+   R  + G         Y  G  G G+ 
Sbjct: 124 ---QYG--RGRSGGQVRDEYRQDYDAGRGGYGKL 152

>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 = 86.5 bits (215), Expect = 5e-21
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 7/80 (8%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           +FV N+  + T ++L+ +F   G +    V++D       + FV+ E   DA  A+  LN
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64

Query: 91  GKKFDDREWYVGKAQKKSER 110
           GK+   +   V  + K  ++
Sbjct: 65  GKEVKGKRINVELSTKGQKK 84

>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 = 76.1 bits (188), Expect = 2e-17
 Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 7/82 (8%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +++ N+  +   ++L+ LF   G +  C V++D         FV      +A  A+A++N
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKDY-------AFVHMEKEADAKAAIAQLN 64

Query: 194 GKMIVSKPLYVAVAQRKEERRA 215
           GK +  K + V ++ + +++  
Sbjct: 65  GKEVKGKRINVELSTKGQKKSG 86

>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 = 86.6 bits (215), Expect = 6e-21
 Identities = 23/91 (25%), Positives = 47/91 (51%), Gaps = 4/91 (4%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
             + L+I  +  ++D++ LK LF EFG I    V++D  +G+ KG  F+ +   E A +A
Sbjct: 12  DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71

Query: 189 LAEMNGKMIV---SKPLYVAVAQRKEERRAR 216
            + ++ +  +   ++P+ V  A  +    + 
Sbjct: 72  QSALHEQKTLPGMNRPIQVKPADSESRGGSG 102

>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 = 81.6 bits (202), Expect = 3e-19
 Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 4/85 (4%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
            +F+  +  +  ++DLK +F E+G I    V++D   G  K   F+ +   + A KA  A
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74

Query: 89  LNGKK---FDDREWYVGKAQKKSER 110
           L+ +K     +R   V  A  +S  
Sbjct: 75  LHEQKTLPGMNRPIQVKPADSESRG 99

>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 = 85.8 bits (213), Expect = 7e-21
 Identities = 20/84 (23%), Positives = 41/84 (48%), Gaps = 6/84 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           N +++ NL  + T +DL+++FG+     +  V          + FV++ + + A +A+E 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIET 63

Query: 89  LNGK-KFDDREWYVGKAQKKSERE 111
           L+GK +   +   V  +  K  R 
Sbjct: 64  LSGKVELHGKIMEVDYSVSKKLRS 87

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 74.6 bits (184), Expect = 8e-17
 Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LYI NL  ++  + L++LF +     + +V+        G  FV +     A RA+  ++
Sbjct: 11  LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLS 65

Query: 194 GKM-IVSKPLYVAVAQRKEERRA 215
           GK+ +  K + V  +  K+ R +
Sbjct: 66  GKVELHGKIMEVDYSVSKKLRSS 88

>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 = 85.8 bits (213), Expect = 1e-20
 Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 5/87 (5%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            +Y   +   + D+ +++ FS FG I   +V  +     KG  FV FST E A+ A+  +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 81

Query: 193 NGKMIVSKPLYVAVAQRKEERRARLQA 219
           NG  I    +     +   +  +   +
Sbjct: 82  NGTTIEGHVVKCYWGKESPDMTSGPSS 108

>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 = 78.5 bits (194), Expect = 5e-18
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 5/84 (5%)

Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 86
           K   V+   +    TD+ +++ F  +G I    V  +     K + FV F   + AA A+
Sbjct: 24  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAI 78

Query: 87  EALNGKKFDDREWYVGKAQKKSER 110
            ++NG   +         ++  + 
Sbjct: 79  VSVNGTTIEGHVVKCYWGKESPDM 102

>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A 1jh4_A Length = 144

 Score = 86.8 bits (214), Expect = 1e-20
 Identities = 44/139 (31%), Positives = 78/139 (56%), Gaps = 1/139 (0%)

Query: 325 PPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMPITALSTALAN 384
           P    A   P  R +  + +  G  +     ++    +  +  +V         ++ LA+
Sbjct: 2   PLGSAAAATPAVRTVPQYKYAAGVRNP-QQHLNAQPQVTMQQPAVHVQGQEPLTASMLAS 60

Query: 385 ASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAME 444
           A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH+LESPE+L++KV EA+ 
Sbjct: 61  APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVA 120

Query: 445 VLRSVAQQQANNPADQLAS 463
           VL++   ++A   A   A+
Sbjct: 121 VLQAHQAKEAAQKAVNSAT 139

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 85.5 bits (212), Expect = 2e-20
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAV--------VMRDGD-GKSKCFGFVNFENA 79
           N +FV+ L E+ T E +   F + G I +          +  D + GK K    V+F++ 
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 80  DDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 112
             A  A++  +GK+F      V  A ++++  +
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 75.1 bits (185), Expect = 9e-17
 Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 9/97 (9%)

Query: 126 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDP-SGISKGSGF 176
            D      ++++ LG+++  E + + F + G I +          +  D  +G  KG   
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 177 VAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEER 213
           V+F  P  A  A+   +GK     P+ V+ A R+ + 
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADF 98

>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 = 85.1 bits (211), Expect = 2e-20
 Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           ++V NL      +D++ +F +YG I    +          F FV FE+  DA  AV   +
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--GGPPFAFVEFEDPRDAEDAVYGRD 82

Query: 91  GKKFDDREWYVGKAQKKSER 110
           G  +D     V   +     
Sbjct: 83  GYDYDGYRLRVEFPRSGRGT 102

>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 = 69.7 bits (171), Expect = 7e-15
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 2/83 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +Y+ NL   I  + ++++F ++G I    +     G      FV F  P +A  A+   +
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFEDPRDAEDAVYGRD 82

Query: 194 GKMIVSKPLYVAVAQRKEERRAR 216
           G       L V   +      + 
Sbjct: 83  GYDYDGYRLRVEFPRSGRGTGSG 105

>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 = 86.1 bits (213), Expect = 3e-20
 Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 4/77 (5%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           V+V NL  +    +L++ FG YG + S  V R+       F FV FE+  DAA AV  L+
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELD 131

Query: 91  GKKFDDREWYVGKAQKK 107
           G+        V  +  +
Sbjct: 132 GRTLCGCRVRVELSNGE 148

>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 = 81.9 bits (202), Expect = 9e-19
 Identities = 32/148 (21%), Positives = 59/148 (39%), Gaps = 8/148 (5%)

Query: 67  KSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETV 126
             K        +A  A K  +        D EW    A K     +          +++ 
Sbjct: 11  TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSC 70

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
                  +Y+ NLG++ +  +L+  F  +G + S  V R+P G      FV F  P +A+
Sbjct: 71  P--LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGF----AFVEFEDPRDAA 124

Query: 187 RALAEMNGKMIVSKPLYVAVAQRKEERR 214
            A+ E++G+ +    + V ++    E+R
Sbjct: 125 DAVRELDGRTLCGCRVRVELS--NGEKR 150

>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 = 85.0 bits (211), Expect = 3e-20
 Identities = 31/92 (33%), Positives = 43/92 (46%), Gaps = 2/92 (2%)

Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAK 84
           T F  +FV  L   TTD  L+K F  +G I  AVV+ D   GKS+ +GFV   +   A +
Sbjct: 15  TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELKG 116
           A +  N    D R+  V  A   ++      G
Sbjct: 75  ACKDPN-PIIDGRKANVNLAYLGAKPRSLQTG 105

>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 = 77.7 bits (192), Expect = 1e-17
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 10/87 (11%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +++  L     D  L++ F  FG I    V+ D  +G S+G GFV  +    A RA  + 
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79

Query: 193 N----GKMIVSKPLYVAVAQRKEERRA 215
           N    G+          +A    + R+
Sbjct: 80  NPIIDGRKANVN-----LAYLGAKPRS 101

>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 = 84.3 bits (209), Expect = 3e-20
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 1/83 (1%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMR-DGDGKSKCFGFVNFENADDAA 83
           K     + V+N+  + + +++   F  Y  I  +V ++ +  G       V FE+ D+A 
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 84  KAVEALNGKKFDDREWYVGKAQK 106
            AV  LN +    R+  +     
Sbjct: 72  AAVIDLNDRPIGSRKVKLSGPSS 94

>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 = 69.3 bits (170), Expect = 6e-15
 Identities = 14/75 (18%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMR-DPSGISKGSGFVAFSTPEEASRALAEM 192
           + ++N+  ++  +++ + F  +  I     ++ +  G+  G   VAF + +EA+ A+ ++
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 193 NGKMIVSKPLYVAVA 207
           N + I S+ + ++  
Sbjct: 78  NDRPIGSRKVKLSGP 92

>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 = 84.1 bits (209), Expect = 3e-20
 Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           +++V N+D   T E+L+  F   G++    ++ D   G  K F ++ F + +    ++ A
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66

Query: 89  LNGKKFDDREWYVGKAQKK 107
           L+   F  R+  V   +  
Sbjct: 67  LDESLFRGRQIKVIPKRTN 85

>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 = 73.3 bits (181), Expect = 2e-16
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           ++Y+ N+      E+L+  F   G++    ++ D  SG  KG  ++ FS  E    +LA 
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 66

Query: 192 MNGKMIVSKPLYVAVAQ 208
           ++  +   + + V   +
Sbjct: 67  LDESLFRGRQIKVIPKR 83

>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 = 84.9 bits (210), Expect = 3e-20
 Identities = 20/102 (19%), Positives = 37/102 (36%), Gaps = 14/102 (13%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             +  KNL   T   ++++ F  +G++   ++      +      V F    +A KA   
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-----PEGGITAIVEFLEPLEARKAFRH 65

Query: 89  LNGKKFDDREWYVGKA---------QKKSEREQELKGQFEQA 121
           L   KF     Y+  A         QKK  + ++   + E  
Sbjct: 66  LAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESG 107

>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 = 67.1 bits (164), Expect = 5e-14
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 5/71 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +  KNL       +++E FS FG++    +          +  V F  P EA +A   + 
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLA 67

Query: 194 GKMIVSKPLYV 204
                  PLY+
Sbjct: 68  YSKFHHVPLYL 78

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 85.4 bits (211), Expect = 7e-20
 Identities = 19/105 (18%), Positives = 45/105 (42%), Gaps = 3/105 (2%)

Query: 23  AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT--ITSAVVMRDGD-GKSKCFGFVNFENA 79
            ++ +   V+V +    TTD+ L ++    G   +       +   G+SK +  V   + 
Sbjct: 50  GLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASE 109

Query: 80  DDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKE 124
           +   K +E L GK  +  +  V  A +++  + E + +  + ++ 
Sbjct: 110 NSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVRV 154

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 80.7 bits (199), Expect = 3e-18
 Identities = 24/148 (16%), Positives = 51/148 (34%), Gaps = 8/148 (5%)

Query: 87  EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGL-----NLYIKNLGD 141
              +G        Y    +      QE   +        +  + GL      +Y+ +   
Sbjct: 6   HHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSW 65

Query: 142 SIDDEKLKELFSEFGT--ITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV 198
              D++L ++    G   +   K   +  +G SKG   V  ++     + L  + GK++ 
Sbjct: 66  WTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLN 125

Query: 199 SKPLYVAVAQRKEERRARLQAQFSQMRP 226
            + + V  A R+   +   QA+  +   
Sbjct: 126 GEKVDVRPATRQNLSQFEAQARKRECVR 153

>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 = 83.1 bits (206), Expect = 1e-19
 Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAA 83
           K     + V+N+  + + +++   F  Y  I  +V +  +  G       V FE+ D+A 
Sbjct: 12  KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 84  KAVEALNGKKFDDREWYVGKAQKKS 108
            AV  LN +    R+  +      S
Sbjct: 72  AAVIDLNDRPIGSRKVKLVLGSGPS 96

>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 = 73.9 bits (182), Expect = 1e-16
 Identities = 14/79 (17%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVM-RDPSGISKGSGFVAFSTPEEASRALAEM 192
           + ++N+  ++  +++ + F  +  I     +  +  G+  G   VAF + +EA+ A+ ++
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 193 NGKMIVSKPLYVAVAQRKE 211
           N + I S+ + + +     
Sbjct: 78  NDRPIGSRKVKLVLGSGPS 96

>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 = 83.2 bits (206), Expect = 1e-19
 Identities = 25/93 (26%), Positives = 42/93 (45%), Gaps = 9/93 (9%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAV--------VMRDGD-GKSKCFGFVNFENA 79
           + ++V+ L++S T +DL   F + G +            +  D + GK K    V++E+ 
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 80  DDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 112
             A  AVE  +GK F   +  V  A+KK     
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 77.8 bits (192), Expect = 9e-18
 Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 9/99 (9%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDP-SGISKGSGFV 177
           +      +Y++ L DS+  + L + F + G +            +  D  +G  KG   V
Sbjct: 11  EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70

Query: 178 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
           ++  P  A  A+   +GK      L V++A++K    + 
Sbjct: 71  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSG 109

>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 = 82.6 bits (205), Expect = 1e-19
 Identities = 19/87 (21%), Positives = 45/87 (51%), Gaps = 2/87 (2%)

Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAK 84
           +K N +FV  +  +  + +L++ F ++G +T  V++ D +  + + FGF+ FE+     +
Sbjct: 8   SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQ 67

Query: 85  AVEALNGKKFDDREWYVGKAQKKSERE 111
           AV   +      ++  V +A+ +  + 
Sbjct: 68  AVNM-HFHDIMGKKVEVKRAEPRDSKS 93

>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 = 73.8 bits (182), Expect = 2e-16
 Identities = 17/84 (20%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +++  +  +  + +L+E F +FG +T   ++ D      +G GF+ F   +   +A+  M
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71

Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
           +   I+ K + V  A+ ++ + + 
Sbjct: 72  HFHDIMGKKVEVKRAEPRDSKSSG 95

>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 = 82.0 bits (203), Expect = 4e-19
 Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 2/83 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           VF   L       DL+  F   G +    ++ D +  +SK   +V F        A+  L
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86

Query: 90  NGKKFDDREWYVGKAQKKSEREQ 112
            G++       V  +Q +  R  
Sbjct: 87  TGQRLLGVPIIVQASQAEKNRLS 109

>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 = 79.7 bits (197), Expect = 2e-18
 Identities = 22/112 (19%), Positives = 46/112 (41%), Gaps = 5/112 (4%)

Query: 106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMR 165
             S  +  ++   +    E  D      ++   L   I    L++ FS  G +   +++ 
Sbjct: 3   SGSSGKSPVREPVDNLSPEERDA---RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIIS 59

Query: 166 DP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
           D  S  SKG  +V F   +    A+  + G+ ++  P+ V  +Q ++ R + 
Sbjct: 60  DRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNRLSG 110

>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 = 81.4 bits (201), Expect = 5e-19
 Identities = 26/83 (31%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           N V V  L  S + +DLK    E G +  A V RDG       G V F   +D   AV  
Sbjct: 16  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG------TGVVEFVRKEDMTYAVRK 69

Query: 89  LNGKKFDDREWYVGKAQKKSERE 111
           L+  KF   E      + K +  
Sbjct: 70  LDNTKFRSHEGETAYIRVKVDGP 92

>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 = 70.6 bits (173), Expect = 3e-15
 Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + +  L  S   + LK+   E G +    V RD      G+G V F   E+ + A+ +++
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 71

Query: 194 GKMIVSKPLYVAVAQRKEERRAR 216
                S     A  + K +    
Sbjct: 72  NTKFRSHEGETAYIRVKVDGPRS 94

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 80.9 bits (200), Expect = 6e-19
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 10/93 (10%)

Query: 11 GHFLRKQERETVAIKTKFNNVFVKNL---DESTTD---EDLKKIFGEYGTITSAVVMRDG 64
          G  L+ + +E   I    + + V N+        +     + KIF ++G IT+     + 
Sbjct: 1  GDVLKDRPQEADGID---SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE- 56

Query: 65 DGKSKCFGFVNFENADDAAKAVEALNGKKFDDR 97
          DGK+K + F+ + +   A  AV+  +G K D +
Sbjct: 57 DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 61.3 bits (149), Expect = 5e-12
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 9/84 (10%)

Query: 122 MKETVDKFQGLN--LYIKNLGDSIDD------EKLKELFSEFGTITSCKVMRDPSGISKG 173
           +K+   +  G++  + + N+     D        + ++FS+FG IT+     +  G +KG
Sbjct: 4   LKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKG 62

Query: 174 SGFVAFSTPEEASRALAEMNGKMI 197
             F+ +++P  A  A+   +G  +
Sbjct: 63  YIFLEYASPAHAVDAVKNADGYKL 86

>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 = 80.4 bits (199), Expect = 7e-19
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
           +L++ +L   +D+  +   F+  G T+ S K++R+  +GI  G  FV F+    A + L 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 191 EMNGKMI 197
           ++NGK +
Sbjct: 71  KINGKPL 77

>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 = 75.4 bits (186), Expect = 5e-17
 Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
          ++++ +L+    +  + + F   G T+ S  ++R+   G    + FV F +   A K + 
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 88 ALNGKKFDDRE 98
           +NGK      
Sbjct: 71 KINGKPLPGAT 81

>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 = 80.4 bits (199), Expect = 8e-19
 Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 5/67 (7%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
            ++V  L  +T+   L + F  +G+I +   ++        F ++ +E+ D A  A   
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAK 72

Query: 89 LNGKKFD 95
          + G    
Sbjct: 73 MRGFPLG 79

>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 = 72.3 bits (178), Expect = 5e-16
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L++  LG +     L   F  FG+I +   ++          ++ + + + A  A A+M
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKM 73

Query: 193 NGKMI--VSKPLYVAVAQRK 210
            G  +    + L V  A+  
Sbjct: 74  RGFPLGGPDRRLRVDFAKSG 93

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 79.4 bits (197), Expect = 1e-18
 Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 88
          +FV  L  +TT ED+K  F ++G +  A++M D    + + FGFV FE+ D   K  E  
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 89 ---LNGKKFD 95
             +N K  +
Sbjct: 62 FHEINNKMVE 71

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 69.8 bits (172), Expect = 3e-15
 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           +++  L  +   E +K  F +FG +    +M D  +   +G GFV F + +   +     
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 191 --EMNGKMI 197
             E+N KM+
Sbjct: 62  FHEINNKMV 70

>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 = 80.9 bits (200), Expect = 1e-18
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           +V+V N+D  +T +DL+  F   G+I    ++ D   G  K + ++ F   +    AV A
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-A 96

Query: 89  LNGKKFDDREWYVGKAQKKSER 110
           ++   F  R   V   +     
Sbjct: 97  MDETVFRGRTIKVLPKRTNMPG 118

>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 = 73.2 bits (180), Expect = 6e-16
 Identities = 20/113 (17%), Positives = 42/113 (37%), Gaps = 2/113 (1%)

Query: 105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVM 164
             K       +G  +    E   +    ++Y+ N+      + L+  FS  G+I    ++
Sbjct: 10  HSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69

Query: 165 RDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
            D  SG  KG  ++ F+       A+A M+  +   + + V   +      + 
Sbjct: 70  CDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFRGRTIKVLPKRTNMPGISS 121

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 79.4 bits (196), Expect = 1e-18
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 7/75 (9%)

Query: 29 NNVFVKNL---DESTTD---EDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDA 82
          + + V N+        +     + KIF ++G IT+     + DGK+K + F+ + +   A
Sbjct: 2  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHA 60

Query: 83 AKAVEALNGKKFDDR 97
            AV+  +G K D +
Sbjct: 61 VDAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 62.4 bits (152), Expect = 1e-12
 Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 146 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 200
             + ++FS+FG IT+     +  G +KG  F+ +++P  A  A+   +G  +  +
Sbjct: 22  NVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75

>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 = 79.6 bits (197), Expect = 2e-18
 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 9/86 (10%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 88
           + V  L   TT++DLK+ F  +G +    V +D   G SK FGFV F   +   K +   
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 89  --LNGKKFDDREWYVGKAQKKSEREQ 112
             ++G+  D           K  ++ 
Sbjct: 78  HMIDGRWCD-----CKLPNSKQSQDS 98

>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 = 74.6 bits (184), Expect = 9e-17
 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 9/86 (10%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L +  L     ++ LKE FS FG +   +V +D  +G SKG GFV F+  E   + +++ 
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 193 ---NGKMIVSKPLYVAVAQRKEERRA 215
              +G+    K         K+ + +
Sbjct: 78  HMIDGRWCDCKL-----PNSKQSQDS 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 = 77.9 bits (193), Expect = 3e-18
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 5/68 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 88
          +FV  L   T +E +++ FG +G + S  +  D    K + F F+ F+  +   K +E  
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 89 ---LNGKK 93
             +   K
Sbjct: 62 YHNVGLSK 69

>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 = 67.9 bits (167), Expect = 1e-14
 Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 5/69 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           +++  L     +EK++E F  FG + S ++  D  +   +G  F+ F   E   + +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 191 --EMNGKMI 197
              +     
Sbjct: 62  YHNVGLSKC 70

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 79.5 bits (196), Expect = 3e-18
 Identities = 26/83 (31%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           N V V  L  S + +DLK    E G +  A V RDG       G V F   +D   AV  
Sbjct: 17  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG------TGVVEFVRKEDMTYAVRK 70

Query: 89  LNGKKFDDREWYVGKAQKKSERE 111
           L+  KF   E      + K +  
Sbjct: 71  LDNTKFRSHEGETAYIRVKVDGP 93

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 69.5 bits (170), Expect = 1e-14
 Identities = 21/99 (21%), Positives = 37/99 (37%), Gaps = 6/99 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + +  L  S   + LK+   E G +    V RD      G+G V F   E+ + A+ +++
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 72

Query: 194 GKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPS 232
                S     A  + K +         S+ R  +   S
Sbjct: 73  NTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRS 111

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 78.5 bits (194), Expect = 5e-18
 Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
            ++ N+    T+ DL  +F  +G I       +     K   F+ ++  + AA  + AL
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVAL 83

Query: 90 NGKKFDDRE 98
              F  R 
Sbjct: 84 ANFPFQGRN 92

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 74.7 bits (184), Expect = 8e-17
 Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 5/70 (7%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
             YI N+     +  L  LF  FG I   K   +     KG  F+ + T E+A+  +  +
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVAL 83

Query: 193 NGKMIVSKPL 202
                  + L
Sbjct: 84  ANFPFQGRNL 93

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 77.1 bits (191), Expect = 6e-18
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 5/70 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 88
          +F+  L   TT E L++ FG++G +   +VMRD    +S+ FGFV F +     K +   
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 89 ---LNGKKFD 95
             L+ K  D
Sbjct: 63 RHELDSKTID 72

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 74.8 bits (185), Expect = 4e-17
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + LA  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 191 --EMNGKMIVSK 200
             E++ K I  K
Sbjct: 63  RHELDSKTIDPK 74

>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 = 78.0 bits (192), Expect = 7e-18
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 29 NNVFVKNLDESTTDEDL---KKIFGEYGTITSAVVMRD----GDGKSKCFGFVNFENADD 81
          N VFV  L +   D ++    + FG++G I   V+       G        +V +  ++D
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 82 AAKAVEALNGKKFDDR 97
          A +A++ +N    D R
Sbjct: 76 ALRAIQCVNNVVVDGR 91

>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 = 64.5 bits (157), Expect = 4e-13
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 134 LYIKNLGDSIDDE---KLKELFSEFGTITSCKVMRDP----SGISKGSGFVAFSTPEEAS 186
           +++  L   + D    K  E F +FG I    +        S     S +V +   E+A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 187 RALAEMNGKMIVSKPLYVAVAQRK 210
           RA+  +N  ++  + L  ++   K
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTTK 101

>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 = 77.7 bits (192), Expect = 8e-18
 Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 9/85 (10%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAV--------VMRDGD-GKSKCFGFVNFENA 79
           N +FV+ L E+ T E +   F + G I +          +  D + GK K    V+F++ 
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 80  DDAAKAVEALNGKKFDDREWYVGKA 104
             A  A++  +GK+F      V  A
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 68.9 bits (169), Expect = 1e-14
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 9/84 (10%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDP-SGISKGSGFVAFSTPE 183
            ++++ LG+++  E + + F + G I +          +  D  +G  KG   V+F  P 
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 184 EASRALAEMNGKMIVSKPLYVAVA 207
            A  A+   +GK     P+ V+ A
Sbjct: 75  SAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 77.3 bits (191), Expect = 1e-17
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +FV  LD STT E L+  F +YG +   V+M+D    +S+ FGFV F++ +     + + 
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS- 77

Query: 90  NGKKFDDREWYVGKAQKKSEREQ 112
                D R         +  +  
Sbjct: 78  RPHTLDGRNIDPKPCTPRGMQPS 100

>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 = 71.5 bits (176), Expect = 1e-15
 Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 10/87 (11%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           L++  L  S   E L+  FS++G +  C +M+D  +  S+G GFV F  P      LA  
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78

Query: 191 --EMNGKMIVSKPLYVAVAQRKEERRA 215
              ++G+ I  KP        +  + +
Sbjct: 79  PHTLDGRNIDPKP-----CTPRGMQPS 100

>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 = 75.3 bits (186), Expect = 3e-17
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA- 88
          +FV  L   T+ +DLK  F ++G +    +  D + G+S+ FGF+ F++A    K ++  
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 89 ---LNGKKFD 95
             L+G+  D
Sbjct: 74 EHRLDGRVID 83

>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 = 73.4 bits (181), Expect = 2e-16
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +++  L      + LK+ F++FG +  C +  DP +G S+G GF+ F       + L + 
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 193 ----NGKMI 197
               +G++I
Sbjct: 74  EHRLDGRVI 82

>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 = 76.2 bits (188), Expect = 4e-17
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +F+  L   TT+E L+  + ++G +T  VVMRD    +S+ FGFV F +  +   A+ A 
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA- 88

Query: 90  NGKKFDDREWYVGKAQKKSEREQ 112
                D R     +A  + E   
Sbjct: 89  RPHSIDGRVVEPKRAVAREESGS 111

>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 = 71.9 bits (177), Expect = 1e-15
 Identities = 29/87 (33%), Positives = 46/87 (52%), Gaps = 10/87 (11%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           L+I  L     +E L+  + ++G +T C VMRDP S  S+G GFV FS+  E   A+A  
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89

Query: 191 --EMNGKMIVSKPLYVAVAQRKEERRA 215
              ++G+++  K      A  +EE  +
Sbjct: 90  PHSIDGRVVEPKR-----AVAREESGS 111

>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 = 75.8 bits (187), Expect = 5e-17
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +F+  L   TT E L++ FG++G +   +VMRD    +S+ FGFV F +     K +   
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 86

Query: 90  NGKKFDDREWYVGKAQKKSEREQ 112
           +  + D +      A  +  + +
Sbjct: 87  SRHELDSKTIDPKVAFPRRAQPK 109

>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 = 70.8 bits (174), Expect = 3e-15
 Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 8/85 (9%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA-- 190
           ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + LA  
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87

Query: 191 --EMNGKMIVSKPLYVAVAQRKEER 213
             E++ K I  K    A  +R + +
Sbjct: 88  RHELDSKTIDPKV---AFPRRAQPK 109

>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 = 75.6 bits (186), Expect = 6e-17
 Identities = 14/101 (13%), Positives = 39/101 (38%), Gaps = 5/101 (4%)

Query: 22  VAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGT-ITSAVVMRDGD--GKSKCFGFVNFEN 78
            +  +    +F+  + +    E++ +   +    +   +V        K++ F FV +E+
Sbjct: 2   SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61

Query: 79  ADDAAKAVEALNGKKF--DDREWYVGKAQKKSEREQELKGQ 117
              AA A   L   +      +  V  A+ + + ++++   
Sbjct: 62  HRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 102

>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 = 67.9 bits (166), Expect = 3e-14
 Identities = 12/92 (13%), Positives = 32/92 (34%), Gaps = 5/92 (5%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGT-ITSCKVMRDP--SGISKGSGFVAFSTPEEASRALA 190
           L+I  +      E++ E  ++    +    V         ++G  FV + +   A+ A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 191 EMNGK--MIVSKPLYVAVAQRKEERRARLQAQ 220
           ++      +    + V  A+ + +    +   
Sbjct: 71  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 102

>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 = 75.5 bits (186), Expect = 7e-17
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAV-VMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
             + N+  S T  D+ +         +AV V+ D +G+      V F+N DDA K+   L
Sbjct: 18  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-L 76

Query: 90  NGKKFDDREWYVGKAQKKSEREQE 113
           + KK + RE +V     +  RE E
Sbjct: 77  HRKKLNGREAFVHVVTLEDMREIE 100

>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 = 64.4 bits (157), Expect = 6e-13
 Identities = 20/104 (19%), Positives = 39/104 (37%), Gaps = 9/104 (8%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTI-TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            +I N+  SI    + +          +  V+ D +G   G   V F   ++A ++   +
Sbjct: 18  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RL 76

Query: 193 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPR 236
           + K +  +  +V V   ++ R         +  P A G S P  
Sbjct: 77  HRKKLNGREAFVHVVTLEDMREI-------EKNPPAQGKSGPSS 113

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 75.0 bits (185), Expect = 8e-17
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
            +V NL  +T   D+  IF +   I S  ++RD D  K K F +V F+  D   +A+   
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TY 75

Query: 90  NGKKFDDREWYVGKAQKKSERE 111
           +G    DR   V  A+ + + +
Sbjct: 76  DGALLGDRSLRVDIAEGRKQDK 97

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 69.2 bits (170), Expect = 8e-15
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 3/84 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
            Y+ NL  +     +  +F +   I S +++RD  +   KG  +V F   +    AL   
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-Y 75

Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
           +G ++  + L V +A+ +++ ++ 
Sbjct: 76  DGALLGDRSLRVDIAEGRKQDKSG 99

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 74.8 bits (184), Expect = 8e-17
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALN 90
           + +       + L  +F + G + +     D   GK+K F FV   + +DA K +++ +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 91 GKKFDDR 97
          GK+ D +
Sbjct: 76 GKRLDLK 82

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 64.4 bits (157), Expect = 4e-13
 Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 193
            I +    +  + L  LFS+ G + + +   D  +G +KG  FV   +  +A + +   +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 194 GKMI 197
           GK +
Sbjct: 76  GKRL 79

>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 = 74.2 bits (183), Expect = 9e-17
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           VFV    E  T E+L++ F +YG +    + +      + F FV F +   A        
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCG--E 67

Query: 91  GKKFDDREWYVGKAQKKSER 110
                    ++  A+ K  +
Sbjct: 68  DLIIKGISVHISNAEPKHNK 87

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 12/84 (14%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM- 192
           +++    + +  E+L++ F ++G +    + +      +   FV F+  + A     E  
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCGEDL 69

Query: 193 --NGKMIVSKPLYVAVAQRKEERR 214
              G  +         A+ K  + 
Sbjct: 70  IIKGISVHISN-----AEPKHNKL 88

>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 = 74.6 bits (184), Expect = 1e-16
 Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG--DGKSKCFGFVNFENADDAAKAVEA 88
            F+ NL    T+E +K+ F     I++  + R+     + K FG+  FE+ D    A+ +
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 89  LNGKKFDDREWYVGKAQKKSERE 111
           LN +   ++   V  A +  +++
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 98

>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 = 66.9 bits (164), Expect = 5e-14
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 4/83 (4%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAE 191
            ++ NL   + +E +KE F     I++ ++ R+P      KG G+  F   +    AL+ 
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 75

Query: 192 MNGKMIVSKPLYVAVAQRKEERR 214
           +N + + +K + V VA + +++ 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 98

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 73.8 bits (182), Expect = 2e-16
 Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 4/81 (4%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG--DGKSKCFGFVNFENADDAAKAVEA 88
            F+ NL    T+E +K+ F     I++  + R+     + K FG+  FE+ D    A+  
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 79

Query: 89  LNGKKFDDREWYVGKAQKKSE 109
           LN +   +R   V  A +  +
Sbjct: 80  LNEESLGNRRIRVDVADQAQD 100

>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 = 65.7 bits (161), Expect = 1e-13
 Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAE 191
            ++ NL   + +E +KE F     I++ ++ R+P      KG G+  F   +    AL  
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79

Query: 192 MNGKMIVSKPLYVAVAQRKEE 212
           +N + + ++ + V VA + ++
Sbjct: 80  LNEESLGNRRIRVDVADQAQD 100

>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 = 73.4 bits (181), Expect = 2e-16
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           VFV       T+++L++ F +YG +    + +      + F FV F +   A        
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--E 61

Query: 91  GKKFDDREWYVGKAQKKSEREQ 112
                    ++  A+ K     
Sbjct: 62  DLIIKGISVHISNAEPKHNSNS 83

>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 = 63.0 bits (154), Expect = 9e-13
 Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 12/83 (14%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM- 192
           +++      + +++L+E FS++G +    + +      +   FV F+  + A     E  
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGEDL 63

Query: 193 --NGKMIVSKPLYVAVAQRKEER 213
              G  +         A+ K   
Sbjct: 64  IIKGISVHISN-----AEPKHNS 81

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 73.0 bits (180), Expect = 3e-16
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 31  VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           +F+ NL  ++ + EDL +IF  YG I    +          FGF+ F+N      A+E  
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA-------FGFIQFDNPQSVRDAIECE 65

Query: 90  NGKKFDDREWYVGKAQKKSER 110
           + +    ++  +  +   +  
Sbjct: 66  SQEMNFGKKLILEVSSSNARP 86

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 63.4 bits (155), Expect = 8e-13
 Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 134 LYIKNL-GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L+I NL   ++  E L  +FS +G I    +           GF+ F  P+    A+   
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIECE 65

Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
           + +M   K L + V+      +  
Sbjct: 66  SQEMNFGKKLILEVSSSNARPQFD 89

>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 = 72.4 bits (178), Expect = 4e-16
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           + + VKNL + +  +++  +  +Y      V       ++K   FV   N + A  A++ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYV------DRNKRTAFVTLLNGEQAQNAIQM 59

Query: 89  LNGKKFDDREWYVGKAQKKS 108
            +   F  ++  V      +
Sbjct: 60  FHQYSFRGKDLIVQLQPTDA 79

>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 = 64.7 bits (158), Expect = 2e-13
 Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + +KNL    + +++ +L  ++  +  C V       +K + FV     E+A  A+   +
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNAIQMFH 61

Query: 194 GKMIVSKPLYVAVAQRK 210
                 K L V +    
Sbjct: 62  QYSFRGKDLIVQLQPTD 78

>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 = 71.9 bits (177), Expect = 6e-16
 Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 6/70 (8%)

Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA- 88
           ++V  L ++ T+ DL+  F ++G I +  V++      +   F+ F     A  A E  
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKS 68

Query: 89 LNGKKFDDRE 98
           N    + R 
Sbjct: 69 FNKLIVNGRR 78

>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 = 71.5 bits (176), Expect = 7e-16
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            LY+  LGD+I +  L+  F +FG I +  V++      +   F+ F+T + A  A  + 
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKS 68

Query: 193 -NGKMIVSKPLYV 204
            N  ++  + L V
Sbjct: 69  FNKLIVNGRRLNV 81

>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 = 74.1 bits (181), Expect = 1e-15
 Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 1/86 (1%)

Query: 28  FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
             +V++K      T +D+K+   + G + +  + R      K   FV F++ + A K VE
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 168

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQE 113
              G+K+ + +  +        ++ E
Sbjct: 169 TP-GQKYKETDLLILFKDDYFAKKNE 193

>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 = 70.6 bits (172), Expect = 2e-14
 Identities = 23/102 (22%), Positives = 41/102 (40%), Gaps = 9/102 (8%)

Query: 117 QFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGF 176
              +   E  +  +  ++YIK        + +KE   + G + + ++ R      KGS F
Sbjct: 95  PLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIF 154

Query: 177 VAFSTPEEASRALAEMNGK------MIVSKPLYVAVAQRKEE 212
           V F + E A + +     K      +I+ K  Y A   +K E
Sbjct: 155 VVFDSIESAKKFVETPGQKYKETDLLILFKDDYFA---KKNE 193

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 71.0 bits (174), Expect = 2e-15
 Identities = 16/89 (17%), Positives = 39/89 (43%), Gaps = 7/89 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL--AE 191
           ++I+ L   + + ++  L   FG +T+  +++      K   F+  +T E A+  +    
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73

Query: 192 MNGKMIVSKPLYVAVAQRKEERRARLQAQ 220
               ++  +P+Y+  +  KE +      Q
Sbjct: 74  SVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 60.3 bits (146), Expect = 1e-11
 Identities = 11/89 (12%), Positives = 31/89 (34%), Gaps = 7/89 (7%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL- 89
           + ++ L    T+ ++  +   +G +T+ ++++      K   F+     + A   V    
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73

Query: 90  -NGKKFDDREWYVGKAQKKSEREQELKGQ 117
                   +  Y+  +  K  +      Q
Sbjct: 74  SVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 70.2 bits (172), Expect = 3e-15
 Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
            +V+V NL       DLK+   E G++   +  +      +   F+++ ++  A +AV  
Sbjct: 20  ADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ----GPRRRAFLHYPDSAAAQQAVSC 75

Query: 89  LNGKKFDDREWYVGKAQKKSER 110
           L G +       V  A+++ ++
Sbjct: 76  LQGLRLGTDTLRVALARQQRDK 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 57.1 bits (138), Expect = 1e-10
 Identities = 16/81 (19%), Positives = 37/81 (45%), Gaps = 4/81 (4%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           ++Y+ NL        LK    E G++      + P    +   F+ +     A +A++ +
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP----RRRAFLHYPDSAAAQQAVSCL 76

Query: 193 NGKMIVSKPLYVAVAQRKEER 213
            G  + +  L VA+A+++ ++
Sbjct: 77  QGLRLGTDTLRVALARQQRDK 97

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 70.0 bits (172), Expect = 4e-15
 Identities = 17/88 (19%), Positives = 30/88 (34%), Gaps = 5/88 (5%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           +VFV           L + F  +G + S V+ +D       F  V   +   A +AV + 
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDV-GAREAVLSQ 64

Query: 90  NGKKFDDREWYVGKAQKKSEREQELKGQ 117
           +          V   ++K  +    K  
Sbjct: 65  SQHSLGGHRLRVRPREQKEFQSPASKSP 92

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 5/84 (5%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           ++++      +D  +L E F  FG + S  + +D          V           L+  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDVGAREAVLS-Q 64

Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
           +   +    L V   ++KE +   
Sbjct: 65  SQHSLGGHRLRVRPREQKEFQSPA 88

>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 = 70.1 bits (172), Expect = 4e-15
 Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 8/68 (11%)

Query: 31 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          VF+ NL+       D++ IF +YG +    V +        + FV + N   A  AV   
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG-------YAFVQYSNERHARAAVLGE 82

Query: 90 NGKKFDDR 97
          NG+    +
Sbjct: 83 NGRVLAGQ 90

>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 = 66.2 bits (162), Expect = 1e-13
 Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 8/84 (9%)

Query: 134 LYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           ++I NL    +    ++ +FS++G +  C        + KG  FV +S    A  A+   
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCS-------VHKGYAFVQYSNERHARAAVLGE 82

Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
           NG+++  + L + +A   +  R+ 
Sbjct: 83  NGRVLAGQTLDINMAGEPKPDRSG 106

>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 = 68.9 bits (169), Expect = 8e-15
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 8/68 (11%)

Query: 31 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
          +F+ NL  ++ + EDL +IF  YG I    +          FGF+ F+N      A+E  
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA-------FGFIQFDNPQSVRDAIEXE 77

Query: 90 NGKKFDDR 97
          + +    +
Sbjct: 78 SQEMNFGK 85

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 10/82 (12%)

Query: 134 LYIKNL-GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L+I NL   ++  E L  +FS +G I    +           GF+ F  P+    A+   
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXE 77

Query: 193 NGKMIVSKPLYVAVAQRKEERR 214
           + +M   K L + V+      R
Sbjct: 78  SQEMNFGKKLILEVS--SSNAR 97

>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 = 69.1 bits (169), Expect = 2e-14
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEAL 89
           V++K L     ++ +   F +   +  ++ +    +GK+   GFV F N  D   A+   
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-R 86

Query: 90  NGKKFDDREWYVGKAQKKSEREQ 112
           + +   +R   V    KK   E+
Sbjct: 87  HKQYMGNRFIQVHPITKKGMLEK 109

>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 = 58.7 bits (142), Expect = 6e-11
 Identities = 15/83 (18%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           +Y+K L    +++ + + F +   +     +   P+G + G GFV F    +   AL   
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CR 86

Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
           + + + ++ + V    +K     
Sbjct: 87  HKQYMGNRFIQVHPITKKGMLEK 109

>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 = 68.4 bits (167), Expect = 3e-14
 Identities = 16/89 (17%), Positives = 39/89 (43%), Gaps = 7/89 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL--AE 191
           ++I+ L   + + ++  L   FG +T+  +++      K   F+  +T E A+  +    
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 88

Query: 192 MNGKMIVSKPLYVAVAQRKEERRARLQAQ 220
               ++  +P+Y+  +  KE +      Q
Sbjct: 89  SVTPVLRGQPIYIQFSNHKELKTDSSPNQ 117

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 59.2 bits (143), Expect = 4e-11
 Identities = 10/81 (12%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE- 87
             + ++ L    T+ ++  +   +G +T+ ++++      K   F+     + A   V  
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNY 86

Query: 88  -ALNGKKFDDREWYVGKAQKK 107
                     +  Y+  +  K
Sbjct: 87  YTSVTPVLRGQPIYIQFSNHK 107

>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 = 66.8 bits (163), Expect = 5e-14
 Identities = 16/80 (20%), Positives = 36/80 (45%), Gaps = 7/80 (8%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA--E 191
           L+I+ L   + + ++  L   FG +T+  +++      K   F+  +T E A   +    
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS 72

Query: 192 MNGKMIVSKPLYVAVAQRKE 211
                + ++P+Y+  +  KE
Sbjct: 73  AVTPHLRNQPIYIQYSNHKE 92

>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 = 59.8 bits (145), Expect = 2e-11
 Identities = 10/79 (12%), Positives = 31/79 (39%), Gaps = 7/79 (8%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE--A 88
           + ++ L    T+ ++  +   +G +T+ ++++      K   F+     + A   V   +
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS 72

Query: 89  LNGKKFDDREWYVGKAQKK 107
                  ++  Y+  +  K
Sbjct: 73  AVTPHLRNQPIYIQYSNHK 91

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 66.8 bits (163), Expect = 7e-14
 Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             + +KNL E  + +DLK +  E    T               G + F + +   +A+E 
Sbjct: 29  YRITMKNLPEGCSWQDLKDLARENSLET--TFSSVNTRDFDGTGALEFPSEEILVEALER 86

Query: 89  LNGKKFDDREWYV 101
           LN  +F      V
Sbjct: 87  LNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 59.1 bits (143), Expect = 3e-11
 Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 3/83 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + +KNL +    + LK+L  E             +    G+G + F + E    AL  +N
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLE--TTFSSVNTRDFDGTGALEFPSEEILVEALERLN 88

Query: 194 GKMIVSKPLYVAVA-QRKEERRA 215
                   + V         RR+
Sbjct: 89  NIEFRGSVITVERDDNPPPIRRS 111

>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 = 65.9 bits (161), Expect = 1e-13
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEAL 89
           V ++ L    + E++ + F     + + + +  D  G+S    FV F + + A KA++  
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-K 76

Query: 90  NGKKFDDREWYVGKAQKKSERE 111
           + ++   R   + K+ +   R 
Sbjct: 77  HKERIGHRYIEIFKSSRAEVRT 98

>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 = 60.9 bits (148), Expect = 6e-12
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVM-RDPSGISKGSGFVAFSTPEEASRALAEM 192
           + ++ L      E++ + FS    + +   +  D  G S G  FV F++ E A +AL + 
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KK 76

Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
           + + I  + + +  + R E R +
Sbjct: 77  HKERIGHRYIEIFKSSRAEVRTS 99

>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 = 65.0 bits (159), Expect = 2e-13
 Identities = 11/67 (16%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V ++    + T++++ +         +  ++R+  G    + FV+F N ++  +A++  N
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CN 70

Query: 91 GKKFDDR 97
           +    R
Sbjct: 71 REYMGGR 77

>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 = 57.7 bits (140), Expect = 7e-11
 Identities = 14/78 (17%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + ++    ++ ++ + E  +      + +++R+  G   G  FV FS  EE  +AL + N
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQAL-KCN 70

Query: 194 GKMIVSKPLYVAVAQRKE 211
            + +  + + V   +   
Sbjct: 71  REYMGGRYIEVFREKSGP 88

>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 = 65.2 bits (159), Expect = 2e-13
 Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 7/90 (7%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            ++++ L +S+ +  L E   +FGTI    +M       K    V F   + A   +   
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFA 71

Query: 193 --NGKMIVSKPLYVAVAQRKEERRARLQAQ 220
                 I  +  +   +  K   R      
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 61.7 bits (150), Expect = 4e-12
 Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 7/91 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             V V+ L ES  + DL +   ++GTI   ++M       K    V FEN D A + V  
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTF 70

Query: 89  LNGKKF--DDREWYVGKAQKKSEREQELKGQ 117
                     ++ +   +  K        G 
Sbjct: 71  AADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101

>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 = 65.7 bits (160), Expect = 3e-13
 Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVM-RDGDGKSKCFGFVNFENADDAAKAVEAL 89
           V ++ L    T E++ + F     + + + +  D +GK     FV F + + A KA+   
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-K 103

Query: 90  NGKKFDDR 97
           + ++   R
Sbjct: 104 HKERIGHR 111

>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 = 61.0 bits (148), Expect = 1e-11
 Identities = 23/108 (21%), Positives = 43/108 (39%), Gaps = 2/108 (1%)

Query: 108 SEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVM-RD 166
           S       GQ       + D      + ++ L      E++ + FS    + +   +  D
Sbjct: 19  SHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVD 78

Query: 167 PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR 214
           P G   G  FV F++ E A +AL   + + I  + + V  + ++E R 
Sbjct: 79  PEGKITGEAFVQFASQELAEKAL-GKHKERIGHRYIEVFKSSQEEVRS 125

>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 = 70.3 bits (171), Expect = 3e-13
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 28  FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 86
           F  +FV  ++  TT+  L++ F  YG I    ++     GK + + F+ +E+  D   A 
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161

Query: 87  EALNGKKFDDRE 98
           +  +GKK D R 
Sbjct: 162 KHADGKKIDGRR 173

>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 = 63.7 bits (154), Expect = 5e-11
 Identities = 31/176 (17%), Positives = 64/176 (36%), Gaps = 8/176 (4%)

Query: 75  NFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQG--- 131
            FE+  DA     A   ++  +R+    + +K   R+QE++ + +          QG   
Sbjct: 47  EFEDPRDAPPPTRAETREERMERK----RREKIERRQQEVETELKMWDPHNDPNAQGDAF 102

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
             L++  +     + KL+  F  +G I    ++    SG  +G  F+ +    +   A  
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 191 EMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVPPRMPMYPPGPSG 246
             +GK I  + + V V + +  +  R +     +     G +            S 
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSR 218

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 64.4 bits (157), Expect = 4e-13
 Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           ++I+ L D + +  L E   EFG I+   VM       K    V F     A  A+    
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAA 78

Query: 194 GK--MIVSKPLYVAVAQRKE 211
                I   P +V  +  ++
Sbjct: 79  DNQIYIAGHPAFVNYSTSQK 98

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 60.2 bits (146), Expect = 1e-11
 Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 5/66 (7%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
            V ++ L +   + DL +   E+G I+  VVM       K    V FE+   A  AV  
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNY 76

Query: 89 LNGKKF 94
              + 
Sbjct: 77 AADNQI 82

>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 = 64.4 bits (157), Expect = 5e-13
 Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 2/81 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           V V  +  S  + D++  F     + +  +++D  G++   G V F +  D  +A++  N
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RN 76

Query: 91  GKKFDDREWYVGKAQKKSERE 111
                 R   V  A ++    
Sbjct: 77  RMLMIQRYVEVSPATERQWVA 97

>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 = 61.3 bits (149), Expect = 6e-12
 Identities = 15/83 (18%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + +  +  S  +  +++ F     + +  +++D  G + G+G V F +P++   AL + N
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRN 76

Query: 194 GKMIVSKPLYVAVAQRKEERRAR 216
             +++ + + V+ A  ++   A 
Sbjct: 77  RMLMIQRYVEVSPATERQWVAAG 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 = 64.6 bits (157), Expect = 5e-13
 Identities = 20/98 (20%), Positives = 40/98 (40%), Gaps = 10/98 (10%)

Query: 14  LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGF 73
           LR +  ETV+  T+   V    L    +   L  +  + G + + ++  +     K + F
Sbjct: 13  LRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSF 67

Query: 74  VNFENADDAAKAVEALNGKKFDDRE-----WYVGKAQK 106
             +   +++ +A   LNGK+  D        Y+   +K
Sbjct: 68  ARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105

>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 = 19/89 (21%), Positives = 38/89 (42%), Gaps = 12/89 (13%)

Query: 133 NLYIKN--LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           +L + N  LG+ +   +L  +  + G + +  +  +     K   F  + T EE+ RA  
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYV 81

Query: 191 EMNGKMIV-----SKPLYVAVAQRKEERR 214
            +NGK +V        LY+   ++ +   
Sbjct: 82  TLNGKEVVDDLGQKITLYLNFVEKVQWSG 110

>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 = 62.8 bits (153), Expect = 2e-12
 Identities = 13/67 (19%), Positives = 22/67 (32%), Gaps = 2/67 (2%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          V ++ L    T+ D+   F          +    DG+      V F   +DA  A+   +
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KD 75

Query: 91 GKKFDDR 97
                R
Sbjct: 76 KANMQHR 82

>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 = 56.6 bits (137), Expect = 2e-10
 Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 2/82 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           ++++ L     +  +   FS         +   P G   G   V F+T E+A  A+   +
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKD 75

Query: 194 GKMIVSKPLYVAVAQRKEERRA 215
              +  + + + +        +
Sbjct: 76  KANMQHRYVELFLNSTAGTSGS 97

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 61.8 bits (150), Expect = 6e-12
 Identities = 19/89 (21%), Positives = 36/89 (40%), Gaps = 6/89 (6%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAV----VMRDGDGKSKCFGFVNFENADDAAKAV 86
           V ++ L  + T E++   FG++  IT        +   DG+     FV F   + A  A+
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 87  EALNGKKFDDREWYVGKAQKKSEREQELK 115
              +      R   + ++   +E +Q L 
Sbjct: 86  R-KHKDLLGKRYIELFRS-TAAEVQQVLN 112

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 51.8 bits (124), Expect = 2e-08
 Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTIT----SCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           + ++ L  +   E++   F +   IT        +  P G   G  FV F+  E A  AL
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRA 215
              +  ++  + + +  +   E ++ 
Sbjct: 86  -RKHKDLLGKRYIELFRSTAAEVQQV 110

>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 = 61.0 bits (148), Expect = 2e-11
 Identities = 12/67 (17%), Positives = 22/67 (32%), Gaps = 2/67 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           V ++ L    T+ D+   F          +    DG+      V F   ++A  A+   +
Sbjct: 49  VHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMS-KD 106

Query: 91  GKKFDDR 97
                 R
Sbjct: 107 RANMQHR 113

>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 = 56.4 bits (136), Expect = 6e-10
 Identities = 19/108 (17%), Positives = 37/108 (34%), Gaps = 2/108 (1%)

Query: 116 GQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSG 175
           G+     + TV    G  ++++ L     +  +   FS         +   P G   G  
Sbjct: 31  GRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEA 89

Query: 176 FVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQ 223
            V F+T EEA  A+   +   +  + + + +            +Q  Q
Sbjct: 90  DVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAYSSQVMQ 136

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 57.7 bits (139), Expect = 1e-10
 Identities = 11/84 (13%), Positives = 28/84 (33%), Gaps = 6/84 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD---GKSKCFGFVNFENADDAAKA 85
             VFV  L     ++++   F  +G +      +         K + F+ F+        
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQA- 67

Query: 86  VEALNGKKFDDREWYVGKAQKKSE 109
              ++    +D + Y+  +    +
Sbjct: 68  --LIDACLEEDGKLYLCVSSPTIK 89

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 45.4 bits (107), Expect = 3e-06
 Identities = 15/96 (15%), Positives = 31/96 (32%), Gaps = 12/96 (12%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS---GISKGSGFVAFSTPEEASRALA 190
           +++  L   ID++++   F  FG +      +  S      KG  F+ F         + 
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 191 EMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRP 226
                    K      +   +++         Q+RP
Sbjct: 71  --ACLEEDGKLYLCVSSPTIKDKPV-------QIRP 97

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 56.8 bits (137), Expect = 2e-10
 Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 5/88 (5%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMR---DGDGKSKCFGFVNFENADDAAKAVE 87
           +  + L  S T ED+   F +         +    + DGK +    +  E+  D  KA+E
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELK 115
             +      R   V +     + +  +K
Sbjct: 74  -KHRMYMGQRYVEVYEI-NNEDVDALMK 99

>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 = 49.5 bits (118), Expect = 7e-08
 Identities = 12/90 (13%), Positives = 30/90 (33%), Gaps = 4/90 (4%)

Query: 134 LYIKNLGDSIDDEKLKELFSEF---GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           +  + L  S   E +   FS+            + +  G  +G   +   + ++  +AL 
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL- 72

Query: 191 EMNGKMIVSKPLYVAVAQRKEERRARLQAQ 220
           E +   +  + + V     ++        Q
Sbjct: 73  EKHRMYMGQRYVEVYEINNEDVDALMKSLQ 102

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 55.5 bits (134), Expect = 3e-10
 Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 7/73 (9%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG------DGKSKCFGFVNFENADDAAK 84
          ++V N+    T+E +   F     +                 + K F F+ F + D+  +
Sbjct: 9  LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 85 AVEALNGKKFDDR 97
          A+ A +G  F  +
Sbjct: 69 AM-AFDGIIFQGQ 80

>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 = 53.2 bits (128), Expect = 2e-09
 Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCK------VMRDPSGISKGSGFVAFSTPEEASR 187
           LY+ N+   I +E + + F+    +          V+       K   F+ F + +E ++
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 188 ALAEMNGKMIVSKPLYV 204
           A+A  +G +   + L +
Sbjct: 69  AMA-FDGIIFQGQSLKI 84

>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 = 55.3 bits (133), Expect = 8e-10
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 31  VFVKNLDESTTDEDLKKIFGEY---GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
           V ++ L  S + ED++    +      +     +   +G+     FV  E+ DD   A++
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELK 115
             + +    R   V K+  ++E +  LK
Sbjct: 80  -KDRESMGHRYIEVFKS-HRTEMDWVLK 105

>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 = 51.5 bits (123), Expect = 2e-08
 Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 4/85 (4%)

Query: 134 LYIKNLGDSIDDEKLKELFSEF---GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           + ++ L  S   E ++   S+      +     +    G   G  FV   + ++   AL 
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL- 78

Query: 191 EMNGKMIVSKPLYVAVAQRKEERRA 215
           + + + +  + + V  + R E    
Sbjct: 79  KKDRESMGHRYIEVFKSHRTEMDWV 103

>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 = 55.5 bits (133), Expect = 2e-09
 Identities = 19/123 (15%), Positives = 44/123 (35%), Gaps = 16/123 (13%)

Query: 75  NFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNL 134
           +  +   A  A++A+N  +  +       A   +      +                L +
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPV-------------LRI 49

Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 194
            ++NL   +  + L ++FS+FGT+         +        + ++ P  A  A   ++G
Sbjct: 50  IVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLDG 106

Query: 195 KMI 197
           + I
Sbjct: 107 QNI 109

>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 = 54.7 bits (131), Expect = 4e-09
 Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 3/68 (4%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           + V+NL    T + L +IF ++GT+   +     +        + + +   A  A  +L+
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ---ALLQYADPVSAQHAKLSLD 105

Query: 91  GKKFDDRE 98
           G+   +  
Sbjct: 106 GQNIYNAC 113

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 54.3 bits (130), Expect = 3e-09
 Identities = 13/66 (19%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + V+NL    T + L +IF ++GT+   +     +        + + +   A  A  +L+
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ---ALLQYADPVSAQHAKLSLD 87

Query: 91 GKKFDD 96
          G+   +
Sbjct: 88 GQNIYN 93

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 53.1 bits (127), Expect = 8e-09
 Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
           L + ++NL   +  + L ++FS+FGT+         +        + ++ P  A  A   
Sbjct: 29  LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLS 85

Query: 192 MNGKMI 197
           ++G+ I
Sbjct: 86  LDGQNI 91

>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 = 53.3 bits (128), Expect = 4e-09
 Identities = 14/56 (25%), Positives = 25/56 (44%)

Query: 42 DEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR 97
          +E   ++  +YG +    V  +         +V F   +DA KAV  LN + F+ +
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96

>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 = 48.7 bits (116), Expect = 1e-07
 Identities = 13/64 (20%), Positives = 30/64 (46%)

Query: 141 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 200
           D   +E   E+  ++G +    V  +      G+ +V F   E+A +A+ ++N +    +
Sbjct: 37  DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96

Query: 201 PLYV 204
           P++ 
Sbjct: 97  PIHA 100

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 57.1 bits (137), Expect = 8e-09
 Identities = 32/171 (18%), Positives = 52/171 (30%), Gaps = 14/171 (8%)

Query: 206 VAQRKEERRARLQAQFSQMRPVAMGPS--VPPRMPMYPPGPSGLGQQFLYGQAPPAIIPP 263
           ++  K+    + Q Q+ Q       P+  +PP+ P       G         A P++   
Sbjct: 1   MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYG-QMGMPPQGAVPSMGQQ 59

Query: 264 QAGFGYQQQLVPGMRPAGAPMPNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQ 323
           Q     Q+QL   +  A   M +  +  V                P    Q   P+   Q
Sbjct: 60  QFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNA------YMQPQVPVQMGTPLQQQQ 113

Query: 324 MPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDASVGQPMP 374
            P    AY  P     Q+             P+D+   +P     +  P P
Sbjct: 114 QPMAAPAYGQPSAAMGQNMRPMNQ-----LYPIDLLTELPPPITDLTLPPP 159

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 54.4 bits (130), Expect = 5e-08
 Identities = 24/157 (15%), Positives = 37/157 (23%), Gaps = 10/157 (6%)

Query: 218 QAQFSQMRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGM 277
           Q     M P     +      M  P    +          PA              +  M
Sbjct: 24  QQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDM 83

Query: 278 RPAGAPM--PNFFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRGHAY---- 331
                P+  PN ++      Q G     ++         QP   M   M P    Y    
Sbjct: 84  HLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDL 143

Query: 332 ----RYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPR 364
                 P+       P  +     + VP ++    P 
Sbjct: 144 LTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPD 180

>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 = 51.1 bits (122), Expect = 1e-08
 Identities = 14/87 (16%), Positives = 36/87 (41%), Gaps = 6/87 (6%)

Query: 131 GLNLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
           G ++ + N+   +  ++L++     F+  G + S ++        +    V     ++A 
Sbjct: 9   GADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAI 66

Query: 187 RALAEMNGKMIVSKPLYVAVAQRKEER 213
            A+  ++   I SK + V++A      
Sbjct: 67  GAVNSLHRYKIGSKKILVSLATGASGP 93

>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 = 50.8 bits (121), Expect = 2e-08
 Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 30  NVFVKNLDESTTDEDLKKI----FGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
           +V V N+D   + ++L+++    F  +G + S  +    D + K    V  EN  DA  A
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKA--VVQMENLQDAIGA 68

Query: 86  VEALNGKKFDDREWYVGKAQKKSERE 111
           V +L+  K   ++  V  A   S   
Sbjct: 69  VNSLHRYKIGSKKILVSLATGASGPS 94

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 54.0 bits (129), Expect = 2e-08
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 5/82 (6%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             +  K+L  +  +  ++ +F   G I     +     +SK  GFV F+   +A  A EA
Sbjct: 144 GALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKFKYQANAEFAKEA 198

Query: 89  LNGKKFDDREWYVGKAQKKSER 110
           ++ +            +++   
Sbjct: 199 MSNQTLLLPSDKEWDDRREGTG 220

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 54.0 bits (129), Expect = 2e-08
 Identities = 18/103 (17%), Positives = 39/103 (37%), Gaps = 17/103 (16%)

Query: 133 NLYIKNLGDSID---------DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPE 183
            LY+  +  +++         + +++ +FS  G I   + +      SK  GFV F    
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQA 190

Query: 184 EASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRP 226
            A  A   M+ + ++         +R+      L  +++   P
Sbjct: 191 NAEFAKEAMSNQTLLLPSDKEWDDRREGT---GLLVKWANEDP 230

>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 = 51.3 bits (123), Expect = 2e-08
 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 43 EDLKKIFGEYGTITSAVVMRDGDGKS---KCFGFVNFENADDAAKAVEALNGKKFDDR 97
          ED++    +YG + S  + R  DG         FV F +  D  KA++ L G+KF +R
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANR 87

>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 = 43.2 bits (102), Expect = 1e-05
 Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 13/74 (17%)

Query: 134 LYIKNL---GDSIDDEKLKELFSE-------FGTITSCKVMRDPSGIS---KGSGFVAFS 180
           L + N+    + +DDE+ +E+  +       +G + S ++ R   G+     G  FV F+
Sbjct: 8   LCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFT 67

Query: 181 TPEEASRALAEMNG 194
           +  +  +A+  + G
Sbjct: 68  SVFDCQKAMQGLTG 81

>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 = 51.1 bits (122), Expect = 2e-08
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 134 LYIKNL-GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA-- 190
           +++ NL      D  + +L   +G I +  +MR      K   F+   T E+A   +   
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHC 82

Query: 191 EMNGKMIVSKPLYVAVAQRKEE 212
                    + + V ++++ ++
Sbjct: 83  LKKALWFQGRCVKVDLSEKYKK 104

>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 = 48.4 bits (115), Expect = 2e-07
 Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 12/88 (13%)

Query: 31  VFVKNL-DESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE-- 87
           + + NL     +D  + K+   YG I + ++M     + K   F+  E  +DA   V+  
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-----RMKSQAFIEMETREDAMAMVDHC 82

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELK 115
                 F  R   V      SE+ ++L 
Sbjct: 83  LKKALWFQGRCVKV----DLSEKYKKLV 106

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 50.4 bits (120), Expect = 6e-08
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 5/88 (5%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMR---DGDGKSKCFGFVNFENADDAAKAVE 87
           V ++ L  S + ED++    +      A  +      +G+     FV   + DD   A++
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK 106

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQELK 115
             + +    R   V K+  ++E +  LK
Sbjct: 107 -KDRESMGHRYIEVFKS-HRTEMDWVLK 132

>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 = 49.6 bits (118), Expect = 1e-07
 Identities = 15/100 (15%), Positives = 35/100 (35%), Gaps = 4/100 (4%)

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEF---GTITSCKVMRDPSGISKGSG 175
             +M    +  +G  + ++ L  S   E ++   S+            +    G   G  
Sbjct: 32  RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91

Query: 176 FVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRA 215
           FV   + ++   AL + + + +  + + V  + R E    
Sbjct: 92  FVELGSEDDVKMAL-KKDRESMGHRYIEVFKSHRTEMDWV 130

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 48.9 bits (116), Expect = 9e-08
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L +KNL   ID   L+ L  + G + S         +++G     ++T EEA++A   +N
Sbjct: 10  LLLKNLTAQIDGPTLRTLCMQHGPLVSFHP-----YLNQGIALCKYTTREEANKAQMALN 64

Query: 194 GKMIVSKPLYVAVAQRKEERR 214
             ++ +  ++       E + 
Sbjct: 65  NCVLANTTIFAESPSENEVQS 85

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.9 bits (126), Expect = 2e-07
 Identities = 37/247 (14%), Positives = 74/247 (29%), Gaps = 50/247 (20%)

Query: 2   LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYG---TITSA 58
           L ND QVF  + + + +     ++       +  L           I G  G   T  + 
Sbjct: 119 LYNDNQVFAKYNVSRLQPYL-KLRQA-----LLELR----PAKNVLIDGVLGSGKTWVAL 168

Query: 59  VVMRDGDGKSKCFGF----VNFENADDAAKAVEALNGKKFD-DREWYVGKAQKKSEREQE 113
            V      + K   F    +N +N +     +E L    +  D  W       +S+    
Sbjct: 169 DVCLSYKVQCK-MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNW-----TSRSDHSSN 222

Query: 114 LKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVM---RDPSGI 170
           +K +     +  + +      Y   L   + + +  + ++ F    SCK++   R     
Sbjct: 223 IKLRIHSI-QAELRRLLKSKPYENCL-LVLLNVQNAKAWNAFN--LSCKILLTTRFKQVT 278

Query: 171 SKGSGFVAFSTP-EEASRALAEMNGKMIVSK-----------------PLYVA-VAQRKE 211
              S         +  S  L     K ++ K                 P  ++ +A+   
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIR 338

Query: 212 ERRARLQ 218
           +  A   
Sbjct: 339 DGLATWD 345

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.8 bits (105), Expect = 5e-05
 Identities = 32/241 (13%), Positives = 71/241 (29%), Gaps = 57/241 (23%)

Query: 12  HFLRKQERETVAIKTKFNNV-------FVKNLDESTTDEDLKKIFG--EYGTITSAVVMR 62
           H     + ET   + ++ ++       FV N D     +  K I    E   I   ++ +
Sbjct: 2   HHHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHI---IMSK 58

Query: 63  DGDGKS-KCFGFVNFENADDAAKAVE-ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
           D    + + F  +  +  +   K VE  L      + ++ +   + +  +   +   + +
Sbjct: 59  DAVSGTLRLFWTLLSKQEEMVQKFVEEVLR----INYKFLMSPIKTEQRQPSMMTRMYIE 114

Query: 121 A---MKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS----KG 173
               +      F   N+        +  + L EL             R    +      G
Sbjct: 115 QRDRLYNDNQVFAKYNVSRLQPYLKL-RQALLEL-------------RPAKNVLIDGVLG 160

Query: 174 SG---FVAFSTPEEASRA---LAEMNGKMIVSKPLYVAVAQRKEERR--ARLQAQFSQMR 225
           SG           +   +     +M+ K+      ++ +            LQ    Q+ 
Sbjct: 161 SGKTWVAL-----DVCLSYKVQCKMDFKI-----FWLNLKNCNSPETVLEMLQKLLYQID 210

Query: 226 P 226
           P
Sbjct: 211 P 211

>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 = 47.0 bits (112), Expect = 7e-07
 Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 43 EDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR 97
          +D+ +   ++G +    V ++   G      +V   +   A  AV AL+G+ F  +
Sbjct: 32 DDVIEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAIAAVNALHGRWFAGK 83

>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 = 39.2 bits (92), Expect = 4e-04
 Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 6/58 (10%)

Query: 140 GDSIDDEKLKELFSE---FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 194
               D E   ++  E    G +    V ++ +    G+ +V   +   A  A+  ++G
Sbjct: 23  EVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNALHG 77

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 96

 Score = 46.2 bits (109), Expect = 8e-07
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 4/79 (5%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY+ NL  + D + +             KV+     I+  S  + F   + A RA   M 
Sbjct: 12  LYVYNLPANKDGKSVSNRLRRLSDNCGGKVLS----ITGCSAILRFINQDSAERAQKRME 67

Query: 194 GKMIVSKPLYVAVAQRKEE 212
            + +    + V+   +  E
Sbjct: 68  NEDVFGNRIIVSFTPKNRE 86

>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} PDB: 3us5_A 2dny_A Length = 118

 Score = 46.3 bits (110), Expect = 1e-06
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 5/60 (8%)

Query: 43 EDLKKIFGEYGTITSAVVMRDGDGKSKCFG-----FVNFENADDAAKAVEALNGKKFDDR 97
           ++ +  G++G +   ++ ++  G+ +        FV F  A +  KA++ALNG+ F  R
Sbjct: 40 GEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR 99

>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} PDB: 3us5_A 2dny_A Length = 118

 Score = 41.3 bits (97), Expect = 7e-05
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 10/71 (14%)

Query: 134 LYIKNL--GDSIDDEKLKELFSE---FGTITSCKVMRDPSGISK-----GSGFVAFSTPE 183
           + ++N+     IDD+   E+  E   FG +    + ++  G  +        FV FS   
Sbjct: 23  MVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIAS 82

Query: 184 EASRALAEMNG 194
           E  +A+  +NG
Sbjct: 83  ETHKAIQALNG 93

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 45.8 bits (108), Expect = 2e-06
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 4/67 (5%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
          + ++N     T + L  +    G +   V+ +    +      V FE+   A KA  ALN
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQ----AMVEFESVLCAQKAKAALN 83

Query: 91 GKKFDDR 97
          G      
Sbjct: 84 GADIYAG 90

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 44.3 bits (104), Expect = 9e-06
 Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 4/66 (6%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
           L L I+N    I  + L  + +  G +    + +     +     V F +   A +A A 
Sbjct: 26  LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR----NGIQAMVEFESVLCAQKAKAA 81

Query: 192 MNGKMI 197
           +NG  I
Sbjct: 82  LNGADI 87

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A Length = 624

 Score = 49.2 bits (117), Expect = 2e-06
 Identities = 33/166 (19%), Positives = 50/166 (30%), Gaps = 30/166 (18%)

Query: 131 GLNLYIKNL--GDSIDDEKLKELFSEFGTITSCKVMRDPS----------GISKGSGFVA 178
              L+  N     S++  K   L+ +   +      +D               K   F A
Sbjct: 460 AAYLFKGNNRWKQSVELCKKDSLYKD--AMQYASESKDTELAEELLQWFLQEEKRECFGA 517

Query: 179 -------FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGP 231
                     P+      A  +  M  + P ++ V +    +  +L A  S  +      
Sbjct: 518 CLFTCYDLLRPDVVLE-TAWRHNIMDFAMPYFIQVMKEYLTKVDKLDASESLRKEEEQAT 576

Query: 232 SVPPRMP-----MYPPGPSGL---GQQFLYGQAPPAIIPPQAGFGY 269
              P +      M   GPS        F YG   PA   PQ GFGY
Sbjct: 577 ETQPIVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGY 622

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 44.4 bits (105), Expect = 4e-06
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 14 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFG- 72
          + K   + V ++    N+      +   + + K+   +YG +   V+             
Sbjct: 3  MGKCPTKVVLLR----NMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVR 58

Query: 73 -FVNFENADDAAKAVEALNGKKFDDR 97
           F+ FE  + A KAV  LNG+ F  R
Sbjct: 59 IFLEFERVESAIKAVVDLNGRYFGGR 84

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 38.3 bits (89), Expect = 6e-04
 Identities = 14/69 (20%), Positives = 31/69 (44%), Gaps = 7/69 (10%)

Query: 134 LYIKNL--GDSIDDEKLKELFSE---FGTITSCKVMRDPSGISKGSG--FVAFSTPEEAS 186
           + ++N+     +D++   E   E   +G +  C +   P      +   F+ F   E A 
Sbjct: 11  VLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAI 70

Query: 187 RALAEMNGK 195
           +A+ ++NG+
Sbjct: 71  KAVVDLNGR 79

>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 Length = 112

 Score = 44.3 bits (105), Expect = 6e-06
 Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 19/92 (20%)

Query: 15 RKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGE--------YGTITSAVVM-RDGD 65
          R +    V IK    N+F  +  +   D  +     E        +G I   ++  R  D
Sbjct: 11 RMRHERVVIIK----NMF--HPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPD 64

Query: 66 GKSKCFGFVNFENADDAAKAVEALNGKKFDDR 97
          G       V+F + ++A   ++ L+G+ F  R
Sbjct: 65 GV----ASVSFRDPEEADYCIQTLDGRWFGGR 92

>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 Length = 112

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 3/49 (6%)

Query: 146 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 194
           E L+   S+FG I    +         G   V+F  PEEA   +  ++G
Sbjct: 41  EDLRVECSKFGQIRKLLLFDRHP---DGVASVSFRDPEEADYCIQTLDG 86

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 12/88 (13%), Positives = 30/88 (34%), Gaps = 12/88 (13%)

Query: 31  VFVKNL-DESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           V + +          L ++   +G I++ +++           F+     +DA  AV+  
Sbjct: 18  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-----NKINEAFIEMATTEDAQAAVDYY 72

Query: 90  NGK--KFDDREWYVGKAQKKSEREQELK 115
                    +   V      S++ + +K
Sbjct: 73  TTTPALVFGKPVRV----HLSQKYKRIK 96

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 39.8 bits (92), Expect = 2e-04
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 140 GDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS 199
                 + L  L  ++G + +  +    S    G+  V F+T + A  A+    G +   
Sbjct: 26  KGGYSKDVLLRLLQKYGEVLNLVL----SSKKPGTAVVEFATVKAAELAVQNEVGLV--D 79

Query: 200 KPLYVAVAQRKEERRA 215
            PL ++  + + +  +
Sbjct: 80  NPLKISWLEGQPQDAS 95

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 16/71 (22%), Positives = 25/71 (35%), Gaps = 6/71 (8%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE--- 87
          V V+ L  +  DE L   F          V+     +  C G + F    DA + +    
Sbjct: 11 VEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--RLGCGGVLTFREPADAERVLAQAD 68

Query: 88 -ALNGKKFDDR 97
            L+G +   R
Sbjct: 69 HELHGAQLSLR 79

>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* Length = 345

 Score = 41.3 bits (96), Expect = 5e-04
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 12/94 (12%)

Query: 133 NLYIKN--LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
           +L + N  LG+ +   +L  +  + G + +  +M      +K   F  + T EE+ RA  
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDAL-LMPP----NKPYSFARYRTTEESKRAYV 74

Query: 191 EMNGKMIVSK-----PLYVAVAQRKEERRARLQA 219
            +NGK +V        LY+   ++ + +  R QA
Sbjct: 75  TLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQA 108

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231

 Score = 40.4 bits (94), Expect = 6e-04
 Identities = 21/106 (19%), Positives = 25/106 (23%), Gaps = 1/106 (0%)

Query: 224 MRPVAMGPSVPPRMPMYPPGPSGLGQQFLYGQAPPAIIPPQAGFGYQQQLVPGMRPAGAP 283
           +      P  P  +     G  G  QQ +  Q    +    A         P   P G  
Sbjct: 114 IPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRG 173

Query: 284 MPN-FFVPVVSQGQQGQRPGGRRGAGPVQQTQQPLPIMPHQMPPRG 328
            P                P G R          P    P  MPP G
Sbjct: 174 GPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPG 219

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	472
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.97
2dyd_A	85	Poly(A)-binding protein; alpha helical protein, RN	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
1ifw_A	92	Polyadenylate-binding protein, cytoplasmic and nuc	99.97
1nmr_A	85	Poly(A)-binding protein; all helical domain, pepti	99.97
3kuj_A	88	Polyadenylate-binding protein 1; protein-protein c	99.97
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.97
1g9l_A	144	Polyadenylate-binding protein 1; all-helical domai	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.96
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
1i2t_A	61	HYD protein; four alpha-helical domain, ligase; 1.	99.95
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.87
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.83
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.82
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.81
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.77
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.77
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.76
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.76
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.76
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.76
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.76
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.76
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.75
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.75
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.75
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.75
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.75
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.75
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.74
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.74
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.74
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.74
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.74
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.74
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.74
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.74
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.74
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.74
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.74
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.74
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.74
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.74
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.73
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.73
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.73
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.73
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.73
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.73
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.73
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.73
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.73
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.73
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.73
2div_A	99	TRNA selenocysteine associated protein; structural	99.72
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.72
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.72
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.72
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.72
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.72
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.72
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.72
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.72
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.72
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.72
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.71
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.71
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.71
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.71
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.71
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.71
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.71
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.71
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.71
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.71
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.71
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.71
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.71
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.71
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.71
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.71
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.71
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.71
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.71
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.7
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.7
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.7
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.7
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.7
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.7
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.7
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.7
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.7
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.7
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.7
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.7
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.7
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.7
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.7
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.7
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.7
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.7
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.7
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.7
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.69
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.69
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.69
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.69
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.69
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.69
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.69
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.69
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.69
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.68
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.68
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.68
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.68
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.68
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.68
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.68
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.68
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.68
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.68
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.68
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.68
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.68
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.68
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.68
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.68
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.68
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.68
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.68
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.68
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.67
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.67
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.67
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.67
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.67
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.67
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.67
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.67
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.67
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.67
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.67
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.67
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.67
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.67
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.66
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.66
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.66
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.66
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.66
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.66
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.66
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.66
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.66
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.66
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.66
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.66
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.66
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.66
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.66
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.66
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.66
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.66
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.66
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.66
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.66
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.66
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.66
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.65
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.65
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.65
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.65
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.65
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.65
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.65
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.65
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.65
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.65
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.65
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.65
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.65
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.65
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.65
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.65
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.65
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.64
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.64
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.64
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.64
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.64
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.64
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.64
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.64
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.45
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.64
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.64
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.64
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.64
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.64
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.64
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.64
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.64
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.64
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.63
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.63
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.63
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.63
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.63
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.63
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.63
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.63
2div_A	99	TRNA selenocysteine associated protein; structural	99.63
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.63
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.63
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.63
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.63
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.63
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.63
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.62
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.62
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.62
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.62
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.62
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.62
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.62
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.62
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.62
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.62
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.62
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.62
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.62
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.62
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.62
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.62
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.62
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.61
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.61
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.61
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.61
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.61
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.61
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.61
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.61
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.61
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.61
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.61
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.61
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.61
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.61
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.61
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.61
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.61
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.6
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.6
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.6
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.6
1x5p_A	97	Negative elongation factor E; structure genomics,	99.6
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.6
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.6
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.6
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.6
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.6
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.6
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.6
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.6
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.59
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.59
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.59
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.59
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.59
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.59
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.59
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.59
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.59
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.58
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.58
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.58
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.58
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.58
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.58
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.58
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.58
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.57
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.57
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.57
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.57
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.57
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.57
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.57
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.56
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.56
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.56
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.56
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.56
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.56
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.56
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.56
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.55
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.55
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.55
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.55
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.55
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.54
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.54
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.54
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.54
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.53
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.3
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.53
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.53
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.53
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.53
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.53
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.53
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.53
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.52
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.52
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.52
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.51
1x5p_A	97	Negative elongation factor E; structure genomics,	99.51
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.5
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.5
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.5
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.5
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.5
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.49
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.49
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.49
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.48
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.48
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.48
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.47
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.46
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.45
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.45
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.45
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.44
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.43
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.43
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.43
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.43
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.42
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.42
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.41
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.36
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.34
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.31
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.29
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.23
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.22
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.2
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.17
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.02
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.99
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.92
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.92
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.86
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.85
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.74
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.69
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.45
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.34
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.84
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.61
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.43
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.33
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.96
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.95
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.84
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.75
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.62
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.08
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.57
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.56
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.32
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.13
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	94.46
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	93.85
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.21
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.64
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	85.82

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=2.2e-35  Score=277.07  Aligned_cols=175  Identities=34%  Similarity=0.512  Sum_probs=158.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++||++|+++|++||+|.+|.|++| .+|+++|||||+|.+.++|.+|++.+|+..+.|+.|.+.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            45789999999999999999999999999999999998 57999999999999999999999999999999999999998


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHH
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE  184 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~  184 (472)
                      .........                ...+|||+||+..+|+++|+++|+.||.|++|+|+++. +.++|||||+|.+.++
T Consensus        93 ~~~~~~~~~----------------~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~-~~~~g~~fV~f~~~~~  155 (213)
T 4f02_A           93 QRDPSLRKS----------------GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEA  155 (213)
T ss_dssp             CCCTHHHHH----------------CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESSHHH
T ss_pred             ccccccccc----------------ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC-CCCceEEEEEeCCHHH
Confidence            765432211                23479999999999999999999999999999999885 4579999999999999


Q ss_pred             HHHHHHHhCCcEecCeeEEEEEcccHHHHHHHH
Q 012034          185 ASRALAEMNGKMIVSKPLYVAVAQRKEERRARL  217 (472)
Q Consensus       185 A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~~~~~  217 (472)
                      |.+|++.|||..|+|++|.|.++..+.++....
T Consensus       156 a~~Ai~~lng~~~~g~~i~V~~a~~~~~~~~~~  188 (213)
T 4f02_A          156 AERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL  188 (213)
T ss_dssp             HHHHHHHHTTCEETTEECEEEECCCHHHHHHHH
T ss_pred             HHHHHHHhCCCEECCEEEEEEEcCCCcccchhh
Confidence            999999999999999999999999987776544

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.1e-33  Score=253.24  Aligned_cols=165  Identities=30%  Similarity=0.532  Sum_probs=152.4

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccch
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  108 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~  108 (472)
                      ++|||+|||.++|+++|+++|++||.|.++.++.+.+++++|||||+|.+.++|.+|++.|++..+.|+.|.|.++....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            58999999999999999999999999999999999989999999999999999999999999999999999999986543


Q ss_pred             hHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC-CCCCcccEEEEEcCCHHHHHH
Q 012034          109 EREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASR  187 (472)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~-~~g~s~g~afV~f~s~~~A~~  187 (472)
                      .                ......++|||+||+..+|+++|+++|+.||.|.++.+..+ .+|.++|||||+|.+.++|.+
T Consensus        81 ~----------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~  144 (166)
T 3md3_A           81 Q----------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN  144 (166)
T ss_dssp             C----------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHH
T ss_pred             C----------------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHH
Confidence            2                12234568999999999999999999999999999999988 478999999999999999999


Q ss_pred             HHHHhCCcEecCeeEEEEEccc
Q 012034          188 ALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       188 Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      |+..|||..++|+.|.|.|+++
T Consensus       145 A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          145 AMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHHHTTCEETTEECEEEESCC
T ss_pred             HHHHhCCCccCCcEEEEEecCC
Confidence            9999999999999999999864

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=6.4e-33  Score=259.73  Aligned_cols=178  Identities=24%  Similarity=0.403  Sum_probs=156.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.++++. +|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            457899999999999999999999999999999999985 8999999999999999999999999999999999999998


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHH
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE  183 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~  183 (472)
                      ..............       ......++|||+||+.++|+++|+++|+.||.|++++|+.+. +|.++|||||+|.+.+
T Consensus       106 ~~~~~~~~~~~~~~-------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~  178 (216)
T 2qfj_A          106 SNIGQAQPIIDQLA-------EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQ  178 (216)
T ss_dssp             SCCGGGHHHHHHHH-------HHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             CCccccchhhhhhh-------cccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHH
Confidence            77665433222111       112245689999999999999999999999999999999985 7899999999999999


Q ss_pred             HHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          184 EASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       184 ~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +|.+|++.|||..|+|+.|.|.++..+
T Consensus       179 ~A~~A~~~l~g~~~~g~~i~V~~a~~~  205 (216)
T 2qfj_A          179 SSQDAVSSMNLFDLGGQYLRVGKAVTP  205 (216)
T ss_dssp             HHHHHHHHHTTCBCSSSBCEEEECSSC
T ss_pred             HHHHHHHHccCCEeCCcEEEEEEecCC
Confidence            999999999999999999999987644

>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=100.00  E-value=1.2e-32  Score=246.78  Aligned_cols=162  Identities=32%  Similarity=0.603  Sum_probs=150.0

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .++|||+|||.++|+++|+++|+.||.|.++.++.+. +|+++|||||+|.+.++|.+|++.|++..+.|+.|.|.++..
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            5889999999999999999999999999999999996 899999999999999999999999999999999999999875


Q ss_pred             chhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHH
Q 012034          107 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA  185 (472)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A  185 (472)
                      ...                  ....++|||+||+..+++++|+++|+.||.|.++++..+. +|.++|||||+|.+.++|
T Consensus        82 ~~~------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A  143 (167)
T 1fxl_A           82 SSA------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA  143 (167)
T ss_dssp             CCG------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             Ccc------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHH
Confidence            532                  1234689999999999999999999999999999999886 788999999999999999


Q ss_pred             HHHHHHhCCcEecCee--EEEEEc
Q 012034          186 SRALAEMNGKMIVSKP--LYVAVA  207 (472)
Q Consensus       186 ~~Ai~~l~g~~i~gk~--l~V~~a  207 (472)
                      .+|++.|||..+.|+.  |.|.||
T Consensus       144 ~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          144 EEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHhcCCccCCCccceEEEeC
Confidence            9999999999999965  888775

>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=100.00  E-value=9.3e-33  Score=254.65  Aligned_cols=177  Identities=24%  Similarity=0.462  Sum_probs=150.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.+ .+|+++|||||+|.+.++|.+|++. ++..+.|+.|.|.+
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            356889999999999999999999999999999999999 4799999999999999999999976 89999999999999


Q ss_pred             cccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCH
Q 012034          104 AQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP  182 (472)
Q Consensus       104 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~  182 (472)
                      +..+......            ......++|||+||+.++|+++|+++|+.||.|.+++|+.+. +|.++|||||+|.+.
T Consensus        89 ~~~~~~~~~~------------~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~  156 (196)
T 1l3k_A           89 AVSREDSQRP------------GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH  156 (196)
T ss_dssp             CCC-----------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             ccCccccccc------------ccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCH
Confidence            8765432211            112244689999999999999999999999999999999985 789999999999999


Q ss_pred             HHHHHHHHHhCCcEecCeeEEEEEcccHHHHHH
Q 012034          183 EEASRALAEMNGKMIVSKPLYVAVAQRKEERRA  215 (472)
Q Consensus       183 ~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~~~  215 (472)
                      ++|.+|+.. ++..++|+.|.|.++..++....
T Consensus       157 ~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          157 DSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             HHHHHHHHC-SCCEETTEECEEEECC-------
T ss_pred             HHHHHHHHh-CCcEECCEEEEEEecCChhHhcc
Confidence            999999976 89999999999999998876643

>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=100.00  E-value=6.5e-33  Score=249.15  Aligned_cols=163  Identities=31%  Similarity=0.566  Sum_probs=151.6

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||.++|+++|+++|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|++.|++..+.|+.|.|.++.
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            4689999999999999999999999999999999998 589999999999999999999999999999999999999987


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEE  184 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~  184 (472)
                      .+..                  ....++|||+||+..+++++|+++|+.||.|.++.+.++. +|.++|||||+|.+.++
T Consensus        82 ~~~~------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~  143 (168)
T 1b7f_A           82 PGGE------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE  143 (168)
T ss_dssp             CCSS------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHH
T ss_pred             CCcc------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHH
Confidence            6542                  1234689999999999999999999999999999999986 88999999999999999


Q ss_pred             HHHHHHHhCCcEecC--eeEEEEEc
Q 012034          185 ASRALAEMNGKMIVS--KPLYVAVA  207 (472)
Q Consensus       185 A~~Ai~~l~g~~i~g--k~l~V~~a  207 (472)
                      |.+|++.|||..+.|  ++|+|.||
T Consensus       144 A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          144 AQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHhcCCEecCCCeEEEEEeC
Confidence            999999999999987  99999986

>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=100.00  E-value=1.9e-32  Score=247.67  Aligned_cols=165  Identities=27%  Similarity=0.503  Sum_probs=147.6

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCC---CceeEEEEEeCCHHHHHHHHHHHCCCccC---Cccee
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG---KSKCFGFVNFENADDAAKAVEALNGKKFD---DREWY  100 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g---~skG~aFV~F~~~e~A~~Av~~lng~~i~---g~~l~  100 (472)
                      ..++|||+|||.++|+++|+++|++||.|.++.++++..+   +++|||||+|.+.++|.+|++.|++..+.   ++.+.
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            4689999999999999999999999999999999999654   89999999999999999999999998876   56777


Q ss_pred             eeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcC
Q 012034          101 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFS  180 (472)
Q Consensus       101 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~  180 (472)
                      +.++.....                 .....++|||+||+..+|+++|+++|+.||.|.++++.++.+|.++|||||+|.
T Consensus        82 ~~~~~~~~~-----------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~  144 (175)
T 3nmr_A           82 MKPADSEKN-----------------NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFT  144 (175)
T ss_dssp             EEECGGGCC-----------------SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEES
T ss_pred             Ecccccccc-----------------ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEEC
Confidence            777654322                 122456899999999999999999999999999999999989999999999999


Q ss_pred             CHHHHHHHHHHhCCcEec---CeeEEEEEcc
Q 012034          181 TPEEASRALAEMNGKMIV---SKPLYVAVAQ  208 (472)
Q Consensus       181 s~~~A~~Ai~~l~g~~i~---gk~l~V~~a~  208 (472)
                      +.++|.+|++.|||..+.   +++|.|.||.
T Consensus       145 ~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          145 TRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             CHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            999999999999998776   4999999974

>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=100.00  E-value=4.9e-32  Score=265.03  Aligned_cols=183  Identities=22%  Similarity=0.308  Sum_probs=166.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|+.||.|.++.++.+ .+|+++|||||+|.+.++|.+|++.|++..+.|+.|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            45689999999999999999999999999999999998 48999999999999999999999999999999999999999


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCc-cHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHH
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSI-DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPE  183 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~-t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~  183 (472)
                      ..+...               ......++|||+|||..+ |+++|+++|+.||.|.+++|+.+.+|.++|||||+|.+.+
T Consensus       173 ~~~~~~---------------~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~  237 (284)
T 3smz_A          173 DAGQLT---------------PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAE  237 (284)
T ss_dssp             CGGGCC---------------TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHH
T ss_pred             CCCCCC---------------cccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHH
Confidence            765321               122456789999999996 9999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCcEecCeeEEEEEcccHHHHHHHHHHhhhc
Q 012034          184 EASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQ  223 (472)
Q Consensus       184 ~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~~~~~~~~~~~  223 (472)
                      +|.+|+..|||..++|++|.|.|+..+..++..+..+...
T Consensus       238 ~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~aa  277 (284)
T 3smz_A          238 MAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAA  277 (284)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECCSSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCccCCeEEEEEEecCCCcccchhhhhhHH
Confidence            9999999999999999999999999998887776665543

>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=100.00  E-value=2e-32  Score=245.86  Aligned_cols=163  Identities=25%  Similarity=0.526  Sum_probs=149.0

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||.++|+++|+++|++||.|.+|.++++ .+|+++|||||+|.+.++|.+|++  ++..+.|+.|.|.++.
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 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            4689999999999999999999999999999999999 579999999999999999999998  4678999999999987


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEE  184 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~  184 (472)
                      .+....                  ...+|||+||+.++|+++|+++|+.||.|.++++..+. +|.++|||||+|.+.++
T Consensus        80 ~~~~~~------------------~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~  141 (167)
T 2cjk_A           80 PRDEQD------------------KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA  141 (167)
T ss_dssp             CHHHHH------------------HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHH
T ss_pred             chhhcc------------------CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHH
Confidence            643211                  23589999999999999999999999999999999885 78999999999999999


Q ss_pred             HHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          185 ASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       185 A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      |.+|++ +++..++|+.|.|.++.++
T Consensus       142 a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          142 VDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             HHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            999997 8999999999999999765

>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=99.97  E-value=2.7e-31  Score=260.87  Aligned_cols=172  Identities=21%  Similarity=0.382  Sum_probs=147.8

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCC-CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG-~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||.++|+++|+++|+.|| .|.+|.++.+..|+++|||||+|.+.++|.+|++.||+..+.|+.|.|.++.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  195 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN  195 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            578999999999999999999999999 9999999999889999999999999999999999999999999999999987


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCC-ccHHHHHHHHhccCceEEEEEeeCCC--CCcccEEEEEcCCH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPS--GISKGSGFVAFSTP  182 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~-~t~e~L~~~F~~~G~I~~v~i~~~~~--g~s~g~afV~f~s~  182 (472)
                      ........           .......++|||+||+.. +|+++|+++|+.||.|.+|+|+.+.+  |.++|||||+|.+.
T Consensus       196 ~~~~~~~~-----------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~  264 (292)
T 2ghp_A          196 PLEKSKRT-----------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK  264 (292)
T ss_dssp             CC--------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSH
T ss_pred             CCcccccc-----------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCH
Confidence            65443221           112335678999999999 99999999999999999999999887  99999999999999


Q ss_pred             HHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          183 EEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       183 ~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ++|.+|+ .|||..|+|+.|.|.|+.++
T Consensus       265 ~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          265 DSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             HHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             HHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            9999999 99999999999999999875

>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=99.97  E-value=9e-31  Score=255.80  Aligned_cols=179  Identities=23%  Similarity=0.408  Sum_probs=149.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHH----HHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLK----KIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~----~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      ....++|||+|||+++|+++|+    ++|++||.|.+|.+++  +|+++|||||+|.+.++|.+|++.||+..|.|+.|.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            3568899999999999999977    8999999999999886  688999999999999999999999999999999999


Q ss_pred             eeccccchhHHHHHHHHHHh-----------------hhh----------------------------------------
Q 012034          101 VGKAQKKSEREQELKGQFEQ-----------------AMK----------------------------------------  123 (472)
Q Consensus       101 V~~a~~~~~~~~~~~~~~~~-----------------~~~----------------------------------------  123 (472)
                      |.++..+..........+..                 ...                                        
T Consensus        84 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  163 (282)
T 3pgw_A           84 IQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPY  163 (282)
T ss_pred             EEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCC
Confidence            99987655321110000000                 000                                        


Q ss_pred             ------------------------------------hhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC
Q 012034          124 ------------------------------------ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP  167 (472)
Q Consensus       124 ------------------------------------~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~  167 (472)
                                                          .......+++|||+||+..+|+++|+++|+.||.|.+|+|+.++
T Consensus       164 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~  243 (282)
T 3pgw_A          164 MPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR  243 (282)
T ss_pred             CCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC
Confidence                                                00112245679999999999999999999999999999999763


Q ss_pred             CCCcccEEEEEcCCHHHHHHHHHHhCCcEec-CeeEEEEEccc
Q 012034          168 SGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPLYVAVAQR  209 (472)
Q Consensus       168 ~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~-gk~l~V~~a~~  209 (472)
                          +|||||+|.+.++|.+|++.|||..|. |+.|+|.|+++
T Consensus       244 ----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~akk  282 (282)
T 3pgw_A          244 ----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK  282 (282)
T ss_pred             ----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEecC
Confidence                689999999999999999999999999 99999999864

>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=99.97  E-value=1.2e-31  Score=242.93  Aligned_cols=165  Identities=27%  Similarity=0.394  Sum_probs=146.3

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|..+.+....+|+++|||||+|.+.++|.+|+ +||+..+.|+.|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEecC
Confidence            46789999999999999999999999999887744444467899999999999999999999 59999999999999999


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHH
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE  184 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~  184 (472)
                      ..+...                .....++|||+||+..+|+++|+++|+.||.|..+    ..++.++|||||+|.+.++
T Consensus        89 ~~~~~~----------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~  148 (175)
T 1fje_B           89 KGRDSK----------------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEAD  148 (175)
T ss_dssp             CCSSCS----------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHH
T ss_pred             CCcccc----------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHH
Confidence            765321                11234689999999999999999999999988776    5578899999999999999


Q ss_pred             HHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          185 ASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       185 A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      |.+|+..|||..++|+.|.|.|+..+
T Consensus       149 A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          149 AEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99999999999999999999999764

>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=99.97  E-value=7.8e-31  Score=236.65  Aligned_cols=158  Identities=24%  Similarity=0.476  Sum_probs=142.9

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcC----C-------CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccC
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEY----G-------TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD   95 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~f----G-------~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~   95 (472)
                      ..++|||+|||.++|+++|+++|++|    |       .|.++.+.     +++|||||+|.+.++|.+|+ .||+..+.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~-----~~~g~afV~f~~~~~A~~A~-~~~~~~~~   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE-----TTTTEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec-----CCCCEEEEEeCCHHHHHHHH-HhCCcEec
Confidence            46899999999999999999999999    6       67776664     45899999999999999999 89999999


Q ss_pred             CcceeeeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccE
Q 012034           96 DREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGS  174 (472)
Q Consensus        96 g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~  174 (472)
                      |+.|.|.++.....                  ....++|||+|||.++|+++|+++|+.||.|.++.+..+. +|.++||
T Consensus        77 g~~i~v~~~~~~~~------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~  138 (172)
T 2g4b_A           77 GQSLKIRRPHDYQP------------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY  138 (172)
T ss_dssp             TEECEEECCSSCCC------------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEE
T ss_pred             CceeeecCCcccCC------------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceE
Confidence            99999998765432                  1125689999999999999999999999999999999985 8899999


Q ss_pred             EEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          175 GFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       175 afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      |||+|.+.++|.+|++.|||..++|+.|.|.+|.
T Consensus       139 afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          139 AFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             EEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            9999999999999999999999999999999873

>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum}

Probab=99.97  E-value=1.5e-32  Score=211.84  Aligned_cols=78  Identities=79%  Similarity=1.074  Sum_probs=74.5

Q ss_pred             cccchhhhhcCCHHHHHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHHHHh
Q 012034          375 ITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQ  452 (472)
Q Consensus       375 ~~~~~~~la~~~~~~q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~~~~  452 (472)
                      +.+++++|+++++++||++|||+|||+|++++|++|+||||||||||++|||+||+|+++|++||+||++||++|+++
T Consensus         7 ~~~~as~La~~~p~~Qkq~LGE~LyplV~~~~p~~AgKITGMLLEmd~~Ell~Lles~e~L~~kv~EA~~vL~~~~~~   84 (85)
T 2dyd_A            7 IGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPDALKAKVAEAMEVLRSAQQH   84 (85)
T ss_dssp             TTTSCHHHHCCCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHCHHHHHHHTTCSHHHHHHHHHHHHHHTSCSSC
T ss_pred             hhhhHHHHHcCCHHHHHHHHHHHHHHHHHHhCccccchhhhhhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHhhc
Confidence            456899999999999999999999999999999999999999999999999999999999999999999999988753

>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=99.97  E-value=5.3e-31  Score=245.72  Aligned_cols=176  Identities=17%  Similarity=0.233  Sum_probs=142.8

Q ss_pred             CcceEEeCCCC-CCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp-~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+||| +++|+++|+++|++||.|.+|+++++    ++|||||+|.+.++|.+||+.|||..+.|+.|.|.++.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            46899999999 89999999999999999999999875    37999999999999999999999999999999999986


Q ss_pred             cchhHHHH---HH------HHHHhhhhhh----------ccccccceeeeecCCCCccHHHHHHHHhccCce--EEEEEe
Q 012034          106 KKSEREQE---LK------GQFEQAMKET----------VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTI--TSCKVM  164 (472)
Q Consensus       106 ~~~~~~~~---~~------~~~~~~~~~~----------~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I--~~v~i~  164 (472)
                      .+......   ..      ..+.......          .....+.+|||+|||+++|+++|+++|+.||.|  .+++++
T Consensus        79 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~  158 (205)
T 3tyt_A           79 QPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVF  158 (205)
T ss_dssp             CSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEEC
T ss_pred             CCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEE
Confidence            43210000   00      0000000000          001235689999999999999999999999999  899998


Q ss_pred             eCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCe----eEEEEEc
Q 012034          165 RDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK----PLYVAVA  207 (472)
Q Consensus       165 ~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk----~l~V~~a  207 (472)
                      .+. +.++|||||+|.+.++|.+|+..|||..|.|+    ++.|+++
T Consensus       159 ~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          159 SGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             cCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            875 55679999999999999999999999999876    6777775

>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.144.1.1

Probab=99.97  E-value=8.9e-32  Score=210.66  Aligned_cols=78  Identities=33%  Similarity=0.445  Sum_probs=75.1

Q ss_pred             ccchhhhhcCCHHHHHHHhhhhhhhhHhh--cCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHHHHhh
Q 012034          376 TALSTALANASPEQQRTLLGESLYPLVEQ--LERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQ  453 (472)
Q Consensus       376 ~~~~~~la~~~~~~q~~~~g~~l~~~v~~--~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~~~~~  453 (472)
                      ++++++|+++++++||++|||+|||+|++  ++|++|+||||||||||++|||+||+|+++|++||+||++||++|++.+
T Consensus         6 p~~a~~la~~~p~~Qkq~LGE~LyplV~~~~~~pelAgKITGMLLEmd~~ElL~LLes~e~L~~kV~EA~~vL~~~~~~~   85 (92)
T 1ifw_A            6 PRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKEQ   85 (92)
T ss_dssp             SSCCSSCCSCSCHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHTTSCHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             ccchHHHhcCChHHHHHHHHHHHHHHHHHhhcCccccchhhHhHhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHHhh
Confidence            57999999999999999999999999999  9999999999999999999999999999999999999999999998643

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1

Probab=99.97  E-value=2.8e-32  Score=210.33  Aligned_cols=77  Identities=55%  Similarity=0.736  Sum_probs=74.3

Q ss_pred             ccccchhhhhcCCHHHHHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHHH
Q 012034          374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVA  450 (472)
Q Consensus       374 ~~~~~~~~la~~~~~~q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~~  450 (472)
                      +.++++++||++++++||++|||+|||+|++++|++|+||||||||||++|||+||+|+++|++||+||++||++|+
T Consensus         7 ~~~l~~s~La~a~p~~Qkq~LGE~LyplV~~~~p~~AgKITGMLLEmd~~ElL~Lle~~e~L~~kV~EA~~vL~~~~   83 (85)
T 1nmr_A            7 QGQNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAKVQEALEVLNRHM   83 (85)
T ss_dssp             CCCTTHHHHTTCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHCSCTHHHHHHTTCCTHHHHHHHHHHHHHHTTCCC
T ss_pred             CCccCHHHHHcCChHHHHHHHHHHHHHHHHHhCccccchhhHhHhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHhh
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999998875

>3kuj_A Polyadenylate-binding protein 1; protein-protein complex, methylation, mRNA processing, mRNA nucleus, phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A

Probab=99.97  E-value=2.5e-31  Score=207.01  Aligned_cols=79  Identities=46%  Similarity=0.793  Sum_probs=75.5

Q ss_pred             ccchhhhhcCCHHHHHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHHHHhhc
Q 012034          376 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA  454 (472)
Q Consensus       376 ~~~~~~la~~~~~~q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~~~~~~  454 (472)
                      ++++++||++++++||++|||+|||+|++++|++|+||||||||||++|||+||+|+++|++||+||++||++|++++.
T Consensus         6 ~l~~s~la~a~p~~Qkq~LGE~Lyp~V~~~~p~~A~KITGMLLEmd~~Ell~lle~~e~L~~kV~EA~~vL~~~~~~~~   84 (88)
T 3kuj_A            6 PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA   84 (88)
T ss_dssp             CCCHHHHHTSCHHHHHHHHHHHHHHHHHHHCTTTHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             cchHHHHHcCCHHHHHHHHHHHhHHHHHhhCCCccchhhhHhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHhhhc
Confidence            5799999999999999999999999999999999999999999999999999999999999999999999999998764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.97  E-value=1.3e-31  Score=247.46  Aligned_cols=178  Identities=22%  Similarity=0.402  Sum_probs=145.8

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCC-----------CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccC
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYG-----------TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD   95 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG-----------~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~   95 (472)
                      ..++|||+|||.++|+++|+++|++||           .|.++.+     ++++|||||+|.+.++|.+|+ .||+..|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~-----~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE-----ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe-----cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            468999999999999999999999994           4555544     456899999999999999999 89999999


Q ss_pred             CcceeeeccccchhHHHHHHH--HHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcc
Q 012034           96 DREWYVGKAQKKSEREQELKG--QFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISK  172 (472)
Q Consensus        96 g~~l~V~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~  172 (472)
                      |+.|.|.++..+.........  ...............++|||+||+.++++++|+++|+.||.|.++.+..+. +|.++
T Consensus        77 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~  156 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK  156 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEE
T ss_pred             CceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcc
Confidence            999999998754221100000  000000111122456799999999999999999999999999999999986 88999


Q ss_pred             cEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          173 GSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       173 g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      |||||+|.+.++|.+|++.|||..++|+.|.|.++..+
T Consensus       157 g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  194 (198)
T 2yh0_A          157 GYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG  194 (198)
T ss_dssp             EEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             eEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            99999999999999999999999999999999998765

>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A 1jh4_A

Probab=99.97  E-value=8.5e-31  Score=222.09  Aligned_cols=80  Identities=45%  Similarity=0.772  Sum_probs=76.3

Q ss_pred             cccchhhhhcCCHHHHHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHHHHhhc
Q 012034          375 ITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA  454 (472)
Q Consensus       375 ~~~~~~~la~~~~~~q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~~~~~~  454 (472)
                      .++++++|+++++++||++|||+|||+|++++|++|+||||||||||++|||+||+|+++|++||+||++||++|++++.
T Consensus        51 ~pl~as~La~a~p~eQkq~LGE~LyplV~~~~p~~A~KITGMLLEmd~~ElL~LLes~e~L~~kV~EA~~vL~~~~~~~~  130 (144)
T 1g9l_A           51 EPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA  130 (144)
T ss_dssp             CCCSHHHHTTCTTTTTTTTTTSSSHHHHHHHTTSCCSSHHHHTTTSSSHHHHHHHHCTTHHHHHHHHHHHHHHTTSSSTT
T ss_pred             chhhHHHHHcCCHHHHHHHHHHHHHHHHHHhCccccchhhhhhccCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHhccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999986543

>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=99.96  E-value=7.6e-30  Score=242.03  Aligned_cols=178  Identities=21%  Similarity=0.314  Sum_probs=147.1

Q ss_pred             cCCcceEEeCCCCC-CCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDE-STTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~-~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||. ++|+++|+++|++||.|.+|.++.+.    +|||||+|.+.++|.+|++.||+..+.|+.|.|.+
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            35688999999999 99999999999999999999999875    78999999999999999999999999999999999


Q ss_pred             cccchhHH-------HHHHHHHHhhh----------hhhccccccceeeeecCCCCccHHHHHHHHhccC-ceEEEEEee
Q 012034          104 AQKKSERE-------QELKGQFEQAM----------KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMR  165 (472)
Q Consensus       104 a~~~~~~~-------~~~~~~~~~~~----------~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G-~I~~v~i~~  165 (472)
                      +..+....       ......+....          ........+++|||+||+..+++++|+++|+.|| .|.+++++.
T Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~  186 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ  186 (229)
T ss_dssp             CSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS
T ss_pred             ecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEE
Confidence            87542110       00000000000          0001112357899999999999999999999999 999999976


Q ss_pred             CCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec-CeeEEEEEcccH
Q 012034          166 DPSGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPLYVAVAQRK  210 (472)
Q Consensus       166 ~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~-gk~l~V~~a~~k  210 (472)
                      +    ++|||||+|.+.++|.+|++.|||..+. |+.|.|.|++.+
T Consensus       187 ~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          187 K----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             S----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             C----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            4    4789999999999999999999999999 999999998753

>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=99.96  E-value=1.7e-29  Score=244.44  Aligned_cols=156  Identities=30%  Similarity=0.524  Sum_probs=144.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.+.+     ++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-----~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~   94 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT   94 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc
Confidence            5678999999999999999999999999999999964     48999999999999999999999999999999999986


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHH
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA  185 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A  185 (472)
                      .                        +++|||+||+..+|+++|+++|+.||.|.+|.|+.+.+|.++|||||+|.+.++|
T Consensus        95 ~------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A  150 (261)
T 3sde_A           95 H------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPA  150 (261)
T ss_dssp             C------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHH
T ss_pred             c------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHH
Confidence            3                        3489999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhCC-cEec---CeeEEEEEcccH
Q 012034          186 SRALAEMNG-KMIV---SKPLYVAVAQRK  210 (472)
Q Consensus       186 ~~Ai~~l~g-~~i~---gk~l~V~~a~~k  210 (472)
                      .+|+..||+ ..+.   +++|.|.++...
T Consensus       151 ~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          151 RKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             HHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             HHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            999999954 4544   999999998754

>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=99.96  E-value=2.1e-29  Score=247.32  Aligned_cols=161  Identities=20%  Similarity=0.280  Sum_probs=141.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|+.||.|.+|.++.+..+ ++|||||+|.+.++|.+|++ +++..+.|+.|.|.++
T Consensus        38 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~  115 (292)
T 2ghp_A           38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL  115 (292)
T ss_dssp             ----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS-SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC-CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEEC
Confidence            567999999999999999999999999999999999998766 58999999999999999995 9999999999999986


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccC-ceEEEEEeeCCCCCcccEEEEEcCCHH
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDPSGISKGSGFVAFSTPE  183 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G-~I~~v~i~~~~~g~s~g~afV~f~s~~  183 (472)
                      .                         .++|||+|||..+++++|+++|+.|| .|.+|.++.+..|.++|||||+|.+.+
T Consensus       116 ~-------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~  170 (292)
T 2ghp_A          116 T-------------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKE  170 (292)
T ss_dssp             C-------------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHH
T ss_pred             C-------------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHH
Confidence            2                         45899999999999999999999999 999999999888899999999999999


Q ss_pred             HHHHHHHHhCCcEecCeeEEEEEcccHHH
Q 012034          184 EASRALAEMNGKMIVSKPLYVAVAQRKEE  212 (472)
Q Consensus       184 ~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~  212 (472)
                      +|.+|+..|+|..+.|+.|.|.++..+..
T Consensus       171 ~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          171 DARYCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECCCC--
T ss_pred             HHHHHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            99999999999999999999999876543

>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=99.96  E-value=8.3e-29  Score=242.10  Aligned_cols=156  Identities=24%  Similarity=0.451  Sum_probs=145.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|+.|| |.++.+     ++++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~   92 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ   92 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEec
Confidence            35678999999999999999999999999 999888     567899999999999999999999999999999999985


Q ss_pred             ccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHH
Q 012034          105 QKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE  183 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~  183 (472)
                      ..                        .++|||+|||.++|+++|+++|+.||.|.+++++.+. +|.++|||||+|.+.+
T Consensus        93 ~~------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~  148 (284)
T 3smz_A           93 PT------------------------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKD  148 (284)
T ss_dssp             CC------------------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             CC------------------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHH
Confidence            42                        2589999999999999999999999999999998875 7899999999999999


Q ss_pred             HHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          184 EASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       184 ~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +|.+|+..++|..++|+.|.|.++..+
T Consensus       149 ~a~~A~~~l~~~~~~g~~i~v~~a~~~  175 (284)
T 3smz_A          149 SAARAKSDLLGKPLGPRTLYVHWTDAG  175 (284)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECCGG
T ss_pred             HHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            999999999999999999999998764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=7.8e-30  Score=235.94  Aligned_cols=176  Identities=20%  Similarity=0.301  Sum_probs=145.1

Q ss_pred             CcceEEeCCCCC-CCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDE-STTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~-~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||. ++|+++|+++|++||.|.+|.++.+.    +|||||+|.+.++|.+|++.||+..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            357999999999 99999999999999999999998874    7899999999999999999999999999999999887


Q ss_pred             cchhHHHHHH-------HHHHhhh----------hhhccccccceeeeecCCCCccHHHHHHHHhccC-ceEEEEEeeCC
Q 012034          106 KKSEREQELK-------GQFEQAM----------KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDP  167 (472)
Q Consensus       106 ~~~~~~~~~~-------~~~~~~~----------~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G-~I~~v~i~~~~  167 (472)
                      ..........       ..+....          ........+++|||+||+..+++++|+++|+.|| .|.+++++.+ 
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-  156 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-  156 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-
Confidence            5431100000       0000000          0000012367899999999999999999999999 9999999775 


Q ss_pred             CCCcccEEEEEcCCHHHHHHHHHHhCCcEec-CeeEEEEEcccH
Q 012034          168 SGISKGSGFVAFSTPEEASRALAEMNGKMIV-SKPLYVAVAQRK  210 (472)
Q Consensus       168 ~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~-gk~l~V~~a~~k  210 (472)
                         ++|||||+|.+.++|.+|+..|||..++ |+.|.|.|++.+
T Consensus       157 ---~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 ---DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             ---TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             ---CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence               3789999999999999999999999999 999999998753

>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo sapiens} SCOP: a.144.1.1 PDB: 3ntw_A

Probab=99.95  E-value=1.1e-28  Score=178.88  Aligned_cols=60  Identities=45%  Similarity=0.720  Sum_probs=59.1

Q ss_pred             HHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHH
Q 012034          390 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSV  449 (472)
Q Consensus       390 q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~  449 (472)
                      ||++|||+|||+|++++|++|+||||||||||++|||+||+|+++|++||+||++||++|
T Consensus         1 qkq~LGe~Lyp~V~~~~p~~A~KITGMLLE~d~~ell~ll~~~e~L~~kv~EA~~vl~~~   60 (61)
T 1i2t_A            1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH   60 (61)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhCcccccchhhhhccCCHHHHHHHHcCHHHHHHHHHHHHHHHHHc
Confidence            799999999999999999999999999999999999999999999999999999999987

>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=99.88  E-value=6.2e-23  Score=173.21  Aligned_cols=110  Identities=37%  Similarity=0.618  Sum_probs=76.4

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      ..+||||+|||+++|+++|+++|++||.|.+|.|+.|. +.+||||||+|++.++|.+||+.||+..|.|+.|.|.++..
T Consensus         4 ~~~~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            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46789999999999999999999999999999999985 44899999999999999999999999999999999999987


Q ss_pred             chhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHH
Q 012034          107 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEK  147 (472)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~  147 (472)
                      +..+.......          ....++|||+||+.++|++.
T Consensus        83 ~~~~~~~~~~~----------~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           83 RKEREAELGAR----------AKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCC--------------------------------------
T ss_pred             ccccccccccc----------cCCCCceEeCCCCCCccccc
Confidence            66544332211          12335799999999999864

>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=99.87  E-value=5.4e-22  Score=176.78  Aligned_cols=148  Identities=21%  Similarity=0.273  Sum_probs=113.0

Q ss_pred             EEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccchhHHHHHHHHHHhhhhhhccccccceeee
Q 012034           57 SAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYI  136 (472)
Q Consensus        57 ~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V  136 (472)
                      ++.|+.+.. +++|||||+|.+.++|++|++.+++....+..+.+...........     ..............++|||
T Consensus         2 ~~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~l~v   75 (158)
T 2kn4_A            2 QYKLILNGK-TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE-----GSHHHHHHMDVEGMTSLKV   75 (158)
T ss_dssp             EEEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEEC-----CCCCSSCCCCCCBCCEEEE
T ss_pred             cEEEEecCc-cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccc-----cccccccccCCCCCCEEEE
Confidence            456777644 6899999999999999999998876544333333322211100000     0000011112234578999


Q ss_pred             ecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          137 KNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       137 ~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +||++++|+++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|++.|||..+.|++|.|.++..+
T Consensus        76 ~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  150 (158)
T 2kn4_A           76 DNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  150 (158)
T ss_dssp             ESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCS
T ss_pred             eCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            9999999999999999999999999999985 7899999999999999999999999999999999999998764

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.83  E-value=2.5e-20  Score=152.86  Aligned_cols=81  Identities=32%  Similarity=0.551  Sum_probs=76.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      -..++|||+|||.++|+++|+++|++||+|.+|.+++| .+|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.+|
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34689999999999999999999999999999999998 47999999999999999999999999999999999999998


Q ss_pred             cc
Q 012034          105 QK  106 (472)
Q Consensus       105 ~~  106 (472)
                      ++
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            64

>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=99.82  E-value=5.3e-21  Score=168.97  Aligned_cols=138  Identities=22%  Similarity=0.320  Sum_probs=113.1

Q ss_pred             CCceeEEEEEeCCHHHHHHHHHHH-CCCccCCcceeeeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCcc
Q 012034           66 GKSKCFGFVNFENADDAAKAVEAL-NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID  144 (472)
Q Consensus        66 g~skG~aFV~F~~~e~A~~Av~~l-ng~~i~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t  144 (472)
                      .+-+|+++|+|.+.++|++|++++ |+..++| .|.+.++..+.........  .............++|||+||++++|
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~~l~V~nl~~~~t   86 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHH--HHHHMHRDSCPLDCKVYVGNLGNNGN   86 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSS--CCCCSCSSSSTTSCEEEEESCCSCCS
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccccc--ccccccccCCCCCCEEEEeCCCCCCC
Confidence            356899999999999999999999 9999999 9999988754321000000  00001112233467899999999999


Q ss_pred             HHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          145 DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       145 ~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +++|+++|+.||.|.+|+|+++    ++|||||+|.+.++|.+|+..|||..+.|++|.|.++..+
T Consensus        87 ~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           87 KTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             CHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            9999999999999999999987    6899999999999999999999999999999999998764

>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=1.6e-19  Score=150.95  Aligned_cols=88  Identities=16%  Similarity=0.173  Sum_probs=81.5

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|++|. +|+++|||||+|++.++|++|++.|||..|.|+.|.|.++
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            456899999999999999999999999999999999995 6999999999999999999999999999999999999999


Q ss_pred             ccchhHHHH
Q 012034          105 QKKSEREQE  113 (472)
Q Consensus       105 ~~~~~~~~~  113 (472)
                      ..+..+...
T Consensus        84 ~~~~~~~~~   92 (110)
T 3s8s_A           84 IKGQQRMKY   92 (110)
T ss_dssp             STTHHHHHH
T ss_pred             CCCcHHHHH
Confidence            877665543

>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=99.79  E-value=3.7e-19  Score=145.80  Aligned_cols=83  Identities=37%  Similarity=0.615  Sum_probs=78.0

Q ss_pred             cccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       127 ~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      ..+++++|||+|||.++|+++|+++|+.||.|.+|+|++++ +|.++|||||+|.+.++|.+|++.|||..++|++|+|.
T Consensus        15 ~~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~   94 (99)
T 4fxv_A           15 LYFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVS   94 (99)
T ss_dssp             -CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            35678899999999999999999999999999999999985 68999999999999999999999999999999999999


Q ss_pred             Eccc
Q 012034          206 VAQR  209 (472)
Q Consensus       206 ~a~~  209 (472)
                      ||++
T Consensus        95 ~AkP   98 (99)
T 4fxv_A           95 YARP   98 (99)
T ss_dssp             ECCB
T ss_pred             EeeC
Confidence            9864

>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=99.77  E-value=7.2e-19  Score=147.95  Aligned_cols=104  Identities=25%  Similarity=0.368  Sum_probs=92.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.++.+  +.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            45789999999999999999999999999999999876  5569999999999999999999999999999999999987


Q ss_pred             cchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCc
Q 012034          106 KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGT  157 (472)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~  157 (472)
                      .+...                          ++++...++++|.++|++||.
T Consensus        84 ~~~~~--------------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           84 ANRAF--------------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHHT--------------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             CChhh--------------------------hhhhHhHhHHHHHHHHHHhCC
Confidence            54321                          356777889999999999984

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.77  E-value=1.9e-18  Score=137.68  Aligned_cols=82  Identities=33%  Similarity=0.518  Sum_probs=75.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            35788999999999999999999999999999999999 58999999999999999999999999999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ..+
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.76  E-value=3.2e-19  Score=144.86  Aligned_cols=82  Identities=18%  Similarity=0.385  Sum_probs=75.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCC--eeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCC----ccCCc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGT--ITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGK----KFDDR   97 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~--I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~----~i~g~   97 (472)
                      ....+||||+|||+++|+++|+++|++||.  |.+|++++| .+|++||||||+|.+.++|.+|++.||+.    .|+|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            356789999999999999999999999995  678999998 47999999999999999999999999997    48999


Q ss_pred             ceeeecccc
Q 012034           98 EWYVGKAQK  106 (472)
Q Consensus        98 ~l~V~~a~~  106 (472)
                      .|.|.+|+.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999864

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.76  E-value=6.3e-18  Score=141.18  Aligned_cols=91  Identities=12%  Similarity=0.256  Sum_probs=83.3

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||++++++++|+++|++||.|.+|+|+.|. +++++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            35689999999999999999999999999999999986 58999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHh
Q 012034          209 RKEERRARLQAQ  220 (472)
Q Consensus       209 ~k~~~~~~~~~~  220 (472)
                      .+..++...+..
T Consensus        85 ~~~~~~~~~~~~   96 (110)
T 3s8s_A           85 KGQQRMKYYELI   96 (110)
T ss_dssp             TTHHHHHHHHHH
T ss_pred             CCcHHHHHHHHh
Confidence            887776555443

>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=99.76  E-value=2.6e-18  Score=135.57  Aligned_cols=79  Identities=33%  Similarity=0.583  Sum_probs=76.0

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      ++|||+|||.++|+++|+++|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|++.|||..+.|+.|.|.++..+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            58999999999999999999999999999999999 68999999999999999999999999999999999999999765

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=2.1e-18  Score=141.40  Aligned_cols=84  Identities=24%  Similarity=0.391  Sum_probs=79.7

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.+.+|+++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        94 ~~~~   97 (100)
T 2do4_A           94 NSGP   97 (100)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7654

>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=99.76  E-value=8e-19  Score=141.09  Aligned_cols=81  Identities=23%  Similarity=0.340  Sum_probs=71.4

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCC--CeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYG--TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG--~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      .+|||+|||+++|+++|+++|++||  .|.++.++.| .+|+++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
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  9999999999 589999999999999999999999999999999999999987


Q ss_pred             cchh
Q 012034          106 KKSE  109 (472)
Q Consensus       106 ~~~~  109 (472)
                      ....
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.76  E-value=1.8e-19  Score=145.36  Aligned_cols=82  Identities=23%  Similarity=0.379  Sum_probs=74.9

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCC-CeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHC-CCccCCcceeeecc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALN-GKKFDDREWYVGKA  104 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG-~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~ln-g~~i~g~~l~V~~a  104 (472)
                      .++|||+|||.++||++|+++|++|| +|.+|.|++| .+|++||||||+|.+.++|.+|++.++ +..+.|+.|.|.++
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 8999999998 579999999999999999999999874 56799999999999


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      .++..
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            77643

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.76  E-value=3.2e-18  Score=141.50  Aligned_cols=84  Identities=30%  Similarity=0.484  Sum_probs=79.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC---cceeee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD---REWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g---~~l~V~  102 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.|..+.+|+++|||||+|.+.++|.+|++.||+..+.|   +.|.|.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            46899999999999999999999999999999999999999999999999999999999999999999998   999999


Q ss_pred             ccccchh
Q 012034          103 KAQKKSE  109 (472)
Q Consensus       103 ~a~~~~~  109 (472)
                      ++..+..
T Consensus        93 ~a~~~~~   99 (105)
T 2dnh_A           93 FADTDKE   99 (105)
T ss_dssp             ESCSSCC
T ss_pred             ECccCcc
Confidence            9987653

>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=3.6e-18  Score=138.48  Aligned_cols=82  Identities=30%  Similarity=0.507  Sum_probs=78.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.+..+.+++++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             cc
Q 012034          105 QK  106 (472)
Q Consensus       105 ~~  106 (472)
                      ..
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2e-18  Score=142.45  Aligned_cols=83  Identities=22%  Similarity=0.286  Sum_probs=77.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.++.|.+|+++|||||+|++.++|.+|++ +++..+.|+.|.|.++.
T Consensus         9 ~~~~~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            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            45688999999999999999999999999999999999779999999999999999999999 89999999999999876


Q ss_pred             cchh
Q 012034          106 KKSE  109 (472)
Q Consensus       106 ~~~~  109 (472)
                      ...+
T Consensus        88 ~~~~   91 (103)
T 1s79_A           88 DYFA   91 (103)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=3.1e-18  Score=141.09  Aligned_cols=84  Identities=46%  Similarity=0.750  Sum_probs=79.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||+++|+++|+++|++||.|.+|.+..+ +++++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            457899999999999999999999999999999999999 9999999999999999999999999999999999999999


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      ..+..
T Consensus        91 ~~~~~   95 (103)
T 2d9p_A           91 QRKEE   95 (103)
T ss_dssp             SSCCC
T ss_pred             ccccc
Confidence            87653

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=5.1e-18  Score=137.55  Aligned_cols=83  Identities=31%  Similarity=0.596  Sum_probs=78.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.++.+. +++++|||||+|++.++|.+|++.||+..|.|+.|.|.++
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            457899999999999999999999999999999999994 6999999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            7654

>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=99.75  E-value=2.4e-18  Score=140.62  Aligned_cols=85  Identities=32%  Similarity=0.491  Sum_probs=80.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.+. +++++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            3567899999999999999999999999999999999996 899999999999999999999999999999999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +..+..
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            987654

>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=99.75  E-value=3.3e-18  Score=135.64  Aligned_cols=81  Identities=32%  Similarity=0.429  Sum_probs=76.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.+..| .+++++|||||+|.+.++|.+|++.||+..+.|+.|.|.+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            356889999999999999999999999999999999888 6889999999999999999999999999999999999998


Q ss_pred             cc
Q 012034          104 AQ  105 (472)
Q Consensus       104 a~  105 (472)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.75  E-value=4e-18  Score=143.80  Aligned_cols=83  Identities=33%  Similarity=0.595  Sum_probs=79.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.+..+.+|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
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~   84 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK   84 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      .+.
T Consensus        85 ~~~   87 (116)
T 2fy1_A           85 KPS   87 (116)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            654

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.74  E-value=3.4e-18  Score=143.82  Aligned_cols=83  Identities=31%  Similarity=0.531  Sum_probs=78.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.|+.+. +++++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            467899999999999999999999999999999999995 8999999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus       103 ~~~~  106 (115)
T 2cpz_A          103 RSKN  106 (115)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.74  E-value=6.3e-18  Score=150.16  Aligned_cols=85  Identities=21%  Similarity=0.311  Sum_probs=78.7

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCC--CeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYG--TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG--~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ..++|||+|||+++|+++|+++|++||  .|.+|.|+.| .+|+++|||||+|.+.++|.+||+.|||..|.|+.|.|.+
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            468999999999999999999999999  9999999999 5899999999999999999999999999999999999999


Q ss_pred             cccchhHH
Q 012034          104 AQKKSERE  111 (472)
Q Consensus       104 a~~~~~~~  111 (472)
                      +..+....
T Consensus       134 a~~~~~~~  141 (156)
T 3n9u_C          134 ATRQNLSQ  141 (156)
T ss_dssp             CCHHHHHH
T ss_pred             cCCCcchh
Confidence            98766544

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=6.6e-18  Score=139.83  Aligned_cols=84  Identities=27%  Similarity=0.395  Sum_probs=78.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.| .+|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            355788999999999999999999999999999999999 4699999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            87653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.5e-18  Score=140.63  Aligned_cols=79  Identities=13%  Similarity=0.260  Sum_probs=73.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCC--CccCCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG--KKFDDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng--~~i~g~~l~V~  102 (472)
                      ....++|||+|||+++||++|+++|++||.|.+|.|+++     ||||||+|++.++|.+|++.|++  ..|.|+.|+|.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            467899999999999999999999999999999999976     79999999999999999998864  78999999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      ++..+.
T Consensus        88 ~A~~~~   93 (105)
T 1sjq_A           88 FSNHKE   93 (105)
T ss_dssp             CCSSSS
T ss_pred             EcCCCC
Confidence            997654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.74  E-value=1.5e-18  Score=142.42  Aligned_cols=100  Identities=25%  Similarity=0.359  Sum_probs=83.6

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccch
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  108 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~  108 (472)
                      ++|||+|||.++|+++|+++|++||.|.+|.+..+    ++|||||+|.+.++|.+|++.||+..+.|+.|.|.++..+.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            58999999999999999999999999999999987    78999999999999999999999999999999999998765


Q ss_pred             hHHHHHHHHHHhhhhhhccccccceeeeecCC
Q 012034          109 EREQELKGQFEQAMKETVDKFQGLNLYIKNLG  140 (472)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~  140 (472)
                      ....        ............+|||+||+
T Consensus        77 ~~~~--------~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           77 RRSR--------FDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CSSC--------CCSCCCSCCCCSCCCSCCCC
T ss_pred             Cccc--------CCCCCccccCCCceecCCCC
Confidence            3210        00111122235689999997

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.74  E-value=8.8e-18  Score=137.39  Aligned_cols=81  Identities=28%  Similarity=0.413  Sum_probs=76.7

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeE--------EEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccC
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS--------AVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFD   95 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~--------v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~   95 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+        +.++.| .+|+++|||||+|.+.++|.+|++.|||..+.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            356899999999999999999999999999999        999999 57999999999999999999999999999999


Q ss_pred             Ccceeeeccc
Q 012034           96 DREWYVGKAQ  105 (472)
Q Consensus        96 g~~l~V~~a~  105 (472)
                      |+.|.|.+|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999874

>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=99.74  E-value=5.8e-18  Score=137.64  Aligned_cols=83  Identities=23%  Similarity=0.407  Sum_probs=78.4

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .++|||+|||.++|+++|+++|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|++.|||..++|+.|.|.++..
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            578999999999999999999999999999999999 4799999999999999999999999999999999999999987


Q ss_pred             chhH
Q 012034          107 KSER  110 (472)
Q Consensus       107 ~~~~  110 (472)
                      +...
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            7654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=5.4e-18  Score=139.88  Aligned_cols=84  Identities=24%  Similarity=0.348  Sum_probs=79.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhc-CCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCc-cCCcceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGE-YGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK-FDDREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~-fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~-i~g~~l~V~~  103 (472)
                      ...++|||+|||.++|+++|+++|++ ||.|.+|.|+.|.+|+++|||||+|.+.++|.+|++.||+.. |.|+.|.|.+
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~   86 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSV   86 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEE
Confidence            56789999999999999999999999 999999999999999999999999999999999999999999 9999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +..+..
T Consensus        87 a~~~~~   92 (104)
T 2dhg_A           87 AIPKAS   92 (104)
T ss_dssp             CCCCCS
T ss_pred             ccCCCc
Confidence            976543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.74  E-value=1e-17  Score=134.95  Aligned_cols=83  Identities=34%  Similarity=0.421  Sum_probs=77.7

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.+.++ +|+++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus         5 ~~~~~~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            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            356789999999999999999999999999999999985 8899999999999999999999999999999999999998


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ....
T Consensus        84 ~~~~   87 (92)
T 2dgv_A           84 RNAS   87 (92)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            7654

>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=99.74  E-value=7.2e-18  Score=140.38  Aligned_cols=84  Identities=32%  Similarity=0.547  Sum_probs=79.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.+ .+|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456889999999999999999999999999999999998 5789999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            98764

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.74  E-value=2e-18  Score=141.68  Aligned_cols=82  Identities=21%  Similarity=0.340  Sum_probs=77.0

Q ss_pred             CcceEEeCCCCC------CCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCC-cc
Q 012034           27 KFNNVFVKNLDE------STTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDD-RE   98 (472)
Q Consensus        27 ~~~~l~V~nLp~------~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g-~~   98 (472)
                      ..++|||+|||.      ++++++|+++|++||.|.+|.|+.|. +|+++|||||+|.+.++|.+|++.|||..|.| +.
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            467899999999      99999999999999999999999995 59999999999999999999999999999999 99


Q ss_pred             eeeeccccch
Q 012034           99 WYVGKAQKKS  108 (472)
Q Consensus        99 l~V~~a~~~~  108 (472)
                      |.|.++..+.
T Consensus        85 l~V~~a~~~~   94 (100)
T 3ns6_A           85 LFLYTMKDVE   94 (100)
T ss_dssp             CEEEESHHHH
T ss_pred             EEEEECchhh
Confidence            9999997543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1e-17  Score=140.63  Aligned_cols=83  Identities=33%  Similarity=0.450  Sum_probs=78.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|+.+.+++++|||||+|++.++|.+|++.||+..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            35678999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ...
T Consensus        92 ~~~   94 (114)
T 2do0_A           92 ERA   94 (114)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            653

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=8.4e-18  Score=137.46  Aligned_cols=83  Identities=23%  Similarity=0.502  Sum_probs=77.8

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.| .+++++|||||+|.+.++|.+|++ ||+..|.|+.|.|.+
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            356789999999999999999999999999999999998 478999999999999999999998 999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        86 a~~~~   90 (99)
T 2dgs_A           86 AEPRD   90 (99)
T ss_dssp             CCCCC
T ss_pred             CCCCc
Confidence            97654

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.74  E-value=9.9e-18  Score=139.01  Aligned_cols=81  Identities=32%  Similarity=0.462  Sum_probs=77.8

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.+.+|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            45688999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             c
Q 012034          105 Q  105 (472)
Q Consensus       105 ~  105 (472)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=6.6e-18  Score=139.13  Aligned_cols=84  Identities=30%  Similarity=0.523  Sum_probs=79.3

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|+.+ .+++++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            356899999999999999999999999999999999999 5899999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        92 a~~~~   96 (103)
T 2cq0_A           92 AKPST   96 (103)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            97654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.73  E-value=1e-17  Score=140.88  Aligned_cols=85  Identities=35%  Similarity=0.560  Sum_probs=79.9

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|+.+ .+++++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            357889999999999999999999999999999999999 4899999999999999999999999999999999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +..+..
T Consensus        92 a~~~~~   97 (115)
T 2dgo_A           92 ATRKPP   97 (115)
T ss_dssp             SSCCCC
T ss_pred             ccCCCC
Confidence            976643

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=9.6e-18  Score=135.85  Aligned_cols=82  Identities=34%  Similarity=0.487  Sum_probs=77.3

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.+. +++++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3567899999999999999999999999999999999994 689999999999999999999999999999999999999


Q ss_pred             ccc
Q 012034          104 AQK  106 (472)
Q Consensus       104 a~~  106 (472)
                      +..
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            864

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=5.2e-18  Score=139.46  Aligned_cols=84  Identities=40%  Similarity=0.667  Sum_probs=78.9

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.+ .+++++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
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            356889999999999999999999999999999999998 4788999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        89 a~~~~   93 (102)
T 1x5s_A           89 AGKSS   93 (102)
T ss_dssp             EECCC
T ss_pred             CCCCC
Confidence            97654

>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=99.73  E-value=6.7e-18  Score=139.56  Aligned_cols=84  Identities=25%  Similarity=0.419  Sum_probs=79.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.+. +++++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4678999999999999999999999999999999999985 899999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        92 a~~~~   96 (105)
T 1x5u_A           92 ASAHN   96 (105)
T ss_dssp             TTTTS
T ss_pred             CCCCC
Confidence            87654

>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=99.73  E-value=7.6e-18  Score=151.14  Aligned_cols=139  Identities=19%  Similarity=0.341  Sum_probs=78.9

Q ss_pred             EEeCCHHHHHHHHHHHCCCccC--CcceeeeccccchhHHHHHHHH----HHhhhhhhccccccceeeeecCCCCccHHH
Q 012034           74 VNFENADDAAKAVEALNGKKFD--DREWYVGKAQKKSEREQELKGQ----FEQAMKETVDKFQGLNLYIKNLGDSIDDEK  147 (472)
Q Consensus        74 V~F~~~e~A~~Av~~lng~~i~--g~~l~V~~a~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~  147 (472)
                      ..|++.++|..|+..+++....  |+.+.+.++....  ...+...    .............+++|||+||+.++++++
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~--~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~   88 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREA--IHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDE   88 (165)
T ss_dssp             ---------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCcccccc--ccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHH
Confidence            7899999999999999887665  5555555432211  1111100    000111122234567899999999999999


Q ss_pred             HHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHHHHH
Q 012034          148 LKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR  214 (472)
Q Consensus       148 L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~~~  214 (472)
                      |+++|+.||.|.+|.|+.+. +|.++|||||+|.+.++|.+||..|||..|.|+.|.|.|+..+..+.
T Consensus        89 L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           89 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             HHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC---
T ss_pred             HHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCC
Confidence            99999999999999999884 78899999999999999999999999999999999999998775544

>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=1e-17  Score=138.09  Aligned_cols=86  Identities=34%  Similarity=0.603  Sum_probs=80.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            34688999999999999999999999999999999998 48999999999999999999999999999999999999999


Q ss_pred             ccchhHH
Q 012034          105 QKKSERE  111 (472)
Q Consensus       105 ~~~~~~~  111 (472)
                      ..+..+.
T Consensus        86 ~~~~~~~   92 (104)
T 1p1t_A           86 ASEKNKE   92 (104)
T ss_dssp             TCTTHHH
T ss_pred             CCccchh
Confidence            8776554

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=9e-18  Score=136.97  Aligned_cols=83  Identities=31%  Similarity=0.508  Sum_probs=77.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC----CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG----DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~----~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.+..+.    +++++|||||+|.+.++|.+|++.||+..|.|+.|.|
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            457899999999999999999999999999999999884    3489999999999999999999999999999999999


Q ss_pred             eccccch
Q 012034          102 GKAQKKS  108 (472)
Q Consensus       102 ~~a~~~~  108 (472)
                      .++..+.
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9997654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=4.1e-18  Score=138.39  Aligned_cols=83  Identities=34%  Similarity=0.550  Sum_probs=78.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEE-EEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v-~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++ .|+.| .+++++|||||+|++.++|.+|++.||+..|.|+.|.|.+
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            457899999999999999999999999999999 99998 6899999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        83 a~~~~   87 (96)
T 1x5t_A           83 AFKKD   87 (96)
T ss_dssp             SCCCC
T ss_pred             ecccC
Confidence            97654

>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=99.73  E-value=1.6e-17  Score=136.82  Aligned_cols=83  Identities=35%  Similarity=0.578  Sum_probs=77.8

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|+.+..+ ++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            467899999999999999999999999999999999998655 8999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        91 ~~~~   94 (103)
T 2cq3_A           91 TARV   94 (103)
T ss_dssp             CSSC
T ss_pred             ccCC
Confidence            7654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.1e-17  Score=138.65  Aligned_cols=84  Identities=23%  Similarity=0.458  Sum_probs=79.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC--CCCceeEEEEEeCCHHHHHHHHHHH-CCCccCCcceee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG--DGKSKCFGFVNFENADDAAKAVEAL-NGKKFDDREWYV  101 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~--~g~skG~aFV~F~~~e~A~~Av~~l-ng~~i~g~~l~V  101 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.+.  +++++|||||+|.+.++|.+|++.| |+..|.|+.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            4568999999999999999999999999999999999984  8999999999999999999999999 999999999999


Q ss_pred             eccccch
Q 012034          102 GKAQKKS  108 (472)
Q Consensus       102 ~~a~~~~  108 (472)
                      .++..+.
T Consensus        92 ~~a~~~~   98 (107)
T 2cph_A           92 EWADSEV   98 (107)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9997654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.4e-17  Score=136.00  Aligned_cols=83  Identities=18%  Similarity=0.354  Sum_probs=77.9

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCee-EEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcc----
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT-SAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDRE----   98 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~-~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~----   98 (472)
                      ....++|||+|||.++|+++|+++|++||.|. ++.++.|. +++++|||||+|.+.++|.+|++.||+..+.|+.    
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            35678999999999999999999999999999 99999994 8999999999999999999999999999999999    


Q ss_pred             eeeeccccc
Q 012034           99 WYVGKAQKK  107 (472)
Q Consensus        99 l~V~~a~~~  107 (472)
                      |.|.++...
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998654

>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=99.72  E-value=7.9e-18  Score=141.76  Aligned_cols=83  Identities=45%  Similarity=0.719  Sum_probs=75.7

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .++|||+|||.++|+++|+++|+.||.|.+|+|+++. +.++|||||+|.+.++|.+|++.|||..|+|+.|.|.++..+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            4589999999999999999999999999999999985 458999999999999999999999999999999999999876


Q ss_pred             HHHH
Q 012034          211 EERR  214 (472)
Q Consensus       211 ~~~~  214 (472)
                      ..+.
T Consensus        84 ~~~~   87 (115)
T 4f25_A           84 KERE   87 (115)
T ss_dssp             CC--
T ss_pred             cccc
Confidence            5443

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=7.7e-18  Score=136.19  Aligned_cols=81  Identities=32%  Similarity=0.457  Sum_probs=76.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.+..+. +++++|||||+|++.++|.+|++.||+..|.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            3567899999999999999999999999999999999984 689999999999999999999999999999999999998


Q ss_pred             cc
Q 012034          104 AQ  105 (472)
Q Consensus       104 a~  105 (472)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=7.4e-18  Score=138.82  Aligned_cols=84  Identities=27%  Similarity=0.459  Sum_probs=78.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|+.+. +++++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3567899999999999999999999999999999999984 699999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +....
T Consensus        90 a~~~~   94 (103)
T 2dnm_A           90 ARYGR   94 (103)
T ss_dssp             CSSCC
T ss_pred             CCcCC
Confidence            97543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=5.8e-18  Score=139.14  Aligned_cols=84  Identities=31%  Similarity=0.405  Sum_probs=79.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|+.| .+++++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
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            457889999999999999999999999999999999998 5789999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        89 a~~~~   93 (102)
T 2cqb_A           89 AKPMR   93 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.72  E-value=1.3e-17  Score=137.28  Aligned_cols=83  Identities=27%  Similarity=0.387  Sum_probs=77.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|+.|..+ ++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            456899999999999999999999999999999999998544 6999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        91 ~~~~   94 (103)
T 2cqi_A           91 TTPS   94 (103)
T ss_dssp             CCTT
T ss_pred             CCCc
Confidence            7654

>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=99.72  E-value=8.5e-18  Score=140.32  Aligned_cols=85  Identities=27%  Similarity=0.417  Sum_probs=79.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHC------CCccCCc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALN------GKKFDDR   97 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~ln------g~~i~g~   97 (472)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|+.| .+++++|||||+|.+.++|.+|++.||      +..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            456889999999999999999999999999999999999 578999999999999999999999999      9999999


Q ss_pred             ceeeeccccchh
Q 012034           98 EWYVGKAQKKSE  109 (472)
Q Consensus        98 ~l~V~~a~~~~~  109 (472)
                      .|.|.++..+..
T Consensus        92 ~l~v~~a~~~~~  103 (111)
T 1x4h_A           92 QLKVDLAVTRDE  103 (111)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCcc
Confidence            999999976543

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.72  E-value=1.6e-17  Score=132.89  Aligned_cols=80  Identities=23%  Similarity=0.454  Sum_probs=75.5

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||.++|+++|+++|++||.|.++.+..+. +++++|||||+|.+.++|.+|+ .||+..+.|+.|.|.++.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            35789999999999999999999999999999999994 8999999999999999999999 899999999999999986


Q ss_pred             cc
Q 012034          106 KK  107 (472)
Q Consensus       106 ~~  107 (472)
                      .+
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=5.7e-18  Score=134.39  Aligned_cols=80  Identities=30%  Similarity=0.473  Sum_probs=75.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
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            46789999999999999999999999999999999998 57999999999999999999999999999999999999886


Q ss_pred             c
Q 012034          105 Q  105 (472)
Q Consensus       105 ~  105 (472)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.72  E-value=1.1e-17  Score=138.40  Aligned_cols=84  Identities=27%  Similarity=0.427  Sum_probs=78.3

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCcc---CCccee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKF---DDREWY  100 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i---~g~~l~  100 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.|. +|+++|||||+|.+.++|.+|++.||+..+   .|+.|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            4568899999999999999999999999999999999984 699999999999999999999999999998   899999


Q ss_pred             eeccccch
Q 012034          101 VGKAQKKS  108 (472)
Q Consensus       101 V~~a~~~~  108 (472)
                      |.++..+.
T Consensus        90 v~~a~~~~   97 (106)
T 2dgp_A           90 VKPADSES   97 (106)
T ss_dssp             EEECCCCS
T ss_pred             EEECCccc
Confidence            99997654

>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=99.72  E-value=1.3e-17  Score=143.47  Aligned_cols=84  Identities=35%  Similarity=0.473  Sum_probs=78.9

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.+++| .+|+++|||||+|.+.++|.+|++.||+..|+|+.|.|.+
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            466889999999999999999999999999999999998 5789999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            97653

>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=99.71  E-value=1.2e-17  Score=139.22  Aligned_cols=84  Identities=26%  Similarity=0.375  Sum_probs=78.9

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.+..+ .+|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
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            356789999999999999999999999999999999998 5899999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            97654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.71  E-value=1.2e-17  Score=145.26  Aligned_cols=85  Identities=25%  Similarity=0.475  Sum_probs=79.3

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||+|.+|.|+.+. +|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
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            3567899999999999999999999999999999999984 689999999999999999999999999999999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +..+..
T Consensus       119 a~~~~~  124 (139)
T 1u6f_A          119 AASGHQ  124 (139)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            976643

>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=99.71  E-value=8.6e-18  Score=134.05  Aligned_cols=81  Identities=27%  Similarity=0.440  Sum_probs=75.0

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CC-CceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DG-KSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g-~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +.++|||+|||.++|+++|+++|++||.|.++.+..+. ++ +++|||||+|.+.++|.+|++.|||..+.|+.|.|.++
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            56899999999999999999999999999999998885 33 38999999999999999999999999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ...
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.71  E-value=7.3e-18  Score=130.43  Aligned_cols=74  Identities=32%  Similarity=0.539  Sum_probs=70.9

Q ss_pred             eEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        30 ~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +|||+|||.++|+++|+++|++||.|.++.+..+. +|+++|||||+|.+.++|++|++ +|+..++|+.|.|.+|
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            59999999999999999999999999999999985 79999999999999999999998 9999999999999875

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.71  E-value=1.4e-17  Score=135.71  Aligned_cols=78  Identities=23%  Similarity=0.332  Sum_probs=72.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCc--cCCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK--FDDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~--i~g~~l~V~  102 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.+++     +||||||+|++.++|.+|++.|++..  +.|+.|+|.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-----CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            35688999999999999999999999999999999985     37999999999999999999999876  789999999


Q ss_pred             ccccc
Q 012034          103 KAQKK  107 (472)
Q Consensus       103 ~a~~~  107 (472)
                      +++.+
T Consensus        93 ~S~~k   97 (100)
T 3r27_A           93 YSTSQ   97 (100)
T ss_dssp             ECSCS
T ss_pred             ecccc
Confidence            99765

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.71  E-value=2.7e-17  Score=131.01  Aligned_cols=79  Identities=28%  Similarity=0.511  Sum_probs=73.8

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|++ +++..+.|+.|.|.+
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            467889999999999999999999999999999999999 479999999999999999999996 588899999999987


Q ss_pred             c
Q 012034          104 A  104 (472)
Q Consensus       104 a  104 (472)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.1e-17  Score=132.88  Aligned_cols=82  Identities=16%  Similarity=0.275  Sum_probs=77.4

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||+++|+++|+++|+.| .|.+|.++.+.+|+++|||||+|.+.++|.+|++ ||+..|.|+.|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            3567899999999999999999999999 9999999999999999999999999999999999 9999999999999998


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7653

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.71  E-value=6.3e-18  Score=146.55  Aligned_cols=121  Identities=19%  Similarity=0.273  Sum_probs=78.4

Q ss_pred             EEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHH
Q 012034           71 FGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE  150 (472)
Q Consensus        71 ~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~  150 (472)
                      ++|++|++...+..|++.+++....|+.- +.+....                  ......++|||+||+.++|+++|++
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~~~------------------~~~~~~~~l~V~nLp~~~te~~L~~   66 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGRPP------------------PDVEGMTSLKVDNLTYRTSPDTLRR   66 (135)
T ss_dssp             ------------------------------CCSCCSC------------------SSGGGCCCEEEECCCSSCHHHHHHH
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCC-CCcCCCC------------------CCCCCCCEEEEeCCCCCCCHHHHHH
Confidence            78899999999999999998877655431 1222111                  1222456899999999999999999


Q ss_pred             HHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          151 LFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       151 ~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+++.+
T Consensus        67 ~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~  127 (135)
T 2lea_A           67 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  127 (135)
T ss_dssp             HHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCC
T ss_pred             HHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            99999999999999885 7889999999999999999999999999999999999998764

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.2e-17  Score=140.05  Aligned_cols=85  Identities=29%  Similarity=0.444  Sum_probs=79.4

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCee--------EEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccC
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT--------SAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFD   95 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~--------~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~   95 (472)
                      ....++|||+|||.++|+++|+++|++||.|.        .|.|+.| .+|+++|||||+|.+.++|.+|++.||+..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            45789999999999999999999999999999        5999998 68999999999999999999999999999999


Q ss_pred             Ccceeeeccccchh
Q 012034           96 DREWYVGKAQKKSE  109 (472)
Q Consensus        96 g~~l~V~~a~~~~~  109 (472)
                      |+.|.|.++..+..
T Consensus        92 g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           92 GSKLKVSLARKKPP  105 (113)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CCEEEEEECCCCCC
Confidence            99999999987653

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.71  E-value=9.4e-18  Score=141.75  Aligned_cols=81  Identities=36%  Similarity=0.552  Sum_probs=76.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||+++|+++|+++|++||.|.+|.++.| .+|+++|||||+|.+.++|.+|++.||+..|+|+.|.|.+
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            356789999999999999999999999999999999998 5789999999999999999999999999999999999998


Q ss_pred             cc
Q 012034          104 AQ  105 (472)
Q Consensus       104 a~  105 (472)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            73

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.71  E-value=2e-17  Score=141.03  Aligned_cols=83  Identities=30%  Similarity=0.428  Sum_probs=79.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|..+.+|+++|||||+|++.++|.+|++.||+..|.|+.|.|.++
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ...
T Consensus       112 ~~~  114 (124)
T 2kt5_A          112 ASQ  114 (124)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            754

>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=99.71  E-value=1.4e-17  Score=135.43  Aligned_cols=81  Identities=26%  Similarity=0.295  Sum_probs=75.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHH----HHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           26 TKFNNVFVKNLDESTTDEDLK----KIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~----~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      ...++|||+|||+++|+++|+    ++|++||.|.+|.|+.|..+  +|||||+|.+.++|.+|++.||+..+.|+.|.|
T Consensus         7 ~~~~~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            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            457899999999999999999    99999999999999998665  899999999999999999999999999999999


Q ss_pred             eccccch
Q 012034          102 GKAQKKS  108 (472)
Q Consensus       102 ~~a~~~~  108 (472)
                      .++....
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9997654

>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=99.71  E-value=7.1e-18  Score=138.33  Aligned_cols=81  Identities=27%  Similarity=0.434  Sum_probs=74.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC--CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG--DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~--~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      ....++|||+|||.++|+++|+++|++|| |.+|.++.+.  +|+++|||||+|.+.++|.+|+ .||+..|.|+.|.|.
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            46789999999999999999999999999 9999999985  7999999999999999999999 899999999999999


Q ss_pred             ccccc
Q 012034          103 KAQKK  107 (472)
Q Consensus       103 ~a~~~  107 (472)
                      ++..+
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            98765

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1.8e-17  Score=137.01  Aligned_cols=84  Identities=27%  Similarity=0.513  Sum_probs=78.8

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|+.+ .+++++|||||+|++.++|.+|++. ++..|.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            467899999999999999999999999999999999999 5799999999999999999999998 99999999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +..+..
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            976643

>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=99.71  E-value=4.5e-17  Score=136.65  Aligned_cols=83  Identities=20%  Similarity=0.434  Sum_probs=76.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCcc--------CC
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF--------DD   96 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i--------~g   96 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.|+.+.+++++|||||+|.+.++|.+|++.|||..|        .+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            3567899999999999999999999999999999999999999999999999999999999999999999        46


Q ss_pred             cceeeeccccc
Q 012034           97 REWYVGKAQKK  107 (472)
Q Consensus        97 ~~l~V~~a~~~  107 (472)
                      +.|.|.++..+
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            67888887643

>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=99.71  E-value=1.3e-17  Score=135.05  Aligned_cols=81  Identities=21%  Similarity=0.292  Sum_probs=73.9

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|++||.|.++.++.+ .+++++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            45689999999999999999999999999998888776 67899999999999999999999999999999999999987


Q ss_pred             cc
Q 012034          105 QK  106 (472)
Q Consensus       105 ~~  106 (472)
                      ..
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            53

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.71  E-value=1.5e-17  Score=140.74  Aligned_cols=82  Identities=18%  Similarity=0.233  Sum_probs=77.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCC---eeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGT---ITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~---I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      ...++|||+|||+++|+++|+++|+.||.   |.+|.|+.|.+|+++|||||+|++.++|++|++ +|++.|.|+.|.|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEE
Confidence            56788999999999999999999999999   899999999889999999999999999999999 99999999999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      ++..+.
T Consensus        94 ~a~~~~   99 (118)
T 2db1_A           94 KSHRTE   99 (118)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            986543

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=1.2e-17  Score=136.18  Aligned_cols=83  Identities=22%  Similarity=0.270  Sum_probs=76.3

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||+++|+++|+++|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
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            356789999999999999999999999999998777776 6899999999999999999999999999999999999999


Q ss_pred             cccc
Q 012034          104 AQKK  107 (472)
Q Consensus       104 a~~~  107 (472)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8653

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.4e-17  Score=138.85  Aligned_cols=82  Identities=34%  Similarity=0.564  Sum_probs=76.8

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.+..|.. .++|||||+|.+.++|.+|++.|||..|+|+.|.|.++
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  104 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA  104 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            46789999999999999999999999999999999999854 48999999999999999999999999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ..+
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            765

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.70  E-value=3.2e-17  Score=135.01  Aligned_cols=82  Identities=28%  Similarity=0.426  Sum_probs=76.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++|| |.+|.++.|. +++++|||||+|++.++|.+|+ .||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            45688999999999999999999999997 9999999995 6999999999999999999999 8999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        90 a~~~~   94 (103)
T 2dng_A           90 AEGRK   94 (103)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            87654

>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=99.70  E-value=1.6e-17  Score=143.78  Aligned_cols=81  Identities=17%  Similarity=0.200  Sum_probs=76.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCC---eeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGT---ITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~---I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      ...++|||+|||+++|+++|+++|+.||.   |.+|.|++|.+|+++|||||+|++.++|++|++ +|++.|.|+.|.|.
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~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            56789999999999999999999999999   899999999889999999999999999999999 99999999999999


Q ss_pred             ccccc
Q 012034          103 KAQKK  107 (472)
Q Consensus       103 ~a~~~  107 (472)
                      ++..+
T Consensus       121 ~a~~~  125 (136)
T 2hgl_A          121 KSHRT  125 (136)
T ss_dssp             ECCHH
T ss_pred             ECChH
Confidence            98654

>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=99.70  E-value=2.1e-17  Score=136.12  Aligned_cols=81  Identities=17%  Similarity=0.187  Sum_probs=74.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||+++|+++|+++|++||.+ +|.|+.|.+|+++|||||+|++.++|++||+ +|++.|.++.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            3567899999999999999999999999955 9999999999999999999999999999995 7999999999999887


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ...
T Consensus        90 ~~~   92 (102)
T 1wez_A           90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.70  E-value=8.8e-18  Score=137.96  Aligned_cols=78  Identities=15%  Similarity=0.220  Sum_probs=71.4

Q ss_pred             CCcceEEeCCCCC-CCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCC--ccCCcceeee
Q 012034           26 TKFNNVFVKNLDE-STTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK--KFDDREWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~-~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~--~i~g~~l~V~  102 (472)
                      ...++|||+|||+ ++|+++|+++|++||.|.+|.|+++     +|||||+|++.++|.+|++.||+.  .|.|+.|+|.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            4678999999999 9999999999999999999999875     689999999999999999999865  4999999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      ++.++.
T Consensus        88 ~a~~~~   93 (102)
T 1x4d_A           88 LSQKYK   93 (102)
T ss_dssp             EECCCT
T ss_pred             ECCCCC
Confidence            998643

>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=99.70  E-value=9.6e-18  Score=140.99  Aligned_cols=85  Identities=24%  Similarity=0.282  Sum_probs=78.9

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCe-eEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTI-TSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I-~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||+++|+++|+++|+.||.| .+|.|+.|.+|+++|||||+|.+.++|.+||+. |+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            3567899999999999999999999999999 899999999999999999999999999999986 99999999999999


Q ss_pred             cccchhH
Q 012034          104 AQKKSER  110 (472)
Q Consensus       104 a~~~~~~  110 (472)
                      +..+..+
T Consensus        91 a~~~~~~   97 (114)
T 2cpy_A           91 VTLEDMR   97 (114)
T ss_dssp             ECHHHHH
T ss_pred             CCHHHHH
Confidence            9766544

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.70  E-value=5e-17  Score=151.84  Aligned_cols=107  Identities=37%  Similarity=0.612  Sum_probs=88.6

Q ss_pred             ccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHH
Q 012034            3 INDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDA   82 (472)
Q Consensus         3 ~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A   82 (472)
                      +.|+.+.+..........    ....++|||+|||+++|+++|+++|++||.|.+|.|+.|.+ .++|||||+|.+.++|
T Consensus        82 ~~g~~i~~~~~~~~~~~~----~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~-~~~g~~fV~f~~~~~a  156 (213)
T 4f02_A           82 IKGKPVRIMWSQRDPSLR----KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAA  156 (213)
T ss_dssp             ETTEECEEEECCCCTHHH----HHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESSHHHH
T ss_pred             cCCccccccccccccccc----ccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC-CCceEEEEEeCCHHHH
Confidence            455666655444333222    23567899999999999999999999999999999999854 4799999999999999


Q ss_pred             HHHHHHHCCCccCCcceeeeccccchhHHHHH
Q 012034           83 AKAVEALNGKKFDDREWYVGKAQKKSEREQEL  114 (472)
Q Consensus        83 ~~Av~~lng~~i~g~~l~V~~a~~~~~~~~~~  114 (472)
                      .+|++.|||..|+|+.|.|.++..+.+++...
T Consensus       157 ~~Ai~~lng~~~~g~~i~V~~a~~~~~~~~~~  188 (213)
T 4f02_A          157 ERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL  188 (213)
T ss_dssp             HHHHHHHTTCEETTEECEEEECCCHHHHHHHH
T ss_pred             HHHHHHhCCCEECCEEEEEEEcCCCcccchhh
Confidence            99999999999999999999998876655443

>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=99.70  E-value=2.3e-17  Score=136.28  Aligned_cols=81  Identities=19%  Similarity=0.245  Sum_probs=75.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeE-EEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~-v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|+.||.|.+ |.|+.|.+|+++|||||+|++.++|.+|++. ++..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEEC
Confidence            56789999999999999999999999999987 8888888999999999999999999999997 999999999999987


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ..+
T Consensus        92 ~~~   94 (104)
T 1wg5_A           92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.70  E-value=1.8e-17  Score=134.46  Aligned_cols=78  Identities=18%  Similarity=0.322  Sum_probs=72.3

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCc--eEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCc----EecCeeEEE
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGT--ITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGK----MIVSKPLYV  204 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~--I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~----~i~gk~l~V  204 (472)
                      .+|||+||+.++|+++|+++|++||.  |.+|++++|+ +|.+||||||+|.+.++|.+|++.|||.    .|+|++|.|
T Consensus        10 ~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V   89 (95)
T 2lkz_A           10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV   89 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEE
Confidence            47999999999999999999999995  6789999986 6899999999999999999999999996    589999999


Q ss_pred             EEccc
Q 012034          205 AVAQR  209 (472)
Q Consensus       205 ~~a~~  209 (472)
                      +||+.
T Consensus        90 ~~Aks   94 (95)
T 2lkz_A           90 DFAKS   94 (95)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            99875

>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=99.70  E-value=4.4e-17  Score=135.63  Aligned_cols=82  Identities=24%  Similarity=0.379  Sum_probs=75.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|..+  ++++|||||+|++.++|.+|++.||+..|.|+.|.|.++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            467899999999999999999999999999999999654  568999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        97 ~~~~  100 (109)
T 1x4a_A           97 RSGR  100 (109)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            7653

>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=99.70  E-value=7.8e-17  Score=127.03  Aligned_cols=79  Identities=34%  Similarity=0.650  Sum_probs=75.4

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC-CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~-~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ++|||+|||.++++++|+++|+.||.|.++.++.+ .+|.++|||||+|.+.++|.+|++.|||..++|+.|+|.++..+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            58999999999999999999999999999999988 47899999999999999999999999999999999999999875

>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=99.70  E-value=1.6e-17  Score=139.53  Aligned_cols=83  Identities=20%  Similarity=0.356  Sum_probs=77.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|+.||.|.+|.|+.|. +|+++|||||+|.+.++|.+|+ .||+..|.|+.|.|.++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            456899999999999999999999999999999999985 5899999999999999999999 99999999999999998


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      ..+..
T Consensus       102 ~~~~~  106 (114)
T 2cq4_A          102 QAEKN  106 (114)
T ss_dssp             HHHHH
T ss_pred             CCCcc
Confidence            76543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.70  E-value=2.3e-17  Score=129.89  Aligned_cols=74  Identities=16%  Similarity=0.224  Sum_probs=69.9

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..+-|||+||++.+||++|+++|.+||+|.++.+..     +||||||+|.+.++|.+|++.||+..+.|+.|+|.+|.
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            456799999999999999999999999999999865     69999999999999999999999999999999999993

>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=99.70  E-value=6.1e-18  Score=135.71  Aligned_cols=81  Identities=30%  Similarity=0.526  Sum_probs=73.0

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .++|||+|||.++|+++|+++|++||.|.++.+..+. +|+++|||||+|.+.+ |.+|++.||+..+.|+.|.|.+|..
T Consensus         1 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANP   79 (90)
T ss_dssp             CEEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC--
T ss_pred             CcEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCC
Confidence            3689999999999999999999999999999999984 6999999999999999 9999999999999999999999976


Q ss_pred             chh
Q 012034          107 KSE  109 (472)
Q Consensus       107 ~~~  109 (472)
                      +..
T Consensus        80 ~~~   82 (90)
T 2ki2_A           80 KKS   82 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.70  E-value=1.4e-17  Score=131.07  Aligned_cols=73  Identities=27%  Similarity=0.506  Sum_probs=68.4

Q ss_pred             ceEEeCCCCCCC------CHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCc-ceee
Q 012034           29 NNVFVKNLDEST------TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR-EWYV  101 (472)
Q Consensus        29 ~~l~V~nLp~~~------tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~-~l~V  101 (472)
                      ++|||+|||.++      |+++|+++|++||.|.++.+. +.+|+++|||||+|.+.++|.+|++.|||..+.|+ .|.|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            789999999999      779999999999999999987 56889999999999999999999999999999999 8877


Q ss_pred             e
Q 012034          102 G  102 (472)
Q Consensus       102 ~  102 (472)
                      .
T Consensus        81 ~   81 (81)
T 2krb_A           81 N   81 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=1.1e-17  Score=130.00  Aligned_cols=75  Identities=29%  Similarity=0.529  Sum_probs=71.7

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ++|||+|||.++|+++|+++|++||.|.++.+..+. +|+++|||||+|.+.++|.+|++.++ ..+.|+.|.|.+|
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            579999999999999999999999999999999984 79999999999999999999999998 9999999999986

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.70  E-value=1.4e-17  Score=134.09  Aligned_cols=79  Identities=20%  Similarity=0.363  Sum_probs=72.9

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccC-ceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhC-CcEecCeeEEEEEcc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN-GKMIVSKPLYVAVAQ  208 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G-~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~-g~~i~gk~l~V~~a~  208 (472)
                      .+|||+|||.++|+++|+++|+.|| .|.+|+|++++ +|.++|||||+|.+.++|.+|++.++ +..++|++|.|.++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            4799999999999999999999999 89999999885 68999999999999999999999874 567999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      ++
T Consensus        82 ~~   83 (91)
T 2lxi_A           82 PK   83 (91)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.70  E-value=8.7e-17  Score=127.92  Aligned_cols=81  Identities=28%  Similarity=0.539  Sum_probs=75.0

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+++++.+. ++.++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
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            35689999999999999999999999999999999985 78999999999999999999999999999999999999998


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            65

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.70  E-value=9.9e-18  Score=144.49  Aligned_cols=82  Identities=18%  Similarity=0.362  Sum_probs=77.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeE--EEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCC----ccCCc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS--AVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGK----KFDDR   97 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~--v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~----~i~g~   97 (472)
                      ....++|||+|||+++|+++|+++|++||.|.+  |+|++|. +|++||||||+|++. +|.+|++.||+.    .|.|+
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            356789999999999999999999999999977  9999996 899999999999999 999999999999    99999


Q ss_pred             ceeeeccccc
Q 012034           98 EWYVGKAQKK  107 (472)
Q Consensus        98 ~l~V~~a~~~  107 (472)
                      .|.|.++..+
T Consensus        99 ~l~V~~a~~~  108 (131)
T 2m2b_A           99 TINVEFAKGS  108 (131)
T ss_dssp             CCCCEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999999764

>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=99.70  E-value=2e-17  Score=138.33  Aligned_cols=83  Identities=23%  Similarity=0.390  Sum_probs=76.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHH---HHHhcCCCeeEEEEEECC----CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcc
Q 012034           26 TKFNNVFVKNLDESTTDEDLK---KIFGEYGTITSAVVMRDG----DGKSKCFGFVNFENADDAAKAVEALNGKKFDDRE   98 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~---~~F~~fG~I~~v~i~~d~----~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~   98 (472)
                      ...++|||+|||+++|+++|+   ++|++||.|.+|.|..+.    +++++|||||+|++.++|.+|++.||+..|+|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            457889999999999999999   999999999999999884    2367799999999999999999999999999999


Q ss_pred             eeeeccccch
Q 012034           99 WYVGKAQKKS  108 (472)
Q Consensus        99 l~V~~a~~~~  108 (472)
                      |.|.++..+.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998764

>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=99.70  E-value=3.6e-17  Score=139.82  Aligned_cols=85  Identities=27%  Similarity=0.388  Sum_probs=79.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.|+.+. +++++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            3567899999999999999999999999999999999984 899999999999999999999999999999999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +..+..
T Consensus        99 a~~~~~  104 (126)
T 3ex7_B           99 CFVRGP  104 (126)
T ss_dssp             SEESSS
T ss_pred             ecCCCC
Confidence            976543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2.6e-17  Score=138.63  Aligned_cols=82  Identities=37%  Similarity=0.531  Sum_probs=77.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      +...++|||+|||+++|+++|+++|++||.|.+|.|+.+ .+++++|||||+|.+.++|.+|++.+++ .|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            467899999999999999999999999999999999998 4799999999999999999999999998 89999999999


Q ss_pred             cccc
Q 012034          104 AQKK  107 (472)
Q Consensus       104 a~~~  107 (472)
                      +..+
T Consensus        93 a~~~   96 (116)
T 2cqd_A           93 AYLG   96 (116)
T ss_dssp             STTT
T ss_pred             cccC
Confidence            8654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=2.7e-17  Score=139.84  Aligned_cols=82  Identities=20%  Similarity=0.213  Sum_probs=75.7

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCe----eEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTI----TSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I----~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      ....++|||+|||+++|+++|+++|++||.|    .+|.|++|.+|+++|||||+|++.++|.+||+. |++.|.++.|.
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            4667899999999999999999999999975    689999999999999999999999999999986 99999999999


Q ss_pred             eeccccc
Q 012034          101 VGKAQKK  107 (472)
Q Consensus       101 V~~a~~~  107 (472)
                      |..+..+
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9888644

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.69  E-value=5.8e-17  Score=138.69  Aligned_cols=84  Identities=18%  Similarity=0.264  Sum_probs=76.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHH----HHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           26 TKFNNVFVKNLDESTTDEDLK----KIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~----~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      ...++|||+|||+++++++|+    ++|++||.|.+|.+.  .++++||||||+|.+.++|.+|++.|||..|.|+.|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~--~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC--CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec--cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            457899999999999999876    699999999988774  46889999999999999999999999999999999999


Q ss_pred             eccccchhHH
Q 012034          102 GKAQKKSERE  111 (472)
Q Consensus       102 ~~a~~~~~~~  111 (472)
                      .++..+....
T Consensus       105 ~~a~~~~~~~  114 (127)
T 2a3j_A          105 TFSETPQSQV  114 (127)
T ss_dssp             EECCCCCHHH
T ss_pred             EEccCcchhc
Confidence            9998876644

>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=99.69  E-value=2.3e-17  Score=136.18  Aligned_cols=83  Identities=25%  Similarity=0.439  Sum_probs=76.9

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-C-CCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-D-GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~-g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      ....++|||+|||.++|+++|+++|++|| |.+|.|+.+. + |+++|||||+|.+.++|.+|+ .||+..|.|+.|.|.
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            35678999999999999999999999999 9999999985 3 899999999999999999999 899999999999999


Q ss_pred             ccccchh
Q 012034          103 KAQKKSE  109 (472)
Q Consensus       103 ~a~~~~~  109 (472)
                      ++..+..
T Consensus        90 ~a~~~~~   96 (104)
T 1wi8_A           90 VADQAQD   96 (104)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9976543

>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=99.69  E-value=3.6e-17  Score=137.82  Aligned_cols=79  Identities=13%  Similarity=0.260  Sum_probs=72.4

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCC--CccCCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG--KKFDDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng--~~i~g~~l~V~  102 (472)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|+++     ||||||+|++.++|.+|++.|++  ..|.|+.|+|.
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            356789999999999999999999999999999999976     79999999999999999998874  68999999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      ++..+.
T Consensus       103 ~a~~k~  108 (119)
T 2ad9_A          103 FSNHKE  108 (119)
T ss_dssp             ECSSSS
T ss_pred             EccCCC
Confidence            997654

>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=99.69  E-value=8.2e-17  Score=142.91  Aligned_cols=83  Identities=27%  Similarity=0.360  Sum_probs=78.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.|+.+. +++++|||||+|++.++|.+||+.||+..|.|+.|.|.++
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            467999999999999999999999999999999999995 6899999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ....
T Consensus       117 ~~~~  120 (156)
T 1h2v_Z          117 AGFK  120 (156)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7644

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.69  E-value=4.1e-17  Score=133.77  Aligned_cols=82  Identities=20%  Similarity=0.304  Sum_probs=77.2

Q ss_pred             cceeeeecCCC------CccHHHHHHHHhccCceEEEEEeeCCC-CCcccEEEEEcCCHHHHHHHHHHhCCcEecC-eeE
Q 012034          131 GLNLYIKNLGD------SIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEMNGKMIVS-KPL  202 (472)
Q Consensus       131 ~~~l~V~nL~~------~~t~e~L~~~F~~~G~I~~v~i~~~~~-g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g-k~l  202 (472)
                      +++|||+|||.      ++++++|+++|+.||.|.+|+|++++. |+++|||||+|.+.++|.+|++.|||..+.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            46899999999      999999999999999999999999874 8999999999999999999999999999999 999


Q ss_pred             EEEEcccHHH
Q 012034          203 YVAVAQRKEE  212 (472)
Q Consensus       203 ~V~~a~~k~~  212 (472)
                      .|.++..++.
T Consensus        86 ~V~~a~~~~~   95 (100)
T 3ns6_A           86 FLYTMKDVER   95 (100)
T ss_dssp             EEEESHHHHH
T ss_pred             EEEECchhhh
Confidence            9999987654

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=8.7e-17  Score=132.37  Aligned_cols=83  Identities=29%  Similarity=0.423  Sum_probs=76.4

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|+.+ .+|+++|||||+|.+.++|.+|++  +++.|.|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            356789999999999999999999999999999999999 479999999999999999999998  57899999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +..+..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            976543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=3.8e-17  Score=136.07  Aligned_cols=78  Identities=21%  Similarity=0.260  Sum_probs=73.5

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      .++|||+|||+++|+++|+++|+.| .|.+|.|+.|.+|+++|||||+|++.++|.+|| .+|++.|.|+.|.|..+..+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            5789999999999999999999999 899999999988999999999999999999999 69999999999999888643

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=1.1e-16  Score=130.91  Aligned_cols=82  Identities=26%  Similarity=0.453  Sum_probs=77.8

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...++|||+||+.++|+++|+++|+.||.|.+|+|+.+.+|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   94 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISN   94 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        95 ~~   96 (100)
T 2do4_A           95 SG   96 (100)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.68  E-value=6.5e-17  Score=132.73  Aligned_cols=78  Identities=13%  Similarity=0.271  Sum_probs=71.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHH--CCCccCCcceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL--NGKKFDDREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~l--ng~~i~g~~l~V~~  103 (472)
                      ...++|||+|||+++|+++|+++|++||.|.+|.++++     ||||||+|++.++|.+|++.|  ++..+.|+.|+|.+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~   87 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQY   87 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEE
Confidence            46789999999999999999999999999999998865     899999999999999999987  46789999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        88 a~~~~   92 (101)
T 2cq1_A           88 SNHKE   92 (101)
T ss_dssp             CSCSS
T ss_pred             cCccc
Confidence            97654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.68  E-value=3e-17  Score=135.87  Aligned_cols=81  Identities=25%  Similarity=0.395  Sum_probs=75.1

Q ss_pred             CCcceEEeCCCCCCC------CHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCc-c
Q 012034           26 TKFNNVFVKNLDEST------TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR-E   98 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~------tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~-~   98 (472)
                      ...++|||+|||+++      |+++|+++|++||.|.+|.+. ..+|+++|||||+|.+.++|.+|++.|||..|.|+ .
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            457899999999999      789999999999999999988 56889999999999999999999999999999999 9


Q ss_pred             eeeeccccc
Q 012034           99 WYVGKAQKK  107 (472)
Q Consensus        99 l~V~~a~~~  107 (472)
                      |.|.++...
T Consensus        92 l~V~~a~~~  100 (105)
T 2nlw_A           92 FRVNLFTDF  100 (105)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEEcchH
Confidence            999998643

>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=99.68  E-value=5.8e-17  Score=153.14  Aligned_cols=83  Identities=24%  Similarity=0.318  Sum_probs=77.1

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCC--CeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYG--TITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG--~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ..++|||+||++++|+++|+++|++||  .|.+|.|++| .+|++||||||+|++.++|.+||+.||++.|.|+.|.|.+
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            567899999999999999999999999  9999999999 5899999999999999999999999999999999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +.....
T Consensus       147 a~~~~~  152 (229)
T 3q2s_C          147 VNKQFL  152 (229)
T ss_dssp             CCHHHH
T ss_pred             CCCCcc
Confidence            976543

>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=99.68  E-value=6.2e-17  Score=133.60  Aligned_cols=78  Identities=26%  Similarity=0.311  Sum_probs=70.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCC--ccCCcceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK--KFDDREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~--~i~g~~l~V~~  103 (472)
                      ...++|||+|||+++|+++|+++|++||.|.+|.++++     ||||||+|++.++|.+|++.|++.  .|.|+.|+|.+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~   87 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            45789999999999999999999999999999998864     799999999999999999998764  49999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        88 a~~~~   92 (104)
T 1wex_A           88 STSKR   92 (104)
T ss_dssp             CSSSS
T ss_pred             ccCcc
Confidence            97654

>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=99.68  E-value=1.4e-16  Score=130.14  Aligned_cols=82  Identities=30%  Similarity=0.491  Sum_probs=77.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   86 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            45789999999999999999999999999999999987 88999999999999999999999999999999999999988


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .+.
T Consensus        87 ~~~   89 (99)
T 1whw_A           87 IKK   89 (99)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            764

>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=99.68  E-value=4.3e-17  Score=135.61  Aligned_cols=84  Identities=17%  Similarity=0.226  Sum_probs=76.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCC-eeEEEEE-EC-CCCCceeEEEEEeCCHHHHHHHHHHHC--CCccCCccee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGT-ITSAVVM-RD-GDGKSKCFGFVNFENADDAAKAVEALN--GKKFDDREWY  100 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~-I~~v~i~-~d-~~g~skG~aFV~F~~~e~A~~Av~~ln--g~~i~g~~l~  100 (472)
                      ...++|||+|||+++|+++|+++|++||. |.++.++ .+ .+|+++|||||+|.+.++|.+|++.|+  +..+.|+.|.
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            46789999999999999999999999998 9999998 55 468999999999999999999999996  5899999999


Q ss_pred             eeccccchh
Q 012034          101 VGKAQKKSE  109 (472)
Q Consensus       101 V~~a~~~~~  109 (472)
                      |.++..+..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987654

>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=99.68  E-value=1.2e-16  Score=126.46  Aligned_cols=79  Identities=29%  Similarity=0.500  Sum_probs=74.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC-CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~-~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||+.++++++|+++|+.||.|.++.++.+ .++.++|||||+|.+.++|.+|++.|||..++|+.|+|.+++
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            4568999999999999999999999999999999887 578899999999999999999999999999999999999974

>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=99.68  E-value=1.3e-16  Score=129.14  Aligned_cols=80  Identities=31%  Similarity=0.529  Sum_probs=76.1

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+|+|..+.++.++|||||+|.+.++|.+|++.||+..++|+.|.|.+++.
T Consensus        15 ~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           15 ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             GGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            45689999999999999999999999999999999998899999999999999999999999999999999999998863

>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=99.68  E-value=3.6e-17  Score=139.58  Aligned_cols=84  Identities=20%  Similarity=0.237  Sum_probs=75.9

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeE-EEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~-v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||+++|+++|+++|+.||.|.+ +.+..+.+|+++|||||+|.+.++|.+||+ ||+..|.|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            356789999999999999999999999999988 455555799999999999999999999999 999999999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +..+..
T Consensus       101 a~~~~~  106 (124)
T 1wel_A          101 ITKKGM  106 (124)
T ss_dssp             ECHHHH
T ss_pred             CCHHHH
Confidence            976543

>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=8.8e-17  Score=131.86  Aligned_cols=77  Identities=21%  Similarity=0.377  Sum_probs=72.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.+.     +++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-----PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-----TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-----cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            3457899999999999999999999999999999998     45899999999999999999999999999999999998


Q ss_pred             cc
Q 012034          105 QK  106 (472)
Q Consensus       105 ~~  106 (472)
                      ..
T Consensus        99 ~~  100 (101)
T 2la4_A           99 KE  100 (101)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=9.1e-17  Score=132.44  Aligned_cols=84  Identities=20%  Similarity=0.301  Sum_probs=77.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+|||.++|+++|+++|+.||.|.+|.|+++..|.++|||||+|.+.++|.+|+. +++..++|+.|.|.++..
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            3468999999999999999999999999999999999889999999999999999999998 999999999999999877


Q ss_pred             HHHHH
Q 012034          210 KEERR  214 (472)
Q Consensus       210 k~~~~  214 (472)
                      ...++
T Consensus        89 ~~~~k   93 (103)
T 1s79_A           89 YFAKK   93 (103)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55443

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.68  E-value=3.3e-17  Score=136.61  Aligned_cols=83  Identities=27%  Similarity=0.451  Sum_probs=74.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.|. +|+++|||||+|.+.++|.+|++.+ +..++|+.|.|.+
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            4678899999999999999999999999999999999994 6999999999999999999999975 5999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus       101 a~~~~  105 (109)
T 2rs2_A          101 AFPRR  105 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            87654

>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=99.68  E-value=2.4e-17  Score=136.93  Aligned_cols=83  Identities=19%  Similarity=0.189  Sum_probs=77.4

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCC---eeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGT---ITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~---I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|.|+.|.+|+++|||||+|.+.++|.+|++ +|+..++|+.|.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            356789999999999999999999999998   899999999889999999999999999999999 9999999999999


Q ss_pred             eccccch
Q 012034          102 GKAQKKS  108 (472)
Q Consensus       102 ~~a~~~~  108 (472)
                      .++..+.
T Consensus        87 ~~a~~~~   93 (107)
T 2lmi_A           87 YEINNED   93 (107)
T ss_dssp             EECCHHH
T ss_pred             EECCHHH
Confidence            9987543

>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=99.68  E-value=3.1e-17  Score=145.81  Aligned_cols=83  Identities=30%  Similarity=0.512  Sum_probs=78.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+.| .+|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45789999999999999999999999999999999999 48999999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus       148 ~~~~  151 (158)
T 2kn4_A          148 RYGR  151 (158)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.68  E-value=2.1e-16  Score=140.31  Aligned_cols=85  Identities=19%  Similarity=0.290  Sum_probs=79.0

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccC--ceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFG--TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G--~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      .++|||+||++++|+++|+++|+.||  .|.+|+|+.|+ +|.++|||||+|.+.++|.+||+.|||..|+|+.|.|.++
T Consensus        55 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a  134 (156)
T 3n9u_C           55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA  134 (156)
T ss_dssp             -CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEc
Confidence            46899999999999999999999999  99999999985 7999999999999999999999999999999999999999


Q ss_pred             ccHHHHHH
Q 012034          208 QRKEERRA  215 (472)
Q Consensus       208 ~~k~~~~~  215 (472)
                      ..+..+..
T Consensus       135 ~~~~~~~~  142 (156)
T 3n9u_C          135 TRQNLSQF  142 (156)
T ss_dssp             CHHHHHHH
T ss_pred             CCCcchhh
Confidence            88765543

>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=99.68  E-value=3e-17  Score=131.85  Aligned_cols=80  Identities=24%  Similarity=0.337  Sum_probs=71.0

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccC--ceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFG--TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G--~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+|||+||++++|+++|+++|+.||  .|.+++++.++ +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            3799999999999999999999999  99999999985 88999999999999999999999999999999999999887


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      ...
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=5.1e-17  Score=136.83  Aligned_cols=83  Identities=31%  Similarity=0.558  Sum_probs=77.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.|+.| .+++++|||||+|.+.++|.+|++. ++..|.|+.|.|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            34689999999999999999999999999999999999 5799999999999999999999997 999999999999999


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      ..+..
T Consensus       104 ~~~~~  108 (116)
T 1x4b_A          104 VAREE  108 (116)
T ss_dssp             SSCCC
T ss_pred             CCCcc
Confidence            87643

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.68  E-value=6.9e-17  Score=137.62  Aligned_cols=81  Identities=25%  Similarity=0.426  Sum_probs=76.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.++.| .+|+++|||||+|.+.++|.+|+ .||+..|.|+.|.|.++
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            45789999999999999999999999999999999998 58999999999999999999999 79999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ...
T Consensus       113 ~~~  115 (124)
T 2jwn_A          113 RTN  115 (124)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            653

>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=99.68  E-value=1.8e-16  Score=128.74  Aligned_cols=83  Identities=25%  Similarity=0.420  Sum_probs=77.6

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      +++|||+||+.++++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.++..
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            4689999999999999999999999999999999885 689999999999999999999999999999999999999987


Q ss_pred             HHHH
Q 012034          210 KEER  213 (472)
Q Consensus       210 k~~~  213 (472)
                      +...
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            7543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=5.3e-17  Score=133.16  Aligned_cols=81  Identities=25%  Similarity=0.421  Sum_probs=74.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|   .++.+.+++++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            3568999999999999999999999999987   5666778999999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        89 ~~~~   92 (101)
T 2fc9_A           89 GPRG   92 (101)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            7653

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.7e-16  Score=127.31  Aligned_cols=78  Identities=24%  Similarity=0.514  Sum_probs=72.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.+.       +|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            3568899999999999999999999999999999997       579999999999999999999999999999999999


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      ..+..
T Consensus        78 ~~~~~   82 (90)
T 2dnq_A           78 KNKSK   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            76543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=9.3e-17  Score=132.18  Aligned_cols=84  Identities=63%  Similarity=1.028  Sum_probs=78.8

Q ss_pred             cccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       127 ~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      .....++|||+||+.++|+++|+++|+.||.|.+|+|..+ ++.++|||||+|.+.++|.+|++.|||..+.|+.|.|.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4456789999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             cccHH
Q 012034          207 AQRKE  211 (472)
Q Consensus       207 a~~k~  211 (472)
                      +..+.
T Consensus        90 a~~~~   94 (103)
T 2d9p_A           90 AQRKE   94 (103)
T ss_dssp             CSSCC
T ss_pred             ecccc
Confidence            98753

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.67  E-value=2.2e-16  Score=124.30  Aligned_cols=75  Identities=23%  Similarity=0.385  Sum_probs=70.3

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +..|||+||++.+|+++|+++|++||.|.++++..     ++|||||+|.+.++|.+|++.||+..+.|++|+|++|...
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e~   81 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSEN   81 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCHH
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCHH
Confidence            45799999999999999999999999999999976     5999999999999999999999999999999999999543

>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=99.67  E-value=3.4e-17  Score=136.51  Aligned_cols=79  Identities=25%  Similarity=0.308  Sum_probs=71.3

Q ss_pred             cCCcceEEeCCCCCC-CCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCC--CccCCcceee
Q 012034           25 KTKFNNVFVKNLDES-TTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG--KKFDDREWYV  101 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~-~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng--~~i~g~~l~V  101 (472)
                      ....++|||+|||++ +|+++|+++|++||.|.+|.|++     +||||||+|++.++|.+|++.|++  ..|.|+.|+|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            356889999999998 99999999999999999999974     489999999999999999998864  5699999999


Q ss_pred             eccccch
Q 012034          102 GKAQKKS  108 (472)
Q Consensus       102 ~~a~~~~  108 (472)
                      .+++++.
T Consensus        97 ~~a~~~~  103 (112)
T 1x4f_A           97 DLSEKYK  103 (112)
T ss_dssp             EEECSCS
T ss_pred             EECcccc
Confidence            9997654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.8e-16  Score=128.31  Aligned_cols=81  Identities=35%  Similarity=0.619  Sum_probs=76.3

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+++|||+||+.++++++|+++|+.||.|.+++++.+. ++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            45689999999999999999999999999999999985 58899999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        84 ~~   85 (95)
T 2dnz_A           84 ER   85 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            65

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.67  E-value=3.3e-16  Score=145.76  Aligned_cols=107  Identities=27%  Similarity=0.518  Sum_probs=91.9

Q ss_pred             cccCeeEEEcCcccchhhhhh-----hccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEE
Q 012034            2 LINDKQVFVGHFLRKQERETV-----AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVN   75 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~-----~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~   75 (472)
                      .|+|+.|.|........+...     ......++|||+|||.++|+++|+++|++||.|.+|.+..+ .+|+++|||||+
T Consensus        94 ~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~  173 (216)
T 2qfj_A           94 MLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIE  173 (216)
T ss_dssp             CCC-CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEE
T ss_pred             eeCCeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEE
Confidence            467888888776655543221     12467899999999999999999999999999999999999 589999999999


Q ss_pred             eCCHHHHHHHHHHHCCCccCCcceeeeccccch
Q 012034           76 FENADDAAKAVEALNGKKFDDREWYVGKAQKKS  108 (472)
Q Consensus        76 F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~  108 (472)
                      |.+.++|.+|++.||+..|+|+.|.|.++..+.
T Consensus       174 F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          174 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             ESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             ecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            999999999999999999999999999987653

>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=99.67  E-value=1.9e-16  Score=145.10  Aligned_cols=108  Identities=24%  Similarity=0.410  Sum_probs=85.7

Q ss_pred             cccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHH
Q 012034            2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENAD   80 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e   80 (472)
                      .|+|+.|.|.....+............++|||+|||.++|+++|+++|++||.|.+|.++.|. +|+++|||||+|.+.+
T Consensus        78 ~~~g~~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~  157 (196)
T 1l3k_A           78 KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD  157 (196)
T ss_dssp             EETTEECEEEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             EECCEEeeeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHH
Confidence            478888888877666554433334567899999999999999999999999999999999994 8999999999999999


Q ss_pred             HHHHHHHHHCCCccCCcceeeeccccchhH
Q 012034           81 DAAKAVEALNGKKFDDREWYVGKAQKKSER  110 (472)
Q Consensus        81 ~A~~Av~~lng~~i~g~~l~V~~a~~~~~~  110 (472)
                      +|.+|++. ++..|+|+.|.|.++..+.+.
T Consensus       158 ~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          158 SVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             HHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             HHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            99999986 899999999999999877654

>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=99.67  E-value=1.6e-16  Score=131.13  Aligned_cols=82  Identities=33%  Similarity=0.603  Sum_probs=77.8

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecC---eeEEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS---KPLYVAV  206 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g---k~l~V~~  206 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+|+|..+.+|.++|||||+|.+.++|.+|++.|||..+.|   +.|.|.+
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~   93 (105)
T 2dnh_A           14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKF   93 (105)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEE
Confidence            4678999999999999999999999999999999999899999999999999999999999999999998   9999999


Q ss_pred             cccHH
Q 012034          207 AQRKE  211 (472)
Q Consensus       207 a~~k~  211 (472)
                      +..+.
T Consensus        94 a~~~~   98 (105)
T 2dnh_A           94 ADTDK   98 (105)
T ss_dssp             SCSSC
T ss_pred             CccCc
Confidence            98764

>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=99.67  E-value=2.9e-16  Score=130.12  Aligned_cols=81  Identities=31%  Similarity=0.490  Sum_probs=76.9

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ....++|||+||+.++|+++|+++|+.||.|.+|+|+.+.+|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             c
Q 012034          208 Q  208 (472)
Q Consensus       208 ~  208 (472)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.67  E-value=1.5e-16  Score=134.18  Aligned_cols=81  Identities=28%  Similarity=0.532  Sum_probs=77.2

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||+.++|+++|+++|+.||.|++|.|..+.+|.++|||||+|.+.++|.+|++.|||..++|+.|.|.++..
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   85 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK   85 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            45689999999999999999999999999999999998899999999999999999999999999999999999999875


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        86 ~   86 (116)
T 2fy1_A           86 P   86 (116)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.67  E-value=1.8e-16  Score=133.27  Aligned_cols=81  Identities=37%  Similarity=0.583  Sum_probs=76.9

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.||+..|.|+.|+|.++.
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  103 (115)
T 2cpz_A           24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR  103 (115)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999986 78999999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus       104 ~~  105 (115)
T 2cpz_A          104 SK  105 (115)
T ss_dssp             CS
T ss_pred             CC
Confidence            65

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.67  E-value=5.1e-17  Score=135.60  Aligned_cols=79  Identities=24%  Similarity=0.243  Sum_probs=72.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCC-CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG-~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|++|| +|..+.|..+   +++|||||+|++.++|++|++.|||..|.|+.|.|.++
T Consensus        26 ~~~~~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           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            5578999999999999999999999999 9999888543   57999999999999999999999999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ...
T Consensus       103 ~~~  105 (111)
T 2jvr_A          103 DNP  105 (111)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            654

>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=99.67  E-value=4.8e-17  Score=132.28  Aligned_cols=84  Identities=26%  Similarity=0.460  Sum_probs=76.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHH----HHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLK----KIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~----~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      ....++|||+|||.++|+++|+    ++|++||.|.+|.+.+  +|+++|||||+|.+.++|.+|++.|||..+.|+.|.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            3567899999999999999999    9999999999998873  577899999999999999999999999999999999


Q ss_pred             eeccccchhH
Q 012034          101 VGKAQKKSER  110 (472)
Q Consensus       101 V~~a~~~~~~  110 (472)
                      |.++..+...
T Consensus        83 v~~a~~~~~~   92 (97)
T 1nu4_A           83 IQYAKTDSDI   92 (97)
T ss_dssp             EEECSSCCTH
T ss_pred             EEEccCCCcc
Confidence            9999877654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=9.8e-17  Score=131.95  Aligned_cols=79  Identities=19%  Similarity=0.367  Sum_probs=71.9

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCC--cEecCeeEEEE
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG--KMIVSKPLYVA  205 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g--~~i~gk~l~V~  205 (472)
                      ....++|||+||++++|+++|+++|++||.|++|+|+++     ||||||+|.+.++|.+|++.+++  ..+.|++|+|.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            345679999999999999999999999999999999976     89999999999999999998864  78999999999


Q ss_pred             EcccHH
Q 012034          206 VAQRKE  211 (472)
Q Consensus       206 ~a~~k~  211 (472)
                      +++.+.
T Consensus        88 ~A~~~~   93 (105)
T 1sjq_A           88 FSNHKE   93 (105)
T ss_dssp             CCSSSS
T ss_pred             EcCCCC
Confidence            987653

>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=99.67  E-value=2.2e-17  Score=170.39  Aligned_cols=162  Identities=18%  Similarity=0.300  Sum_probs=110.2

Q ss_pred             HHHHHhcCCCeeEEEEEEC---CCCCceeEE-----EEEeCCHHHHHHHHHHHCCCccCCcceeeeccccchhHHHHHHH
Q 012034           45 LKKIFGEYGTITSAVVMRD---GDGKSKCFG-----FVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKG  116 (472)
Q Consensus        45 L~~~F~~fG~I~~v~i~~d---~~g~skG~a-----FV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~~~~~~~~~  116 (472)
                      |.++|..+|+|..|..+..   ...+..+|+     |+.|.+.+++..++..++......+..    ..+....+..+..
T Consensus         9 L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~----~~k~~~~~~~~~~   84 (437)
T 3pgw_S            9 LLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKR----REKIERRQQEVET   84 (437)
T ss_pred             HHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHH----HHHHHHHHHHHHH
Confidence            8899999999988744332   111223344     888888777666654433222211110    0000000111110


Q ss_pred             HHH---hhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHh
Q 012034          117 QFE---QAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM  192 (472)
Q Consensus       117 ~~~---~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l  192 (472)
                      ...   ............++|||+||+..+|+++|+++|+.||.|+.|.|+.+. +|.++|||||+|.+.++|.+||..|
T Consensus        85 ~~~~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~l  164 (437)
T 3pgw_S           85 ELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA  164 (437)
T ss_pred             hhhhcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHc
Confidence            000   001111122344689999999999999999999999999999999884 7899999999999999999999999


Q ss_pred             CCcEecCeeEEEEEcccH
Q 012034          193 NGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       193 ~g~~i~gk~l~V~~a~~k  210 (472)
                      ||..|.|+.|.|.|+..+
T Consensus       165 ng~~i~gr~i~V~~a~~~  182 (437)
T 3pgw_S          165 DGKKIDGRRVLVDVERGR  182 (437)
T ss_pred             CCCEECCEEEEEEEeCCC
Confidence            999999999999998754

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=3e-16  Score=126.76  Aligned_cols=79  Identities=24%  Similarity=0.471  Sum_probs=74.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||.++++++|+++|+.||.|.++++..+. ++.++|||||+|.+.++|.+|++.||+..+.|+.|+|.|++
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            45689999999999999999999999999999999886 58899999999999999999999999999999999999974

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.5e-16  Score=133.70  Aligned_cols=86  Identities=17%  Similarity=0.250  Sum_probs=79.9

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCce-EEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTI-TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I-~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||+++|+++|+++|+.||.| .+|+|+.+.+|.++|||||+|.+.++|.+|++. |+..|+|+.|.|.++.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~   92 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVT   92 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEEC
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECC
Confidence            45789999999999999999999999999 899999999999999999999999999999977 9999999999999999


Q ss_pred             cHHHHHHH
Q 012034          209 RKEERRAR  216 (472)
Q Consensus       209 ~k~~~~~~  216 (472)
                      .++.+...
T Consensus        93 ~~~~~~~~  100 (114)
T 2cpy_A           93 LEDMREIE  100 (114)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88766544

>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=99.66  E-value=2.2e-16  Score=141.60  Aligned_cols=85  Identities=26%  Similarity=0.379  Sum_probs=78.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+.+ .+|+++|||||+|.+.++|.+||+.||+..|.|+.|.|.++
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  149 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  149 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45678999999999999999999999999999999999 58999999999999999999999999999999999999999


Q ss_pred             ccchhH
Q 012034          105 QKKSER  110 (472)
Q Consensus       105 ~~~~~~  110 (472)
                      ..+..+
T Consensus       150 ~~~~~~  155 (165)
T 1rk8_A          150 FVKGPK  155 (165)
T ss_dssp             EECC--
T ss_pred             cCCCCC
Confidence            876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.66  E-value=3.1e-16  Score=139.46  Aligned_cols=101  Identities=29%  Similarity=0.494  Sum_probs=87.3

Q ss_pred             cccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHH
Q 012034            2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENAD   80 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e   80 (472)
                      .|+|+.+.|.........    .....++|||+|||.++|+++|+++|++||.|.++.+..+ .+|+++|||||+|.+.+
T Consensus        65 ~~~g~~i~v~~~~~~~~~----~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~  140 (166)
T 3md3_A           65 QIENNIVKINWAFQSQQS----SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQD  140 (166)
T ss_dssp             EETTEECEEEECCCCCCC----CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHH
T ss_pred             ccCCCeeEEEEcCCCCCC----CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHH
Confidence            356677777655443321    2356789999999999999999999999999999999999 68999999999999999


Q ss_pred             HHHHHHHHHCCCccCCcceeeecccc
Q 012034           81 DAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        81 ~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      +|.+|++.|||..++|+.|.|.++.+
T Consensus       141 ~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          141 DAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             HHHHHHHHhCCCccCCcEEEEEecCC
Confidence            99999999999999999999999863

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2.1e-16  Score=130.07  Aligned_cols=83  Identities=30%  Similarity=0.452  Sum_probs=77.8

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ....++|||+||+.++++++|+++|+.||.|.+|+|+.++ ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            3456799999999999999999999999999999999985 789999999999999999999999999999999999999


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      +..+
T Consensus        92 a~~~   95 (103)
T 2cq0_A           92 AKPS   95 (103)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8765

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.66  E-value=1.1e-16  Score=139.05  Aligned_cols=80  Identities=33%  Similarity=0.428  Sum_probs=75.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
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            456899999999999999999999999999999999998 6799999999999999999999999999999999999987


Q ss_pred             c
Q 012034          104 A  104 (472)
Q Consensus       104 a  104 (472)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

>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=6.9e-17  Score=132.74  Aligned_cols=82  Identities=30%  Similarity=0.552  Sum_probs=76.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|+.||.|.+|.++.|.+|+++|||||+|++.++|.+|++  ++..+.|+.|.|.++.
T Consensus         7 ~~~~~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            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            45689999999999999999999999999999999999999999999999999999999998  9999999999999997


Q ss_pred             cchh
Q 012034          106 KKSE  109 (472)
Q Consensus       106 ~~~~  109 (472)
                      .+..
T Consensus        85 ~~~~   88 (102)
T 2xs2_A           85 RKQN   88 (102)
T ss_dssp             ECC-
T ss_pred             cCcc
Confidence            6654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3.5e-16  Score=126.52  Aligned_cols=81  Identities=25%  Similarity=0.343  Sum_probs=75.6

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+|||.++++++|+++|+.||.|.+|.++.+. ++.++|||||+|.+.++|.+|++.|||..++|+.|.|.++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP   92 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            345689999999999999999999999999999999885 5789999999999999999999999999999999999998


Q ss_pred             cc
Q 012034          208 QR  209 (472)
Q Consensus       208 ~~  209 (472)
                      +.
T Consensus        93 ~~   94 (95)
T 2cqc_A           93 SS   94 (95)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.66  E-value=3.3e-16  Score=131.55  Aligned_cols=82  Identities=30%  Similarity=0.556  Sum_probs=77.4

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||+.++++++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.|||..|+|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   92 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            356789999999999999999999999999999999985 7899999999999999999999999999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        93 ~~~   95 (115)
T 2dgo_A           93 TRK   95 (115)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            765

>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=99.66  E-value=4e-17  Score=126.18  Aligned_cols=74  Identities=23%  Similarity=0.424  Sum_probs=69.8

Q ss_pred             eEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        30 ~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +|||+|||.++|+++|+++|++||.|.++.+..+ .+|+++|||||+|++.++|.+|++. ++..+.|+.|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            5999999999999999999999999999999988 4689999999999999999999985 899999999999875

>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=99.66  E-value=4.1e-16  Score=128.28  Aligned_cols=82  Identities=28%  Similarity=0.508  Sum_probs=76.2

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ....++|||+||+.++|+++|+++|+.||.|.+|+|+.+..+ ++|||||+|.+.++|.+|+..||+..|+|+.|.|.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            345678999999999999999999999999999999998655 8999999999999999999999999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        91 ~~~   93 (103)
T 2cq3_A           91 TAR   93 (103)
T ss_dssp             CSS
T ss_pred             ccC
Confidence            765

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=3.6e-16  Score=131.02  Aligned_cols=81  Identities=31%  Similarity=0.571  Sum_probs=77.0

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+|+|+.++++.++|||||+|.+.++|.+|++.||+..|+|+.|.|.++..
T Consensus        14 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   93 (114)
T 2do0_A           14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDER   93 (114)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEccc
Confidence            45789999999999999999999999999999999998899999999999999999999999999999999999999865


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      .
T Consensus        94 ~   94 (114)
T 2do0_A           94 A   94 (114)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.6e-16  Score=128.98  Aligned_cols=82  Identities=35%  Similarity=0.640  Sum_probs=76.9

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEE-EEeeC-CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v-~i~~~-~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      .+++|||+|||.++++++|+++|+.||.|.++ +|+.+ .++.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45789999999999999999999999999999 99988 57899999999999999999999999999999999999998


Q ss_pred             ccHH
Q 012034          208 QRKE  211 (472)
Q Consensus       208 ~~k~  211 (472)
                      ..+.
T Consensus        84 ~~~~   87 (96)
T 1x5t_A           84 FKKD   87 (96)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            7653

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.66  E-value=1.7e-16  Score=129.22  Aligned_cols=78  Identities=24%  Similarity=0.318  Sum_probs=71.5

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcE--ecCeeEEEE
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKM--IVSKPLYVA  205 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~--i~gk~l~V~  205 (472)
                      ...+.+|||+|||+++|+++|+++|++||.|++++++++     ||||||+|.+.++|.+|++.+++..  +.|++|+|.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            345678999999999999999999999999999999864     8999999999999999999999875  789999999


Q ss_pred             EcccH
Q 012034          206 VAQRK  210 (472)
Q Consensus       206 ~a~~k  210 (472)
                      |++.+
T Consensus        93 ~S~~k   97 (100)
T 3r27_A           93 YSTSQ   97 (100)
T ss_dssp             ECSCS
T ss_pred             ecccc
Confidence            99875

>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=99.66  E-value=2e-16  Score=128.72  Aligned_cols=79  Identities=22%  Similarity=0.385  Sum_probs=73.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccC--Ccceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD--DREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~--g~~l~V~  102 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.+..+     +|||||+|.+.++|.+|++.||+..|.  |+.|.|.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            356789999999999999999999999999999988764     789999999999999999999999999  9999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      ++..+.
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            997653

>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=99.66  E-value=2.9e-16  Score=127.64  Aligned_cols=79  Identities=19%  Similarity=0.301  Sum_probs=74.1

Q ss_pred             ccceeeeecCCCCccHHHHH----HHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~----~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      .+++|||+||++++++++|+    ++|+.||.|.+|+|+.+..+  +|||||+|.+.++|.+|++.|||..++|+.|+|.
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   85 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVS   85 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            45789999999999999999    99999999999999988765  8999999999999999999999999999999999


Q ss_pred             EcccH
Q 012034          206 VAQRK  210 (472)
Q Consensus       206 ~a~~k  210 (472)
                      ++..+
T Consensus        86 ~a~~~   90 (96)
T 2dgx_A           86 LATGA   90 (96)
T ss_dssp             ECCCS
T ss_pred             EcCCC
Confidence            98654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.66  E-value=2.4e-16  Score=131.13  Aligned_cols=78  Identities=28%  Similarity=0.555  Sum_probs=73.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.+.       +|||||+|.+.++|.+|++.|||..+.|+.|.|.++
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  100 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS  100 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            4678999999999999999999999999999999998       689999999999999999999999999999999999


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      ..+..
T Consensus       101 ~~~~~  105 (108)
T 2jvo_A          101 KLPAK  105 (108)
T ss_dssp             SCCC-
T ss_pred             cCCCC
Confidence            87654

>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=99.66  E-value=1.7e-16  Score=132.01  Aligned_cols=77  Identities=32%  Similarity=0.337  Sum_probs=72.5

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC-----ccee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD-----REWY  100 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g-----~~l~  100 (472)
                      ...++|||+|||+++|+++|+++|++||+|.+|.|+.|      |||||+|++.++|.+||+.||++.|.|     +.|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~   86 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   86 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEE
Confidence            46789999999999999999999999999999999887      899999999999999999999999999     9999


Q ss_pred             eeccccch
Q 012034          101 VGKAQKKS  108 (472)
Q Consensus       101 V~~a~~~~  108 (472)
                      |.++..+.
T Consensus        87 V~~a~~~~   94 (108)
T 1x4c_A           87 VKVDGPRS   94 (108)
T ss_dssp             EEESSCCS
T ss_pred             EEeCCCCC
Confidence            99997654

>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=99.66  E-value=1.4e-16  Score=150.43  Aligned_cols=86  Identities=21%  Similarity=0.282  Sum_probs=79.1

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccC--ceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFG--TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G--~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ..++|||+||++++|+++|+++|+.||  .|++|+|++++ +|+++|||||+|.+.++|.+||+.||+..|.|+.|+|.+
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  99999999985 899999999999999999999999999999999999999


Q ss_pred             cccHHHHHH
Q 012034          207 AQRKEERRA  215 (472)
Q Consensus       207 a~~k~~~~~  215 (472)
                      +..+.....
T Consensus       147 a~~~~~~~~  155 (229)
T 3q2s_C          147 VNKQFLSQF  155 (229)
T ss_dssp             CCHHHHHHH
T ss_pred             CCCCccchh
Confidence            988765544

>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=99.66  E-value=2e-16  Score=131.82  Aligned_cols=84  Identities=24%  Similarity=0.458  Sum_probs=78.0

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ...+++|||+||+.++|+++|+++|+.||.|.+|.++.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            3456789999999999999999999999999999998884 788999999999999999999999999999999999999


Q ss_pred             cccHH
Q 012034          207 AQRKE  211 (472)
Q Consensus       207 a~~k~  211 (472)
                      +..+.
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            97653

>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=99.66  E-value=1.6e-16  Score=129.81  Aligned_cols=78  Identities=28%  Similarity=0.459  Sum_probs=72.9

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.+.++     +|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   87 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcC
Confidence            56789999999999999999999999999999999854     7999999999999999999999999999999999997


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      .+.
T Consensus        88 ~~~   90 (99)
T 2cpj_A           88 HSA   90 (99)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            653

>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=99.66  E-value=2.8e-16  Score=130.75  Aligned_cols=79  Identities=22%  Similarity=0.382  Sum_probs=74.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.++.+     +|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            467899999999999999999999999999999999987     789999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        97 ~~~~  100 (109)
T 1x4g_A           97 KESP  100 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3.1e-16  Score=129.65  Aligned_cols=82  Identities=24%  Similarity=0.484  Sum_probs=77.0

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..+++|||+||+.++++++|+++|+.||.|.+|.|..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.++
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            456789999999999999999999999999999999885 5889999999999999999999999999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus       101 ~~~  103 (106)
T 1p27_B          101 FVR  103 (106)
T ss_dssp             EES
T ss_pred             cCC
Confidence            765

>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=99.66  E-value=2.6e-16  Score=129.92  Aligned_cols=83  Identities=28%  Similarity=0.456  Sum_probs=77.8

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||+.++++++|+++|+.||.|.+|.|+.+. ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   92 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   92 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            456789999999999999999999999999999999986 7899999999999999999999999999999999999998


Q ss_pred             ccHH
Q 012034          208 QRKE  211 (472)
Q Consensus       208 ~~k~  211 (472)
                      ..+.
T Consensus        93 ~~~~   96 (105)
T 1x5u_A           93 SAHN   96 (105)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            7653

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.65  E-value=5.2e-17  Score=140.72  Aligned_cols=83  Identities=30%  Similarity=0.524  Sum_probs=78.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+.+. +++++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a  124 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  124 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            457899999999999999999999999999999999984 7999999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus       125 ~~~~  128 (135)
T 2lea_A          125 RYGR  128 (135)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.65  E-value=5.4e-16  Score=127.56  Aligned_cols=82  Identities=32%  Similarity=0.482  Sum_probs=75.9

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...++|||+||+.++++++|+++|+.||.|.+|+|+.+..+ ++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   91 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   91 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECC
Confidence            34678999999999999999999999999999999998544 79999999999999999999999999999999999988


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .+.
T Consensus        92 ~~~   94 (103)
T 2cqi_A           92 TPS   94 (103)
T ss_dssp             CTT
T ss_pred             CCc
Confidence            753

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=3.7e-16  Score=127.59  Aligned_cols=81  Identities=21%  Similarity=0.429  Sum_probs=75.7

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||+.++++++|+++|+.||.|.+|+|+.++ ++.++|||||+|.+.++|.+|++ +|+..+.|+.|.|.++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            345789999999999999999999999999999999885 68899999999999999999998 9999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        87 ~~~   89 (99)
T 2dgs_A           87 EPR   89 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=2.3e-16  Score=128.40  Aligned_cols=80  Identities=21%  Similarity=0.355  Sum_probs=72.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||+++|+++|+++|++||.|. +.++.+   +++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            35578999999999999999999999999997 666654   67899999999999999999999999999999999998


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.65  E-value=3.4e-16  Score=127.89  Aligned_cols=80  Identities=25%  Similarity=0.495  Sum_probs=75.1

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEE--------EEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecC
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVS  199 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~--------v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g  199 (472)
                      ...++|||+||+.++++++|+++|+.||.|.+        ++++.++ +|.++|||||+|.+.++|.+|++.|||..+.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            34578999999999999999999999999999        9999884 68999999999999999999999999999999


Q ss_pred             eeEEEEEcc
Q 012034          200 KPLYVAVAQ  208 (472)
Q Consensus       200 k~l~V~~a~  208 (472)
                      +.|+|.+++
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999874

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.65  E-value=3.6e-16  Score=132.18  Aligned_cols=83  Identities=17%  Similarity=0.271  Sum_probs=77.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCc---eEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGT---ITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~---I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ..++|||+||++++|+++|+++|+.||.   |.+|+|+.+.+|+++|||||+|.+.++|.+|++ +|+..|+|+.|.|.+
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~   94 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFK   94 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEE
Confidence            4578999999999999999999999999   899999999889999999999999999999998 999999999999999


Q ss_pred             cccHHHH
Q 012034          207 AQRKEER  213 (472)
Q Consensus       207 a~~k~~~  213 (472)
                      +..++..
T Consensus        95 a~~~~~~  101 (118)
T 2db1_A           95 SHRTEMD  101 (118)
T ss_dssp             ECHHHHH
T ss_pred             CCHHHHH
Confidence            9876643

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=2.7e-16  Score=129.05  Aligned_cols=81  Identities=28%  Similarity=0.467  Sum_probs=76.3

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   90 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   90 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCC
Confidence            45789999999999999999999999999999998884 68899999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        91 ~~   92 (102)
T 2cqb_A           91 PM   92 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.65  E-value=3.4e-16  Score=140.36  Aligned_cols=98  Identities=18%  Similarity=0.399  Sum_probs=85.8

Q ss_pred             cccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHH
Q 012034            2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENAD   80 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e   80 (472)
                      .|+|+.+.|........      ....++|||+|||.++|+++|+++|++||.|.++.+..+. +|+++|||||+|.+.+
T Consensus        74 ~~~g~~i~v~~~~~~~~------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~  147 (172)
T 2g4b_A           74 IFQGQSLKIRRPHDYQP------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN  147 (172)
T ss_dssp             EETTEECEEECCSSCCC------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTT
T ss_pred             EecCceeeecCCcccCC------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHH
Confidence            46677777765433221      2447889999999999999999999999999999999994 8999999999999999


Q ss_pred             HHHHHHHHHCCCccCCcceeeeccc
Q 012034           81 DAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        81 ~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      +|.+|++.|||..++|+.|.|.+|.
T Consensus       148 ~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          148 VTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHHHcCCCEECCeEEEEEeCC
Confidence            9999999999999999999999874

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=3.5e-16  Score=129.52  Aligned_cols=83  Identities=23%  Similarity=0.479  Sum_probs=77.6

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC--CCCcccEEEEEcCCHHHHHHHHHHh-CCcEecCeeEEE
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEM-NGKMIVSKPLYV  204 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~--~g~s~g~afV~f~s~~~A~~Ai~~l-~g~~i~gk~l~V  204 (472)
                      ....++|||+||+.++++++|+++|+.||.|.+|+|+.+.  ++.++|||||+|.+.++|.+|++.| |+..|.|+.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            3456789999999999999999999999999999999884  7899999999999999999999999 999999999999


Q ss_pred             EEcccH
Q 012034          205 AVAQRK  210 (472)
Q Consensus       205 ~~a~~k  210 (472)
                      .++..+
T Consensus        92 ~~a~~~   97 (107)
T 2cph_A           92 EWADSE   97 (107)
T ss_dssp             EECCCC
T ss_pred             EeCCCC
Confidence            998765

>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=99.65  E-value=1.3e-16  Score=133.36  Aligned_cols=77  Identities=21%  Similarity=0.298  Sum_probs=71.5

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.+..     ++|||||+|.+.++|.+|++.||+..|.|+.|.|.|+.
T Consensus         8 ~~~~~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            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            3578999999999999999999999999999998864     58999999999999999999999999999999999986


Q ss_pred             cc
Q 012034          106 KK  107 (472)
Q Consensus       106 ~~  107 (472)
                      ..
T Consensus        83 ~~   84 (111)
T 1whx_A           83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.65  E-value=2.1e-16  Score=125.20  Aligned_cols=76  Identities=22%  Similarity=0.388  Sum_probs=71.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHH-CCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL-NGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~l-ng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.+.++     +|||||+|.+.++|.+|++.| ++..+.|+.|.|.+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            356789999999999999999999999999999999864     899999999999999999999 99999999999998


Q ss_pred             cc
Q 012034          104 AQ  105 (472)
Q Consensus       104 a~  105 (472)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.65  E-value=1.8e-17  Score=136.00  Aligned_cols=81  Identities=31%  Similarity=0.454  Sum_probs=73.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+ .++.+ .+|+++|||||+|.+.++|.+|++ ||+..|.|+.|.|.++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            46789999999999999999999999999988 44444 678999999999999999999998 9999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        93 ~~~~   96 (101)
T 1fj7_A           93 KGRD   96 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=2.7e-16  Score=128.07  Aligned_cols=81  Identities=37%  Similarity=0.667  Sum_probs=75.1

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCC--C--CcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS--G--ISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~--g--~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+|+|..+..  |  .++|||||+|.+.++|.+|++.|||..+.|+.|.|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            356899999999999999999999999999999988753  3  789999999999999999999999999999999999


Q ss_pred             EcccH
Q 012034          206 VAQRK  210 (472)
Q Consensus       206 ~a~~k  210 (472)
                      ++..+
T Consensus        84 ~a~~~   88 (98)
T 2cpf_A           84 ISERA   88 (98)
T ss_dssp             CSSCS
T ss_pred             EccCC
Confidence            98765

>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=99.65  E-value=5.1e-17  Score=141.15  Aligned_cols=82  Identities=16%  Similarity=0.168  Sum_probs=75.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||+++|+++|+++|++|| |.+|.|++|.+|+++|||||+|++.++|++|| .+|+..|.++.|.|.++.
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECC
Confidence            5677899999999999999999999999 67999999988999999999999999999999 789999999999999887


Q ss_pred             cchh
Q 012034          106 KKSE  109 (472)
Q Consensus       106 ~~~~  109 (472)
                      ....
T Consensus       122 ~~~~  125 (139)
T 2hgn_A          122 TTGA  125 (139)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            6543

>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=99.65  E-value=4.9e-16  Score=126.61  Aligned_cols=76  Identities=24%  Similarity=0.423  Sum_probs=71.2

Q ss_pred             cCCcceEEeCCCCC-CCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDE-STTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~-~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||. ++|+++|+++|++||.|.++.+.       +|||||+|.+.++|.+|++.|||..+.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   91 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV   91 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            46789999999998 99999999999999999999882       78999999999999999999999999999999999


Q ss_pred             cccc
Q 012034          104 AQKK  107 (472)
Q Consensus       104 a~~~  107 (472)
                      +..+
T Consensus        92 a~~~   95 (97)
T 2xnq_A           92 SSSN   95 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8764

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=3.2e-16  Score=130.54  Aligned_cols=82  Identities=28%  Similarity=0.474  Sum_probs=76.0

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ....++|||+||+.++++++|+++|+.||.|.+|++..+.. .++|||||+|.+.++|.+|++.|||..++|+.|.|.++
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  104 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA  104 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            44567899999999999999999999999999999998854 48999999999999999999999999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            764

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=1.9e-16  Score=130.45  Aligned_cols=82  Identities=37%  Similarity=0.567  Sum_probs=77.6

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhc-cCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcE-ecCeeEEEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSE-FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKM-IVSKPLYVAV  206 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~-~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~-i~gk~l~V~~  206 (472)
                      ...++|||+||+.++|+++|+++|+. ||.|.+|+|+.+.+|.++|||||+|.+.++|.+|++.||+.. ++|+.|.|.+
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~   86 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSV   86 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEE
Confidence            35678999999999999999999999 999999999999899999999999999999999999999999 9999999999


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      +..+
T Consensus        87 a~~~   90 (104)
T 2dhg_A           87 AIPK   90 (104)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8765

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.64  E-value=3.1e-16  Score=132.35  Aligned_cols=81  Identities=36%  Similarity=0.548  Sum_probs=75.1

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ....++|||+||++++++++|+++|++||.|.+|+|+.++ +|.++|||||+|.+.++|.+|++.|||..++|+.|+|.|
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            3456789999999999999999999999999999999884 689999999999999999999999999999999999998


Q ss_pred             cc
Q 012034          207 AQ  208 (472)
Q Consensus       207 a~  208 (472)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>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=99.64  E-value=5.4e-16  Score=123.87  Aligned_cols=79  Identities=20%  Similarity=0.418  Sum_probs=74.4

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .++|||+|||.++++++|+++|+.||.|.++++..+. ++.++|||||+|.+.++|.+|+ .+||..+.|+.|.|.+++.
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            3589999999999999999999999999999999885 7899999999999999999999 9999999999999999865


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.64  E-value=3.2e-16  Score=129.04  Aligned_cols=86  Identities=27%  Similarity=0.490  Sum_probs=79.7

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .++|||+||+.++++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++..
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            3589999999999999999999999999999999885 788999999999999999999999999999999999999998


Q ss_pred             HHHHHHH
Q 012034          210 KEERRAR  216 (472)
Q Consensus       210 k~~~~~~  216 (472)
                      +..+...
T Consensus        88 ~~~~~~~   94 (104)
T 1p1t_A           88 EKNKEEL   94 (104)
T ss_dssp             TTHHHHH
T ss_pred             ccchhhh
Confidence            8766543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=3.3e-16  Score=128.57  Aligned_cols=82  Identities=37%  Similarity=0.515  Sum_probs=74.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||.++|+++|+++|+.|+   ++.++.+ .+++++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            46789999999999999999999999874   5677777 5899999999999999999999999999999999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +..+..
T Consensus        89 a~~~~~   94 (102)
T 2fc8_A           89 AKPKGE   94 (102)
T ss_dssp             CCCCCS
T ss_pred             ecCCCC
Confidence            987653

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.64  E-value=3.4e-16  Score=133.29  Aligned_cols=77  Identities=21%  Similarity=0.401  Sum_probs=73.3

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ++|||+||+.++|+++|+++|+.||.|.+|+|+.++ +|.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.++..
T Consensus        37 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             TEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            589999999999999999999999999999999884 7899999999999999999999 8999999999999999864

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.64  E-value=2.8e-16  Score=142.52  Aligned_cols=83  Identities=30%  Similarity=0.428  Sum_probs=78.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.|..+.+|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      ...
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            643

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=3.1e-16  Score=128.76  Aligned_cols=82  Identities=28%  Similarity=0.525  Sum_probs=76.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.||+..|.|+.|+|.++.
T Consensus        11 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   90 (102)
T 1x5s_A           11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   90 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            45689999999999999999999999999999999885 67899999999999999999999999999999999999987


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .+.
T Consensus        91 ~~~   93 (102)
T 1x5s_A           91 KSS   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.64  E-value=1.2e-16  Score=136.18  Aligned_cols=80  Identities=23%  Similarity=0.260  Sum_probs=73.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCee--EEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTIT--SAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~--~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ...++|||+|||+++|+++|+++|+.| .|.  +|.|++|.+|+++|||||+|++.++|++||+. ++..|.|+.|.|.+
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEE
Confidence            457889999999999999999999999 676  89999998899999999999999999999985 78999999999998


Q ss_pred             cccc
Q 012034          104 AQKK  107 (472)
Q Consensus       104 a~~~  107 (472)
                      +..+
T Consensus       118 a~~~  121 (126)
T 2hgm_A          118 SSQE  121 (126)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.45  E-value=1.3e-17  Score=140.57  Aligned_cols=86  Identities=27%  Similarity=0.413  Sum_probs=79.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeE--------EEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccC
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS--------AVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFD   95 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~--------v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~   95 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+        |.++.| .+++++|||||+|.+.++|.+|++.||+..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            356789999999999999999999999999999        889988 57999999999999999999999999999999


Q ss_pred             CcceeeeccccchhH
Q 012034           96 DREWYVGKAQKKSER  110 (472)
Q Consensus        96 g~~l~V~~a~~~~~~  110 (472)
                      |+.|.|.++..+..+
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999876543

>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=99.64  E-value=4.8e-16  Score=130.38  Aligned_cols=82  Identities=23%  Similarity=0.477  Sum_probs=76.7

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .++|||+||+.++++++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.++..
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            4589999999999999999999999999999999886 4889999999999999999999 9999999999999999987


Q ss_pred             HHHH
Q 012034          210 KEER  213 (472)
Q Consensus       210 k~~~  213 (472)
                      +..+
T Consensus       104 ~~~~  107 (114)
T 2cq4_A          104 EKNR  107 (114)
T ss_dssp             HHHH
T ss_pred             CccC
Confidence            7654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.64  E-value=1.1e-16  Score=129.94  Aligned_cols=80  Identities=28%  Similarity=0.412  Sum_probs=73.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|+.||.|..+    +.+++++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            3567899999999999999999999999998766    457889999999999999999999999999999999999998


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        89 ~~~~   92 (96)
T 1fjc_A           89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            7653

>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=99.64  E-value=6.4e-16  Score=128.82  Aligned_cols=82  Identities=30%  Similarity=0.519  Sum_probs=76.9

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhC------CcEecCee
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN------GKMIVSKP  201 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~------g~~i~gk~  201 (472)
                      ...++|||+||++++|+++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.+|      +..|+|+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            356789999999999999999999999999999999885 68899999999999999999999999      99999999


Q ss_pred             EEEEEcccH
Q 012034          202 LYVAVAQRK  210 (472)
Q Consensus       202 l~V~~a~~k  210 (472)
                      |.|.++..+
T Consensus        93 l~v~~a~~~  101 (111)
T 1x4h_A           93 LKVDLAVTR  101 (111)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEECCCC
Confidence            999998765

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.64  E-value=5.9e-16  Score=131.91  Aligned_cols=82  Identities=29%  Similarity=0.482  Sum_probs=77.6

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..+++|||+||+.++++++|+++|+.||.|.+|+|..+.+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  112 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  112 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeC
Confidence            45678999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      ..
T Consensus       113 ~~  114 (124)
T 2kt5_A          113 SQ  114 (124)
T ss_dssp             CT
T ss_pred             CC
Confidence            54

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=3.1e-16  Score=129.04  Aligned_cols=82  Identities=26%  Similarity=0.422  Sum_probs=76.7

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||+.++++++|+++|+.||.|.+|.|..+. ++.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            345789999999999999999999999999999999886 5889999999999999999999999999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        91 ~~~   93 (103)
T 2dnm_A           91 RYG   93 (103)
T ss_dssp             SSC
T ss_pred             CcC
Confidence            764

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.64  E-value=4.2e-16  Score=125.38  Aligned_cols=80  Identities=29%  Similarity=0.470  Sum_probs=75.4

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+|||.++++++|+++|+.||.|.+++|.++ ++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++..
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   85 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRN   85 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            4578999999999999999999999999999999985 788999999999999999999999999999999999999876


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      .
T Consensus        86 ~   86 (92)
T 2dgv_A           86 A   86 (92)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.64  E-value=3.2e-16  Score=135.59  Aligned_cols=83  Identities=17%  Similarity=0.270  Sum_probs=77.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCc---eEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGT---ITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~---I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ..++|||+||++++|+++|+++|+.||.   |.+|+|+++++|+++|||||+|.+.++|.+|++ +|+..++|+.|.|.+
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~  121 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFK  121 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            4578999999999999999999999999   899999999889999999999999999999998 999999999999999


Q ss_pred             cccHHHH
Q 012034          207 AQRKEER  213 (472)
Q Consensus       207 a~~k~~~  213 (472)
                      +..++..
T Consensus       122 a~~~e~~  128 (136)
T 2hgl_A          122 SHRTEMD  128 (136)
T ss_dssp             CCHHHHH
T ss_pred             CChHHHH
Confidence            9877643

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.64  E-value=4.5e-16  Score=126.49  Aligned_cols=78  Identities=23%  Similarity=0.419  Sum_probs=71.3

Q ss_pred             cCCcceEEeCCCCC-CCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDE-STTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~-~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||. ++|+++|+++|++||.|.+|.+.       +|||||+|.+.++|.+|++.||+..+.|+.|.|.+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            35688999999998 99999999999999999999984       78999999999999999999999999999999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +..+..
T Consensus        80 a~~~~~   85 (96)
T 2kvi_A           80 SSSNAR   85 (96)
T ss_dssp             EECCCC
T ss_pred             cCcCCC
Confidence            976554

>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=99.64  E-value=2.5e-16  Score=132.23  Aligned_cols=83  Identities=20%  Similarity=0.320  Sum_probs=72.9

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++.+..+ .+++++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            45789999999999999999999999999954332222 27899999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus       103 ~~~~  106 (115)
T 2cpx_A          103 KNKK  106 (115)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            7654

>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=99.64  E-value=4.3e-16  Score=137.29  Aligned_cols=79  Identities=32%  Similarity=0.479  Sum_probs=74.3

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||+++|+++|+++|++||.|.+|.++.+    ++|||||+|.+.++|.+|++.|||..|.|+.|.|.++
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  145 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS  145 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            356899999999999999999999999999999999887    6899999999999999999999999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ..+
T Consensus       146 ~~~  148 (150)
T 2i2y_A          146 NGE  148 (150)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=5.2e-16  Score=129.94  Aligned_cols=83  Identities=25%  Similarity=0.469  Sum_probs=77.1

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceE--------EEEEeeC-CCCCcccEEEEEcCCHHHHHHHHHHhCCcEec
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTIT--------SCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIV  198 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~--------~v~i~~~-~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~  198 (472)
                      ....++|||+||+.++|+++|+++|+.||.|.        .|+|+.+ .++.++|||||+|.+.++|.+|++.|||..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            34567999999999999999999999999999        6999988 57899999999999999999999999999999


Q ss_pred             CeeEEEEEcccH
Q 012034          199 SKPLYVAVAQRK  210 (472)
Q Consensus       199 gk~l~V~~a~~k  210 (472)
                      |+.|+|.++..+
T Consensus        92 g~~l~V~~a~~~  103 (113)
T 2cpe_A           92 GSKLKVSLARKK  103 (113)
T ss_dssp             TEECEEECSSCC
T ss_pred             CCEEEEEECCCC
Confidence            999999998765

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=9.1e-16  Score=123.22  Aligned_cols=79  Identities=18%  Similarity=0.280  Sum_probs=75.2

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+|||+++++++|+++|+.| .|.+|+|+.+.+|.++|||||+|.+.++|.+|+. +|+..++|+.|.|.++..
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~   86 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKS   86 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESS
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCc
Confidence            45789999999999999999999999 9999999999889999999999999999999999 999999999999999876


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        87 ~   87 (91)
T 2dgw_A           87 G   87 (91)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.63  E-value=2.6e-16  Score=125.36  Aligned_cols=81  Identities=25%  Similarity=0.443  Sum_probs=74.2

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCC--CCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS--GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~--g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..++|||+||+.++|+++|+++|+.||.|.++.+..+..  +.++|||||+|.+.++|.+|++.|||..++|+.|.|.++
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            356899999999999999999999999999999988763  338999999999999999999999999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ...
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.63  E-value=4.9e-16  Score=129.24  Aligned_cols=81  Identities=35%  Similarity=0.621  Sum_probs=76.3

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+|+++++. +|.++|||||+|.+.++|.+|++.+||..+.|+.|.|.++.
T Consensus        25 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~  104 (108)
T 2jrs_A           25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVT  104 (108)
T ss_dssp             SCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcc
Confidence            45789999999999999999999999999999999884 68899999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus       105 ~k  106 (108)
T 2jrs_A          105 ER  106 (108)
T ss_dssp             SS
T ss_pred             cC
Confidence            65

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.3e-15  Score=126.75  Aligned_cols=80  Identities=19%  Similarity=0.415  Sum_probs=74.8

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .++|||+|||+++|+++|+++|+.| .|.+|+|+.+++|+++|||||+|.+.++|.+|+ .+|+..++|+.|.|..+..+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            3589999999999999999999999 899999999988999999999999999999999 79999999999999998766


Q ss_pred             HH
Q 012034          211 EE  212 (472)
Q Consensus       211 ~~  212 (472)
                      +-
T Consensus        94 ~~   95 (109)
T 2dnn_A           94 QW   95 (109)
T ss_dssp             HH
T ss_pred             ch
Confidence            43

>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=99.63  E-value=6.9e-16  Score=127.22  Aligned_cols=81  Identities=26%  Similarity=0.442  Sum_probs=75.4

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCC--CCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS--GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~--g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ...++|||+||+.++++++|+++|+.|| |.+|.|+.+..  +.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4557999999999999999999999999 99999998864  899999999999999999999 9999999999999999


Q ss_pred             cccHH
Q 012034          207 AQRKE  211 (472)
Q Consensus       207 a~~k~  211 (472)
                      +..+.
T Consensus        91 a~~~~   95 (104)
T 1wi8_A           91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            87653

>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=99.63  E-value=5.7e-16  Score=129.44  Aligned_cols=83  Identities=22%  Similarity=0.359  Sum_probs=75.6

Q ss_pred             ccccceeeeecCCCCccHHHHH---HHHhccCceEEEEEeeCCC----CCcccEEEEEcCCHHHHHHHHHHhCCcEecCe
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLK---ELFSEFGTITSCKVMRDPS----GISKGSGFVAFSTPEEASRALAEMNGKMIVSK  200 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~---~~F~~~G~I~~v~i~~~~~----g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk  200 (472)
                      ....++|||+|||+++++++|+   ++|++||.|.+|+|.++..    +.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3456789999999999999999   9999999999999988752    35679999999999999999999999999999


Q ss_pred             eEEEEEcccH
Q 012034          201 PLYVAVAQRK  210 (472)
Q Consensus       201 ~l~V~~a~~k  210 (472)
                      .|.|.++..+
T Consensus        92 ~l~V~~a~~k  101 (111)
T 2cpi_A           92 TLKASLGTTK  101 (111)
T ss_dssp             EEEEESCCCC
T ss_pred             EEEEEecccc
Confidence            9999998765

>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=99.63  E-value=1.9e-16  Score=127.80  Aligned_cols=78  Identities=23%  Similarity=0.501  Sum_probs=70.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCC-eeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCC-CccCCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGT-ITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG-KKFDDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~-I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng-~~i~g~~l~V~  102 (472)
                      ....++|||+|||.++|+++|+++|++||. |..+.+.      ++|||||+|.+.++|.+|++.||+ ..+.|+.|.|.
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            356789999999999999999999999999 6666663      479999999999999999999999 99999999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      ++..+.
T Consensus        79 ~a~~~~   84 (93)
T 2cqh_A           79 YSVSKK   84 (93)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            997654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=6.6e-16  Score=126.05  Aligned_cols=81  Identities=25%  Similarity=0.456  Sum_probs=75.8

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceE-EEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCee----EE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTIT-SCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP----LY  203 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~-~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~----l~  203 (472)
                      ..++|||+||+.++++++|+++|+.||.|. +++|++++ ++.++|||||+|.+.++|.+|++.|||..+.|+.    |+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~   87 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFK   87 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEE
Confidence            457899999999999999999999999999 99999985 7899999999999999999999999999999999    99


Q ss_pred             EEEcccH
Q 012034          204 VAVAQRK  210 (472)
Q Consensus       204 V~~a~~k  210 (472)
                      |.|+...
T Consensus        88 v~~a~~~   94 (99)
T 2div_A           88 LNYATYS   94 (99)
T ss_dssp             EEETTCC
T ss_pred             EeecCCC
Confidence            9988643

>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=99.63  E-value=2.9e-16  Score=128.87  Aligned_cols=76  Identities=20%  Similarity=0.315  Sum_probs=70.1

Q ss_pred             ccceeeeecCCC-CccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCc--EecCeeEEEEE
Q 012034          130 QGLNLYIKNLGD-SIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK--MIVSKPLYVAV  206 (472)
Q Consensus       130 ~~~~l~V~nL~~-~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~--~i~gk~l~V~~  206 (472)
                      .+++|||+||++ ++|+++|+++|+.||.|.+|.|+++     +|||||+|.+.++|.+|++.||+.  .|.|++|+|.+
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~   88 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   88 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEE
Confidence            467899999999 9999999999999999999999876     689999999999999999998864  59999999999


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      ++.+
T Consensus        89 a~~~   92 (102)
T 1x4d_A           89 SQKY   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            9854

>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=99.63  E-value=1.4e-15  Score=121.05  Aligned_cols=78  Identities=22%  Similarity=0.465  Sum_probs=72.1

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+|||.++++++|+++|+.||.|.+++++.++ +|.++|||||+|.+.++|.+|++ +++..++|+.|.|++|
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            356789999999999999999999999999999999885 68999999999999999999995 5888999999999875

>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=99.63  E-value=4.6e-16  Score=128.11  Aligned_cols=77  Identities=30%  Similarity=0.553  Sum_probs=71.5

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.++       +|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   81 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK   81 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcC
Confidence            567899999999999999999999999999999886       4599999999999999999999999999999999997


Q ss_pred             cchh
Q 012034          106 KKSE  109 (472)
Q Consensus       106 ~~~~  109 (472)
                      .+..
T Consensus        82 ~~~~   85 (103)
T 2dgu_A           82 PPDQ   85 (103)
T ss_dssp             CCCC
T ss_pred             CCcc
Confidence            6543

>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=99.63  E-value=2.4e-16  Score=140.61  Aligned_cols=99  Identities=24%  Similarity=0.496  Sum_probs=87.1

Q ss_pred             cccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHH
Q 012034            2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENAD   80 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e   80 (472)
                      .|+|+.|.|.....+...      ...++|||+|||.++|+++|+++|++||.|.++.+..| .+|+++|||||+|.+.+
T Consensus        67 ~~~g~~i~v~~~~~~~~~------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~  140 (167)
T 2cjk_A           67 ILDGKVIDPKRAIPRDEQ------DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD  140 (167)
T ss_dssp             EETTEECCCEECCCHHHH------HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHH
T ss_pred             ccCCeEcccccccchhhc------cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHH
Confidence            367788777766554433      23678999999999999999999999999999999998 47999999999999999


Q ss_pred             HHHHHHHHHCCCccCCcceeeeccccc
Q 012034           81 DAAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        81 ~A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      +|.+|++ +++..+.|+.|.|.++.++
T Consensus       141 ~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          141 AVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             HHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            9999998 8999999999999999765

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.63  E-value=3.5e-16  Score=120.85  Aligned_cols=74  Identities=22%  Similarity=0.384  Sum_probs=70.2

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      +|||+|||.++++++|+++|+.||.|.++.+..++ +|.++|||||+|.+.++|.+|++ +|+..++|+.|.|.+|
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            48999999999999999999999999999999886 78999999999999999999997 9999999999999875

>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=99.63  E-value=5.9e-16  Score=127.99  Aligned_cols=82  Identities=28%  Similarity=0.591  Sum_probs=76.4

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEe---cCeeEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMI---VSKPLYV  204 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i---~gk~l~V  204 (472)
                      ...++|||+||+.++++++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.||+..+   .|+.|.|
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v   90 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQV   90 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEE
Confidence            345789999999999999999999999999999999986 588999999999999999999999999988   8999999


Q ss_pred             EEcccH
Q 012034          205 AVAQRK  210 (472)
Q Consensus       205 ~~a~~k  210 (472)
                      .++..+
T Consensus        91 ~~a~~~   96 (106)
T 2dgp_A           91 KPADSE   96 (106)
T ss_dssp             EECCCC
T ss_pred             EECCcc
Confidence            998765

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=6.9e-16  Score=124.27  Aligned_cols=77  Identities=23%  Similarity=0.483  Sum_probs=71.7

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.+|.+.+       +||||+|++.++|.+|++.||+..|.|+.|.|.++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS-------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            45689999999999999999999999999999999874       49999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        80 ~~~~   83 (92)
T 2dgt_A           80 TSRL   83 (92)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            7654

>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=99.62  E-value=5.7e-16  Score=133.05  Aligned_cols=82  Identities=26%  Similarity=0.355  Sum_probs=76.8

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||+.++++++|+++|+.||.|.+|+|+.++ ++.++|||||+|.+.++|.+|++.|||..|+|++|.|.|+
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a  123 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS  123 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356789999999999999999999999999999999885 6789999999999999999999999999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus       124 ~~~  126 (129)
T 2kxn_B          124 ITK  126 (129)
T ss_dssp             SSS
T ss_pred             cCC
Confidence            765

>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=99.62  E-value=2.5e-16  Score=131.36  Aligned_cols=77  Identities=17%  Similarity=0.361  Sum_probs=69.0

Q ss_pred             cCCcceEEe--CCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCcc-----CCc
Q 012034           25 KTKFNNVFV--KNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF-----DDR   97 (472)
Q Consensus        25 ~~~~~~l~V--~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i-----~g~   97 (472)
                      ....++|||  +||++++|+++|+++|++||+|.+|.+..     +||||||+|++.++|++|++.|||+.+     .|+
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            456788999  77999999999999999999999988764     379999999999999999999999988     678


Q ss_pred             ceeeecccc
Q 012034           98 EWYVGKAQK  106 (472)
Q Consensus        98 ~l~V~~a~~  106 (472)
                      .|+|.++..
T Consensus        97 ~l~v~~a~~  105 (114)
T 2cq2_A           97 TLYLNFVEK  105 (114)
T ss_dssp             ECEEEEESC
T ss_pred             EEEEEeccc
Confidence            899988754

>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=99.62  E-value=1.1e-15  Score=125.45  Aligned_cols=78  Identities=21%  Similarity=0.342  Sum_probs=71.1

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHh--CCcEecCeeEEEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM--NGKMIVSKPLYVAV  206 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l--~g~~i~gk~l~V~~  206 (472)
                      ..+++|||+||++++++++|+++|+.||.|.+|.++++     ||||||+|.+.++|.+|++.+  ++..+.|++|+|.|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~   87 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQY   87 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEE
Confidence            35678999999999999999999999999999999875     899999999999999999976  56789999999999


Q ss_pred             cccHH
Q 012034          207 AQRKE  211 (472)
Q Consensus       207 a~~k~  211 (472)
                      +..+.
T Consensus        88 a~~~~   92 (101)
T 2cq1_A           88 SNHKE   92 (101)
T ss_dssp             CSCSS
T ss_pred             cCccc
Confidence            98653

>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=1.1e-15  Score=140.25  Aligned_cols=107  Identities=17%  Similarity=0.367  Sum_probs=90.4

Q ss_pred             cccCeeEEEcCcccchhhhh--------------hhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CC
Q 012034            2 LINDKQVFVGHFLRKQERET--------------VAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DG   66 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~--------------~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g   66 (472)
                      .|+|+.|.|...........              .......++|||+|||.++|+++|+++|++||.|.++.+..+. +|
T Consensus        74 ~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~  153 (198)
T 2yh0_A           74 IFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATG  153 (198)
T ss_dssp             EETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTC
T ss_pred             EEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCC
Confidence            46788888876554422110              0012467999999999999999999999999999999999995 89


Q ss_pred             CceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccch
Q 012034           67 KSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  108 (472)
Q Consensus        67 ~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~  108 (472)
                      +++|||||+|.+.++|.+|++.|||..|+|+.|.|.++..+.
T Consensus       154 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          154 LSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             SEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            999999999999999999999999999999999999987653

>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=99.62  E-value=1.3e-15  Score=126.73  Aligned_cols=80  Identities=20%  Similarity=0.318  Sum_probs=73.8

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...++|||+||+.++|+++|+++|+.||.|.+|+|..+  +.++|||||+|.+.++|.+|++.||+..|+|+.|.|.++.
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   97 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   97 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcc
Confidence            34578999999999999999999999999999999765  5689999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        98 ~~   99 (109)
T 1x4a_A           98 SG   99 (109)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.62  E-value=2e-15  Score=134.69  Aligned_cols=97  Identities=30%  Similarity=0.488  Sum_probs=84.2

Q ss_pred             cccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHH
Q 012034            2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENAD   80 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e   80 (472)
                      .|+|+.|.|........      ....++|||+|||.++|+++|+++|++||.|.++.+..+. +|+++|||||+|.+.+
T Consensus        69 ~~~g~~l~v~~~~~~~~------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~  142 (168)
T 1b7f_A           69 TVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE  142 (168)
T ss_dssp             EETTEECEEEECCCCSS------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             EeCCcEEEEEecCCCcc------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHH
Confidence            35677777765443322      2457899999999999999999999999999999999996 8999999999999999


Q ss_pred             HHHHHHHHHCCCccCC--cceeeecc
Q 012034           81 DAAKAVEALNGKKFDD--REWYVGKA  104 (472)
Q Consensus        81 ~A~~Av~~lng~~i~g--~~l~V~~a  104 (472)
                      +|.+|++.|||..+.|  +.|.|.+|
T Consensus       143 ~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          143 EAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            9999999999999988  99999875

>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=99.62  E-value=3e-16  Score=128.59  Aligned_cols=79  Identities=24%  Similarity=0.448  Sum_probs=73.6

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC--CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~--~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..++|||+||+.++++++|+++|+.|| |.+|+|+.+.  +|+++|||||+|.+.++|.+|+ .|||..++|+.|.|.++
T Consensus        18 ~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a   95 (100)
T 2j76_E           18 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVA   95 (100)
T ss_dssp             --CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEec
Confidence            457899999999999999999999999 9999999986  7899999999999999999999 99999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        96 ~~~   98 (100)
T 2j76_E           96 DQA   98 (100)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.62  E-value=8.6e-16  Score=133.48  Aligned_cols=82  Identities=34%  Similarity=0.521  Sum_probs=76.8

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||+.++++++|+++|+.||.|++|+|+.++ ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|.++
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  119 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            345789999999999999999999999999999999885 5789999999999999999999999999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus       120 ~~~  122 (139)
T 1u6f_A          120 ASG  122 (139)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            865

>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=5e-16  Score=124.08  Aligned_cols=76  Identities=18%  Similarity=0.365  Sum_probs=70.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||+++|+++|+++|++| .|.++.+.     +++|||||+|.+.++|.+|++.||+..+.|+.|.|.++.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            457889999999999999999999999 99999884     679999999999999999999999999999999999986


Q ss_pred             cc
Q 012034          106 KK  107 (472)
Q Consensus       106 ~~  107 (472)
                      .+
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.62  E-value=2.6e-16  Score=137.54  Aligned_cols=85  Identities=28%  Similarity=0.386  Sum_probs=74.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEE------EEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcce
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA------VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREW   99 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v------~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l   99 (472)
                      ...++|||+|||+++|+++|+++|++||.|.++      .+....+|+++|||||+|.+.++|.+|++.|||..|.|+.|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            467899999999999999999999999999874      12222578999999999999999999999999999999999


Q ss_pred             eeeccccchhH
Q 012034          100 YVGKAQKKSER  110 (472)
Q Consensus       100 ~V~~a~~~~~~  110 (472)
                      .|.++.....+
T Consensus       123 ~V~~a~~~~~~  133 (143)
T 3egn_A          123 VVQFARSARPK  133 (143)
T ss_dssp             EEEECCCSCC-
T ss_pred             EEEECCCCCCc
Confidence            99999765543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.62  E-value=1.3e-15  Score=125.26  Aligned_cols=80  Identities=23%  Similarity=0.397  Sum_probs=74.6

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||+.++++++|+++|+.|| |.+|+|+.+. ++.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEe
Confidence            3467899999999999999999999997 9999999986 5889999999999999999999 99999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        91 ~~~   93 (103)
T 2dng_A           91 EGR   93 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            765

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.3e-15  Score=128.22  Aligned_cols=82  Identities=27%  Similarity=0.399  Sum_probs=75.8

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ....++|||+||+.++|+++|+++|+.||.|.+|+|++++ ++.++|||||+|.+.++|.+|++.+++ .|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            3456789999999999999999999999999999999885 689999999999999999999999998 89999999999


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      +..+
T Consensus        93 a~~~   96 (116)
T 2cqd_A           93 AYLG   96 (116)
T ss_dssp             STTT
T ss_pred             cccC
Confidence            8654

>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=99.62  E-value=9.7e-16  Score=130.85  Aligned_cols=82  Identities=24%  Similarity=0.484  Sum_probs=77.3

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..+++|||+||+.++|+++|+++|+.||.|.+|.|+.+. ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++
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            446789999999999999999999999999999999885 7889999999999999999999999999999999999999


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus       100 ~~~  102 (126)
T 3ex7_B          100 FVR  102 (126)
T ss_dssp             EES
T ss_pred             cCC
Confidence            765

>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=99.62  E-value=8.7e-16  Score=129.38  Aligned_cols=78  Identities=19%  Similarity=0.376  Sum_probs=71.6

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCC--cEecCeeEEEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG--KMIVSKPLYVAV  206 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g--~~i~gk~l~V~~  206 (472)
                      ..+++|||+||++++|+++|+++|+.||.|++|+|+++     ||||||+|.+.++|.+|++.+++  ..|.|++|+|.+
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~  103 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF  103 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEE
Confidence            34678999999999999999999999999999999986     89999999999999999999874  689999999999


Q ss_pred             cccHH
Q 012034          207 AQRKE  211 (472)
Q Consensus       207 a~~k~  211 (472)
                      ++.++
T Consensus       104 a~~k~  108 (119)
T 2ad9_A          104 SNHKE  108 (119)
T ss_dssp             CSSSS
T ss_pred             ccCCC
Confidence            97653

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=8.7e-16  Score=123.12  Aligned_cols=77  Identities=26%  Similarity=0.454  Sum_probs=71.4

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.+++       +||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            35688999999999999999999999999999999974       49999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        79 ~~~~   82 (90)
T 2dnp_A           79 TKGQ   82 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.62  E-value=8.8e-16  Score=131.31  Aligned_cols=84  Identities=23%  Similarity=0.320  Sum_probs=75.5

Q ss_pred             cccceeeeecCCCCccHHHHH----HHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  204 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~----~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V  204 (472)
                      ..+++|||+||++.+++++|+    ++|++||.|.+|.+.+  ++.++|||||+|.+.++|.+|+..|||..+.|++|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            346789999999999999876    6999999999988864  5789999999999999999999999999999999999


Q ss_pred             EEcccHHHHH
Q 012034          205 AVAQRKEERR  214 (472)
Q Consensus       205 ~~a~~k~~~~  214 (472)
                      .|+..+....
T Consensus       105 ~~a~~~~~~~  114 (127)
T 2a3j_A          105 TFSETPQSQV  114 (127)
T ss_dssp             EECCCCCHHH
T ss_pred             EEccCcchhc
Confidence            9998876544

>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=99.62  E-value=1.2e-15  Score=136.80  Aligned_cols=80  Identities=23%  Similarity=0.397  Sum_probs=75.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccC---Ccceeee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD---DREWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~---g~~l~V~  102 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++.+..+.+|+++|||||+|.+.++|.+|++.|||..+.   ++.|.|.
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            3678999999999999999999999999999999999999999999999999999999999999998876   4899999


Q ss_pred             ccc
Q 012034          103 KAQ  105 (472)
Q Consensus       103 ~a~  105 (472)
                      +|.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            873

>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=99.61  E-value=1.5e-15  Score=134.48  Aligned_cols=79  Identities=16%  Similarity=0.290  Sum_probs=72.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC--cceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD--REWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g--~~l~V~~  103 (472)
                      .+-.+|||+||++++|+++|+++|++||+|.+|+|..+   +++|||||+|++.++|.+|++.|||..|.|  +.|+|.+
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k---~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES---SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEE
Confidence            45677999999999999999999999999999999765   358999999999999999999999999965  9999999


Q ss_pred             cccc
Q 012034          104 AQKK  107 (472)
Q Consensus       104 a~~~  107 (472)
                      ++.+
T Consensus       121 Ak~~  124 (164)
T 1sjr_A          121 SKLT  124 (164)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            9765

>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=99.61  E-value=1.2e-15  Score=127.82  Aligned_cols=81  Identities=33%  Similarity=0.650  Sum_probs=75.8

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEe--------cCee
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI--------VSKP  201 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i--------~gk~  201 (472)
                      ..++|||+||+.++|+++|+++|+.||.|.+|+|+.+.++.++|||||+|.+.++|.+|++.|||..+        .+++
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~  103 (114)
T 1x5o_A           24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP  103 (114)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCc
Confidence            45789999999999999999999999999999999998899999999999999999999999999999        5788


Q ss_pred             EEEEEcccH
Q 012034          202 LYVAVAQRK  210 (472)
Q Consensus       202 l~V~~a~~k  210 (472)
                      |.|.|+..+
T Consensus       104 l~v~~a~p~  112 (114)
T 1x5o_A          104 LLCKFSGPS  112 (114)
T ss_dssp             BEEEECCCS
T ss_pred             eeEEccCCC
Confidence            999998743

>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=99.61  E-value=8.6e-16  Score=138.29  Aligned_cols=98  Identities=22%  Similarity=0.345  Sum_probs=85.8

Q ss_pred             cccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHH
Q 012034            2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADD   81 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~   81 (472)
                      .|+|++|.|.....+....    ....++|||+|||.++|+++|+++|++||.|..+    +.+++++|||||+|.+.++
T Consensus        77 ~~~g~~l~v~~~~~~~~~~----~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~  148 (175)
T 1fje_B           77 KVFGNEIKLEKPKGRDSKK----VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEAD  148 (175)
T ss_dssp             EETTEEEEEECCCCSSCST----TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHH
T ss_pred             EeCCeEEEEecCCCccccc----cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHH
Confidence            4678888888776554332    2467899999999999999999999999998766    6788999999999999999


Q ss_pred             HHHHHHHHCCCccCCcceeeeccccc
Q 012034           82 AAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        82 A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      |.+|++.|||..|.|+.|.|.++..+
T Consensus       149 A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          149 AEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99999999999999999999999765

>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=99.61  E-value=3.3e-15  Score=132.81  Aligned_cols=97  Identities=26%  Similarity=0.439  Sum_probs=82.7

Q ss_pred             cccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHH
Q 012034            2 LINDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENAD   80 (472)
Q Consensus         2 ~~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e   80 (472)
                      .++|+.+.|........      ....++|||+|||.++|+++|+++|++||.|.++.+..+. +|+++|||||+|.+.+
T Consensus        68 ~~~g~~l~v~~~~~~~~------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~  141 (167)
T 1fxl_A           68 RLQTKTIKVSYARPSSA------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI  141 (167)
T ss_dssp             EETTEECEEEECCCCCG------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             ccCCceEEEEecCCCcc------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHH
Confidence            35667777755443322      2356889999999999999999999999999999999985 8999999999999999


Q ss_pred             HHHHHHHHHCCCccCCcc--eeeecc
Q 012034           81 DAAKAVEALNGKKFDDRE--WYVGKA  104 (472)
Q Consensus        81 ~A~~Av~~lng~~i~g~~--l~V~~a  104 (472)
                      +|.+|++.|||..+.|+.  |.|.||
T Consensus       142 ~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          142 EAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHhcCCccCCCccceEEEeC
Confidence            999999999999999975  777765

>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=99.61  E-value=6e-16  Score=126.02  Aligned_cols=81  Identities=17%  Similarity=0.354  Sum_probs=74.1

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC-CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~-~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||.++++++|+++|+.||.|.++.++.+ .+|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.++.
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   93 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGS   93 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcC
Confidence            4568999999999999999999999999988777665 478899999999999999999999999999999999999986


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        94 ~~   95 (98)
T 2cqp_A           94 GP   95 (98)
T ss_dssp             CS
T ss_pred             CC
Confidence            53

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=1.6e-15  Score=123.86  Aligned_cols=77  Identities=31%  Similarity=0.476  Sum_probs=71.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcC--CCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEY--GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~f--G~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      ....++|||+|||+++|+++|+++|++|  |.|.++.+.       +|||||+|.+.++|.+|++.||+..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   84 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3568899999999999999999999999  999988764       6799999999999999999999999999999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      ++..+.
T Consensus        85 ~a~~~~   90 (99)
T 2cpd_A           85 LAKPVD   90 (99)
T ss_dssp             CCCCCC
T ss_pred             ECCCCC
Confidence            997654

>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=99.61  E-value=1.1e-15  Score=127.43  Aligned_cols=75  Identities=27%  Similarity=0.479  Sum_probs=70.1

Q ss_pred             CCcceEEeCCCCCC-CCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDES-TTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~-~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||++ +|+++|+++|++||.|.+|.+       ++|||||+|++.++|.+|++.||+..|.|+.|.|.++
T Consensus        25 ~~~~~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           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            34589999999999 999999999999999999998       5789999999999999999999999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ...
T Consensus        98 ~~~  100 (110)
T 1wf1_A           98 GEP  100 (110)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            743

>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=99.61  E-value=4.7e-16  Score=129.07  Aligned_cols=84  Identities=12%  Similarity=0.156  Sum_probs=78.0

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCc---eEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGT---ITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~---I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      ...++|||+||++++|+++|+++|+.||.   |.+|+|+.+.+|+++|||||+|.+.++|.+|++ +|+..++|+.|.|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVY   87 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEE
Confidence            35678999999999999999999999998   899999999889999999999999999999998 99999999999999


Q ss_pred             EcccHHHH
Q 012034          206 VAQRKEER  213 (472)
Q Consensus       206 ~a~~k~~~  213 (472)
                      ++..++..
T Consensus        88 ~a~~~~~~   95 (107)
T 2lmi_A           88 EINNEDVD   95 (107)
T ss_dssp             ECCHHHHH
T ss_pred             ECCHHHHH
Confidence            99877644

>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=99.61  E-value=9.8e-16  Score=126.42  Aligned_cols=81  Identities=21%  Similarity=0.276  Sum_probs=75.1

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEE-EEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITS-CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~-v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+|||+++|+++|+++|+.||.|.+ |.|+.+.+|+++|||||+|.+.++|.+|++. ++..++|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEEC
Confidence            34578999999999999999999999999998 8898888899999999999999999999987 999999999999988


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        92 ~~~   94 (104)
T 1wg5_A           92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.61  E-value=1.4e-15  Score=126.85  Aligned_cols=79  Identities=22%  Similarity=0.215  Sum_probs=71.6

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccC-ceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G-~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+++|||+||++++++++|+++|+.|| .|..+.|..+   .++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~  103 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDD  103 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            356899999999999999999999999 9999998643   479999999999999999999999999999999999987


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      ...
T Consensus       104 ~~p  106 (111)
T 2jvr_A          104 NPP  106 (111)
T ss_dssp             C--
T ss_pred             CCC
Confidence            653

>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=9.4e-16  Score=122.85  Aligned_cols=77  Identities=25%  Similarity=0.437  Sum_probs=63.5

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCc--cCCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK--FDDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~--i~g~~l~V~  102 (472)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|+.+    +||||||+|++.++|.+    +++..  +.|+.|.|.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            467899999999999999999999999999999999875    79999999999999983    55655  458999999


Q ss_pred             ccccchh
Q 012034          103 KAQKKSE  109 (472)
Q Consensus       103 ~a~~~~~  109 (472)
                      ++..+..
T Consensus        80 ~a~~k~~   86 (89)
T 3d2w_A           80 NAEPKHN   86 (89)
T ss_dssp             ECC----
T ss_pred             EcCCCCc
Confidence            9876543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.61  E-value=8.9e-16  Score=126.91  Aligned_cols=80  Identities=20%  Similarity=0.297  Sum_probs=73.9

Q ss_pred             ccceeeeecCCCCc------cHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCe-eE
Q 012034          130 QGLNLYIKNLGDSI------DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK-PL  202 (472)
Q Consensus       130 ~~~~l~V~nL~~~~------t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk-~l  202 (472)
                      .+++|||+|||+.+      |+++|+++|+.||.|.+|.|. ..+|.++|||||+|.+.++|.+|+..|||..+.|+ .|
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            35689999999999      789999999999999999998 45789999999999999999999999999999998 99


Q ss_pred             EEEEcccH
Q 012034          203 YVAVAQRK  210 (472)
Q Consensus       203 ~V~~a~~k  210 (472)
                      .|.++...
T Consensus        93 ~V~~a~~~  100 (105)
T 2nlw_A           93 RVNLFTDF  100 (105)
T ss_dssp             EEECSCCC
T ss_pred             EEEEcchH
Confidence            99998653

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.61  E-value=4.6e-16  Score=122.23  Aligned_cols=72  Identities=22%  Similarity=0.359  Sum_probs=67.3

Q ss_pred             ceeeeecCCCCc------cHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCe-eEEE
Q 012034          132 LNLYIKNLGDSI------DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK-PLYV  204 (472)
Q Consensus       132 ~~l~V~nL~~~~------t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk-~l~V  204 (472)
                      ++|||+|||..+      ++++|+++|++||.|.++.+. ..+|.++|||||+|.+.++|.+|++.|||..++|+ +|+|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            589999999999      779999999999999999988 45789999999999999999999999999999999 8876

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.61  E-value=3.1e-16  Score=135.03  Aligned_cols=81  Identities=20%  Similarity=0.343  Sum_probs=76.0

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEE--EEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCc----EecCee
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITS--CKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGK----MIVSKP  201 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~--v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~----~i~gk~  201 (472)
                      ...++|||+||++++|+++|+++|+.||.|..  |+|++|+ +|+++|||||+|.+. +|.+|+..|||.    .++|+.
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            34568999999999999999999999999977  9999997 899999999999999 999999999999    999999


Q ss_pred             EEEEEcccH
Q 012034          202 LYVAVAQRK  210 (472)
Q Consensus       202 l~V~~a~~k  210 (472)
                      |.|.++..+
T Consensus       100 l~V~~a~~~  108 (131)
T 2m2b_A          100 INVEFAKGS  108 (131)
T ss_dssp             CCCEECCCS
T ss_pred             EEEEECCCC
Confidence            999999764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=6.6e-16  Score=119.81  Aligned_cols=75  Identities=35%  Similarity=0.578  Sum_probs=71.3

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ++|||+|||.++++++|+++|+.||.|.++.+..++ +|.++|||||+|.+.++|.+|++.++ ..++|+.|.|+++
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            479999999999999999999999999999999885 68999999999999999999999999 9999999999986

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.61  E-value=2.1e-15  Score=125.56  Aligned_cols=81  Identities=33%  Similarity=0.557  Sum_probs=73.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||+.++|+++|+++|+.||.|.+|+|+++. +|.++|||||+|.+.++|.+|++.+ +..++|+.|.|.++.
T Consensus        24 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a~  102 (109)
T 2rs2_A           24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVAF  102 (109)
T ss_dssp             --CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEcc
Confidence            45689999999999999999999999999999999986 5899999999999999999999886 499999999999987


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .+.
T Consensus       103 ~~~  105 (109)
T 2rs2_A          103 PRR  105 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.61  E-value=7.5e-16  Score=124.64  Aligned_cols=80  Identities=18%  Similarity=0.348  Sum_probs=72.6

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC-CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~-~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.+ .++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
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            3468999999999999999999999999998887765 477899999999999999999999999999999999999875


Q ss_pred             c
Q 012034          209 R  209 (472)
Q Consensus       209 ~  209 (472)
                      .
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=1.7e-15  Score=122.47  Aligned_cols=77  Identities=18%  Similarity=0.365  Sum_probs=68.5

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||+++|+++|+++|++||.|.+| +....+|+   ||||+|.+.++|.+|++ ||+..|.|+.|.|.++.
T Consensus         6 ~~~~~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            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            457899999999999999999999999999987 33334554   99999999999999999 99999999999999886


Q ss_pred             cc
Q 012034          106 KK  107 (472)
Q Consensus       106 ~~  107 (472)
                      .+
T Consensus        81 ~~   82 (94)
T 2e5g_A           81 QK   82 (94)
T ss_dssp             CS
T ss_pred             cC
Confidence            54

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=2.1e-15  Score=123.56  Aligned_cols=78  Identities=29%  Similarity=0.452  Sum_probs=72.3

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||+.++|+++|+++|+.||.|   +++.+.++.++|||||+|.+.++|.+|++.||+..|.|+.|+|.++..
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   90 (101)
T 2fc9_A           14 ESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGP   90 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCC
Confidence            46789999999999999999999999987   666667889999999999999999999999999999999999999876


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        91 ~   91 (101)
T 2fc9_A           91 R   91 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.1e-15  Score=126.26  Aligned_cols=82  Identities=24%  Similarity=0.432  Sum_probs=76.0

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||++++++++|+++|+.||.|.+|+|+.++ ++.++|||||+|.+.++|.+|++. ++..|.|+.|.|.++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a   92 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPC   92 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEc
Confidence            355789999999999999999999999999999999984 789999999999999999999998 999999999999988


Q ss_pred             ccHH
Q 012034          208 QRKE  211 (472)
Q Consensus       208 ~~k~  211 (472)
                      ..+.
T Consensus        93 ~~~~   96 (105)
T 2dh8_A           93 TPRG   96 (105)
T ss_dssp             CCSS
T ss_pred             cCCC
Confidence            7653

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=3.4e-16  Score=124.00  Aligned_cols=79  Identities=27%  Similarity=0.442  Sum_probs=73.2

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+++|||+|||.++++++|+++|+.||.|.+++++.++ ++.++|||||+|.+.++|.+|++.|||..+.|+.|++.++.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            45689999999999999999999999999999999885 68899999999999999999999999999999998887654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=2e-15  Score=122.79  Aligned_cols=76  Identities=26%  Similarity=0.393  Sum_probs=70.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+||  ++|+++|+++|++||.|.+|.+.     +++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~   85 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   85 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCS
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            46789999996  89999999999999999999984     568999999999999999999999999999999999997


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      .+.
T Consensus        86 ~~~   88 (97)
T 1x5p_A           86 KQP   88 (97)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=99.60  E-value=9.2e-16  Score=126.19  Aligned_cols=80  Identities=16%  Similarity=0.246  Sum_probs=73.0

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...++|||+|||+++|+++|+++|+.||. .+|+|+.+++|+++|||||+|.+.++|.+|+ .+|+..++|+.|.|.++.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEECC
Confidence            34568999999999999999999999995 5999999999999999999999999999999 579999999999999776


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      ..
T Consensus        91 ~~   92 (102)
T 1wez_A           91 TA   92 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.60  E-value=4.1e-16  Score=124.93  Aligned_cols=80  Identities=33%  Similarity=0.522  Sum_probs=71.9

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ++|||+||+.++++++|+++|+.||.|.++++.++. +|.++|||||+|.+.+ |.+|+..|||..++|+.|.|.++..+
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            479999999999999999999999999999999886 5899999999999999 99999999999999999999998876


Q ss_pred             HH
Q 012034          211 EE  212 (472)
Q Consensus       211 ~~  212 (472)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.60  E-value=8.9e-16  Score=128.91  Aligned_cols=81  Identities=17%  Similarity=0.194  Sum_probs=71.5

Q ss_pred             ceEEeCCC----CCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCC----HHH----HHHHHH--HHCCCc
Q 012034           29 NNVFVKNL----DESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFEN----ADD----AAKAVE--ALNGKK   93 (472)
Q Consensus        29 ~~l~V~nL----p~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~----~e~----A~~Av~--~lng~~   93 (472)
                      ++|||+||    |+++++++|+++|+.||+|.++.++.| .||+++|||||+|.+    .++    |.+|++  .|||..
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            68999999    999999999999999999999999999 589999999999996    333    899998  789999


Q ss_pred             cCCcceeeeccccchh
Q 012034           94 FDDREWYVGKAQKKSE  109 (472)
Q Consensus        94 i~g~~l~V~~a~~~~~  109 (472)
                      |+|+.|.|..-.....
T Consensus        83 I~Gr~irV~ln~~g~~   98 (136)
T 2j8a_A           83 IMGFKFEVILNKHSIL   98 (136)
T ss_dssp             ETTEEEEEEECCTTHH
T ss_pred             ecCcEEEEEECcccHH
Confidence            9999999987654433

>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=99.60  E-value=3.3e-15  Score=125.38  Aligned_cols=79  Identities=23%  Similarity=0.392  Sum_probs=74.0

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .+++|||+|||.++|+++|+++|+.||.|.+|.++.+  +.++|||||+|.+.++|.+|+..|||..++|+.|.|.++..
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   84 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA   84 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            4568999999999999999999999999999999875  56799999999999999999999999999999999999986


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        85 ~   85 (115)
T 3lqv_A           85 N   85 (115)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.60  E-value=1.5e-15  Score=125.27  Aligned_cols=77  Identities=19%  Similarity=0.277  Sum_probs=70.0

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCc--EecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK--MIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~--~i~gk~l~V~~a  207 (472)
                      .+++|||+||++++++++|+++|++||.|.+|.++++     ||||||+|.+.++|.+|++.|++.  .+.|++|+|.|+
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a   88 (104)
T 1wex_A           14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            4568999999999999999999999999999999874     899999999999999999988764  589999999999


Q ss_pred             ccHH
Q 012034          208 QRKE  211 (472)
Q Consensus       208 ~~k~  211 (472)
                      ..+.
T Consensus        89 ~~~~   92 (104)
T 1wex_A           89 TSKR   92 (104)
T ss_dssp             SSSS
T ss_pred             cCcc
Confidence            7653

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=2.3e-15  Score=119.66  Aligned_cols=74  Identities=22%  Similarity=0.358  Sum_probs=66.4

Q ss_pred             CcceEEeCCCCCCCCHHH----HHHHHhcC-CCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           27 KFNNVFVKNLDESTTDED----LKKIFGEY-GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~----L~~~F~~f-G~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      ..|.|||+|||+++++++    |+++|++| |+|.+|      ++   |||||.|.+.++|.+|++.|+|..+.||.|+|
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v   78 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            455699999999999988    55899999 599998      33   99999999999999999999999999999999


Q ss_pred             eccccchh
Q 012034          102 GKAQKKSE  109 (472)
Q Consensus       102 ~~a~~~~~  109 (472)
                      .+|..+++
T Consensus        79 ~~A~~~sd   86 (96)
T 2diu_A           79 SFTPKNRE   86 (96)
T ss_dssp             ESSCCSCC
T ss_pred             EecCCCcc
Confidence            99987654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=1.6e-15  Score=128.98  Aligned_cols=85  Identities=18%  Similarity=0.272  Sum_probs=77.1

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCce----EEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTI----TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I----~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      ..++|||+|||+++|+++|+++|+.||.|    .+|.|+.+.+|+++|||||+|.+.++|.+|++. |+..+.|+.|.|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~  100 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEE
Confidence            45689999999999999999999999875    689999988999999999999999999999986 9999999999999


Q ss_pred             EcccHHHHHH
Q 012034          206 VAQRKEERRA  215 (472)
Q Consensus       206 ~a~~k~~~~~  215 (472)
                      .+..++....
T Consensus       101 ~a~~~e~~~~  110 (123)
T 2dha_A          101 RSTAAEVQQV  110 (123)
T ss_dssp             EECHHHHHHH
T ss_pred             ECCHHHHHHH
Confidence            9987765544

>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=99.60  E-value=3.5e-15  Score=132.36  Aligned_cols=81  Identities=23%  Similarity=0.300  Sum_probs=76.3

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||+.++|+++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.|+.
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  117 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA  117 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            45789999999999999999999999999999999886 58899999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus       118 ~~  119 (156)
T 1h2v_Z          118 GF  119 (156)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=2e-15  Score=122.47  Aligned_cols=79  Identities=20%  Similarity=0.338  Sum_probs=71.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEE-EEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v-~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|++||.|.++ .++.+..   .|.|||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            457899999999999999999999999999999 5777732   344999999999999999999999999999999999


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ..+
T Consensus        90 ~~~   92 (96)
T 2e44_A           90 PDE   92 (96)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            765

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=2.4e-15  Score=126.51  Aligned_cols=79  Identities=33%  Similarity=0.505  Sum_probs=74.4

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .++|||+||+.++|+++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++. ++..|+|+.|.|.++..
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            3589999999999999999999999999999999985 688999999999999999999988 99999999999999876


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus       106 ~  106 (116)
T 1x4b_A          106 R  106 (116)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.59  E-value=4.3e-15  Score=123.40  Aligned_cols=75  Identities=24%  Similarity=0.325  Sum_probs=71.1

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecC-----eeEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS-----KPLYV  204 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g-----k~l~V  204 (472)
                      ..++|||+||++++|+++|+++|+.||.|.+|+|+.+      |||||+|.+.++|.+||+.||+..|.|     +.|.|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V   87 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   87 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEE
Confidence            4578999999999999999999999999999999876      899999999999999999999999999     99999


Q ss_pred             EEcccH
Q 012034          205 AVAQRK  210 (472)
Q Consensus       205 ~~a~~k  210 (472)
                      .++..+
T Consensus        88 ~~a~~~   93 (108)
T 1x4c_A           88 KVDGPR   93 (108)
T ss_dssp             EESSCC
T ss_pred             EeCCCC
Confidence            999874

>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=99.59  E-value=1.5e-15  Score=123.41  Aligned_cols=82  Identities=33%  Similarity=0.522  Sum_probs=75.5

Q ss_pred             ccceeeeecCCCCccHHHHH----HHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~----~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      .+++|||+||+.++++++|+    ++|+.||.|.+|.+.+  +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   84 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            45789999999999999999    9999999999999874  46789999999999999999999999999999999999


Q ss_pred             EcccHHHH
Q 012034          206 VAQRKEER  213 (472)
Q Consensus       206 ~a~~k~~~  213 (472)
                      ++..+...
T Consensus        85 ~a~~~~~~   92 (97)
T 1nu4_A           85 YAKTDSDI   92 (97)
T ss_dssp             ECSSCCTH
T ss_pred             EccCCCcc
Confidence            99876544

>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=99.59  E-value=5.6e-15  Score=121.42  Aligned_cols=81  Identities=28%  Similarity=0.409  Sum_probs=74.4

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||++++++++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+|+.  ++..++|+.|.|.++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a   90 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLP   90 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEec
Confidence            345789999999999999999999999999999999985 68999999999999999999998  578999999999998


Q ss_pred             ccHH
Q 012034          208 QRKE  211 (472)
Q Consensus       208 ~~k~  211 (472)
                      ..+.
T Consensus        91 ~~~~   94 (103)
T 2cqg_A           91 NSKQ   94 (103)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            8763

>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=99.59  E-value=1.5e-15  Score=127.69  Aligned_cols=70  Identities=34%  Similarity=0.375  Sum_probs=63.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      ...++|||+|||+++|+++|+++|++||+|.+|.|+.|      |||||+|++.++|.+||+.||++.|.|+.|.|
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~   83 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET   83 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeee
Confidence            45688999999999999999999999999999999876      89999999999999999999999999998433

>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=99.59  E-value=2.4e-15  Score=124.97  Aligned_cols=82  Identities=15%  Similarity=0.175  Sum_probs=74.4

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCc-eEEEEEe-eCC-CCCcccEEEEEcCCHHHHHHHHHHhC--CcEecCeeEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGT-ITSCKVM-RDP-SGISKGSGFVAFSTPEEASRALAEMN--GKMIVSKPLYV  204 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~-I~~v~i~-~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~--g~~i~gk~l~V  204 (472)
                      ..++|||+||+.++|+++|+++|+.||. |.++.++ .+. +|.++|||||+|.+.++|.+|++.|+  +..+.|+.|.|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            4568999999999999999999999998 9999998 554 57899999999999999999999996  58999999999


Q ss_pred             EEcccHH
Q 012034          205 AVAQRKE  211 (472)
Q Consensus       205 ~~a~~k~  211 (472)
                      .|+..+.
T Consensus        87 ~~a~~~~   93 (109)
T 2dis_A           87 DWAEPEI   93 (109)
T ss_dssp             EESCSSC
T ss_pred             EEcCCCC
Confidence            9997653

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.59  E-value=1.9e-15  Score=123.76  Aligned_cols=76  Identities=22%  Similarity=0.345  Sum_probs=71.1

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .+++|||+||+.++++++|+++|+.||.|.++++.+     ++|||||+|.+.++|.+|+..|||..++|+.|+|.|++.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            457899999999999999999999999999999984     589999999999999999999999999999999999875


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus       101 ~  101 (101)
T 2la4_A          101 R  101 (101)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.59  E-value=4.6e-15  Score=117.37  Aligned_cols=75  Identities=27%  Similarity=0.451  Sum_probs=70.3

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHh-CCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM-NGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l-~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||+.++++++|+++|+.||.|.++++.++     +|||||+|.+.++|.+|++.| ++..++|++|.|.|+
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            34578999999999999999999999999999999874     899999999999999999999 999999999999997


Q ss_pred             c
Q 012034          208 Q  208 (472)
Q Consensus       208 ~  208 (472)
                      +
T Consensus        85 k   85 (85)
T 2ytc_A           85 R   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.58  E-value=2.1e-15  Score=128.55  Aligned_cols=84  Identities=19%  Similarity=0.381  Sum_probs=75.8

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEE-EEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v-~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||+++|+++|+++|+.||.|.++ .+..+.+|.++|||||+|.+.++|.+||+ +|+..|+|+.|.|.++.
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            45789999999999999999999999999884 45555689999999999999999999998 99999999999999998


Q ss_pred             cHHHHH
Q 012034          209 RKEERR  214 (472)
Q Consensus       209 ~k~~~~  214 (472)
                      .++...
T Consensus       103 ~~~~~~  108 (124)
T 1wel_A          103 KKGMLE  108 (124)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=99.58  E-value=4e-15  Score=121.00  Aligned_cols=76  Identities=21%  Similarity=0.358  Sum_probs=71.3

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec--CeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~--gk~l~V~~a  207 (472)
                      ..++|||+||+.++|+++|+++|++||.|.+|.+.++     +|||||+|.+.++|.+|++.||+..+.  |+.|.|.++
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a   90 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEEC
Confidence            3468999999999999999999999999999999865     789999999999999999999999999  999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        91 ~~~   93 (97)
T 1why_A           91 KSG   93 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.58  E-value=1.1e-15  Score=127.43  Aligned_cols=77  Identities=21%  Similarity=0.302  Sum_probs=69.8

Q ss_pred             ccceeeeecCCCC-ccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCC--cEecCeeEEEEE
Q 012034          130 QGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG--KMIVSKPLYVAV  206 (472)
Q Consensus       130 ~~~~l~V~nL~~~-~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g--~~i~gk~l~V~~  206 (472)
                      .+++|||+||+++ +++++|+++|+.||.|.+|.|++     ++|||||+|.+.++|.+|++.|++  ..|.|++|+|.+
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   98 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL   98 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEE
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            4678999999998 99999999999999999999975     489999999999999999998864  569999999999


Q ss_pred             cccHH
Q 012034          207 AQRKE  211 (472)
Q Consensus       207 a~~k~  211 (472)
                      ++.+.
T Consensus        99 a~~~~  103 (112)
T 1x4f_A           99 SEKYK  103 (112)
T ss_dssp             ECSCS
T ss_pred             Ccccc
Confidence            97653

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.58  E-value=5.1e-15  Score=128.51  Aligned_cols=78  Identities=29%  Similarity=0.488  Sum_probs=73.3

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..++|||+|||.++++++|+++|+.||.|.+++|++++ ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|.+|
T Consensus        62 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45789999999999999999999999999999999884 7889999999999999999999999999999999999875

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.58  E-value=7.7e-15  Score=121.22  Aligned_cols=82  Identities=23%  Similarity=0.285  Sum_probs=73.1

Q ss_pred             cCCcceEEeCCCCC-----CCCHHHHHHHHhcCCCeeEEEEEECC--CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCc
Q 012034           25 KTKFNNVFVKNLDE-----STTDEDLKKIFGEYGTITSAVVMRDG--DGKSKCFGFVNFENADDAAKAVEALNGKKFDDR   97 (472)
Q Consensus        25 ~~~~~~l~V~nLp~-----~~tee~L~~~F~~fG~I~~v~i~~d~--~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~   97 (472)
                      ....++|+|+|+-.     +-++++|+++|++||.|.+|.|.++.  +++++|||||+|++.++|.+|++.|||..+.|+
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            35678999999962     33789999999999999999999984  368999999999999999999999999999999


Q ss_pred             ceeeecccc
Q 012034           98 EWYVGKAQK  106 (472)
Q Consensus        98 ~l~V~~a~~  106 (472)
                      .|.|.++..
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

>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=99.58  E-value=4.9e-15  Score=123.20  Aligned_cols=77  Identities=27%  Similarity=0.472  Sum_probs=72.7

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...++|||+||+..+++++|+++|+.||.|.+|+++.+     +|||||+|.+.++|.+|+..|||..+.|+.|.|.|+.
T Consensus        23 ~~~~~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           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   97 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecC
Confidence            45679999999999999999999999999999999986     8999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        98 ~~   99 (109)
T 1x4g_A           98 ES   99 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.58  E-value=3.8e-15  Score=123.83  Aligned_cols=78  Identities=26%  Similarity=0.574  Sum_probs=72.0

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ....++|||+||+.++|+++|+++|+.||.|.+|++.       +|||||+|.+.++|.+|++.|||..++|+.|.|.++
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  100 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS  100 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            3456799999999999999999999999999999987       789999999999999999999999999999999999


Q ss_pred             ccHHH
Q 012034          208 QRKEE  212 (472)
Q Consensus       208 ~~k~~  212 (472)
                      ..+..
T Consensus       101 ~~~~~  105 (108)
T 2jvo_A          101 KLPAK  105 (108)
T ss_dssp             SCCC-
T ss_pred             cCCCC
Confidence            87643

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.58  E-value=2e-15  Score=123.67  Aligned_cols=76  Identities=26%  Similarity=0.543  Sum_probs=72.0

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      ++|||+||+.++|+++|+++|+.||.|.+|.+..+    ++|||||+|.+.++|.+|++.|||..+.|+.|.|.++..+.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            47999999999999999999999999999999987    79999999999999999999999999999999999988753

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=5.7e-15  Score=118.34  Aligned_cols=74  Identities=22%  Similarity=0.478  Sum_probs=69.8

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||+.++++++|+++|+.||.|.++++.       +|||||+|.+.++|.+|++.||+..++|+.|.|.++..
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   79 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKN   79 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSC
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCC
Confidence            45789999999999999999999999999999997       57999999999999999999999999999999999876


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        80 ~   80 (90)
T 2dnq_A           80 K   80 (90)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.57  E-value=3.6e-15  Score=124.59  Aligned_cols=76  Identities=24%  Similarity=0.304  Sum_probs=70.9

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+|.|..     ++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+..
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            356899999999999999999999999999999875     488999999999999999999999999999999999875


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      .
T Consensus        84 ~   84 (111)
T 1whx_A           84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.57  E-value=8.8e-15  Score=119.10  Aligned_cols=74  Identities=26%  Similarity=0.453  Sum_probs=69.5

Q ss_pred             ccceeeeecCCC-CccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGD-SIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~-~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+++|||+||+. ++++++|+++|+.||.|.++++.       +|||||+|.+.++|.+|++.+||..++|+.|.|.++.
T Consensus        21 ~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   93 (97)
T 2xnq_A           21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSS   93 (97)
T ss_dssp             TTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            467899999998 99999999999999999999983       7899999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        94 ~~   95 (97)
T 2xnq_A           94 SN   95 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.57  E-value=5.7e-15  Score=125.97  Aligned_cols=78  Identities=18%  Similarity=0.321  Sum_probs=70.9

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeE-EEEEeCCHHHHHHHHHHHCCCccCC--cceeee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF-GFVNFENADDAAKAVEALNGKKFDD--REWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~-aFV~F~~~e~A~~Av~~lng~~i~g--~~l~V~  102 (472)
                      .+--.|||+||++.+|+++|+++|++||.|.+|++..+    ++|| |||+|++.++|.+|++.|||..|.|  +.|+|.
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            45667899999999999999999999999999988864    3677 9999999999999999999999988  899999


Q ss_pred             ccccc
Q 012034          103 KAQKK  107 (472)
Q Consensus       103 ~a~~~  107 (472)
                      +++.+
T Consensus       102 ~ak~~  106 (130)
T 3zzy_A          102 FSKLT  106 (130)
T ss_dssp             ECSCS
T ss_pred             ecCCC
Confidence            99765

>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=99.57  E-value=3.4e-15  Score=121.88  Aligned_cols=77  Identities=29%  Similarity=0.439  Sum_probs=71.9

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...++|||+||+.++|+++|+++|+.||.|.+|++.++     +|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   87 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcC
Confidence            34568999999999999999999999999999999865     8999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        88 ~~   89 (99)
T 2cpj_A           88 HS   89 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.57  E-value=2.6e-15  Score=119.30  Aligned_cols=72  Identities=22%  Similarity=0.475  Sum_probs=67.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcC----C-------CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCcc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEY----G-------TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF   94 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~f----G-------~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i   94 (472)
                      ...++|||+|||.++|+++|+++|++|    |       .|.++.+..+     +|||||+|.+.++|.+|+ .||+..+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            457899999999999999999999999    8       9999988765     899999999999999999 9999999


Q ss_pred             CCcceeeec
Q 012034           95 DDREWYVGK  103 (472)
Q Consensus        95 ~g~~l~V~~  103 (472)
                      .|+.|.|++
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            999999975

>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=99.57  E-value=5.4e-15  Score=135.93  Aligned_cols=82  Identities=22%  Similarity=0.292  Sum_probs=74.7

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      ..++|||+|||.++|+++|+++|++||.|.+|.+.++.+|+++|||||+|++.++|.+|++.+ +..+.|+.|.|.++..
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            468999999999999999999999999999999999988999999999999999999999765 5689999999999876


Q ss_pred             chh
Q 012034          107 KSE  109 (472)
Q Consensus       107 ~~~  109 (472)
                      ..+
T Consensus       187 y~~  189 (193)
T 2voo_A          187 YFA  189 (193)
T ss_dssp             C--
T ss_pred             HHH
Confidence            543

>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=99.56  E-value=4.3e-15  Score=123.88  Aligned_cols=77  Identities=22%  Similarity=0.431  Sum_probs=69.4

Q ss_pred             cccceeee--ecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEe-----cCee
Q 012034          129 FQGLNLYI--KNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI-----VSKP  201 (472)
Q Consensus       129 ~~~~~l~V--~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i-----~gk~  201 (472)
                      ....+|||  +||++++|+++|+++|++||.|++|.|..+     ||||||+|.+.++|.+|++.|||+.+     .|++
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            34568999  669999999999999999999999988753     89999999999999999999999998     6899


Q ss_pred             EEEEEcccH
Q 012034          202 LYVAVAQRK  210 (472)
Q Consensus       202 l~V~~a~~k  210 (472)
                      |+|.+++..
T Consensus        98 l~v~~a~~~  106 (114)
T 2cq2_A           98 LYLNFVEKV  106 (114)
T ss_dssp             CEEEEESCC
T ss_pred             EEEEecccC
Confidence            999998653

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.56  E-value=1.1e-14  Score=123.65  Aligned_cols=77  Identities=22%  Similarity=0.206  Sum_probs=68.6

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeE-EEEEeCCHHHHHHHHHHHCCCccCC--cceeeec
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF-GFVNFENADDAAKAVEALNGKKFDD--REWYVGK  103 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~-aFV~F~~~e~A~~Av~~lng~~i~g--~~l~V~~  103 (472)
                      +--.|||+||++.+|+++|+++|++||.|.+|+|...     .|| |||+|.+.++|.+|++.|||..|.|  +.|.|.+
T Consensus        24 ~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           24 KVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             cEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            3445789999999999999999999999999999763     286 9999999999999999999999987  6899999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        99 Ak~~~  103 (124)
T 2e5i_A           99 ARPTR  103 (124)
T ss_dssp             CSCSC
T ss_pred             ecCCc
Confidence            97654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.2e-14  Score=116.98  Aligned_cols=75  Identities=20%  Similarity=0.458  Sum_probs=70.0

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...++|||+||+.++++++|+++|+.||.|.+|.+.++       ||||+|.+.++|.+|++.||+..+.|+.|.|.++.
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~-------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   80 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLST   80 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS-------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC-------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            35678999999999999999999999999999999743       99999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        81 ~~   82 (92)
T 2dgt_A           81 SR   82 (92)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.56  E-value=3e-15  Score=122.81  Aligned_cols=81  Identities=22%  Similarity=0.496  Sum_probs=75.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+|+++.+.+|.++|||||+|.+.++|.+|++  ++..++|+.|.|.++..
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCc
Confidence            4568999999999999999999999999999999999889999999999999999999998  99999999999999887


Q ss_pred             HHH
Q 012034          210 KEE  212 (472)
Q Consensus       210 k~~  212 (472)
                      +..
T Consensus        86 ~~~   88 (102)
T 2xs2_A           86 KQN   88 (102)
T ss_dssp             CC-
T ss_pred             Ccc
Confidence            643

>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=99.56  E-value=1.9e-15  Score=116.60  Aligned_cols=74  Identities=20%  Similarity=0.392  Sum_probs=69.2

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      +|||+|||.++++++|+++|+.||.|.++.+..+. +|.++|||||+|.+.++|.+|++. ++..+.|+.|.|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            58999999999999999999999999999998885 588999999999999999999974 889999999999875

>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=99.56  E-value=5.5e-15  Score=152.41  Aligned_cols=82  Identities=27%  Similarity=0.525  Sum_probs=77.4

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||.++|+++|+++|++||.|.+|.|+.+ .+|+++|||||+|.+.++|.+||+.|||..|.|+.|.|.++.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            4579999999999999999999999999999999999 589999999999999999999999999999999999999997


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      .+.
T Consensus       181 ~~~  183 (437)
T 3pgw_S          181 GRT  183 (437)
T ss_pred             CCC
Confidence            543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=5.8e-15  Score=120.04  Aligned_cols=77  Identities=19%  Similarity=0.366  Sum_probs=70.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||++++++++|+++|+.||.|. +.++.+   .++|||||+|.+.++|.+|++.|||..++|+.|.|.++..
T Consensus        18 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   93 (97)
T 2e5j_A           18 LAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ   93 (97)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCC
T ss_pred             CCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            457899999999999999999999999997 666653   6799999999999999999999999999999999999876


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        94 ~   94 (97)
T 2e5j_A           94 Q   94 (97)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.55  E-value=3.8e-15  Score=126.98  Aligned_cols=80  Identities=24%  Similarity=0.338  Sum_probs=73.2

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceE--EEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTIT--SCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~--~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..++|||+|||+++|+++|+++|+.| .|.  +|+|+.+++|+++|||||+|.+.++|.+|++. ++..|+|+.|.|..+
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a  118 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKS  118 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEEC
Confidence            45689999999999999999999999 566  89999998899999999999999999999974 779999999999998


Q ss_pred             ccHH
Q 012034          208 QRKE  211 (472)
Q Consensus       208 ~~k~  211 (472)
                      ..++
T Consensus       119 ~~~e  122 (126)
T 2hgm_A          119 SQEE  122 (126)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7665

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.55  E-value=6.8e-15  Score=133.33  Aligned_cols=82  Identities=29%  Similarity=0.482  Sum_probs=77.8

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..+++|||+||+..+++++|+++|+.||.|++|.|..+.++.++|||||+|.+.++|.+|++.|||..|+|+.|.|.|+.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            34679999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      ..
T Consensus       166 ~~  167 (177)
T 2f3j_A          166 SQ  167 (177)
T ss_dssp             SG
T ss_pred             CC
Confidence            65

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=1.3e-14  Score=116.22  Aligned_cols=75  Identities=24%  Similarity=0.506  Sum_probs=69.8

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...++|||+||+.++|+++|+++|+.||.|.++++.++       ||||+|.+.++|.+|++.|||..++|+.|.|.++.
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~-------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   79 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELST   79 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS-------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC-------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECC
Confidence            34578999999999999999999999999999999843       99999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        80 ~~   81 (90)
T 2dnp_A           80 KG   81 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=3.9e-15  Score=124.91  Aligned_cols=77  Identities=14%  Similarity=0.271  Sum_probs=67.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-C---CCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-D---GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~---g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      ...++|||+|||+++|+++|+++|++||.|. +.++.+. +   |+++|||||+|++.++|.+|++.|+  .++|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            5678999999999999999999999999999 7777663 4   7999999999999999999999984  377888877


Q ss_pred             eccc
Q 012034          102 GKAQ  105 (472)
Q Consensus       102 ~~a~  105 (472)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6553

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.55  E-value=5.4e-15  Score=119.83  Aligned_cols=77  Identities=27%  Similarity=0.412  Sum_probs=70.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||+.++++++|+++|+.||.|..+    ..++.++|||||+|.+.++|.+|+..|||..++|+.|.|.++..
T Consensus        15 ~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   90 (96)
T 1fjc_A           15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCC
Confidence            45689999999999999999999999988766    34678999999999999999999999999999999999999876


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        91 ~   91 (96)
T 1fjc_A           91 K   91 (96)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.54  E-value=1.9e-15  Score=131.24  Aligned_cols=123  Identities=14%  Similarity=0.161  Sum_probs=74.3

Q ss_pred             eEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHH
Q 012034           70 CFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK  149 (472)
Q Consensus        70 G~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~  149 (472)
                      |++|..|...+.+..+...+... ..+...--.....                .........++|||+|||+++|+++|+
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g~~----------------~~~~~~~~~~~lfV~nLp~~~te~dL~   64 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSGDS----------------EFTVQSTTGHCVHMRGLPYKATENDIY   64 (139)
T ss_dssp             ------------------------------------------------------------CCCCEECCSCCTTCCHHHHH
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCCCc----------------ccCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            67888888877777666654322 2222110000000                001122345689999999999999999


Q ss_pred             HHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHH
Q 012034          150 ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       150 ~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      ++|+.|| |++|+|+.+++|+++|||||+|.+.++|.+|| .+|+..|.|+.|.|.++..++
T Consensus        65 ~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           65 NFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             HHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSC
T ss_pred             HHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCC
Confidence            9999999 77999999988999999999999999999999 899999999999999877653

>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=99.54  E-value=2.5e-14  Score=114.52  Aligned_cols=76  Identities=16%  Similarity=0.391  Sum_probs=63.4

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEe--cCeeEEEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVAV  206 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i--~gk~l~V~~  206 (472)
                      ...++|||+||++++|+++|+++|++||.|.+|+|+++    ++|||||+|.+.++|.+    +++..+  .|+.|.|.+
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~   80 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISN   80 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEE
Confidence            35679999999999999999999999999999999885    79999999999999883    566554  599999999


Q ss_pred             cccHHH
Q 012034          207 AQRKEE  212 (472)
Q Consensus       207 a~~k~~  212 (472)
                      +..+..
T Consensus        81 a~~k~~   86 (89)
T 3d2w_A           81 AEPKHN   86 (89)
T ss_dssp             CC----
T ss_pred             cCCCCc
Confidence            987754

>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=99.54  E-value=2e-14  Score=118.15  Aligned_cols=75  Identities=28%  Similarity=0.544  Sum_probs=69.9

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||+.++|+++|+++|+.||.|.+|+++       ++||||+|.+.++|.+|++.||+..|.|+.|.|.++..
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   82 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKP   82 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCC
Confidence            45689999999999999999999999999999987       45999999999999999999999999999999999876


Q ss_pred             HH
Q 012034          210 KE  211 (472)
Q Consensus       210 k~  211 (472)
                      +.
T Consensus        83 ~~   84 (103)
T 2dgu_A           83 PD   84 (103)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>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=99.54  E-value=8.6e-15  Score=122.79  Aligned_cols=79  Identities=29%  Similarity=0.484  Sum_probs=71.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCce----EEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTI----TSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I----~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      ..++|||+||+.++|+++|+++|+.||.|    ..+++.   ++.++|||||+|.+.++|.+|++.|||..+.|+.|.|.
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            45789999999999999999999999998    445544   67899999999999999999999999999999999999


Q ss_pred             EcccHH
Q 012034          206 VAQRKE  211 (472)
Q Consensus       206 ~a~~k~  211 (472)
                      ++..+.
T Consensus       101 ~a~~~~  106 (115)
T 2cpx_A          101 FGKNKK  106 (115)
T ss_dssp             ECCCCS
T ss_pred             EccCCC
Confidence            988753

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=2e-14  Score=117.81  Aligned_cols=80  Identities=30%  Similarity=0.432  Sum_probs=71.7

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ...++|||+||+.++|+++|+++|+.|+   +++++.+. ++.++|||||+|.+.++|.+|++.||+..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA   89 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            4567899999999999999999999874   56676664 7889999999999999999999999999999999999998


Q ss_pred             ccHH
Q 012034          208 QRKE  211 (472)
Q Consensus       208 ~~k~  211 (472)
                      ..+.
T Consensus        90 ~~~~   93 (102)
T 2fc8_A           90 KPKG   93 (102)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.30  E-value=5.8e-16  Score=130.32  Aligned_cols=84  Identities=25%  Similarity=0.510  Sum_probs=77.2

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEE--------EEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCe
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITS--------CKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSK  200 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~--------v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk  200 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+        |+|+.++ ++.++|||||+|.+.++|.+|++.|||..+.|+
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            3468999999999999999999999999999        8888884 688999999999999999999999999999999


Q ss_pred             eEEEEEcccHHHH
Q 012034          201 PLYVAVAQRKEER  213 (472)
Q Consensus       201 ~l~V~~a~~k~~~  213 (472)
                      .|.|.++..+..+
T Consensus        86 ~l~V~~a~~~~~~   98 (116)
T 2lcw_A           86 PIKVSFATRRADF   98 (116)
Confidence            9999999877543

>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=99.53  E-value=1.5e-14  Score=128.05  Aligned_cols=76  Identities=20%  Similarity=0.344  Sum_probs=70.3

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecC--eeEEEEEccc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS--KPLYVAVAQR  209 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g--k~l~V~~a~~  209 (472)
                      .+|||+||++.+|+++|+++|++||.|++|+|+.+   .++|||||+|.+.++|.+|++.|||..|.|  +.|+|.|++.
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k---~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~  123 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  123 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES---SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecC
Confidence            46999999999999999999999999999999765   258899999999999999999999999965  9999999987


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus       124 ~  124 (164)
T 1sjr_A          124 T  124 (164)
T ss_dssp             S
T ss_pred             C
Confidence            6

>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=99.53  E-value=1.6e-14  Score=115.26  Aligned_cols=74  Identities=20%  Similarity=0.350  Sum_probs=69.0

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .++|||+|||+++++++|+++|++| .|.++++.     .++|||||+|.+.++|.+|++.|||..++|++|+|.++..+
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            4689999999999999999999999 99999885     57999999999999999999999999999999999998653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.53  E-value=1.5e-14  Score=121.54  Aligned_cols=80  Identities=19%  Similarity=0.338  Sum_probs=71.6

Q ss_pred             ceeeeecC----CCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCC----HHH----HHHHHH--HhCCcE
Q 012034          132 LNLYIKNL----GDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFST----PEE----ASRALA--EMNGKM  196 (472)
Q Consensus       132 ~~l~V~nL----~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s----~~~----A~~Ai~--~l~g~~  196 (472)
                      ++|||+||    ++.+++++|+++|+.||.|.+|.++.|+ +|.|+|||||+|.+    +++    |.+|+.  .++|..
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            47999999    9999999999999999999999999997 78999999999996    333    899998  789999


Q ss_pred             ecCeeEEEEEcccHH
Q 012034          197 IVSKPLYVAVAQRKE  211 (472)
Q Consensus       197 i~gk~l~V~~a~~k~  211 (472)
                      |+|++|+|.+.....
T Consensus        83 I~Gr~irV~ln~~g~   97 (136)
T 2j8a_A           83 IMGFKFEVILNKHSI   97 (136)
T ss_dssp             ETTEEEEEEECCTTH
T ss_pred             ecCcEEEEEECcccH
Confidence            999999999986643

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.53  E-value=1.2e-14  Score=118.06  Aligned_cols=75  Identities=25%  Similarity=0.435  Sum_probs=70.0

Q ss_pred             ccceeeeecCCC-CccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGD-SIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~-~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||++ ++++++|+++|+.||.|.++.+.       +|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus         9 ~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   81 (96)
T 2kvi_A            9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSS   81 (96)
T ss_dssp             CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcC
Confidence            467899999998 99999999999999999999984       7899999999999999999999999999999999987


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .+.
T Consensus        82 ~~~   84 (96)
T 2kvi_A           82 SNA   84 (96)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            653

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.53  E-value=2.9e-14  Score=121.59  Aligned_cols=75  Identities=20%  Similarity=0.363  Sum_probs=69.4

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccE-EEEEcCCHHHHHHHHHHhCCcEecC--eeEEEEEcc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS-GFVAFSTPEEASRALAEMNGKMIVS--KPLYVAVAQ  208 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~-afV~f~s~~~A~~Ai~~l~g~~i~g--k~l~V~~a~  208 (472)
                      ..|||+||++.+|+++|+++|++||.|.+|+++.+    ++|| |||+|.+.++|.+|++.|||..|.|  +.|+|.|++
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak  104 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  104 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECS
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecC
Confidence            36899999999999999999999999999998875    3678 9999999999999999999999988  899999997


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus       105 ~~  106 (130)
T 3zzy_A          105 LT  106 (130)
T ss_dssp             CS
T ss_pred             CC
Confidence            65

>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=99.53  E-value=2.8e-15  Score=119.61  Aligned_cols=77  Identities=19%  Similarity=0.368  Sum_probs=66.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||+++|+++|+++|++||.|.+|.++.+    ++|||||+|++.++|++|+..  ...+.++.|.|.++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecC
Confidence            45789999999999999999999999999999999865    789999999999999865321  334589999999987


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      .+.
T Consensus        77 ~~~   79 (88)
T 1wf0_A           77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.53  E-value=1e-14  Score=117.53  Aligned_cols=75  Identities=24%  Similarity=0.378  Sum_probs=68.1

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCc-eEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCC-cEecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGT-ITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG-KMIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~-I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g-~~i~gk~l~V~~a  207 (472)
                      ..++|||+||+.++|+++|+++|+.||. |..+.+.      ++|||||+|.+.++|.+|++.||| ..++|+.|+|.++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a   80 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYS   80 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEc
Confidence            4568999999999999999999999999 6666653      489999999999999999999999 9999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        81 ~~~   83 (93)
T 2cqh_A           81 VSK   83 (93)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            765

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.52  E-value=1.6e-15  Score=124.25  Aligned_cols=80  Identities=23%  Similarity=0.387  Sum_probs=72.0

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC-CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~-~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||+.++|+++|+++|+.||.|.+ .++.+ .+|.++|||||+|.+.++|.+|++ |||..+.|+.|.|.++.
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            4568999999999999999999999999888 55444 468899999999999999999998 99999999999999987


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .+.
T Consensus        94 ~~~   96 (101)
T 1fj7_A           94 GRD   96 (101)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.52  E-value=6.9e-14  Score=115.46  Aligned_cols=82  Identities=16%  Similarity=0.266  Sum_probs=72.4

Q ss_pred             ccceeeeecCCC-----CccHHHHHHHHhccCceEEEEEeeCC--CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeE
Q 012034          130 QGLNLYIKNLGD-----SIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL  202 (472)
Q Consensus       130 ~~~~l~V~nL~~-----~~t~e~L~~~F~~~G~I~~v~i~~~~--~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l  202 (472)
                      .+.+|+|+|+-.     +-++++|+++|++||.|++|.|++++  ++.++|||||+|.+.++|.+|++.|||+.++|+.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            456899999963     23689999999999999999999875  36899999999999999999999999999999999


Q ss_pred             EEEEcccHH
Q 012034          203 YVAVAQRKE  211 (472)
Q Consensus       203 ~V~~a~~k~  211 (472)
                      +|.++....
T Consensus        87 ~v~~a~~~~   95 (105)
T 2pe8_A           87 KACFYNLDK   95 (105)
T ss_dssp             EEEECCHHH
T ss_pred             EEEEcCHHH
Confidence            999997643

>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=99.52  E-value=1.8e-14  Score=119.88  Aligned_cols=74  Identities=26%  Similarity=0.550  Sum_probs=69.2

Q ss_pred             ccceeeeecCCCC-ccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~-~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||+++ +++++|+++|+.||.|.+|.+       ++|||||+|.+.++|.+|++.||+..++|+.|.|.++.
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   98 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAG   98 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            3468999999999 999999999999999999998       48899999999999999999999999999999999986


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      ..
T Consensus        99 ~~  100 (110)
T 1wf1_A           99 EP  100 (110)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.51  E-value=1.2e-14  Score=126.98  Aligned_cols=83  Identities=27%  Similarity=0.474  Sum_probs=72.4

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEE------EEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCee
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSC------KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP  201 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v------~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~  201 (472)
                      ...+++|||+||++++|+++|+++|+.||.|.++      .+....+|.++|||||+|.+.++|.+|+..|||..|.|+.
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            3456789999999999999999999999998774      1211236889999999999999999999999999999999


Q ss_pred             EEEEEcccH
Q 012034          202 LYVAVAQRK  210 (472)
Q Consensus       202 l~V~~a~~k  210 (472)
                      |.|.++...
T Consensus       122 l~V~~a~~~  130 (143)
T 3egn_A          122 MVVQFARSA  130 (143)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999999764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=5.6e-14  Score=114.18  Aligned_cols=75  Identities=29%  Similarity=0.469  Sum_probs=69.0

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...++|||+||  ++|+++|+++|+.||.|.+|.|.     .++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~   85 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   85 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCS
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            35678999996  89999999999999999999985     468999999999999999999999999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        86 ~~   87 (97)
T 1x5p_A           86 KQ   87 (97)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.50  E-value=2e-14  Score=135.53  Aligned_cols=81  Identities=22%  Similarity=0.386  Sum_probs=71.7

Q ss_pred             cCCcceEEeCCCCCCC---------CHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCcc-
Q 012034           25 KTKFNNVFVKNLDEST---------TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF-   94 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~---------tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i-   94 (472)
                      ....++|||+||+.++         +|++|+++|++||+|.+|.|+.     +||||||+|.+.++|+.|+++|++..| 
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-----~kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-----CCCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            4678999999999998         7999999999999999999985     489999999999999999999999999 


Q ss_pred             -----------CCcceeeeccccchhH
Q 012034           95 -----------DDREWYVGKAQKKSER  110 (472)
Q Consensus        95 -----------~g~~l~V~~a~~~~~~  110 (472)
                                 .|+.|.|.||..+...
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                       8999999999876543

>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=99.50  E-value=8.1e-14  Score=128.03  Aligned_cols=123  Identities=16%  Similarity=0.209  Sum_probs=93.1

Q ss_pred             CHHHHHHHHHHH--CCCccCCcceeeeccccchhH--HHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHh
Q 012034           78 NADDAAKAVEAL--NGKKFDDREWYVGKAQKKSER--EQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFS  153 (472)
Q Consensus        78 ~~e~A~~Av~~l--ng~~i~g~~l~V~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~  153 (472)
                      +.+.+..|++..  ....+.+....|.+.......  ..+..           .....++|||+|||.++|+++|+++|+
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~-----------~~~~~~~l~V~nLp~~~t~~~L~~~F~  131 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYK-----------NDVKNRSVYIKGFPTDATLDDIKEWLE  131 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHH-----------HHHHHTEEEEECCCTTCCHHHHHHHHT
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhh-----------hccccCEEEecCCCCcCCHHHHHHHHh
Confidence            567777788765  344566666777665321110  00000           111235899999999999999999999


Q ss_pred             ccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHHH
Q 012034          154 EFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEE  212 (472)
Q Consensus       154 ~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~~  212 (472)
                      .||.|.+|+|.++.++.++|||||+|.+.++|.+|+..++ ..++|+.|.|.++..-..
T Consensus       132 ~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~y~~  189 (193)
T 2voo_A          132 DKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDDYFA  189 (193)
T ss_dssp             TSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTTC--
T ss_pred             cCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHHHHH
Confidence            9999999999999889999999999999999999997665 589999999998776433

>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=99.50  E-value=4.3e-14  Score=131.13  Aligned_cols=77  Identities=17%  Similarity=0.405  Sum_probs=71.8

Q ss_pred             ccceeeeecCC-CCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~-~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+++|||+||+ +.+|+++|+++|+.||.|.+|+|+++    ++|||||+|.+.++|.+|++.|||..+.|++|+|.+++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            45789999999 89999999999999999999999876    48999999999999999999999999999999999986


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        79 ~~   80 (205)
T 3tyt_A           79 QP   80 (205)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=7.8e-14  Score=113.72  Aligned_cols=74  Identities=30%  Similarity=0.492  Sum_probs=69.0

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhcc--CceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~--G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..++|||+||++++|+++|+++|+.|  |.|.++++.       +|||||+|.+.++|.+|+..|||..+.|+.|.|.++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpd_A           14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   86 (99)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             CcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            45789999999999999999999999  999999875       569999999999999999999999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        87 ~~~   89 (99)
T 2cpd_A           87 KPV   89 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.50  E-value=3.6e-14  Score=119.23  Aligned_cols=74  Identities=24%  Similarity=0.333  Sum_probs=66.2

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCee-----EEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP-----LYV  204 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~-----l~V  204 (472)
                      ..++|||+||++++|+++|+++|+.||.|.+|.|+.+      |||||+|.+.++|.+||+.|||..|+|+.     |.|
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v   88 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   88 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEe
Confidence            3568999999999999999999999999999999875      89999999999999999999999999988     666


Q ss_pred             EEccc
Q 012034          205 AVAQR  209 (472)
Q Consensus       205 ~~a~~  209 (472)
                      ..+..
T Consensus        89 ~~~~~   93 (115)
T 3beg_B           89 KVDGP   93 (115)
T ss_dssp             EECC-
T ss_pred             ccCCC
Confidence            66554

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=4.8e-14  Score=114.18  Aligned_cols=78  Identities=27%  Similarity=0.391  Sum_probs=70.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEE-EeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCK-VMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~-i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||++++++++|+++|+.||.|.+++ |+.++.   .|.|||+|.+.++|.+|+..|||..+.|+.|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   90 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIP   90 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            457899999999999999999999999999994 777642   3349999999999999999999999999999999998


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        91 ~~   92 (96)
T 2e44_A           91 DE   92 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            76

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=4e-14  Score=112.49  Aligned_cols=70  Identities=24%  Similarity=0.391  Sum_probs=63.6

Q ss_pred             ceeeeecCCCCccHHH----HHHHHhcc-CceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          132 LNLYIKNLGDSIDDEK----LKELFSEF-GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~----L~~~F~~~-G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      +.|||+||++.+++++    |+++|++| |.|.+|.      +   |+|||+|.+.++|.+|++.|+|..+.||+|+|.+
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt------g---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT------G---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC------T---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe------c---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            3499999999999987    55899999 5999982      2   9999999999999999999999999999999999


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      ++.+
T Consensus        81 A~~~   84 (96)
T 2diu_A           81 TPKN   84 (96)
T ss_dssp             SCCS
T ss_pred             cCCC
Confidence            9765

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.49  E-value=8.5e-14  Score=118.10  Aligned_cols=74  Identities=24%  Similarity=0.276  Sum_probs=67.4

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccE-EEEEcCCHHHHHHHHHHhCCcEecC--eeEEEEEcc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS-GFVAFSTPEEASRALAEMNGKMIVS--KPLYVAVAQ  208 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~-afV~f~s~~~A~~Ai~~l~g~~i~g--k~l~V~~a~  208 (472)
                      ..|||+||++.+|+++|+++|++||.|.+|+|+..     .|| |||+|.+.++|.+|++.|||..|.|  +.|+|.+++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            35789999999999999999999999999999763     386 9999999999999999999999987  589999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus       101 ~~  102 (124)
T 2e5i_A          101 PT  102 (124)
T ss_dssp             CS
T ss_pred             CC
Confidence            65

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.48  E-value=1.1e-14  Score=120.05  Aligned_cols=72  Identities=21%  Similarity=0.325  Sum_probs=65.3

Q ss_pred             eCCCCCCCCHHHHHHHH------------hcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           33 VKNLDESTTDEDLKKIF------------GEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        33 V~nLp~~~tee~L~~~F------------~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      +.||++++|+++|++.|            ++||.|.+|.|.++.+++++|||||+|++.++|.+|++.|||+.+.|+.|.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56777788888777666            999999999999998899999999999999999999999999999999999


Q ss_pred             eecc
Q 012034          101 VGKA  104 (472)
Q Consensus       101 V~~a  104 (472)
                      |.++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9876

>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=99.48  E-value=1.2e-13  Score=132.89  Aligned_cols=82  Identities=29%  Similarity=0.374  Sum_probs=74.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCC-CccC---Ccceee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG-KKFD---DREWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng-~~i~---g~~l~V  101 (472)
                      ...++|||+|||.++|+++|+++|+.||.|.+|.++.|.+|+++|||||+|.+.++|.+|++.||+ ..+.   ++.|.|
T Consensus        94 ~~~~~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           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            346789999999999999999999999999999999999999999999999999999999999954 4444   899999


Q ss_pred             eccccc
Q 012034          102 GKAQKK  107 (472)
Q Consensus       102 ~~a~~~  107 (472)
                      .++...
T Consensus       174 ~~~~~~  179 (261)
T 3sde_A          174 EPMEQF  179 (261)
T ss_dssp             EECCCE
T ss_pred             eecccc
Confidence            988754

>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=99.48  E-value=8e-13  Score=128.28  Aligned_cols=81  Identities=33%  Similarity=0.520  Sum_probs=74.7

Q ss_pred             cccceeeeecCCCCccHHHHH----HHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  204 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~----~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V  204 (472)
                      ...++|||+||+.++|+++|+    ++|+.||.|.+|++++  +++++|||||+|.+.++|.+|++.|||..|.|+.|+|
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            346789999999999999977    8999999999999987  5789999999999999999999999999999999999


Q ss_pred             EEcccHH
Q 012034          205 AVAQRKE  211 (472)
Q Consensus       205 ~~a~~k~  211 (472)
                      .++..+.
T Consensus        85 ~~a~~~~   91 (282)
T 3pgw_A           85 QYAKTDS   91 (282)
T ss_pred             EEeccCc
Confidence            9997654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=7.2e-14  Score=112.81  Aligned_cols=75  Identities=20%  Similarity=0.342  Sum_probs=65.6

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ..+|||+||++++|+++|+++|+.||.|.+| +....++.   ||||+|.+.++|.+|++ |||..|+|+.|.|.++..+
T Consensus         8 ~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v-~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~   82 (94)
T 2e5g_A            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcC
Confidence            3589999999999999999999999999988 33323343   99999999999999999 9999999999999876544

>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=99.46  E-value=1.5e-13  Score=109.00  Aligned_cols=69  Identities=22%  Similarity=0.491  Sum_probs=65.4

Q ss_pred             cceeeeecCCCCccHHHHHHHHhcc----C-------ceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecC
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEF----G-------TITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS  199 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~----G-------~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g  199 (472)
                      .++|||+||+.++++++|+++|+.|    |       .|.++++.++     +|||||+|.+.++|.+|+ .|||..+.|
T Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~~g   79 (87)
T 2hzc_A            6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIFQG   79 (87)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEECC
Confidence            4689999999999999999999999    8       8999999865     899999999999999999 999999999


Q ss_pred             eeEEEE
Q 012034          200 KPLYVA  205 (472)
Q Consensus       200 k~l~V~  205 (472)
                      +.|.|+
T Consensus        80 ~~l~V~   85 (87)
T 2hzc_A           80 QSLKIR   85 (87)
T ss_dssp             EECEEE
T ss_pred             eEEEEe
Confidence            999987

>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=99.45  E-value=1.7e-13  Score=114.54  Aligned_cols=81  Identities=20%  Similarity=0.318  Sum_probs=70.1

Q ss_pred             cCCcceEEeCCCCCCCC-----------HHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCc
Q 012034           25 KTKFNNVFVKNLDESTT-----------DEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK   93 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~t-----------ee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~   93 (472)
                      ....++|+|+||-...+           +++|+++|++||.|.+|.| .|.  .++|||||+|.+.++|.+|++.|||..
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            46788999999944332           5899999999999999965 554  379999999999999999999999999


Q ss_pred             cCCcceeeeccccch
Q 012034           94 FDDREWYVGKAQKKS  108 (472)
Q Consensus        94 i~g~~l~V~~a~~~~  108 (472)
                      |.|+.|.|.++..+.
T Consensus        89 ~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           89 FGGRQITAQAWDGTT  103 (112)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCcEEEEEEeCCCC
Confidence            999999999987653

>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=1.7e-13  Score=115.37  Aligned_cols=81  Identities=20%  Similarity=0.381  Sum_probs=71.2

Q ss_pred             CCcceEEeCCCC--CCC---CHHHHHHHHhcCCCeeEEEEEECC-----CCCceeEEEEEeCCHHHHHHHHHHHCCCccC
Q 012034           26 TKFNNVFVKNLD--EST---TDEDLKKIFGEYGTITSAVVMRDG-----DGKSKCFGFVNFENADDAAKAVEALNGKKFD   95 (472)
Q Consensus        26 ~~~~~l~V~nLp--~~~---tee~L~~~F~~fG~I~~v~i~~d~-----~g~skG~aFV~F~~~e~A~~Av~~lng~~i~   95 (472)
                      ...++|+|+|+-  .++   .+++|++.|++||.|.+|+|.++.     +++++||+||+|++.++|.+|++.|||..+.
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            468899999983  233   368999999999999999999984     3578899999999999999999999999999


Q ss_pred             Ccceeeecccc
Q 012034           96 DREWYVGKAQK  106 (472)
Q Consensus        96 g~~l~V~~a~~  106 (472)
                      |+.|.|.++..
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999998754

>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=99.44  E-value=2.2e-13  Score=128.41  Aligned_cols=77  Identities=16%  Similarity=0.341  Sum_probs=71.2

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCC-CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccC-Ccceeeecc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD-DREWYVGKA  104 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG-~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~-g~~l~V~~a  104 (472)
                      ..++|||+|||.++|+++|+++|++|| .|.+|.++.+    ++|||||+|.+.++|.+|++.|||..+. |+.|.|.++
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a  225 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS  225 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEe
Confidence            368999999999999999999999999 9999999764    3789999999999999999999999999 999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ..+
T Consensus       226 ~~~  228 (229)
T 2adc_A          226 KST  228 (229)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            753

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.43  E-value=1.7e-13  Score=125.80  Aligned_cols=77  Identities=16%  Similarity=0.341  Sum_probs=71.3

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCC-CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccC-Ccceeeecc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD-DREWYVGKA  104 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG-~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~-g~~l~V~~a  104 (472)
                      ..++|||+|||.++|+++|+++|++|| .|.++.++.+    ++|||||+|.+.++|.+|++.|||..+. |+.|.|.++
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  194 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS  194 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEee
Confidence            378899999999999999999999999 9999998764    3789999999999999999999999999 999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ..+
T Consensus       195 ~~~  197 (198)
T 1qm9_A          195 KST  197 (198)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            653

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.43  E-value=1.8e-13  Score=129.02  Aligned_cols=82  Identities=22%  Similarity=0.375  Sum_probs=70.6

Q ss_pred             cccceeeeecCCCCc---------cHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEe--
Q 012034          129 FQGLNLYIKNLGDSI---------DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI--  197 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~---------t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i--  197 (472)
                      ...++|||+||+..+         ++++|+++|++||.|++|+|+.+     +|||||+|.+.++|..|++.|+|..|  
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-----kG~AFV~F~~~~~Ae~A~~am~g~~l~~  206 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQTLLL  206 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHHHTTCCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-----CCEEEEEeCCHHHHHHHHHHhCCCEEec
Confidence            356799999999998         79999999999999999999864     89999999999999999999999999  


Q ss_pred             ----------cCeeEEEEEcccHHHHHH
Q 012034          198 ----------VSKPLYVAVAQRKEERRA  215 (472)
Q Consensus       198 ----------~gk~l~V~~a~~k~~~~~  215 (472)
                                .|+.|.|.||..+.....
T Consensus       207 ~~~~e~~~~~~gr~L~V~wA~~~pnp~~  234 (240)
T 3u1l_A          207 PSDKEWDDRREGTGLLVKWANEDPDPAA  234 (240)
T ss_dssp             TTSTTGGGGGGSCCCEEEECC-------
T ss_pred             cccccccccCCCCEEEEEEccCCCCHHH
Confidence                      899999999988765443

>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=99.43  E-value=1.4e-13  Score=113.65  Aligned_cols=81  Identities=25%  Similarity=0.290  Sum_probs=70.4

Q ss_pred             CCcceEEeCCC--CCCCC--------HHHHHHHHhcCCCeeEEEEEECCC---CCceeEEEEEeCCHHHHHHHHHHHCCC
Q 012034           26 TKFNNVFVKNL--DESTT--------DEDLKKIFGEYGTITSAVVMRDGD---GKSKCFGFVNFENADDAAKAVEALNGK   92 (472)
Q Consensus        26 ~~~~~l~V~nL--p~~~t--------ee~L~~~F~~fG~I~~v~i~~d~~---g~skG~aFV~F~~~e~A~~Av~~lng~   92 (472)
                      ...+.|.++|+  +.++.        +++|++.|++||.|.+|.|.++..   ++++|||||+|++.++|.+|++.|||+
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            35678899998  44443        369999999999999999998854   468999999999999999999999999


Q ss_pred             ccCCcceeeecccc
Q 012034           93 KFDDREWYVGKAQK  106 (472)
Q Consensus        93 ~i~g~~l~V~~a~~  106 (472)
                      .+.|+.|.|.++..
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            99999999998754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=1.9e-13  Score=114.49  Aligned_cols=76  Identities=16%  Similarity=0.242  Sum_probs=65.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-C---CCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-S---GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~---g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      ..++|||+||++++|+++|+++|++||.|. +.++.+. +   |+++|||||+|.+.++|.+|++.++  .++|+.+.+.
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            356899999999999999999999999999 7777765 3   7899999999999999999999984  3677777776


Q ss_pred             Ecc
Q 012034          206 VAQ  208 (472)
Q Consensus       206 ~a~  208 (472)
                      .+.
T Consensus        84 ~~~   86 (114)
T 2dnl_A           84 SSP   86 (114)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            543

>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=99.42  E-value=1e-13  Score=110.50  Aligned_cols=75  Identities=17%  Similarity=0.357  Sum_probs=64.2

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+|||+++|+++|+++|+.||.|.+|+|+.+    ++|||||+|.+.++|.+|+..  ...+.|+.|.|.++..
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCC
Confidence            3568999999999999999999999999999999875    799999999999999764321  3345899999998876


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        78 ~   78 (88)
T 1wf0_A           78 K   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.42  E-value=1.2e-13  Score=113.87  Aligned_cols=71  Identities=17%  Similarity=0.403  Sum_probs=61.8

Q ss_pred             ecCCCCccHHHHH-----------HHH-hccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEE
Q 012034          137 KNLGDSIDDEKLK-----------ELF-SEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  204 (472)
Q Consensus       137 ~nL~~~~t~e~L~-----------~~F-~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V  204 (472)
                      .+|++.+++++|+           ++| ++||.|++|+|.++..++++|||||+|.+.++|.+|+..|||+.++|+.|+|
T Consensus        21 ~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v  100 (104)
T 1jmt_A           21 DGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA  100 (104)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCE
T ss_pred             CCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEE
Confidence            4455555555555           455 9999999999999888899999999999999999999999999999999999


Q ss_pred             EEc
Q 012034          205 AVA  207 (472)
Q Consensus       205 ~~a  207 (472)
                      .|+
T Consensus       101 ~~s  103 (104)
T 1jmt_A          101 ELS  103 (104)
T ss_dssp             EEC
T ss_pred             EEc
Confidence            986

>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=99.41  E-value=6.4e-13  Score=109.65  Aligned_cols=81  Identities=17%  Similarity=0.315  Sum_probs=69.9

Q ss_pred             cceeeeecC--CCCcc--------HHHHHHHHhccCceEEEEEeeCCCC---CcccEEEEEcCCHHHHHHHHHHhCCcEe
Q 012034          131 GLNLYIKNL--GDSID--------DEKLKELFSEFGTITSCKVMRDPSG---ISKGSGFVAFSTPEEASRALAEMNGKMI  197 (472)
Q Consensus       131 ~~~l~V~nL--~~~~t--------~e~L~~~F~~~G~I~~v~i~~~~~g---~s~g~afV~f~s~~~A~~Ai~~l~g~~i  197 (472)
                      +..|.|.|+  +.++.        +++|++.|++||.|++|+|+++..+   .++||+||+|.+.++|.+|++.|||+.+
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f   84 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   84 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEe
Confidence            457888888  33333        3799999999999999999988643   6899999999999999999999999999


Q ss_pred             cCeeEEEEEcccHH
Q 012034          198 VSKPLYVAVAQRKE  211 (472)
Q Consensus       198 ~gk~l~V~~a~~k~  211 (472)
                      +|+.|.|.++....
T Consensus        85 ~GR~i~v~~~~~~~   98 (105)
T 3v4m_A           85 ANRVVVTKYCDPDS   98 (105)
T ss_dssp             TTEECEEEEECHHH
T ss_pred             CCCEEEEEEeCHHH
Confidence            99999999987654

>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=99.36  E-value=2.3e-12  Score=107.53  Aligned_cols=79  Identities=24%  Similarity=0.333  Sum_probs=68.1

Q ss_pred             cccceeeeecCCCCcc-----------HHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEe
Q 012034          129 FQGLNLYIKNLGDSID-----------DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI  197 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t-----------~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i  197 (472)
                      ....+|+|.||-...+           +++|+++|++||.|.+|.| .++  .++|||||+|.+.++|.+|+..|||..+
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~~   89 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRWF   89 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCEE
Confidence            3456899999954332           5899999999999999966 443  4899999999999999999999999999


Q ss_pred             cCeeEEEEEcccH
Q 012034          198 VSKPLYVAVAQRK  210 (472)
Q Consensus       198 ~gk~l~V~~a~~k  210 (472)
                      +|+.|.|.++..+
T Consensus        90 ~gr~l~v~~a~~~  102 (112)
T 2dit_A           90 GGRQITAQAWDGT  102 (112)
T ss_dssp             TTEECEEEECCSC
T ss_pred             CCcEEEEEEeCCC
Confidence            9999999998764

>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=99.34  E-value=2.4e-12  Score=108.41  Aligned_cols=81  Identities=19%  Similarity=0.350  Sum_probs=70.4

Q ss_pred             ccceeeeecCCC--Cc---cHHHHHHHHhccCceEEEEEeeCCC-----CCcccEEEEEcCCHHHHHHHHHHhCCcEecC
Q 012034          130 QGLNLYIKNLGD--SI---DDEKLKELFSEFGTITSCKVMRDPS-----GISKGSGFVAFSTPEEASRALAEMNGKMIVS  199 (472)
Q Consensus       130 ~~~~l~V~nL~~--~~---t~e~L~~~F~~~G~I~~v~i~~~~~-----g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g  199 (472)
                      .+.+|+|+|+-.  ++   .++||++.|++||.|.+|+|+++..     +.++||+||+|.+.++|.+|++.|||+.++|
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            456899999842  22   3689999999999999999998753     4678999999999999999999999999999


Q ss_pred             eeEEEEEcccH
Q 012034          200 KPLYVAVAQRK  210 (472)
Q Consensus       200 k~l~V~~a~~k  210 (472)
                      +.|.|.++...
T Consensus        99 R~i~v~~~~~~  109 (118)
T 3ue2_A           99 RKVVAEVYDQE  109 (118)
T ss_dssp             EECEEEEECHH
T ss_pred             cEEEEEEcChH
Confidence            99999998764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=9.3e-12  Score=101.52  Aligned_cols=65  Identities=17%  Similarity=0.229  Sum_probs=57.7

Q ss_pred             CCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccch
Q 012034           38 ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  108 (472)
Q Consensus        38 ~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~  108 (472)
                      .++|+++|+++|++||+|.+|.|+    ++++|||||+|++.++|.+|++.+  ..+.++.|.|.|+..+.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~--~~~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNE--VGLVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTC--CBCSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhc--CCCCCCeEEEEEccCCC
Confidence            468999999999999999999998    478999999999999999999974  44689999999987653

>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=99.29  E-value=2.4e-12  Score=127.64  Aligned_cols=76  Identities=17%  Similarity=0.368  Sum_probs=66.3

Q ss_pred             cCCcceEEeCC--CCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccC---Cc--
Q 012034           25 KTKFNNVFVKN--LDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD---DR--   97 (472)
Q Consensus        25 ~~~~~~l~V~n--Lp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~---g~--   97 (472)
                      ....++|||+|  |+.++||++|+++|++||+|.+|.+..     +||||||+|++.++|++|+++|||+.+.   |+  
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            46788999999  579999999999999999999987642     5899999999999999999999999873   44  


Q ss_pred             ceeeeccc
Q 012034           98 EWYVGKAQ  105 (472)
Q Consensus        98 ~l~V~~a~  105 (472)
                      .|+|.+..
T Consensus        90 ~ly~~~~~   97 (345)
T 3tht_A           90 TLYLNFVE   97 (345)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEee
Confidence            58888874

>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=99.23  E-value=3.9e-11  Score=100.21  Aligned_cols=79  Identities=14%  Similarity=0.176  Sum_probs=66.6

Q ss_pred             cceeeeecCCCCc----------cHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCe
Q 012034          131 GLNLYIKNLGDSI----------DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK  200 (472)
Q Consensus       131 ~~~l~V~nL~~~~----------t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk  200 (472)
                      +.+|.++|+=..-          .++||++.|++||.|++|.|.++.   ++||+||+|.+.++|.+|++.|||+.++|+
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR   83 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFAGK   83 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            4567788873321          236899999999999999997763   599999999999999999999999999999


Q ss_pred             eEEEEEcccHHH
Q 012034          201 PLYVAVAQRKEE  212 (472)
Q Consensus       201 ~l~V~~a~~k~~  212 (472)
                      .|+|.++....-
T Consensus        84 ~i~v~~~~~~~y   95 (114)
T 3s6e_A           84 MITAAYVPLPTY   95 (114)
T ss_dssp             ECEEEEECHHHH
T ss_pred             EEEEEEEcHHHH
Confidence            999999976543

>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=99.22  E-value=1.7e-11  Score=121.55  Aligned_cols=75  Identities=25%  Similarity=0.490  Sum_probs=65.7

Q ss_pred             cccceeeeec--CCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec---Ce--e
Q 012034          129 FQGLNLYIKN--LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV---SK--P  201 (472)
Q Consensus       129 ~~~~~l~V~n--L~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~---gk--~  201 (472)
                      ..+.+|||+|  |+..+|+++|+++|++||.|++|.+..     +||||||+|.+.++|.+|++.|||+.+.   |+  .
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~   90 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   90 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceE
Confidence            3456899999  578999999999999999999988764     4899999999999999999999999883   34  6


Q ss_pred             EEEEEcc
Q 012034          202 LYVAVAQ  208 (472)
Q Consensus       202 l~V~~a~  208 (472)
                      |+|.+++
T Consensus        91 ly~~~~~   97 (345)
T 3tht_A           91 LYLNFVE   97 (345)
T ss_dssp             CEEEECS
T ss_pred             EEEEEee
Confidence            8888874

>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=99.20  E-value=1.3e-11  Score=103.14  Aligned_cols=77  Identities=16%  Similarity=0.166  Sum_probs=64.5

Q ss_pred             CcceEEeCCCCCCC----------CHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC
Q 012034           27 KFNNVFVKNLDEST----------TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD   96 (472)
Q Consensus        27 ~~~~l~V~nLp~~~----------tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g   96 (472)
                      ..+.|.++|+=...          .+++|++.|++||.|.+|.|.++.   ++|||||+|++.++|.+|++.|||..++|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            45678888873211          235889999999999999886552   58999999999999999999999999999


Q ss_pred             cceeeecccc
Q 012034           97 REWYVGKAQK  106 (472)
Q Consensus        97 ~~l~V~~a~~  106 (472)
                      +.|.|.++..
T Consensus        83 R~i~v~~~~~   92 (114)
T 3s6e_A           83 KMITAAYVPL   92 (114)
T ss_dssp             EECEEEEECH
T ss_pred             EEEEEEEEcH
Confidence            9999999854

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=3.9e-11  Score=97.79  Aligned_cols=64  Identities=20%  Similarity=0.367  Sum_probs=57.3

Q ss_pred             CCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          141 DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       141 ~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ..+++++|+++|++||.|.+|.|+    +.++|||||+|.+.++|.+|++.+++  +.|++|.|.|+..+
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~   90 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQ   90 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCC
Confidence            568999999999999999999998    36899999999999999999998554  67999999998755

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.02  E-value=9.7e-10  Score=92.08  Aligned_cols=84  Identities=23%  Similarity=0.255  Sum_probs=74.1

Q ss_pred             ccccccceeeeecCCCC-ccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCC-HHHHHHHHHHhC--CcEecCee
Q 012034          126 VDKFQGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFST-PEEASRALAEMN--GKMIVSKP  201 (472)
Q Consensus       126 ~~~~~~~~l~V~nL~~~-~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s-~~~A~~Ai~~l~--g~~i~gk~  201 (472)
                      .....++.|||+||++. ++.++|+++|+.||.|.+|.+.++.     -.|||.|.+ .++|..|+..++  +..|.|..
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-----~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~   87 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-----SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-----CEEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            44567889999999999 9999999999999999999998873     269999999 899999999995  67899999


Q ss_pred             EEEEEcccHHHHH
Q 012034          202 LYVAVAQRKEERR  214 (472)
Q Consensus       202 l~V~~a~~k~~~~  214 (472)
                      +.+++....++..
T Consensus        88 ~~~evL~GeeE~~  100 (121)
T 1owx_A           88 VTWEVLEGEVEKE  100 (121)
T ss_dssp             EEEEECCHHHHHH
T ss_pred             EEEEECCCHHHHH
Confidence            9999888776654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.99  E-value=2e-09  Score=90.20  Aligned_cols=80  Identities=19%  Similarity=0.181  Sum_probs=69.8

Q ss_pred             CCcceEEeCCCCCC-CCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCC-HHHHHHHHHHHC--CCccCCcceee
Q 012034           26 TKFNNVFVKNLDES-TTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFEN-ADDAAKAVEALN--GKKFDDREWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~-~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~-~e~A~~Av~~ln--g~~i~g~~l~V  101 (472)
                      .+.+.|||+||+.+ +|+++|+++|++||+|..|.+..+.+     .|||.|.+ .++|..|++++|  +..|.+..+.+
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-----tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~   90 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-----EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   90 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-----EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-----EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEE
Confidence            56888999999999 99999999999999999999988743     69999999 899999999995  77789988888


Q ss_pred             eccccchhH
Q 012034          102 GKAQKKSER  110 (472)
Q Consensus       102 ~~a~~~~~~  110 (472)
                      +......+.
T Consensus        91 evL~GeeE~   99 (121)
T 1owx_A           91 EVLEGEVEK   99 (121)
T ss_dssp             EECCHHHHH
T ss_pred             EECCCHHHH
Confidence            776654443

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.92  E-value=1.1e-09  Score=86.17  Aligned_cols=73  Identities=21%  Similarity=0.299  Sum_probs=61.7

Q ss_pred             CcceEEeCCCC----CCCCH----HHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcc
Q 012034           27 KFNNVFVKNLD----ESTTD----EDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDRE   98 (472)
Q Consensus        27 ~~~~l~V~nLp----~~~te----e~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~   98 (472)
                      ..-||+|.-.+    .++-+    .+|.+.|+.||+|.++++..|       .+||+|.+.++|.+|++ |||..++|+.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-------~~fVtF~d~~sAlaAi~-mnG~~v~Gr~   77 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-------KMWVTFLEGSSALNVLS-LNGKELLNRT   77 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-------SEEEEESSHHHHHHGGG-GTTCEETTEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-------CEEEEECChHHHHHHHh-cCCeEeCCeE
Confidence            34577777766    34444    678899999999999999987       38999999999999998 9999999999


Q ss_pred             eeeeccccc
Q 012034           99 WYVGKAQKK  107 (472)
Q Consensus        99 l~V~~a~~~  107 (472)
                      |+|+.+.+.
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999988653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.92  E-value=3.1e-09  Score=83.58  Aligned_cols=72  Identities=21%  Similarity=0.407  Sum_probs=61.4

Q ss_pred             ccceeeeecCC----CCccH----HHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCee
Q 012034          130 QGLNLYIKNLG----DSIDD----EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP  201 (472)
Q Consensus       130 ~~~~l~V~nL~----~~~t~----e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~  201 (472)
                      .+.||+|...+    .++.+    .+|.+.|+.||.|..+++..+       .+||+|.+.++|.+|++ |||..++||.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-------~~fVtF~d~~sAlaAi~-mnG~~v~Gr~   77 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-------KMWVTFLEGSSALNVLS-LNGKELLNRT   77 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-------SEEEEESSHHHHHHGGG-GTTCEETTEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-------CEEEEECChHHHHHHHh-cCCeEeCCeE
Confidence            34577877766    24444    678899999999999999987       38999999999999997 9999999999


Q ss_pred             EEEEEccc
Q 012034          202 LYVAVAQR  209 (472)
Q Consensus       202 l~V~~a~~  209 (472)
                      |+|+++.+
T Consensus        78 LkV~lkt~   85 (91)
T 2dnr_A           78 ITIALKSP   85 (91)
T ss_dssp             EEEEECCC
T ss_pred             EEEEeCCC
Confidence            99998864

>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=98.86  E-value=4.6e-09  Score=98.16  Aligned_cols=79  Identities=20%  Similarity=0.391  Sum_probs=66.5

Q ss_pred             cceEEeCCC-----CCCCCHHHHHHHHhcCCCeeEEEEEECC-----CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCc
Q 012034           28 FNNVFVKNL-----DESTTDEDLKKIFGEYGTITSAVVMRDG-----DGKSKCFGFVNFENADDAAKAVEALNGKKFDDR   97 (472)
Q Consensus        28 ~~~l~V~nL-----p~~~tee~L~~~F~~fG~I~~v~i~~d~-----~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~   97 (472)
                      .+.+.+.|+     ..+-.+++|++.|++||.|.++.|.++.     +++++|++||+|.+.++|.+|++.|||..+.||
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            444555554     2344678999999999999999998763     458999999999999999999999999999999


Q ss_pred             ceeeecccc
Q 012034           98 EWYVGKAQK  106 (472)
Q Consensus        98 ~l~V~~a~~  106 (472)
                      .|.|.+...
T Consensus       204 ~i~~~~~~~  212 (222)
T 3dxb_A          204 KVVAEVYDQ  212 (222)
T ss_dssp             BCEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999998753

>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=98.85  E-value=7e-09  Score=96.94  Aligned_cols=70  Identities=17%  Similarity=0.305  Sum_probs=62.6

Q ss_pred             CccHHHHHHHHhccCceEEEEEeeCC-----CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHH
Q 012034          142 SIDDEKLKELFSEFGTITSCKVMRDP-----SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       142 ~~t~e~L~~~F~~~G~I~~v~i~~~~-----~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      +-.+++|++.|++||.|.++.|.++.     ++.++|++||+|.+.++|.+|+..|||+.++|+.|.+.++....
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~~  214 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQER  214 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHHH
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHHH
Confidence            34568999999999999999998654     34899999999999999999999999999999999999987554

>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=98.74  E-value=4e-09  Score=83.35  Aligned_cols=72  Identities=19%  Similarity=0.298  Sum_probs=61.8

Q ss_pred             CCcceEEeCCCCCC-----CCH----HHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC
Q 012034           26 TKFNNVFVKNLDES-----TTD----EDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD   96 (472)
Q Consensus        26 ~~~~~l~V~nLp~~-----~te----e~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g   96 (472)
                      -..-||+|.-++.+     +-+    .+|.+.|+.||+|..+++..|+       +||+|.+.++|.+||+ |||..++|
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHh-cCCeeeCC
Confidence            35678999988643     333    5688999999999999999883       9999999999999998 99999999


Q ss_pred             cceeeeccc
Q 012034           97 REWYVGKAQ  105 (472)
Q Consensus        97 ~~l~V~~a~  105 (472)
                      |.|+|.+..
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999998754

>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=98.69  E-value=1.9e-08  Score=79.57  Aligned_cols=72  Identities=13%  Similarity=0.208  Sum_probs=61.1

Q ss_pred             cccceeeeecCCCC-----ccH----HHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecC
Q 012034          129 FQGLNLYIKNLGDS-----IDD----EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS  199 (472)
Q Consensus       129 ~~~~~l~V~nL~~~-----~t~----e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g  199 (472)
                      ....|++|..++..     +.+    .+|.+.|+.||.|..+++..+       -+||+|.+.++|.+||+ |+|..++|
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-------~~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-------cEEEEEcChHHHHHHHh-cCCeeeCC
Confidence            34568999888632     333    568899999999999999988       29999999999999998 99999999


Q ss_pred             eeEEEEEcc
Q 012034          200 KPLYVAVAQ  208 (472)
Q Consensus       200 k~l~V~~a~  208 (472)
                      +.|+|++..
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999998753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.45  E-value=1.4e-06  Score=70.26  Aligned_cols=71  Identities=15%  Similarity=0.214  Sum_probs=66.2

Q ss_pred             cceeeeecCCCCccHHHHHHHHhcc-----CceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEF-----GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~-----G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      ..+|-+-|||+.++++.|+.+++++     |.|+.+.+..|     -+-|+|+|.|..+|.+|...|+|.+|.|++|+|.
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-----H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-----FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-----TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-----CCceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            5578899999999999999999999     99999999988     5579999999999999999999999999999998


Q ss_pred             E
Q 012034          206 V  206 (472)
Q Consensus       206 ~  206 (472)
                      -
T Consensus        96 T   96 (117)
T 2l9w_A           96 T   96 (117)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.34  E-value=1.4e-06  Score=70.22  Aligned_cols=73  Identities=18%  Similarity=0.187  Sum_probs=67.7

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcC-----CCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEY-----GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~f-----G~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      ..++|-+-|||..+++..|+.+++++     |.|..+.+..|-     +=|+|+|.|..+|-+|.-+|+|..|.|++|.|
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH-----~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-----NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT-----TEEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC-----CceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            47899999999999999999999999     999999999984     45999999999999999999999999999999


Q ss_pred             ecc
Q 012034          102 GKA  104 (472)
Q Consensus       102 ~~a  104 (472)
                      .-.
T Consensus        95 gTv   97 (117)
T 2l9w_A           95 GTI   97 (117)
T ss_dssp             ECH
T ss_pred             cCH
Confidence            754

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.84  E-value=8.1e-05  Score=59.48  Aligned_cols=89  Identities=19%  Similarity=0.261  Sum_probs=72.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhc-C----CCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGE-Y----GTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~-f----G~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      ....+|.|.|||.+++++.|.-+|++ .    |+|.++....       +-|+|+|.+.+.|++.++. ..+.|.+..|.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k-~~H~L~~~~Ls   77 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            45678999999999999999999997 2    5888877643       3689999999999999973 47889999999


Q ss_pred             eeccccchhHHHHHHHHHHhhhhhhccccccceeeeecCCCCcc
Q 012034          101 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID  144 (472)
Q Consensus       101 V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t  144 (472)
                      |.....+                      ...+|++.+|+..++
T Consensus        78 V~P~~~~----------------------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           78 LRPAPPR----------------------APARLLLQGLPPGTS   99 (104)
T ss_dssp             EEECCCC----------------------CCCCCCCCSCCCCCC
T ss_pred             EEcCCCC----------------------CcceEeeecCCCCCC
Confidence            9765433                      234789999988765

>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=97.61  E-value=0.00012  Score=58.77  Aligned_cols=72  Identities=19%  Similarity=0.220  Sum_probs=62.3

Q ss_pred             ceeeeecCCCCcc-----HHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          132 LNLYIKNLGDSID-----DEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       132 ~~l~V~nL~~~~t-----~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      ++|+|.||+.++-     .+.++++|..|+.+.+...++.     =.-..|.|.+.++|.+|-..||+..+.|+.++|.+
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YF   80 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYF   80 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECEEEC
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecCceeEEEe
Confidence            5799999987662     2577899999999888888765     33579999999999999999999999999999999


Q ss_pred             cc
Q 012034          207 AQ  208 (472)
Q Consensus       207 a~  208 (472)
                      ++
T Consensus        81 gq   82 (104)
T 1wey_A           81 AQ   82 (104)
T ss_dssp             CC
T ss_pred             cC
Confidence            88

>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=97.43  E-value=0.00012  Score=58.67  Aligned_cols=75  Identities=19%  Similarity=0.166  Sum_probs=63.5

Q ss_pred             CcceEEeCCCCCCC-CH----HHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           27 KFNNVFVKNLDEST-TD----EDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        27 ~~~~l~V~nLp~~~-te----e~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      --++|+|.||+.++ +.    +.++++|..|+++.+....+.     -.-..|.|.+.++|.+|-..|++..+.|+.++|
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            35789999999766 32    577899999999998777765     224689999999999999999999999999999


Q ss_pred             ecccc
Q 012034          102 GKAQK  106 (472)
Q Consensus       102 ~~a~~  106 (472)
                      -+++.
T Consensus        79 YFgq~   83 (104)
T 1wey_A           79 YFAQT   83 (104)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99873

>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=97.33  E-value=0.00086  Score=52.82  Aligned_cols=69  Identities=17%  Similarity=0.251  Sum_probs=56.7

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCC--C-CceeEEEEEeCCHHHHHHHHHHHCCCccCCc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD--G-KSKCFGFVNFENADDAAKAVEALNGKKFDDR   97 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~--g-~skG~aFV~F~~~e~A~~Av~~lng~~i~g~   97 (472)
                      ++|.|++||..+||+++.+.++.+.++........+.  + ..-.-|||.|.+.|++....+.++|+.+.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~   73 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcC
Confidence            6799999999999999999999998877666655421  1 2335799999999999999999999987543

>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=96.96  E-value=0.0023  Score=50.54  Aligned_cols=56  Identities=20%  Similarity=0.345  Sum_probs=46.0

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHC
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN   90 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~ln   90 (472)
                      ...-++| ++|+++...||.++|+.||-|. |..+.|.      .|||.|.+++.|..|+..++
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidDT------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            3444566 9999999999999999999644 5666662      79999999999999998763

>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=96.95  E-value=0.0018  Score=53.43  Aligned_cols=91  Identities=19%  Similarity=0.238  Sum_probs=58.7

Q ss_pred             EcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHH
Q 012034           10 VGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL   89 (472)
Q Consensus        10 v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~l   89 (472)
                      +.+|....+..........+-|.|-++|... ...|.+.|++||+|.+...  . +  ...+-.|.|.+..+|++||.+ 
T Consensus         6 ~~pf~~~~~~l~~~~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~--~-~--~~NWihI~Y~s~~~A~rAL~k-   78 (119)
T 1wwh_A            6 SGPFYTQGDSLTSEDHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM--S-N--TGNWMHIRYQSKLQARKALSK-   78 (119)
T ss_dssp             ---------------CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE--C-S--SSSEEEEEESSHHHHHHHHTT-
T ss_pred             cCcceeCCcccCCCCCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc--C-C--CCCeEEEEeCCHHHHHHHHHh-
Confidence            3344444444333334457789999999885 6677888999999998775  2 1  235999999999999999975 


Q ss_pred             CCCccCC-cceeeeccccc
Q 012034           90 NGKKFDD-REWYVGKAQKK  107 (472)
Q Consensus        90 ng~~i~g-~~l~V~~a~~~  107 (472)
                      ||..|.+ -.|-|.+...+
T Consensus        79 NG~ii~g~~mIGV~p~~d~   97 (119)
T 1wwh_A           79 DGRIFGESIMIGVKPCIDK   97 (119)
T ss_dssp             TTCEETTTEECEEEECCCH
T ss_pred             CCeEecCCEEEEEEECCCH
Confidence            9999875 44555554433

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.84  E-value=0.0049  Score=49.23  Aligned_cols=69  Identities=23%  Similarity=0.372  Sum_probs=56.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhc-----cCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSE-----FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  204 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~-----~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V  204 (472)
                      .+.+|.|.|||..++++.|.-+|++     -|.|.++....       +-|+|+|.+.+.|++.++ -..+.+.+..|.|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV   78 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLA-QADHELHGAQLSL   78 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhc-CCcceecCeEEEE
Confidence            4568999999999999999999987     26888888754       368999999999999884 3356778888888


Q ss_pred             EE
Q 012034          205 AV  206 (472)
Q Consensus       205 ~~  206 (472)
                      .-
T Consensus        79 ~P   80 (104)
T 2dhx_A           79 RP   80 (104)
T ss_dssp             EE
T ss_pred             Ec
Confidence            74

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.75  E-value=0.0022  Score=50.75  Aligned_cols=52  Identities=19%  Similarity=0.360  Sum_probs=44.2

Q ss_pred             EEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHC
Q 012034           31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN   90 (472)
Q Consensus        31 l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~ln   90 (472)
                      ++| ++|+++...||.++|+.||- ..|..+.|.      .|||.|.+++.|..|+..++
T Consensus         9 ~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            9 LHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            555 99999999999999999994 345666662      79999999999999999775

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.62  E-value=0.0078  Score=47.28  Aligned_cols=68  Identities=12%  Similarity=0.214  Sum_probs=56.1

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC---CCCcccEEEEEcCCHHHHHHHHHHhCCcEecC
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---SGISKGSGFVAFSTPEEASRALAEMNGKMIVS  199 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~---~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g  199 (472)
                      ++|.|++||..+|++++.+.++....+.........   .-..-.-|+|.|.+.+++....+.++|..+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            468999999999999999999999888777665543   11234569999999999999999999998743

>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=96.08  E-value=0.046  Score=44.94  Aligned_cols=75  Identities=12%  Similarity=0.156  Sum_probs=57.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecC-eeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS-KPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g-k~l~V~~a~  208 (472)
                      ..+-|.|-+.+... .+.+.+.|++||.|.+.....     ......|.|.+..+|.+|+ ..||..++| -.|-|....
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~-----~~NWihI~Y~s~~~A~rAL-~kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEEECC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC-----CCCeEEEEeCCHHHHHHHH-HhCCeEecCCEEEEEEECC
Confidence            34568888888764 567788999999999887622     2347899999999999999 569999975 556666655


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .+.
T Consensus        96 d~~   98 (119)
T 1wwh_A           96 DKN   98 (119)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            443

>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=95.57  E-value=0.036  Score=43.66  Aligned_cols=54  Identities=28%  Similarity=0.431  Sum_probs=43.7

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhC
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN  193 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~  193 (472)
                      .+|+-.+|.++.-.||.++|+.||.|. |+.+.|      .-|||.|.+.+.|..|+..+.
T Consensus        17 HVf~l~FP~ewKt~DI~~lFs~fggv~-I~WidD------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEEeCChhhhhHHHHHHhhccCCEE-EEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            455449999999999999999999543 455554      269999999999999998763

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.56  E-value=0.0079  Score=47.63  Aligned_cols=70  Identities=19%  Similarity=0.179  Sum_probs=50.4

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC--CCC-ceeEEEEEeCCHHHHHHHHHHHCCCccCCc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG--DGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR   97 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~--~g~-skG~aFV~F~~~e~A~~Av~~lng~~i~g~   97 (472)
                      .-+|.|+.||..+||+++.+.++.+=++........+  .+. .-.-|||.|.+.|+.....+.++|..+-+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~   81 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDS   81 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECT
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeC
Confidence            3469999999999999999888876554322221111  111 124689999999999999999999887543

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.32  E-value=0.0081  Score=50.16  Aligned_cols=78  Identities=19%  Similarity=0.225  Sum_probs=55.7

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-C---------CC-----CceeEEEEEeCCHHHHHHHHHHHCC
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-G---------DG-----KSKCFGFVNFENADDAAKAVEALNG   91 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~---------~g-----~skG~aFV~F~~~e~A~~Av~~lng   91 (472)
                      ..+-|.|-++|.+.+. .+.+.|++||.|.+-.-..+ .         ..     ....+-.|.|.+..+|.+||.+ ||
T Consensus         6 ~e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG   83 (132)
T 3p3d_A            6 GELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NG   83 (132)
T ss_dssp             --CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TT
T ss_pred             CceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CC
Confidence            4567889999776554 66788999999876221100 0         00     1245889999999999999985 99


Q ss_pred             CccCCcceeeecccc
Q 012034           92 KKFDDREWYVGKAQK  106 (472)
Q Consensus        92 ~~i~g~~l~V~~a~~  106 (472)
                      ..|.|..|-|.+..+
T Consensus        84 ~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           84 AVFNGVLLGVIPYTK   98 (132)
T ss_dssp             CEETTEECEEEECCH
T ss_pred             eEeCcEEEEEEECCH
Confidence            999999888877753

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.13  E-value=0.0096  Score=60.87  Aligned_cols=58  Identities=12%  Similarity=0.267  Sum_probs=43.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHH
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA   88 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~   88 (472)
                      ...++|||. .+.++++.+|.++|+.||.|.++...++ .   .-||.|+|.+.+++..++..
T Consensus        51 qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~-~---g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           51 QAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES-F---GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS-S---SEEEEEECC---CCHHHHSS
T ss_pred             HhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc-C---CeEEEEEeCCHHHHHHHHhc
Confidence            457889997 8999999999999999999999877654 2   25999999999999977653

>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=94.46  E-value=0.042  Score=43.45  Aligned_cols=53  Identities=26%  Similarity=0.403  Sum_probs=43.5

Q ss_pred             eeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhC
Q 012034          134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN  193 (472)
Q Consensus       134 l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~  193 (472)
                      +|+-++|.++.-.||.++|+.||. ..|+.+.|      .-|||.|.+++.|..|+..+.
T Consensus         8 V~~l~FP~ewKt~Di~~lFs~fgg-v~I~WidD------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHVTFPKEWKTSDLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEECCTTCCHHHHHHHTTTSEE-EEEEEEET------TEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEEeCChhhhhHHHHHHHhccCC-EEEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            444499999999999999999994 34565655      269999999999999998774

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=93.85  E-value=0.069  Score=42.23  Aligned_cols=68  Identities=12%  Similarity=0.215  Sum_probs=50.8

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC--C-CCcccEEEEEcCCHHHHHHHHHHhCCcEecC
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--S-GISKGSGFVAFSTPEEASRALAEMNGKMIVS  199 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~--~-g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g  199 (472)
                      .+|.|+.||..+|++++.+.++..-.++........  . ...-.-|+|.|.+.++.....+..+|..+.+
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            469999999999999999988876555443332221  1 1122458999999999999999999998743

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.21  E-value=0.21  Score=41.68  Aligned_cols=75  Identities=23%  Similarity=0.324  Sum_probs=53.6

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEE-EEeeCCC-------------C-CcccEEEEEcCCHHHHHHHHHHhCCcEe
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPS-------------G-ISKGSGFVAFSTPEEASRALAEMNGKMI  197 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v-~i~~~~~-------------g-~s~g~afV~f~s~~~A~~Ai~~l~g~~i  197 (472)
                      -+.|-+.|.+. ...+-+.|++||.|.+- ...++..             . .......|+|++..+|.+|+ ..||..|
T Consensus         9 ~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG~ii   86 (132)
T 3p3d_A            9 AILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENGAVF   86 (132)
T ss_dssp             EEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTTCEE
T ss_pred             EEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCCeEe
Confidence            46677776544 45567889999998772 2221100             0 12456789999999999999 7899999


Q ss_pred             cCeeEEEEEccc
Q 012034          198 VSKPLYVAVAQR  209 (472)
Q Consensus       198 ~gk~l~V~~a~~  209 (472)
                      .|.-|-|....+
T Consensus        87 ~G~mIGV~Py~~   98 (132)
T 3p3d_A           87 NGVLLGVIPYTK   98 (132)
T ss_dssp             TTEECEEEECCH
T ss_pred             CcEEEEEEECCH
Confidence            999888887753

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.64  E-value=0.069  Score=54.57  Aligned_cols=55  Identities=18%  Similarity=0.230  Sum_probs=41.1

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE  191 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~  191 (472)
                      ++|+|. .+..+++.+|.++|+.||.|.++....+ .   .-|+.|+|.+.+++..++..
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~-~---g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES-F---GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS-S---SEEEEEECC---CCHHHHSS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc-C---CeEEEEEeCCHHHHHHHHhc
Confidence            379997 7999999999999999999999988765 2   35999999999998877643

>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=85.82  E-value=1.3  Score=45.86  Aligned_cols=56  Identities=20%  Similarity=0.308  Sum_probs=44.6

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCC
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNG   91 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng   91 (472)
                      ...++|+ +|..|...+|.++|+.||.| +|..+.|      ..|||.|.+.++|..+++.++.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC------CeEEEEECCHHHHHHHHHHHHh
Confidence            3455565 99999999999999999964 4444433      3799999999999999998853

---

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	472
d1nmra_	85	a.144.1.1 (A:) poly(A) binding protein {Protozoan	8e-32
d1g9la_	144	a.144.1.1 (A:) poly(A) binding protein {Human (Hom	2e-28
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-27
d1ifwa_	92	a.144.1.1 (A:) poly(A) binding protein {Baker's ye	5e-27
d1i2ta_	61	a.144.1.1 (A:) hyperplastic discs protein {Human (	5e-26
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-21
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-18
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-21
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-18
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-20
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	7e-20
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-19
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-16
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-19
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-18
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-19
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-17
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-18
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-16
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-18
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-16
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-18
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-18
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-17
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-18
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-15
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-18
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-17
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-17
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-17
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-17
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-16
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-17
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	8e-16
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-17
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-15
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-17
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-14
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-16
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	7e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-16
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-16
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-16
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-14
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-16
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-16
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	7e-14
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-16
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-13
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:) 4e-16
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:) 1e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-16
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-15
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-16
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-16
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-15
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-15
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-14
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-15
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	7e-10
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-15
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	6e-15
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-15
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	7e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-15
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-15
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-14
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	9e-15
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-13
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	9e-15
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	7e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-14
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-13
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-14
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-12
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-14
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-14
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	7e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	4e-14
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-14
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-12
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	6e-14
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-14
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	8e-14
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-13
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-11
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-13
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-13
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-13
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-11
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-13
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-13
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	5e-13
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	5e-13
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-09
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	7e-13
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-13
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	9e-12
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	8e-13
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-11
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-12
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	8e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-12
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-11
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-12
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	8e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-12
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-11
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-10
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-12
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-09
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	6e-12
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-11
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	8e-09
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-11
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	6e-10
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	3e-11
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	2e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-11
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-11
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	8e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-10
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-10
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	7e-10
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-09
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-09
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	1e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	5e-09
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	3e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-08
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-07
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-07
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-07
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	3e-06
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	5e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	5e-07
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	8e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	7e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	7e-07

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]} Length = 85

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Protozoan (Trypanosoma cruzi) [TaxId: 5693]

 Score =  114 bits (288), Expect = 8e-32
 Identities = 42/72 (58%), Positives = 52/72 (72%)

Query: 377 ALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALK 436
            LST LAN +PEQQ+ +LGE LY  +  +   AAAKVTGMLLEMD  E+L+LL++P  L 
Sbjct: 10  NLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLD 69

Query: 437 AKVAEAMEVLRS 448
           AKV EA+EVL  
Sbjct: 70  AKVQEALEVLNR 81

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 144

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  107 bits (268), Expect = 2e-28
 Identities = 50/156 (32%), Positives = 81/156 (51%), Gaps = 17/156 (10%)

Query: 308 GPVQQTQQPLPIMPHQMPPRGHAYRYPLGRNMQDFPFDMGAGSMLPVPVDMGAGIPRRDA 367
           GP+       P +   +P     Y+Y  G        +      +  P            
Sbjct: 1   GPLGSAAAATPAVR-TVPQ----YKYAAGVRNPQQHLNAQPQVTMQQPA----------V 45

Query: 368 SVGQPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLH 427
            V    P+TA  + LA+A P++Q+ +LGE L+PL++ +    A K+TGMLLE+D +E+LH
Sbjct: 46  HVQGQEPLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 103

Query: 428 LLESPEALKAKVAEAMEVLRSVAQQQANNPADQLAS 463
           +LESPE+L++KV EA+ VL++   ++A   A   A+
Sbjct: 104 MLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNSAT 139

>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 =  105 bits (263), Expect = 3e-27
 Identities = 39/187 (20%), Positives = 75/187 (40%), Gaps = 16/187 (8%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +F+  L   TTDE L+  F ++GT+T  VVMRD +  +S+ FGFV +   ++   A+ A 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 90  NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 149
             K                      +    +  +          +++  + +  ++  L+
Sbjct: 69  PHKVDGRVVEPK-------------RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLR 115

Query: 150 ELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 208
           + F ++G I   ++M D   G  +G  FV F   +   + +       +      V  A 
Sbjct: 116 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKAL 174

Query: 209 RKEERRA 215
            K+E  +
Sbjct: 175 SKQEMAS 181

>d1ifwa_ a.144.1.1 (A:) poly(A) binding protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 92

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  101 bits (254), Expect = 5e-27
 Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 2/87 (2%)

Query: 372 PMPITALSTALANASPEQQRTLLGESLYPLVEQL--ERDAAAKVTGMLLEMDQTEVLHLL 429
           P+     +        ++QR  LGE LY  V       +AA K+TGM+L++   EV  LL
Sbjct: 2   PLGSPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLL 61

Query: 430 ESPEALKAKVAEAMEVLRSVAQQQANN 456
           ES E  +    EA     S  ++Q   
Sbjct: 62  ESDELFEQHYKEASAAYESFKKEQEQQ 88

>d1i2ta_ a.144.1.1 (A:) hyperplastic discs protein {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: hyperplastic discs protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 97.8 bits (244), Expect = 5e-26
 Identities = 27/59 (45%), Positives = 42/59 (71%)

Query: 390 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRS 448
            R  LGE LYP V+ ++   A+K+TGMLLE+   ++L LL S ++L+A+V EAME++ +
Sbjct: 1   HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIA 59

>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 = 86.5 bits (214), Expect = 2e-21
 Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 3/93 (3%)

Query: 22  VAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD--GKSKCFGFVNFENA 79
           V  K   + + V+N+       +++++F  +G + +  + +     G  + FGFV+F   
Sbjct: 2   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 61

Query: 80  DDAAKAVEAL-NGKKFDDREWYVGKAQKKSERE 111
            DA KA  AL +      R   +  A  +   +
Sbjct: 62  QDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 77.3 bits (190), Expect = 3e-18
 Identities = 18/85 (21%), Positives = 43/85 (50%), Gaps = 3/85 (3%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALA 190
            + ++N+    +  +++ELFS FG + + ++ +    +G  +G GFV F T ++A +A  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 191 EM-NGKMIVSKPLYVAVAQRKEERR 214
            + +   +  + L +  A  +   +
Sbjct: 70  ALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 85.1 bits (210), Expect = 6e-21
 Identities = 34/86 (39%), Positives = 55/86 (63%), Gaps = 1/86 (1%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           K+   N+F+KNLD+S  ++ L   F  +G I S  V+ D +G SK +GFV+FE  + A +
Sbjct: 5   KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAER 63

Query: 85  AVEALNGKKFDDREWYVGKAQKKSER 110
           A+E +NG   +DR+ +VG+ + + ER
Sbjct: 64  AIEKMNGMLLNDRKVFVGRFKSRKER 89

>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 = 77.4 bits (190), Expect = 2e-18
 Identities = 38/81 (46%), Positives = 55/81 (67%), Gaps = 1/81 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           N++IKNL  SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 68

Query: 193 NGKMIVSKPLYVAVAQRKEER 213
           NG ++  + ++V   + ++ER
Sbjct: 69  NGMLLNDRKVFVGRFKSRKER 89

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 82.3 bits (203), Expect = 4e-20
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           +++V +L    T+  L + F   G I S  V RD    +S  + +VNF+   DA +A++ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 89  LNGKKFDDREWYVGKAQK 106
           +N      +   +  +Q+
Sbjct: 62  MNFDVIKGKPVRIMWSQR 79

>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 = 81.5 bits (201), Expect = 7e-20
 Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           +LY+ +L   + +  L E FS  G I S +V RD  +  S G  +V F  P +A RAL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 192 MNGKMIVSKPLYVAVAQR 209
           MN  +I  KP+ +  +QR
Sbjct: 62  MNFDVIKGKPVRIMWSQR 79

>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 = 80.8 bits (199), Expect = 3e-19
 Identities = 23/105 (21%), Positives = 48/105 (45%), Gaps = 3/105 (2%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             ++++NL    T E++  IFG+YG I    +      +++   +V +E+  DA  A + 
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQ--IRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN 133
           L+G    +R   V         ++    + E+ +K  + +  G+N
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKL-LKEKYGIN 109

>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 = 73.5 bits (180), Expect = 1e-16
 Identities = 18/93 (19%), Positives = 44/93 (47%), Gaps = 3/93 (3%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LYI+NL   I  E++ ++F ++G I         +  ++G+ +V +    +A  A   ++
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQI--RVGNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 194 GKMIVSKPLYVAVAQ-RKEERRARLQAQFSQMR 225
           G  + ++ L V      +  ++   + +  Q++
Sbjct: 68  GFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLK 100

>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 = 78.8 bits (194), Expect = 7e-19
 Identities = 26/71 (36%), Positives = 39/71 (54%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           + V NLD   +D D++++F E+GT+  A V  D  G+S     V+FE   DA KA++  N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 91  GKKFDDREWYV 101
           G   D R   +
Sbjct: 63  GVPLDGRPMNI 73

>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 = 77.7 bits (191), Expect = 2e-18
 Identities = 24/75 (32%), Positives = 40/75 (53%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L + NL   + D  ++ELF+EFGT+    V  D SG S G+  V F    +A +A+ + N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 194 GKMIVSKPLYVAVAQ 208
           G  +  +P+ + +  
Sbjct: 63  GVPLDGRPMNIQLVT 77

>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 = 78.5 bits (193), Expect = 8e-19
 Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 4/81 (4%)

Query: 32  FVKNLDESTTDEDLKKIFGEYGTITSAVVMRD----GDGKSKCFGFVNFENADDAAKAVE 87
           F+KNL+ STT+E LK +F + G I S  + +     G   S  FGFV ++  + A KA++
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 88  ALNGKKFDDREWYVGKAQKKS 108
            L G   D  +  V  +++ +
Sbjct: 62  QLQGHTVDGHKLEVRISERAT 82

>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 = 74.7 bits (183), Expect = 2e-17
 Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 4/82 (4%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP----SGISKGSGFVAFSTPEEASRAL 189
           L+IKNL  S  +E LK +FS+ G I SC + +        +S G GFV +  PE+A +AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 190 AEMNGKMIVSKPLYVAVAQRKE 211
            ++ G  +    L V +++R  
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 82

>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 = 78.5 bits (193), Expect = 1e-18
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           ++V NL   TT+E + ++F + G I   ++  D     +  F FV + +  DA  A+  +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 90  NGKKFDDREWYVGKAQKKSEREQ 112
           NG + DDR           E  Q
Sbjct: 70  NGTRLDDRIIRTDWDAGFKEGRQ 92

>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 = 71.5 bits (175), Expect = 4e-16
 Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 7/97 (7%)

Query: 119 EQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGS-GFV 177
           E+ +K++        LY+ NL     +E++ ELFS+ G I    +  D    +     FV
Sbjct: 1   EKLLKKSC------TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 54

Query: 178 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR 214
            + +  +A  A+  +NG  +  + +        +E R
Sbjct: 55  EYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR 91

>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 = 77.7 bits (191), Expect = 2e-18
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L +  TD +L  +F   G I +  +MRD   G S  + FV+F +  D+ +A++ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 89  LNGKKFDDREWYVGKAQ 105
           LNG    ++   V  A+
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>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 = 72.3 bits (177), Expect = 1e-16
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAE 191
           NL +  L   + D +L  LF   G I +C++MRD   G S G  FV F++  ++ RA+  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K L V+ A+
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>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 = 78.2 bits (192), Expect = 2e-18
 Identities = 28/83 (33%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           K+    + V N+     D DL+++FG++G I    ++ + +  SK FGFV FEN+ DA +
Sbjct: 8   KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFENSADADR 66

Query: 85  AVEALNGKKFDDREWYVGKAQKK 107
           A E L+G   + R+  V  A  +
Sbjct: 67  AREKLHGTVVEGRKIEVNNATAR 89

>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 = 68.2 bits (166), Expect = 5e-15
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L++ N+     D  L+++F +FG I   +++ +    SKG GFV F    +A RA  ++
Sbjct: 13  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKL 71

Query: 193 NGKMIVSKPLYVAVAQRK 210
           +G ++  + + V  A  +
Sbjct: 72  HGTVVEGRKIEVNNATAR 89

>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 = 77.1 bits (189), Expect = 3e-18
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSA--VVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           +F+ NLD    ++ L   F  +G I     ++     G SK + F+NF + D +  A+EA
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 89  LNGKKFDDREWYVGKAQKKSER 110
           +NG+   +R   V  A KK  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 73.6 bits (180), Expect = 4e-17
 Identities = 25/82 (30%), Positives = 47/82 (57%), Gaps = 2/82 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMR--DPSGISKGSGFVAFSTPEEASRALAE 191
           ++I NL   ID++ L + FS FG I     +     +G SKG  F+ F++ + +  A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 192 MNGKMIVSKPLYVAVAQRKEER 213
           MNG+ + ++P+ V+ A +K+ +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 76.6 bits (188), Expect = 5e-18
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 89
           ++V  L E   D+ L   F  +G IT   +  D + +  + F FV FE A+DAA A++ +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 90  NGKKFDDREWYVGKAQKKSERE 111
           N  +   R   V  A+    +E
Sbjct: 68  NESELFGRTIRVNLAKPMRIKE 89

>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 = 68.5 bits (167), Expect = 4e-15
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           LY+  L + +DD+ L   F  FG IT  ++  D  +   +G  FV F   E+A+ A+  M
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 193 NGKMIVSKPLYVAVAQRKEER 213
           N   +  + + V +A+    +
Sbjct: 68  NESELFGRTIRVNLAKPMRIK 88

>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 = 76.1 bits (187), Expect = 8e-18
 Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 3/83 (3%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAA 83
             K  N++V NL  + TD+ L  IFG+YG+I    ++RD   G+ +   FV +   ++A 
Sbjct: 3   SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 62

Query: 84  KAVEALNGKKFD--DREWYVGKA 104
           +A+ ALN    +   +   V  A
Sbjct: 63  EAISALNNVIPEGGSQPLSVRLA 85

>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 = 74.6 bits (183), Expect = 3e-17
 Identities = 27/84 (32%), Positives = 49/84 (58%), Gaps = 3/84 (3%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 185
           +  +  NLY+ NL  +I D++L  +F ++G+I    ++RD  +G  +G  FV ++  EEA
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 186 SRALAEMNGKMI--VSKPLYVAVA 207
             A++ +N  +    S+PL V +A
Sbjct: 62  QEAISALNNVIPEGGSQPLSVRLA 85

>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 = 76.1 bits (187), Expect = 1e-17
 Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 8/84 (9%)

Query: 29  NNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
           + VF+ NL+       D++ IF +YG I    V +        F FV + N  +A  AV 
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG-------FAFVQYVNERNARAAVA 68

Query: 88  ALNGKKFDDREWYVGKAQKKSERE 111
             +G+    +   +  A +     
Sbjct: 69  GEDGRMIAGQVLDINLAAEPKVNR 92

>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 = 74.1 bits (182), Expect = 4e-17
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 8/83 (9%)

Query: 133 NLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
            ++I NL    +    ++ +FS++G I  C V +       G  FV +     A  A+A 
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK-------GFAFVQYVNERNARAAVAG 69

Query: 192 MNGKMIVSKPLYVAVAQRKEERR 214
            +G+MI  + L + +A   +  R
Sbjct: 70  EDGRMIAGQVLDINLAAEPKVNR 92

>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 = 74.7 bits (183), Expect = 3e-17
 Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 6/90 (6%)

Query: 29  NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           + +++ NL+E    ++LKK    IF  +G I   +V R      +   FV F+    A  
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATN 61

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQEL 114
           A+ ++ G  F D+   +  A+  S+   ++
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>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 = 70.8 bits (173), Expect = 5e-16
 Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 134 LYIKNLGDSIDDEKLK----ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           +YI NL + I  ++LK     +FS FG I    V R      +G  FV F     A+ AL
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 63

Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARL 217
             M G     KP+ +  A+   +  A++
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>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 = 74.7 bits (183), Expect = 3e-17
 Identities = 26/83 (31%), Positives = 47/83 (56%), Gaps = 1/83 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
            N+F+ +L +   D+DL ++F  +G + SA V  D     SKCFGFV+++N   A  A++
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 88  ALNGKKFDDREWYVGKAQKKSER 110
           ++NG +   +   V   + K++ 
Sbjct: 79  SMNGFQIGMKRLKVQLKRSKNDS 101

>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 = 70.9 bits (173), Expect = 8e-16
 Identities = 30/86 (34%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRA 188
           +G NL+I +L     D+ L ++F  FG + S KV  D    +SK  GFV++  P  A  A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERR 214
           +  MNG  I  K L V + + K + +
Sbjct: 77  IQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 74.3 bits (182), Expect = 4e-17
 Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             V+V  LDE  ++  L ++F + G + +  + +D   G+ + +GFV F + +DA  A++
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 88  ALNGKKFDDREWYVGKAQKKSE 109
            ++  K   +   V KA   ++
Sbjct: 70  IMDMIKLYGKPIRVNKASAHNK 91

>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 = 69.7 bits (170), Expect = 2e-15
 Identities = 23/87 (26%), Positives = 44/87 (50%), Gaps = 1/87 (1%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 185
           ++ Q   +Y+  L + + +  L ELF + G + +  + +D  +G  +G GFV F + E+A
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 64

Query: 186 SRALAEMNGKMIVSKPLYVAVAQRKEE 212
             A+  M+   +  KP+ V  A    +
Sbjct: 65  DYAIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 73.9 bits (181), Expect = 4e-17
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             ++V NL    T+  + ++F + G   S  ++ +    +  + FV F    DAA A+ A
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRDAAAALAA 67

Query: 89  LNGKKFDDREWYVGKAQKKSERE 111
           +NG+K   +E  V  A   S ++
Sbjct: 68  MNGRKILGKEVKVNWATTPSSQK 90

>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 = 66.6 bits (162), Expect = 2e-14
 Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 1/81 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY+ NL   + +  + +LFS+ G   SCK++ +    +    FV F    +A+ ALA MN
Sbjct: 11  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-TSNDPYCFVEFYEHRDAAAALAAMN 69

Query: 194 GKMIVSKPLYVAVAQRKEERR 214
           G+ I+ K + V  A     ++
Sbjct: 70  GRKILGKEVKVNWATTPSSQK 90

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 72.3 bits (177), Expect = 1e-16
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
           T+ + +FV NL    T+E+++K+F +YG      + +D     K FGF+  E    A  A
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIA 60

Query: 86  VEALNGKKFDDREWYVGKAQKKS 108
              L+      ++  V  A   +
Sbjct: 61  KVELDNMPLRGKQLRVRFACHSA 83

>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 = 61.9 bits (150), Expect = 7e-13
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 128 KFQGLN-LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
            F   + L++ NL   I +E++++LF ++G      + +D        GF+   T   A 
Sbjct: 4   TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAE 58

Query: 187 RALAEMNGKMIVSKPLYVAVAQRK 210
            A  E++   +  K L V  A   
Sbjct: 59  IAKVELDNMPLRGKQLRVRFACHS 82

>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 = 72.8 bits (178), Expect = 1e-16
 Identities = 14/92 (15%), Positives = 37/92 (40%), Gaps = 5/92 (5%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVM---RDGDGKSKCFGFVNFENADDAAKAVE 87
           +F+  + +    E++ +   +       V++        K++ F FV +E+   AA A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 88  ALNGKKF--DDREWYVGKAQKKSEREQELKGQ 117
            L   +      +  V  A+ + + ++++   
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>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 = 64.3 bits (156), Expect = 1e-13
 Identities = 11/92 (11%), Positives = 32/92 (34%), Gaps = 5/92 (5%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVM---RDPSGISKGSGFVAFSTPEEASRALA 190
           L+I  +      E++ E  ++        ++         ++G  FV + +   A+ A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 191 EMNGK--MIVSKPLYVAVAQRKEERRARLQAQ 220
           ++      +    + V  A+ + +    +   
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>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 = 72.8 bits (178), Expect = 2e-16
 Identities = 28/85 (32%), Positives = 44/85 (51%), Gaps = 1/85 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVE 87
             +FV+NL  ++++EDL+K+F  YG ++      D   K  K F FV F   + A KA  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 88  ALNGKKFDDREWYVGKAQKKSEREQ 112
            ++G+ F  R  +V  +  K E  Q
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 67.4 bits (164), Expect = 1e-14
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAE 191
            L+++NL  +  +E L++LFS +G ++      D      KG  FV F  PE A +A AE
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 192 MNGKMIVSKPLYVAVAQRKEERRAR 216
           ++G++   + L+V  +  K+E    
Sbjct: 70  VDGQVFQGRMLHVLPSTIKKEASQS 94

>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 = 72.0 bits (176), Expect = 2e-16
 Identities = 17/80 (21%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +F+  L     D+ +K++   +G + +  +++D   G SK + F  + + +   +A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 90  NGKKFDDREWYVGKAQKKSE 109
           NG +  D++  V +A   ++
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 83

>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 = 65.4 bits (159), Expect = 4e-14
 Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L+I  L + ++D+++KEL + FG + +  +++D  +G+SKG  F  +       +A+A +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 193 NGKMIVSKPLYVAVAQRKEE 212
           NG  +  K L V  A    +
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.7 bits (175), Expect = 2e-16
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVE 87
             + V  L   TT+ DL+++F +YG I    ++ D    +S+ F FV FEN DDA +A E
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 88  ALNGKKFDDREWYV 101
             NG + D R   V
Sbjct: 70  RANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.8 bits (152), Expect = 3e-13
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            L +  L     +  L+E+FS++G I    ++ D  S  S+G  FV F   ++A  A   
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 192 MNGKMIVSKPLYV 204
            NG  +  + + V
Sbjct: 71  ANGMELDGRRIRV 83

>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 = 71.7 bits (175), Expect = 2e-16
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
           N+ V  L ++ T E+ + +FG  G I S  ++RD   G+S  +GFVN+ +  DA KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 89  LNGKKFDDREWYVGKAQ 105
           LNG +   +   V  A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>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 = 64.7 bits (157), Expect = 7e-14
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
           NL +  L  ++  E+ + LF   G I SCK++RD  +G S G GFV +  P++A +A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 192 MNGKMIVSKPLYVAVAQ 208
           +NG  + +K + V+ A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>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 = 71.6 bits (175), Expect = 3e-16
 Identities = 25/81 (30%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 87
             + V NL E T + DL+++F  +G+I+   + +D   G+SK F F++F   +DAA+A+ 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 88  ALNGKKFDDREWYVGKAQKKS 108
            ++G  +D     V  A+  +
Sbjct: 69  GVSGFGYDHLILNVEWAKPST 89

>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 = 63.9 bits (155), Expect = 2e-13
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            + + NL +   +  L+ELF  FG+I+   + +D  +G SKG  F++F   E+A+RA+A 
Sbjct: 10  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 69

Query: 192 MNGKMIVSKPLYVAVAQRKE 211
           ++G       L V  A+   
Sbjct: 70  VSGFGYDHLILNVEWAKPST 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 = 71.6 bits (175), Expect = 4e-16
 Identities = 15/77 (19%), Positives = 34/77 (44%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
           ++  ++V ++   +   +E   ++  +YG +    V  +         +V F   +DA K
Sbjct: 24  RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEK 83

Query: 85  AVEALNGKKFDDREWYV 101
           AV  LN + F+ +  + 
Sbjct: 84  AVIDLNNRWFNGQPIHA 100

>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 = 67.8 bits (165), Expect = 1e-14
 Identities = 13/72 (18%), Positives = 34/72 (47%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           ++ ++   D   +E   E+  ++G +    V  +      G+ +V F   E+A +A+ ++
Sbjct: 29  DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 193 NGKMIVSKPLYV 204
           N +    +P++ 
Sbjct: 89  NNRWFNGQPIHA 100

>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 = 71.2 bits (174), Expect = 4e-16
 Identities = 20/73 (27%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKA 85
          +  N++V  L ++ T ++L+++F +YG I ++ ++ D     S+  GF+ F+   +A +A
Sbjct: 5  RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 86 VEALNGKKFDDRE 98
          ++ LNG+K     
Sbjct: 65 IKGLNGQKPSGAT 77

>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 = 70.1 bits (171), Expect = 1e-15
 Identities = 24/78 (30%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG-ISKGSGFVAFSTPEEASRALAE 191
           NLY+  L  ++  ++L++LFS++G I + +++ D    +S+G GF+ F    EA  A+  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 192 MNGKMI--VSKPLYVAVA 207
           +NG+     ++P+ V  A
Sbjct: 68  LNGQKPSGATEPITVKFA 85

>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 = 71.2 bits (174), Expect = 5e-16
 Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKA 85
           K +++ V  L   TT++DLK+ F  +G +    V +D   G SK FGFV F   +   K 
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

Query: 86  VEALNGKKFDDREWYVGKAQKKSERE 111
           +   +    D R         K  ++
Sbjct: 67  MSQRH--MIDGRWCDCKLPNSKQSQD 90

>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 = 68.8 bits (168), Expect = 3e-15
 Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 5/93 (5%)

Query: 122 MKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFS 180
           +K  V K    +L +  L     ++ LKE FS FG +   +V +D  +G SKG GFV F+
Sbjct: 1   VKRAVQK--TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 58

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEER 213
             E   + +++ +  MI  +     +   K+ +
Sbjct: 59  EYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ 89

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.2 bits (174), Expect = 5e-16
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 5/78 (6%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
            V+   +    TD+ +++ F  +G I    V  +     K + FV F   + AA A+ ++
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 74

Query: 90  NGKKFDDREWYVGKAQKK 107
           NG   +         ++ 
Sbjct: 75  NGTTIEGHVVKCYWGKES 92

>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 = 68.5 bits (167), Expect = 4e-15
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 7/93 (7%)

Query: 118 FEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFV 177
           FE  + ++  K     +Y   +   + D+ +++ FS FG I   +V  +         FV
Sbjct: 7   FEDVVNQSSPK--NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-----YSFV 59

Query: 178 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK 210
            FST E A+ A+  +NG  I    +     +  
Sbjct: 60  RFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>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 = 70.4 bits (172), Expect = 1e-15
 Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 2/83 (2%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVE 87
             VF   L       DL+  F   G +    ++ D +  +SK   +V F        A+ 
Sbjct: 19  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 78

Query: 88  ALNGKKFDDREWYVGKAQKKSER 110
            L G++       V  +Q +  R
Sbjct: 79  -LTGQRLLGVPIIVQASQAEKNR 100

>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 = 65.8 bits (160), Expect = 4e-14
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            ++   L   I    L++ FS  G +   +++ D  S  SKG  +V F   +    A+  
Sbjct: 20  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-G 78

Query: 192 MNGKMIVSKPLYVAVAQRKEER 213
           + G+ ++  P+ V  +Q ++ R
Sbjct: 79  LTGQRLLGVPIIVQASQAEKNR 100

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.6 bits (172), Expect = 1e-15
 Identities = 23/103 (22%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFEN-ADDAAKAVEA 88
             F  +LD+ T  EDL  +F  +G I     +R         G + F+  A +A    + 
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKD 67

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQG 131
            N      R   V     + E E+E   +  +  +E+++K++ 
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKS 110

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (130), Expect = 7e-10
 Identities = 18/95 (18%), Positives = 30/95 (31%), Gaps = 6/95 (6%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTP-EEASRALA 190
           L  +  +L D    E L  LFS  G I     +R         G + F    +EA     
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAK 66

Query: 191 EMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMR 225
           + N   +  +   V     + E       +  + +
Sbjct: 67  DANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQ 101

>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 = 69.7 bits (170), Expect = 1e-15
 Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 5/87 (5%)

Query: 24  IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 83
             +    ++V+NL  ST++E ++K F          V      K + + FV+F N +DA 
Sbjct: 4   TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAV 58

Query: 84  KAVEALNGKKFDDREWYVGKAQKKSER 110
           +A++ALNGK  D     V  A+   + 
Sbjct: 59  EAMKALNGKVLDGSPIEVTLAKPVDKD 85

>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 = 60.0 bits (145), Expect = 3e-12
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LY++NL  S  +E +++ F+        +V        +   FV FS  E+A  A+  +N
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKALN 65

Query: 194 GKMIVSKPLYVAVAQRKEER 213
           GK++   P+ V +A+  ++ 
Sbjct: 66  GKVLDGSPIEVTLAKPVDKD 85

>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 = 69.2 bits (169), Expect = 2e-15
 Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           ++I  L      E L+E F +FG +  C VMRDP +  S+G GFV F       + L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 193 NGKMIVSKPLYVAVA 207
           +   + SK +   VA
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 67.7 bits (165), Expect = 6e-15
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           +F+  L   TT E L++ FG++G +   +VMRD    +S+ FGFV F +     K +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 90  NGKKFDDREWYVGKA 104
           +  + D +      A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 69.8 bits (170), Expect = 2e-15
 Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 9/91 (9%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---------GDGKSKCFGFVNFENA 79
           + ++V+ L++S T +DL   F + G +                   GK K    V++E+ 
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 80  DDAAKAVEALNGKKFDDREWYVGKAQKKSER 110
             A  AVE  +GK F   +  V  A+KK   
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 62.5 bits (151), Expect = 7e-13
 Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 9/96 (9%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFV 177
           +      +Y++ L DS+  + L + F + G +   K    P         +G  KG   V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 178 AFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEER 213
           ++  P  A  A+   +GK      L V++A++K   
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 68.5 bits (167), Expect = 3e-15
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 89
           +F+  L   TT +DLK  F ++G +    +  D     S+ FGFV F+ ++   K ++  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 90  NGKKFDDREWYVGKA 104
              K + +     +A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.0 bits (145), Expect = 2e-12
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           ++I  L      + LK+ FS+FG +  C +  DP +G S+G GFV F   E   + + + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 193 NGKMIVSKPLYVAVA 207
               +  K +    A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>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 = 68.9 bits (168), Expect = 4e-15
 Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 6/98 (6%)

Query: 14  LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFG 72
           L +++RE    K +F  +F+  L   TT+E L+  + ++G +T  VVMRD    +S+ FG
Sbjct: 10  LERKKRE----KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 65

Query: 73  FVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSER 110
           FV F +  +   A+        D R     +A  + E 
Sbjct: 66  FVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES 102

>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 = 67.0 bits (163), Expect = 2e-14
 Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            L+I  L     +E L+  + ++G +T C VMRDP S  S+G GFV FS+  E   A+  
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 80

Query: 192 MNGKMIVSKPLYVAVAQRKEER 213
                I  + +    A  +EE 
Sbjct: 81  ARPHSIDGRVVEPKRAVAREES 102

>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 = 67.0 bits (163), Expect = 9e-15
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 6/83 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           N +++ NL  + T +DL+++FG+     +  V+         + FV++ + + A +A+E 
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIET 56

Query: 89  LNGK-KFDDREWYVGKAQKKSER 110
           L+GK +   +   V  +  K  R
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKLR 79

>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 = 62.0 bits (150), Expect = 6e-13
 Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           LYI NL  ++  + L++LF +     + +V+        G  FV +     A RA+  ++
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLS 58

Query: 194 GKMIV-SKPLYVAVAQRKEER 213
           GK+ +  K + V  +  K+ R
Sbjct: 59  GKVELHGKIMEVDYSVSKKLR 79

>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 = 67.5 bits (164), Expect = 9e-15
 Identities = 34/81 (41%), Positives = 52/81 (64%), Gaps = 1/81 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 89
           +FV  L   T ++ L+++F +YG I+  VV++D + + S+ FGFV FEN DDA  A+ A+
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 90  NGKKFDDREWYVGKAQKKSER 110
           NGK  D R+  V +A K S+ 
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDN 88

>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 = 64.8 bits (157), Expect = 7e-14
 Identities = 23/83 (27%), Positives = 45/83 (54%), Gaps = 1/83 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCK-VMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L++  L    +++ L+++FS++G I+    V    +  S+G GFV F   ++A  A+  M
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
           NGK +  + + V  A +  + R+
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDNRS 90

>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 = 67.4 bits (164), Expect = 1e-14
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             +  KNL  + T+++LK++F +   I          G      ++ F++  DA K +E 
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG----IAYIEFKSEADAEKNLEE 72

Query: 89  LNGKKFDDREWYVGKAQKKSER 110
             G + D R   +    +K   
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGT 94

>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 = 63.5 bits (154), Expect = 2e-13
 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 4/82 (4%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L  KNL  +I +++LKE+F +   I          G SKG  ++ F +  +A + L E 
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEK 73

Query: 193 NGKMIVSKPLYVAVAQRKEERR 214
            G  I  + + +     K   R
Sbjct: 74  QGAEIDGRSVSLYYTGEKGGTR 95

>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 = 66.6 bits (162), Expect = 2e-14
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +F+  L   TTDE L+  F ++GT+T  VVMRD +  +S+ FGFV +   ++   A+ A 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 67

Query: 90  NGKKFDDREWYVGKA 104
              K D R     +A
Sbjct: 68  RPHKVDGRVVEPKRA 82

>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 = 60.0 bits (145), Expect = 3e-12
 Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           L+I  L     DE L+  F ++GT+T C VMRDP +  S+G GFV ++T EE   A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 67

Query: 193 NGKMIVSKPLYVAVA 207
               +  + +    A
Sbjct: 68  RPHKVDGRVVEPKRA 82

>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 = 65.5 bits (159), Expect = 3e-14
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
           +FV  L  +TT ED+K  F ++G +  A++M D    + + FGFV FE+ D   K  E +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 90  NGKKFDDREWYVGKA 104
           +  + +++     KA
Sbjct: 61  HFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.8 bits (139), Expect = 1e-11
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +++  L  +   E +K  F +FG +    +M D  +   +G GFV F + +   +   E+
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 193 NGKMIVSKPLYVAVA 207
           +   I +K +    A
Sbjct: 61  HFHEINNKMVECKKA 75

>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 = 65.4 bits (159), Expect = 4e-14
 Identities = 15/84 (17%), Positives = 29/84 (34%), Gaps = 6/84 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           + VFV       T+++L++ F +YG +    + +        F FV F +   A      
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRA----FAFVTFADDQIAQSLCG- 60

Query: 89  LNGKKFDDREWYVGKAQKKSEREQ 112
                      ++  A+ K     
Sbjct: 61  -EDLIIKGISVHISNAEPKHNSNS 83

>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 = 59.3 bits (143), Expect = 7e-12
 Identities = 12/82 (14%), Positives = 34/82 (41%), Gaps = 6/82 (7%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            +++      + +++L+E FS++G +    + +     +    FV F+  + A       
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFA----FVTFADDQIAQSLC--G 60

Query: 193 NGKMIVSKPLYVAVAQRKEERR 214
              +I    ++++ A+ K    
Sbjct: 61  EDLIIKGISVHISNAEPKHNSN 82

>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 = 65.0 bits (158), Expect = 4e-14
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
           +FV  L   T +E +++ FG +G + S  +  D    K + F F+ F+  +   K +E  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 90  NGKKFDDREWYVGKA 104
                   +  +  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 60.4 bits (146), Expect = 2e-12
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           +++  L     +EK++E F  FG + S ++  D  +   +G  F+ F   E   + + E 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 193 NGKMIVSKPLYVAVA 207
               +      + VA
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 65.1 bits (158), Expect = 5e-14
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 87
             +FV ++ E   ++++++ F +YG I +  +  D   G SK +  V +E    A  A E
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 88  ALNGKKFDDREWYVGKAQKK 107
           ALNG +   +   V     K
Sbjct: 68  ALNGAEIMGQTIQVDWCFVK 87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 60.1 bits (145), Expect = 3e-12
 Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRA 188
           +G  L++ ++ +   +++++E F ++G I +  +  D     SKG   V + T ++A  A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 189 LAEMNGKMIVSKPLYVAVAQRK 210
              +NG  I+ + + V     K
Sbjct: 66  KEALNGAEIMGQTIQVDWCFVK 87

>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 = 65.5 bits (159), Expect = 6e-14
 Identities = 20/99 (20%), Positives = 40/99 (40%), Gaps = 10/99 (10%)

Query: 13  FLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFG 72
            LR +  ETV+  T+   V    L    +   L  +  + G + + ++  +     K + 
Sbjct: 5   LLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYS 59

Query: 73  FVNFENADDAAKAVEALNGKKFDDRE-----WYVGKAQK 106
           F  +   +++ +A   LNGK+  D        Y+   +K
Sbjct: 60  FARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 98

>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 = 52.8 bits (126), Expect = 2e-09
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 10/84 (11%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           Q L +    LG+ +   +L  +  + G + +  +  +         F  + T EE+ RA 
Sbjct: 19  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP-----YSFARYRTTEESKRAY 73

Query: 190 AEMNGKMIV-----SKPLYVAVAQ 208
             +NGK +V        LY+   +
Sbjct: 74  VTLNGKEVVDDLGQKITLYLNFVE 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 = 65.1 bits (158), Expect = 7e-14
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           ++V NL      +D++ +F +YG I    +          F FV FE+  DA  AV   +
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDAVYGRD 74

Query: 91  GKKFDDREWYVGKAQKKSER 110
           G  +D     V     +S R
Sbjct: 75  GYDYDGYRLRVEFP--RSGR 92

>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 = 62.0 bits (150), Expect = 8e-13
 Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 2/77 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           +Y+ NL   I  + ++++F ++G I    +            FV F  P +A  A+   +
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--GGPPFAFVEFEDPRDAEDAVYGRD 74

Query: 194 GKMIVSKPLYVAVAQRK 210
           G       L V   +  
Sbjct: 75  GYDYDGYRLRVEFPRSG 91

>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 = 64.7 bits (157), Expect = 8e-14
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             + V+N+  + + +++   F  Y  I  +V ++  + G       V FE+ D+A  AV 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 88  ALNGKKFDDREWYV 101
            LN +    R+  +
Sbjct: 70  DLNDRPIGSRKVKL 83

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 14/76 (18%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
            + ++N+  ++  +++ + F  +  I     ++    G+  G   VAF + +EA+ A+ +
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 192 MNGKMIVSKPLYVAVA 207
           +N + I S+ + + + 
Sbjct: 71  LNDRPIGSRKVKLVLG 86

>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 = 64.0 bits (155), Expect = 2e-13
 Identities = 27/91 (29%), Positives = 46/91 (50%), Gaps = 1/91 (1%)

Query: 23  AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC-FGFVNFENADD 81
           A+     +VFV N+    T+E LK IF E G + S  ++ D +      +GF  +++ + 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 82  AAKAVEALNGKKFDDREWYVGKAQKKSEREQ 112
           A  A+  LNG++F  R   V  A  +  +E+
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNKEE 93

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.5 bits (138), Expect = 4e-11
 Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 3/96 (3%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAE 191
           ++++ N+     +E+LK++FSE G + S +++ D      KG GF  +   E A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 192 MNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPV 227
           +NG+    + L V  A  ++ +            PV
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEEL--KSLGTGAPV 103

>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 = 64.3 bits (156), Expect = 2e-13
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
           L + ++NL   +  + L ++FS+FGT+         +   +    + ++ P  A  A   
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN---QFQALLQYADPVSAQHAKLS 64

Query: 192 MNGKMIV--SKPLYVAVAQRKEERRAR 216
           ++G+ I      L +  ++        
Sbjct: 65  LDGQNIYNACCTLRIDFSKLTSLNVKY 91

>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 = 63.5 bits (154), Expect = 3e-13
 Identities = 14/87 (16%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
           +    + V+NL    T + L +IF ++GT+   +        ++    + + +   A  A
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHA 61

Query: 86  VEALNGKKFDDREWYVGKAQKKSEREQ 112
             +L+G+   +    +     K     
Sbjct: 62  KLSLDGQNIYNACCTLRIDFSKLTSLN 88

>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 = 63.3 bits (153), Expect = 2e-13
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTIT-SAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
           +++ N   S T  +++ +  +   +  S  +       S+ F +++  + +DA   VE L
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 90  NGKKFDDREWYVGKAQ 105
           NG K +        + 
Sbjct: 64  NGLKIEGYTLVTKVSN 79

>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 = 57.1 bits (137), Expect = 3e-11
 Identities = 12/76 (15%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAEM 192
           L++ N   S     +++L  +   +     +       S+   ++  ++ E+A   + ++
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 193 NGKMIVSKPLYVAVAQ 208
           NG  I    L   V+ 
Sbjct: 64  NGLKIEGYTLVTKVSN 79

>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 = 63.3 bits (153), Expect = 3e-13
 Identities = 17/77 (22%), Positives = 34/77 (44%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
            N+++ NL  S  +++L+ +   +G + S  ++RD  G S+  GF   E+ +     +  
Sbjct: 19  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 89  LNGKKFDDREWYVGKAQ 105
            NGK            +
Sbjct: 79  FNGKFIKTPPGVSAPTE 95

>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 = 62.5 bits (151), Expect = 7e-13
 Identities = 31/95 (32%), Positives = 48/95 (50%)

Query: 114 LKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKG 173
           LK    QA      +    NLYI NL  S+D+++L+ +   FG + S +++RD SG S+G
Sbjct: 1   LKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG 60

Query: 174 SGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 208
            GF    + E+    +   NGK I + P   A  +
Sbjct: 61  VGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>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 = 62.9 bits (152), Expect = 5e-13
 Identities = 16/103 (15%), Positives = 31/103 (30%), Gaps = 10/103 (9%)

Query: 133 NLYIKNLGDSIDDEK-----LKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASR 187
            L      D +  E       + LF  +   T+ +  +           + FS P  A+ 
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAAD 61

Query: 188 ALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMG 230
           A   ++    + K + +  AQ      + L          + G
Sbjct: 62  ARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGPSSG 104

>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 = 55.2 bits (132), Expect = 2e-10
 Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 10/92 (10%)

Query: 29  NNVFVKNLDES-----TTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 83
           + +     ++       T    + +F  Y   T+    +           +NF N   AA
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAA 60

Query: 84  KAVEALNGKKFDDREWYVGKAQKKSEREQELK 115
            A   L+  +F  +E  +  AQ        L 
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIGSSHLA 92

>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 = 62.5 bits (151), Expect = 5e-13
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 4/82 (4%)

Query: 29  NNVFVKNLDESTTDED-LKKIFGEYGTITSAVVMR--DGDGKSKCFGFVNFENADDAAKA 85
             + ++NL     DE+ L++ F  +G+I    +         + C  F+ FEN D A +A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 86  VEALNGKKFDDREWYVGKAQKK 107
           ++ +N     +RE  V  A KK
Sbjct: 65  LQ-MNRSLLGNREISVSLADKK 85

>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 = 52.4 bits (125), Expect = 1e-09
 Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 130 QGLNLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVA--FSTPEEAS 186
           +G  + I+NL  + +D+  L+E F  FG+I    +       S  +      F   + A 
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 187 RALAEMNGKMIVSKPLYVAVAQRK 210
           RAL +MN  ++ ++ + V++A +K
Sbjct: 63  RAL-QMNRSLLGNREISVSLADKK 85

>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 = 62.3 bits (150), Expect = 7e-13
 Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 25  KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
            T   N+F+ NL+ + +  +LK    E        V+    G ++ FG+V+FE+A+D  K
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEK 69

Query: 85  AVEALNGKKFDDREWYVGKAQKK 107
           A+E L G K    E  + K + +
Sbjct: 70  ALE-LTGLKVFGNEIKLEKPKGR 91

>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 = 62.5 bits (151), Expect = 7e-13
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             +++KNL    T+ DL  +F  +       +      G+ +   F+ F N + A +A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 88  ALNGKKFDDREWYVGKAQKKSER 110
            +NG K   +   +   + K +R
Sbjct: 79  LVNGYKLYGKILVIEFGKNKKQR 101

>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 = 59.4 bits (143), Expect = 9e-12
 Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
            LY+KNL   + +  L  LF+ F       +     +G  +G  F+ F   E A +AL  
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 192 MNGKMIVSKPLYVAVAQRKEER 213
           +NG  +  K L +   + K++R
Sbjct: 80  VNGYKLYGKILVIEFGKNKKQR 101

>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 = 62.2 bits (151), Expect = 8e-13
 Identities = 17/96 (17%), Positives = 38/96 (39%), Gaps = 5/96 (5%)

Query: 15  RKQERETVAIKTKFNNVFVKNLDESTTD--EDLKKIFGEYGTITSAVVMRDGDGKSKCFG 72
           R +    V IK  F+ +  ++      +  EDL+    ++G I   ++            
Sbjct: 4   RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVA 60

Query: 73  FVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS 108
            V+F + ++A   ++ L+G+ F  R+         +
Sbjct: 61  SVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT 96

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.0 bits (140), Expect = 2e-11
 Identities = 19/111 (17%), Positives = 36/111 (32%), Gaps = 16/111 (14%)

Query: 102 GKAQKKSEREQELKGQFEQA-MKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITS 160
           G ++ + ER   +K  F     ++       +             E L+   S+FG I  
Sbjct: 1   GPSRMRHERVVIIKNMFHPMDFEDDPLVLNEI------------REDLRVECSKFGQIRK 48

Query: 161 CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE 211
             +         G   V+F  PEEA   +  ++G+    + +         
Sbjct: 49  LLLFDRHP---DGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT 96

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.3 bits (148), Expect = 1e-12
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
            K  +V++K      T +D+K+   + G + +  + R      K   FV F++ + A K 
Sbjct: 4   VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF 63

Query: 86  VEALNGKKFDDREWYV 101
           VE   G+K+ + +  +
Sbjct: 64  VE-TPGQKYKETDLLI 78

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 8e-10
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 4/80 (5%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           ++YIK        + +KE   + G + + ++ R      KGS FV F + E A + + E 
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 66

Query: 193 NGKMIVSKPLYVAVAQRKEE 212
            G+      L +     K++
Sbjct: 67  PGQKYKETDLLI---LFKDD 83

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.7 bits (149), Expect = 1e-12
 Identities = 31/94 (32%), Positives = 45/94 (47%), Gaps = 3/94 (3%)

Query: 26  TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAK 84
           T F  +FV  L   TTD  L+K F  +G I  AVV+ D    KS+ +GFV   +   A +
Sbjct: 8   TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 67

Query: 85  AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
           A +  N    D R+  V  A   + + + L+  F
Sbjct: 68  ACKDPNP-IIDGRKANVNLAYLGA-KPRSLQTGF 99

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 4e-10
 Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAE 191
            +++  L     D  L++ F  FG I    V+ D     S+G GFV  +    A RA  +
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 192 MNGKMIVSKPLYVAVAQRKEERRARLQAQFS 222
            N  +I  +   V +A    + R+ LQ  F+
Sbjct: 72  PNP-IIDGRKANVNLAYLGAKPRS-LQTGFA 100

>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 = 61.8 bits (149), Expect = 1e-12
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 7/89 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVE 87
             VF++NL   + +E L ++  ++G +    V+       SK   F  F   + A K + 
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 88  ALN------GKKFDDREWYVGKAQKKSER 110
           A +      G K D R+  V  A  + E 
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 57.9 bits (139), Expect = 3e-11
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 7/94 (7%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEA 185
           D  +G  ++I+NL    ++E L E+  +FG +   +V+  P    SKG  F  F T E A
Sbjct: 4   DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 63

Query: 186 SRALAEMN------GKMIVSKPLYVAVAQRKEER 213
            + LA  +      G  +  + L V +A  ++E 
Sbjct: 64  QKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 60.9 bits (147), Expect = 2e-12
 Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEAL 89
           +FV  + E T +  L+  F +YG I    +M D      + F FV F++ D   K V   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-Q 63

Query: 90  NGKKFDDREWYVGKA 104
                +     V KA
Sbjct: 64  KYHTVNGHNCEVRKA 78

>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 = 53.2 bits (127), Expect = 8e-10
 Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 7/84 (8%)

Query: 125 TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPE 183
           TV K     +++  + +  ++  L++ F ++G I   ++M D  SG  +G  FV F   +
Sbjct: 1   TVKK-----IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 55

Query: 184 EASRALAEMNGKMIVSKPLYVAVA 207
              + +       +      V  A
Sbjct: 56  SVDKIV-IQKYHTVNGHNCEVRKA 78

>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 = 60.4 bits (146), Expect = 2e-12
 Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 27  KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAV 86
           K N ++V   D   T   L+  F  +G I    +        +   FV +E  + A +AV
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAV 56

Query: 87  EALNGKKFDDREWYVGKAQKK 107
             LNG + +  +  V  A+K+
Sbjct: 57  AELNGTQVESVQLKVNIARKQ 77

>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 = 57.7 bits (139), Expect = 2e-11
 Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 7/81 (8%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
           +G  LY+      +    L+  FS FG I    +            FV +   E A +A+
Sbjct: 4   KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR-----NCAFVTYEKMESADQAV 56

Query: 190 AEMNGKMIVSKPLYVAVAQRK 210
           AE+NG  + S  L V +A+++
Sbjct: 57  AELNGTQVESVQLKVNIARKQ 77

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 4e-12
 Identities = 12/81 (14%), Positives = 29/81 (35%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
            F+ NL    T+E +K+ F         +     + +             D+  +  +LN
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLN 77

Query: 91  GKKFDDREWYVGKAQKKSERE 111
            +   ++   V  A +  +++
Sbjct: 78  EESLGNKRIRVDVADQAQDKD 98

>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 = 55.1 bits (132), Expect = 3e-10
 Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKV-MRDPSGISKGSGFVAFSTPEEASRALAEM 192
            ++ NL   + +E +KE F                    KG G+  F   +    AL  +
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SL 76

Query: 193 NGKMIVSKPLYVAVAQRKEERR 214
           N + + +K + V VA + +++ 
Sbjct: 77  NEESLGNKRIRVDVADQAQDKD 98

>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 = 59.4 bits (143), Expect = 5e-12
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 29 NNVFVKNLDESTTDEDLKKIF---GEYGTITSAVVMRD----GDGKSKCFGFVNFENADD 81
          N VFV  L +   D ++ K     G++G I   V+       G        +V +  ++D
Sbjct: 9  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 82 AAKAVEALNGKKFDDR 97
          A +A++ +N    D R
Sbjct: 69 ALRAIQCVNNVVVDGR 84

>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 = 52.9 bits (126), Expect = 1e-09
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 130 QGLNLYIKNLGDSIDDE---KLKELFSEFGTITSCKVMRDP----SGISKGSGFVAFSTP 182
           Q   +++  L   + D    K  E F +FG I    +        S     S +V +   
Sbjct: 7   QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 183 EEASRALAEMNGKMIVSKPLYVA 205
           E+A RA+  +N  ++  + L  +
Sbjct: 67  EDALRAIQCVNNVVVDGRTLKAS 89

>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 = 59.9 bits (144), Expect = 6e-12
 Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 2/85 (2%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA 88
              + N+  S T  D+ +         +AV +   + G+      V F+N DDA K+   
Sbjct: 10  CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER- 68

Query: 89  LNGKKFDDREWYVGKAQKKSEREQE 113
           L+ KK + RE +V     +  RE E
Sbjct: 69  LHRKKLNGREAFVHVVTLEDMREIE 93

>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 = 52.5 bits (125), Expect = 2e-09
 Identities = 13/86 (15%), Positives = 32/86 (37%), Gaps = 2/86 (2%)

Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 190
           +  +I N+  SI    + +         +   +    +G   G   V F   ++A ++  
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE- 67

Query: 191 EMNGKMIVSKPLYVAVAQRKEERRAR 216
            ++ K +  +  +V V   ++ R   
Sbjct: 68  RLHRKKLNGREAFVHVVTLEDMREIE 93

>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 = 59.0 bits (142), Expect = 1e-11
 Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 7/80 (8%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG------DGKSKCFGFVNFENADDAAK 84
           ++V N+    T+E +   F     +                 + K F F+ F + D+  +
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 85  AVEALNGKKFDDREWYVGKA 104
           A+   +G  F  +   + + 
Sbjct: 64  AMA-FDGIIFQGQSLKIRRP 82

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (131), Expect = 3e-10
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 7/77 (9%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP------SGISKGSGFVAFSTPEEASR 187
           LY+ N+   I +E + + F+    +                   K   F+ F + +E ++
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 188 ALAEMNGKMIVSKPLYV 204
           A+   +G +   + L +
Sbjct: 64  AM-AFDGIIFQGQSLKI 79

>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 = 58.2 bits (140), Expect = 1e-11
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
          ++++ L   TTD+DL K+   YG I S   + D    K K +GFV+F++   A KAV AL
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 90 NGKKFDDR 97
                 +
Sbjct: 61 KASGVQAQ 68

>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 = 50.2 bits (119), Expect = 8e-09
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
           LYI+ L     D+ L +L   +G I S K + D  +   KG GFV F +P  A +A+  +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 193 NGKMIVSKPL 202
               + ++  
Sbjct: 61  KASGVQAQMA 70

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.6 bits (141), Expect = 1e-11
 Identities = 20/82 (24%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             V V  L  S + +DLK    E G       +   D +    G V +   +D   A+  
Sbjct: 16  FRVLVSGLPPSGSWQDLKDHMREAGD------VCYADVQKDGMGMVEYLRKEDMEYALRK 69

Query: 89  LNGKKFDDREWYVGKAQKKSER 110
           L+  KF   E      +   ER
Sbjct: 70  LDDTKFRSHEGETSYIRVYPER 91

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.1 bits (124), Expect = 3e-09
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + +  L  S   + LK+   E G +    V +D  G       V +   E+   AL +++
Sbjct: 18  VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMG------MVEYLRKEDMEYALRKLD 71

Query: 194 GKMIVSKPLYVAVAQRKEERRA 215
                S     +  +   ER +
Sbjct: 72  DTKFRSHEGETSYIRVYPERSS 93

>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 = 59.1 bits (142), Expect = 2e-11
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF-GFVNFENADDAAKAVE 87
            N+ V  +  +  +  L+++F  YG I S  ++ D + +     GFV F++   A +A+ 
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 88  ALNGKKFDDREWYVGKAQKKSER 110
            LNG    ++   V  A    +R
Sbjct: 103 GLNGFNILNKRLKVALAASGHQR 125

>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 = 55.3 bits (132), Expect = 6e-10
 Identities = 26/111 (23%), Positives = 52/111 (46%), Gaps = 1/111 (0%)

Query: 107 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD 166
           + ++ Q+ + Q     +   +     NL +  +  ++D+ +L++LF  +G I S K++ D
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77

Query: 167 PSGISKGSGFVA-FSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRAR 216
                        F +   A +A+A +NG  I++K L VA+A    +R   
Sbjct: 78  RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGI 128

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.2 bits (137), Expect = 3e-11
 Identities = 22/84 (26%), Positives = 30/84 (35%), Gaps = 6/84 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           N V V  L  S + +DLK    E G       +   D      G V F   +D   AV  
Sbjct: 1   NRVVVSGLPPSGSWQDLKDHMREAGD------VCYADVYRDGTGVVEFVRKEDMTYAVRK 54

Query: 89  LNGKKFDDREWYVGKAQKKSEREQ 112
           L+  KF   E      + K +  +
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPR 78

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.1 bits (103), Expect = 2e-06
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 6/81 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + +  L  S   + LK+   E G +    V RD       +G V F   E+ + A+ +++
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG------TGVVEFVRKEDMTYAVRKLD 56

Query: 194 GKMIVSKPLYVAVAQRKEERR 214
                S     A  + K +  
Sbjct: 57  NTKFRSHEGETAYIRVKVDGP 77

>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 = 57.7 bits (139), Expect = 4e-11
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 35 NLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS---KCFGFVNFENADDAAKAVEALNG 91
          + +     ED++    +YG + S  + R  DG         FV F +  D  KA++ L G
Sbjct: 21 DEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80

Query: 92 KKFDDRE 98
          +KF +R 
Sbjct: 81 RKFANRV 87

>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 = 50.4 bits (120), Expect = 1e-08
 Identities = 16/94 (17%), Positives = 38/94 (40%), Gaps = 13/94 (13%)

Query: 134 LYIKNL---GDSIDD-------EKLKELFSEFGTITSCKVMRDP---SGISKGSGFVAFS 180
           L + N+    + +DD       E +++  S++G + S ++ R          G  FV F+
Sbjct: 7   LCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFT 66

Query: 181 TPEEASRALAEMNGKMIVSKPLYVAVAQRKEERR 214
           +  +  +A+  + G+   ++ +           R
Sbjct: 67  SVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHR 100

>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 = 56.7 bits (136), Expect = 5e-11
 Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 6/80 (7%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
           + + VKNL + +  +++  +  +Y      V             FV   N + A  A++ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKR------TAFVTLLNGEQAQNAIQM 59

Query: 89  LNGKKFDDREWYVGKAQKKS 108
            +   F  ++  V      +
Sbjct: 60  FHQYSFRGKDLIVQLQPTDA 79

>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 = 53.2 bits (127), Expect = 8e-10
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 6/78 (7%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            + +KNL    + +++ +L  ++               +K + FV     E+A  A+   
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR------NKRTAFVTLLNGEQAQNAIQMF 60

Query: 193 NGKMIVSKPLYVAVAQRK 210
           +      K L V +    
Sbjct: 61  HQYSFRGKDLIVQLQPTD 78

>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 = 55.1 bits (132), Expect = 3e-10
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             ++V  L  +T+   L + F  +G+I +   ++        F ++ +E+ D A  A   
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAK 72

Query: 89  LNGKKFD--DREWYVGKAQKK 107
           + G      DR   V  A+  
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSG 93

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 7/80 (8%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L++  LG +     L   F  FG+I +   ++  S       ++ + + + A  A A+M
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS-----FAYIQYESLDAAQAACAKM 73

Query: 193 NGKMI--VSKPLYVAVAQRK 210
            G  +    + L V  A+  
Sbjct: 74  RGFPLGGPDRRLRVDFAKSG 93

>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 = 54.8 bits (131), Expect = 4e-10
 Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 7/84 (8%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             V V+ L ES  + DL +   ++GTI   ++M       K    V FEN D A + V  
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTF 70

Query: 89  LNGKKF--DDREWYVGKAQKKSER 110
                     ++ +   +  K   
Sbjct: 71  AADVPVYIAGQQAFFNYSTSKRIT 94

>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 = 54.8 bits (131), Expect = 4e-10
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           ++++ L +S+ +  L E   +FGTI    +M            V F   + A   +    
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-----QALVEFENIDSAKECVTFAA 72

Query: 194 GK--MIVSKPLYVAVAQRKEERR 214
                I  +  +   +  K   R
Sbjct: 73  DVPVYIAGQQAFFNYSTSKRITR 95

>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 = 53.3 bits (127), Expect = 7e-10
 Identities = 20/75 (26%), Positives = 25/75 (33%), Gaps = 2/75 (2%)

Query: 30  NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
            V VKNL +S     + K F   G I    V      K+  F  + F   D A  A+   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS-LKKNFRFARIEFARYDGALAAITK- 59

Query: 90  NGKKFDDREWYVGKA 104
             K     E  V   
Sbjct: 60  THKVVGQNEIIVSHL 74

>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 = 42.9 bits (100), Expect = 3e-06
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 2/72 (2%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            + +KNL  S +  K+ + F   G I    V        +    + F+  + A  A+   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-FARIEFARYDGALAAI-TK 59

Query: 193 NGKMIVSKPLYV 204
             K++    + V
Sbjct: 60  THKVVGQNEIIV 71

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.3 bits (124), Expect = 3e-09
 Identities = 17/96 (17%), Positives = 30/96 (31%), Gaps = 5/96 (5%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             +  KNL   T   ++++ F  +G++   ++             V F    +A KA   
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEARKAFRH 65

Query: 89  LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKE 124
           L   KF     Y+  A          K   +     
Sbjct: 66  LAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPA 101

>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 = 44.9 bits (105), Expect = 1e-06
 Identities = 22/102 (21%), Positives = 35/102 (34%), Gaps = 5/102 (4%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            +  KNL       +++E FS FG++    +          +  V F  P EA +A   +
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-----ITAIVEFLEPLEARKAFRHL 66

Query: 193 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPVAMGPSVP 234
                   PLY+  A       A  +      +P     S P
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESGP 108

>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 = 52.1 bits (124), Expect = 4e-09
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 29  NNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
           + + V NL+ E  T + L  +FG YG +    ++ +     K    V   + + A  A+ 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMS 58

Query: 88  ALNGKKFDDREWYVGKAQKKS 108
            LNG K   +   +  ++ ++
Sbjct: 59  HLNGHKLHGKPIRITLSKHQN 79

>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 = 50.5 bits (120), Expect = 1e-08
 Identities = 16/84 (19%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 134 LYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
           L + NL  + +  + L  LF  +G +   K++ +          V  +   +A  A++ +
Sbjct: 5   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN----ALVQMADGNQAQLAMSHL 60

Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
           NG  +  KP+ + +++ +  +  R
Sbjct: 61  NGHKLHGKPIRITLSKHQNVQLPR 84

>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 = 50.7 bits (121), Expect = 5e-09
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 8/82 (9%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           V V    +++    L + F +YG I   V+          +  + +++   A KA+   +
Sbjct: 7   VTVFGFPQASASYILLQ-FAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALS-KD 59

Query: 91  GKKFDDRE-WYVGKAQKKSERE 111
           G+ F +     V     K+  E
Sbjct: 60  GRIFGESIMIGVKPCIDKNVME 81

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.3 bits (94), Expect = 3e-05
 Identities = 10/78 (12%), Positives = 26/78 (33%), Gaps = 8/78 (10%)

Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNG 194
            +     +     L + F+++G I    +             + + +  +A +AL   +G
Sbjct: 8   TVFGFPQASASYILLQ-FAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKAL-SKDG 60

Query: 195 KMIVSKP-LYVAVAQRKE 211
           ++      + V     K 
Sbjct: 61  RIFGESIMIGVKPCIDKN 78

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 13/80 (16%), Positives = 24/80 (30%), Gaps = 2/80 (2%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           V ++ L    T+ D+   F     +    +    DG+      V F   +DA  A+   +
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMRV-HIEIGPDGRVTGEADVEFATHEDAVAAMA-KD 75

Query: 91  GKKFDDREWYVGKAQKKSER 110
                 R   +         
Sbjct: 76  KANMQHRYVELFLNSTAGTS 95

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 13/91 (14%), Positives = 31/91 (34%), Gaps = 2/91 (2%)

Query: 124 ETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPE 183
            +     G  ++++ L     +  +   FS    +    +   P G   G   V F+T E
Sbjct: 8   SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPDGRVTGEADVEFATHE 66

Query: 184 EASRALAEMNGKMIVSKPLYVAVAQRKEERR 214
           +A  A+   +   +  + + + +        
Sbjct: 67  DAVAAM-AKDKANMQHRYVELFLNSTAGTSG 96

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.1 bits (116), Expect = 3e-08
 Identities = 15/83 (18%), Positives = 36/83 (43%), Gaps = 2/83 (2%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
             V ++ L    + E++ + F     + + + +     G+S    FV F + + A KA++
Sbjct: 16  GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK 75

Query: 88  ALNGKKFDDREWYVGKAQKKSER 110
             + ++   R   + K+ +   R
Sbjct: 76  -KHKERIGHRYIEIFKSSRAEVR 97

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (106), Expect = 8e-07
 Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 2/90 (2%)

Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEA 185
           D      + ++ L      E++ + FS    + +   +     G S G  FV F++ E A
Sbjct: 11  DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70

Query: 186 SRALAEMNGKMIVSKPLYVAVAQRKEERRA 215
            +AL + + + I  + + +  + R E R +
Sbjct: 71  EKAL-KKHKERIGHRYIEIFKSSRAEVRTS 99

>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 = 47.1 bits (111), Expect = 1e-07
 Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L++ N+  S+ +E LK LFS  G +                  +   + EEA +AL ++
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA---LIQMGSVEEAVQALIDL 68

Query: 193 NGKMIV-SKPLYVAVAQ 208
           +   +  +  L V+ ++
Sbjct: 69  HNHDLGENHHLRVSFSK 85

>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 = 47.1 bits (111), Expect = 1e-07
 Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 3/68 (4%)

Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
            + + N+  S ++EDLK +F   G +   V       K +    +   + ++A +A+  
Sbjct: 11 ATLHLSNIPPSVSEEDLKVLFSSNGGV---VKGFKFFQKDRKMALIQMGSVEEAVQALID 67

Query: 89 LNGKKFDD 96
          L+     +
Sbjct: 68 LHNHDLGE 75

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

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 = 48.0 bits (113), Expect = 1e-07
 Identities = 22/99 (22%), Positives = 41/99 (41%), Gaps = 3/99 (3%)

Query: 15  RKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGF 73
           +K+ R     +  F  V++K L     ++ +   F +   +  ++ +  G  GK+   GF
Sbjct: 6   QKRSRSRSPHEAGFC-VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGF 64

Query: 74  VNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQ 112
           V F N  D   A+   + +   +R   V    KK   E+
Sbjct: 65  VEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEK 102

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

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 = 41.4 bits (96), Expect = 2e-05
 Identities = 16/87 (18%), Positives = 36/87 (41%), Gaps = 2/87 (2%)

Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRA 188
            G  +Y+K L    +++ + + F +   +     +   P+G + G GFV F    +   A
Sbjct: 17  AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 76

Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRA 215
           L   + + + ++ + V    +K     
Sbjct: 77  L-CRHKQYMGNRFIQVHPITKKGMLEK 102

>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 = 46.5 bits (109), Expect = 2e-07
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 6/78 (7%)

Query: 31  VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
           + ++ L    T++++  +  +Y      V       K K   FV   N + A  A+   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 91  GKKFDDREWYVGKAQKKS 108
             +  +RE  V      +
Sbjct: 55  QSRLRERELSVQLQPTDA 72

>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 = 43.0 bits (100), Expect = 3e-06
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           + I+ L   + ++++ +L S+       ++        KG+ FV     E+A  A+   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSD------YELKYCFVDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 194 GKMIVSKPLYVAVAQRK 210
              +  + L V +    
Sbjct: 55  QSRLRERELSVQLQPTD 71

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (106), Expect = 5e-07
 Identities = 15/83 (18%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
            L+I+ L   + + ++  L   FG +T+  +++  +       F+  +T E A   +   
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN-----QAFLELATEEAAITMVNYY 64

Query: 193 NGK--MIVSKPLYVAVAQRKEER 213
           +     + ++P+Y+  +  KE +
Sbjct: 65  SAVTPHLRNQPIYIQYSNHKELK 87

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.7 bits (102), Expect = 2e-06
 Identities = 10/81 (12%), Positives = 26/81 (32%), Gaps = 7/81 (8%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             + ++ L    T+ ++  +   +G +           K K   F+     + A   V  
Sbjct: 9   RVLHIRKLPGEVTETEVIALGLPFGKV-----TNILMLKGKNQAFLELATEEAAITMVNY 63

Query: 89  LNGKK--FDDREWYVGKAQKK 107
            +       ++  Y+  +  K
Sbjct: 64  YSAVTPHLRNQPIYIQYSNHK 84

>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 = 45.2 bits (106), Expect = 5e-07
 Identities = 18/79 (22%), Positives = 27/79 (34%), Gaps = 5/79 (6%)

Query: 29  NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
             +F+ NL E T +  L  +F ++                    FV F     +  A EA
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGF----KEVRLVPNRHDIAFVEFTTELQSNAAKEA 64

Query: 89  LNGKKFDD-REWYVGKAQK 106
           L G K        +  A+K
Sbjct: 65  LQGFKITPTHAMKITFAKK 83

>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 = 41.8 bits (97), Expect = 8e-06
 Identities = 16/77 (20%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
           L++ NL +  ++  L  LF++F      +++ +   I+    FV F+T  +++ A   + 
Sbjct: 11  LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIA----FVEFTTELQSNAAKEALQ 66

Query: 194 GKMIV-SKPLYVAVAQR 209
           G  I  +  + +  A++
Sbjct: 67  GFKITPTHAMKITFAKK 83

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.1 bits (106), Expect = 7e-07
 Identities = 15/84 (17%), Positives = 37/84 (44%), Gaps = 8/84 (9%)

Query: 134 LYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA-- 190
           ++I +         +L +L   FG I++  ++   +       F+  +T E+A  A+   
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN-----EAFIEMATTEDAQAAVDYY 65

Query: 191 EMNGKMIVSKPLYVAVAQRKEERR 214
                ++  KP+ V ++Q+ +  +
Sbjct: 66  TTTPALVFGKPVRVHLSQKYKRIK 89

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.1 bits (106), Expect = 7e-07
 Identities = 12/83 (14%), Positives = 27/83 (32%), Gaps = 8/83 (9%)

Query: 31  VFVKNLDES-TTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA- 88
           V + +          L ++   +G I++ +++           F+     +DA  AV+  
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYY 65

Query: 89  -LNGKKFDDREWYVGKAQKKSER 110
                    +   V  +QK    
Sbjct: 66  TTTPALVFGKPVRVHLSQKYKRI 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	472
d1g9la_	144	poly(A) binding protein {Human (Homo sapiens) [Tax	99.97
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1nmra_	85	poly(A) binding protein {Protozoan (Trypanosoma cr	99.96
d1ifwa_	92	poly(A) binding protein {Baker's yeast (Saccharomy	99.95
d1i2ta_	61	hyperplastic discs protein {Human (Homo sapiens) [	99.95
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.8
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.8
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.8
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.8
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.8
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.79
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.78
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.78
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.78
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.78
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.78
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.77
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.77
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.77
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.76
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.76
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.76
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.76
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.76
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.75
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.75
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.75
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.74
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.74
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.74
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.74
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.74
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.74
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.73
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.73
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.73
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.73
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.73
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.73
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.72
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.72
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.72
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.72
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.71
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.71
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.71
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.71
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.71
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.71
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.71
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.7
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.7
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.7
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.7
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.69
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.69
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.69
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.69
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.69
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.69
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.68
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.68
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.68
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.68
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.68
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.68
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.68
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.68
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.68
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.68
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.67
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.67
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.67
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.67
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.67
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.67
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.66
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.66
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.66
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.66
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.66
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.65
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.65
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.65
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.65
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.65
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.65
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.64
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.64
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.64
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.63
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.63
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.63
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.63
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.63
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.62
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.62
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.62
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.61
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.61
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.61
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.61
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.61
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.6
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.6
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.59
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	99.59
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.59
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.59
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.58
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.58
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.57
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.57
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.56
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.56
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.56
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.56
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.56
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.55
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.55
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	99.55
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.54
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.54
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.52
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.51
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.49
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.49
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.49
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.46
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.41
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.36
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.36
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.36
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.34
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.3
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.24
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.23
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.23
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.65
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.28
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.05
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.87
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.79
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.48
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.03
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	89.02

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.8e-32  Score=230.78  Aligned_cols=86  Identities=42%  Similarity=0.699  Sum_probs=80.7

Q ss_pred             CCCccccchhhhhcCCHHHHHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHHH
Q 012034          371 QPMPITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVA  450 (472)
Q Consensus       371 ~~~~~~~~~~~la~~~~~~q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~~  450 (472)
                      .+.+.++++++||++++++||++|||+|||+|++++|++|+||||||||||++|||+||+|+++|++||+||++||++|+
T Consensus        47 ~~~q~pltas~la~a~p~eQkq~LGE~Lyp~I~~~~p~~A~KITGMLLEmd~~ell~lL~~~~~L~~kV~EA~~vL~~~~  126 (144)
T d1g9la_          47 VQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQ  126 (144)
T ss_dssp             CCSCCCCSHHHHTTCTTTTTTTTTTSSSHHHHHHHTTSCCSSHHHHTTTSSSHHHHHHHHCTTHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCcccHHHHhhCCHHHHHHHHHHHHHHHHHHhChhhccchhhhhhcCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHh
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcCC
Q 012034          451 QQQANN  456 (472)
Q Consensus       451 ~~~~~~  456 (472)
                      .+++.+
T Consensus       127 ~~~~~~  132 (144)
T d1g9la_         127 AKEAAQ  132 (144)
T ss_dssp             SSTTCC
T ss_pred             ccHHHH
Confidence            877554

>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=99.97  E-value=2.3e-30  Score=234.62  Aligned_cols=173  Identities=25%  Similarity=0.462  Sum_probs=150.9

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .++|||+|||+++|+++|+++|++||.|.++.++.+ .++.++|||||+|.+.++|.+|++. ++..+.++.+.+.+...
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhh
Confidence            478999999999999999999999999999999998 5899999999999999999999974 67778888888877654


Q ss_pred             chhHHHHHHHHHHhhhhhhccccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHH
Q 012034          107 KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA  185 (472)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A  185 (472)
                      +....            .........+|||+|||..+|+++|+++|+.||.|..+.|..+. +|.++|||||+|.+.++|
T Consensus        85 ~~~~~------------~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A  152 (183)
T d1u1qa_          85 REDSQ------------RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV  152 (183)
T ss_dssp             TTGGG------------STTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHH
T ss_pred             ccccc------------ccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHH
Confidence            43211            11122344689999999999999999999999999999999875 588999999999999999


Q ss_pred             HHHHHHhCCcEecCeeEEEEEcccHHHHH
Q 012034          186 SRALAEMNGKMIVSKPLYVAVAQRKEERR  214 (472)
Q Consensus       186 ~~Ai~~l~g~~i~gk~l~V~~a~~k~~~~  214 (472)
                      .+|++ +++..++|+.|.|.+|..|+++.
T Consensus       153 ~~Al~-~~~~~~~G~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         153 DKIVI-QKYHTVNGHNCEVRKALSKQEMA  180 (183)
T ss_dssp             HHHHT-SSCEEETTEEEEEEECCCHHHHH
T ss_pred             HHHHH-hCCCeECCEEEEEEecCCccccc
Confidence            99996 78899999999999999887664

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Protozoan (Trypanosoma cruzi) [TaxId: 5693]

Probab=99.96  E-value=5e-31  Score=201.48  Aligned_cols=75  Identities=56%  Similarity=0.776  Sum_probs=72.6

Q ss_pred             ccchhhhhcCCHHHHHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHHH
Q 012034          376 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVA  450 (472)
Q Consensus       376 ~~~~~~la~~~~~~q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~~  450 (472)
                      ..++++|++++|++||++|||+|||+|++++|++|+||||||||||++||++||+|++.|++||+||++||++|+
T Consensus         9 ~~~a~~la~~~p~eqK~~LGE~Lyp~V~~~~p~~AgKITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~h~   83 (85)
T d1nmra_           9 QNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDAKVQEALEVLNRHM   83 (85)
T ss_dssp             CTTHHHHTTCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHCSCTHHHHHHTTCCTHHHHHHHHHHHHHHTTCCC
T ss_pred             hHHHHHHhhCCHHHHHHHHHHHHHHHHHHHCcccccchhHHhhCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHhc
Confidence            358999999999999999999999999999999999999999999999999999999999999999999999875

>d1ifwa_ a.144.1.1 (A:) poly(A) binding protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.95  E-value=3.7e-29  Score=194.28  Aligned_cols=80  Identities=33%  Similarity=0.439  Sum_probs=74.5

Q ss_pred             cchhhhhcCCHHHHHHHhhhhhhhhHhhc--CCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHHHHhhc
Q 012034          377 ALSTALANASPEQQRTLLGESLYPLVEQL--ERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSVAQQQA  454 (472)
Q Consensus       377 ~~~~~la~~~~~~q~~~~g~~l~~~v~~~--~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~~~~~~  454 (472)
                      .+++.++.+++++||++|||+|||+|+++  +|++|+||||||||||++||++||+|++.|++||+||++||++|+++++
T Consensus         7 ~~~~~~~~~~~~~qk~~LGe~Lyp~V~~~~~~pe~A~KITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~~~~~~~   86 (92)
T d1ifwa_           7 RNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKEQE   86 (92)
T ss_dssp             SCCSSCCSCSCHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHTTSCHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHSCT
T ss_pred             CChHHHhhcCHHHHHHHHHHHHHHHHHHhccCccccccchhhhcCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHhccc
Confidence            46777888999999999999999999998  5899999999999999999999999999999999999999999998765


Q ss_pred             CC
Q 012034          455 NN  456 (472)
Q Consensus       455 ~~  456 (472)
                      +.
T Consensus        87 ~~   88 (92)
T d1ifwa_          87 QQ   88 (92)
T ss_dssp             TS
T ss_pred             cc
Confidence            53

>d1i2ta_ a.144.1.1 (A:) hyperplastic discs protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: hyperplastic discs protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=8.8e-29  Score=177.15  Aligned_cols=60  Identities=45%  Similarity=0.720  Sum_probs=59.2

Q ss_pred             HHHHhhhhhhhhHhhcCCccchhhhHhhcCCChHHHHHhhCChHHHHHHHHHHHHHHHHH
Q 012034          390 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVLRSV  449 (472)
Q Consensus       390 q~~~~g~~l~~~v~~~~~~~a~kitgmll~~~~~e~~~~~~~~~~l~~~v~~a~~~l~~~  449 (472)
                      ||++|||+|||+|++++|++|+||||||||||++||++||+|++.|++||+||++||++|
T Consensus         1 qk~~LGE~Ly~~V~~~~p~~A~KITGMLLEm~~~ell~lL~~~~~L~~kV~EA~~vL~~h   60 (61)
T d1i2ta_           1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH   60 (61)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGHHHHHHHHTTSCHHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHhHHHHHHHChhhhcchhHHHhcCCHHHHHHHHCCHHHHHHHHHHHHHHHHHc
Confidence            799999999999999999999999999999999999999999999999999999999987

>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=99.82  E-value=1.2e-20  Score=147.37  Aligned_cols=79  Identities=30%  Similarity=0.503  Sum_probs=75.5

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .++|||+|||.++|+++|+++|++||.|.++.+.+| .+|+++|||||+|++.++|++|++.|||..+.|+.|.|.+|++
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            578999999999999999999999999999999987 5799999999999999999999999999999999999999864

>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=3e-20  Score=144.96  Aligned_cols=79  Identities=34%  Similarity=0.585  Sum_probs=75.3

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .++|||+|||.++|+++|+++|++||.|.++.+++| .+|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.+|++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            468999999999999999999999999999999998 5789999999999999999999999999999999999999864

>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=99.81  E-value=4.1e-20  Score=146.16  Aligned_cols=82  Identities=27%  Similarity=0.382  Sum_probs=77.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||+|.+|.+++| .+|+++|||||+|++.++|++|++.|||..+.|+.|.|.||
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45678999999999999999999999999999999998 57999999999999999999999999999999999999999


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ..+
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            764

>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=99.81  E-value=6.8e-20  Score=143.96  Aligned_cols=79  Identities=33%  Similarity=0.562  Sum_probs=74.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC--cceeee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDD--REWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g--~~l~V~  102 (472)
                      .+.++|||+|||+++|+++|+++|++||.|.++++++| .+|++||||||+|.+.++|.+|++.||+..+.|  +.|.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            46788999999999999999999999999999999998 579999999999999999999999999999987  789999


Q ss_pred             cc
Q 012034          103 KA  104 (472)
Q Consensus       103 ~a  104 (472)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.81  E-value=7.5e-20  Score=143.68  Aligned_cols=79  Identities=29%  Similarity=0.523  Sum_probs=73.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCc--ceeee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDR--EWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~--~l~V~  102 (472)
                      .+.++|||+|||.++|+++|+++|++||+|.++.++.| .+|+++|||||+|.++++|.+|++.|||..+.|+  +|.|.
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            45688999999999999999999999999999999998 4799999999999999999999999999999984  58888


Q ss_pred             cc
Q 012034          103 KA  104 (472)
Q Consensus       103 ~a  104 (472)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            76

>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=99.80  E-value=4.1e-20  Score=146.82  Aligned_cols=83  Identities=30%  Similarity=0.531  Sum_probs=78.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++.+..| .+|++||||||+|.+.++|.+|++.|||..++|+.|.|.||
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            45688999999999999999999999999999999998 47999999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      .+++
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8654

>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=3.7e-20  Score=142.98  Aligned_cols=76  Identities=34%  Similarity=0.521  Sum_probs=74.0

Q ss_pred             eEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        30 ~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      +|||+|||+++|+++|+++|++||.|.++.+..|.+|+++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            5999999999999999999999999999999999999999999999999999999999999999999999999875

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=5e-20  Score=142.99  Aligned_cols=77  Identities=26%  Similarity=0.380  Sum_probs=73.9

Q ss_pred             eEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        30 ~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      +|||+|||.++|+++|+++|++||+|.+++|++| .+|+++|||||+|.+.++|.+|++.|||..+.|+.|.|.+++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            5999999999999999999999999999999998 4699999999999999999999999999999999999999864

>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=99.80  E-value=1.1e-20  Score=149.79  Aligned_cols=83  Identities=31%  Similarity=0.399  Sum_probs=77.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|++||+|.+|.+++|. +|+++|||||+|.+.++|.+|++.||+..|+|+.|.|.+|
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            456789999999999999999999999999999999984 6999999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      .++.
T Consensus        83 ~p~~   86 (89)
T d2cqba1          83 KPMR   86 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=99.80  E-value=9.7e-20  Score=145.54  Aligned_cols=82  Identities=27%  Similarity=0.354  Sum_probs=77.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +..++|||+|||.++|+++|+++|++||+|.+|.++.| .+|+++|||||+|.+.++|..|++.||+..++|+.|.|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            46789999999999999999999999999999999998 57899999999999999999999999999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.80  E-value=4.8e-20  Score=147.32  Aligned_cols=83  Identities=25%  Similarity=0.404  Sum_probs=77.9

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++.|++| .+|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.+|
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            34678999999999999999999999999999999998 57999999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            7654

>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=99.80  E-value=6.4e-20  Score=149.20  Aligned_cols=83  Identities=31%  Similarity=0.542  Sum_probs=78.3

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||+++|+++|+++|++||.|.++.++.+ .+|++||||||+|.+.++|.+|++.|||..|.|+.|+|.++.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            4578999999999999999999999999999999998 579999999999999999999999999999999999999998


Q ss_pred             cchh
Q 012034          106 KKSE  109 (472)
Q Consensus       106 ~~~~  109 (472)
                      ++.+
T Consensus        97 ~k~~  100 (102)
T d2cpza1          97 SKND  100 (102)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7754

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=4.2e-20  Score=145.13  Aligned_cols=80  Identities=21%  Similarity=0.498  Sum_probs=75.8

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKK  107 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~  107 (472)
                      .+|||+|||+++|+++|+++|++||+|.++.|++| .+|+++|||||+|.++++|..|++.||+..|.|+.|.|.+|...
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            46999999999999999999999999999999998 57999999999999999999999999999999999999999764


Q ss_pred             h
Q 012034          108 S  108 (472)
Q Consensus       108 ~  108 (472)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.79  E-value=8.8e-20  Score=146.08  Aligned_cols=83  Identities=23%  Similarity=0.491  Sum_probs=77.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC--CCCCceeEEEEEeCCHHHHHHHHHHH-CCCccCCcceeee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENADDAAKAVEAL-NGKKFDDREWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d--~~g~skG~aFV~F~~~e~A~~Av~~l-ng~~i~g~~l~V~  102 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.|+.|  .+|+++|||||+|.+.++|.+|++.| |+..|.|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            45788999999999999999999999999999999887  47899999999999999999999998 8999999999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      ||..+.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            997654

>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=99.79  E-value=1.5e-19  Score=147.55  Aligned_cols=84  Identities=33%  Similarity=0.604  Sum_probs=78.1

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||.++|+++|+++|++||+|.+|.++.+ .+|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            3568999999999999999999999999999999998 579999999999999999999999999999999999999987


Q ss_pred             cchhH
Q 012034          106 KKSER  110 (472)
Q Consensus       106 ~~~~~  110 (472)
                      .+..+
T Consensus        87 ~~~~~   91 (104)
T d1p1ta_          87 SEKNK   91 (104)
T ss_dssp             CTTHH
T ss_pred             CCCCc
Confidence            66543

>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=99.78  E-value=1.3e-19  Score=146.63  Aligned_cols=84  Identities=31%  Similarity=0.463  Sum_probs=78.7

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||+++|+++|+++|++||.|.+|.++.| .+|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            355778999999999999999999999999999999988 5799999999999999999999999999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        85 a~~~~   89 (99)
T d1whwa_          85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98754

>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=99.78  E-value=1.3e-19  Score=143.90  Aligned_cols=84  Identities=40%  Similarity=0.680  Sum_probs=78.0

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +..++|||+|||+++|+++|+++|++||.|..+.++.+ .+|+++|||||+|.++++|++|++.||+..|.|+.|.|.++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            45678999999999999999999999999999998887 57999999999999999999999999999999999999999


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      .++.+
T Consensus        83 ~~~~~   87 (90)
T d1x5sa1          83 GKSSD   87 (90)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            76643

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.4e-19  Score=140.09  Aligned_cols=76  Identities=37%  Similarity=0.529  Sum_probs=72.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceee
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYV  101 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V  101 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.|++| .+|+++|||||+|.+.++|.+|++.||+..|+|+.|.|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            45678999999999999999999999999999999998 46999999999999999999999999999999999987

>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=99.78  E-value=2.3e-19  Score=142.28  Aligned_cols=81  Identities=30%  Similarity=0.436  Sum_probs=74.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|++| .+|++||||||+|.+.++|.+|++.  .+.|+|+.|.|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            46788999999999999999999999999999999999 4799999999999999999999984  55899999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            7754

>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=99.78  E-value=5.4e-20  Score=145.81  Aligned_cols=83  Identities=37%  Similarity=0.689  Sum_probs=76.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...+||||+|||.++|+++|+++|++||.|.++.|+.+.+ .++|||||+|++.++|.+|++.|||..|+|+.|.|.++.
T Consensus         6 s~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           6 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            3567899999999999999999999999999999999864 478999999999999999999999999999999999998


Q ss_pred             cchh
Q 012034          106 KKSE  109 (472)
Q Consensus       106 ~~~~  109 (472)
                      ++.+
T Consensus        85 ~~~~   88 (89)
T d1cvja2          85 SRKE   88 (89)
T ss_dssp             CTTT
T ss_pred             CCCC
Confidence            7654

>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=99.78  E-value=3.9e-19  Score=139.13  Aligned_cols=78  Identities=33%  Similarity=0.565  Sum_probs=73.3

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||+++|+++|+++|++||+|.++.|++| .+|+++|||||+|.+.++|.+|++ ++++.|.|+.|.|.+|.
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            4578999999999999999999999999999999999 469999999999999999999997 69999999999999874

>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=99.78  E-value=1.7e-19  Score=155.25  Aligned_cols=83  Identities=25%  Similarity=0.483  Sum_probs=77.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|++||+|.+|.|+.| .+|++||||||+|.+.++|.+||+.||+..|+|+.|.|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34578999999999999999999999999999999998 57999999999999999999999999999999999999998


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      ..+.
T Consensus       120 ~~~~  123 (139)
T d1u6fa1         120 ASGH  123 (139)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7654

>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=99.78  E-value=4.5e-19  Score=141.61  Aligned_cols=83  Identities=35%  Similarity=0.578  Sum_probs=77.1

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ....++|||+|||.++|+++|+++|++||+|.+|.++.|..+ ++|||||+|.+.++|.+|++.||+..|.|+.|.|.+|
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            456788999999999999999999999999999999998654 6999999999999999999999999999999999999


Q ss_pred             ccch
Q 012034          105 QKKS  108 (472)
Q Consensus       105 ~~~~  108 (472)
                      .++.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            8764

>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=99.77  E-value=1.7e-19  Score=140.28  Aligned_cols=79  Identities=16%  Similarity=0.320  Sum_probs=68.6

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .++|||+|||+++|+++|+++|++||.|..+.++.+ .+|+++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.+
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            368999999999999999999999999988877666 6789999999999999999999999999999999999998864

>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=99.77  E-value=4.2e-19  Score=144.05  Aligned_cols=82  Identities=21%  Similarity=0.443  Sum_probs=77.0

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +...++|||+|||.++|+++|+++|++||.|.++.+..+.+++++|||||+|.+.++|.+|++.|||..|.|+.+.|.++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999877


Q ss_pred             cc
Q 012034          105 QK  106 (472)
Q Consensus       105 ~~  106 (472)
                      .+
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>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=99.77  E-value=1.9e-19  Score=146.60  Aligned_cols=82  Identities=37%  Similarity=0.531  Sum_probs=75.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      +...++|||+|||+++|+++|+++|++||.|.+|.|+.| .+|+++|||||+|.+.++|.+|++.+|+ .|.|+.|.|.+
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEE
Confidence            456788999999999999999999999999999999998 4699999999999999999999998875 79999999999


Q ss_pred             cccc
Q 012034          104 AQKK  107 (472)
Q Consensus       104 a~~~  107 (472)
                      +..+
T Consensus        86 a~~~   89 (103)
T d2cqda1          86 AYLG   89 (103)
T ss_dssp             STTT
T ss_pred             cCCC
Confidence            8654

>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=99.77  E-value=1.1e-19  Score=139.88  Aligned_cols=75  Identities=29%  Similarity=0.530  Sum_probs=71.2

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ++|||+|||+++|+++|+++|++||.|.++.|..|+ +|++||||||+|.+.++|.+|++ ++++.++|+.|.|.+|
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            579999999999999999999999999999999985 69999999999999999999997 7999999999999876

>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=99.77  E-value=2.7e-19  Score=136.93  Aligned_cols=74  Identities=27%  Similarity=0.508  Sum_probs=70.1

Q ss_pred             eEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        30 ~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +|||+|||+++||++|+++|++||+|.++.+..| .+|+++|||||+|.+.++|++|++ +++..|.|+.|.|.+|
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            4999999999999999999999999999999998 579999999999999999999997 7999999999999875

>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=99.77  E-value=4.2e-19  Score=139.33  Aligned_cols=77  Identities=34%  Similarity=0.567  Sum_probs=71.6

Q ss_pred             EEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCC----CCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD----GKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        31 l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~----g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      |||+|||+++|+++|+++|++||.|.++.|..+.+    +++||||||+|++.++|.+|++.||+..++|+.|.|.++..
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            79999999999999999999999999999998742    25799999999999999999999999999999999999865


Q ss_pred             c
Q 012034          107 K  107 (472)
Q Consensus       107 ~  107 (472)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
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=99.77  E-value=6.1e-19  Score=137.42  Aligned_cols=79  Identities=34%  Similarity=0.594  Sum_probs=74.9

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      +++|||+|||.++|+++|+++|++||.|.+++|.+++ +|.++|||||+|.+.++|.+|++.|||..+.|++|+|.|+++
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            4689999999999999999999999999999998874 789999999999999999999999999999999999999864

>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=99.76  E-value=2.2e-19  Score=145.60  Aligned_cols=80  Identities=21%  Similarity=0.366  Sum_probs=74.7

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||.++|+++|+++|+.||+|.+|.|++| .+|++||||||+|.+.++|.+|++ |||..|.|+.|.|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            3578999999999999999999999999999999998 579999999999999999999995 99999999999999885


Q ss_pred             cc
Q 012034          106 KK  107 (472)
Q Consensus       106 ~~  107 (472)
                      .+
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            44

>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=99.76  E-value=5.6e-19  Score=140.19  Aligned_cols=82  Identities=27%  Similarity=0.389  Sum_probs=75.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|+.||.|.+|.+..|..+ .+|||||+|++.++|.+|++.||+..|.|+.|.|.||.
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999998544 38999999999999999999999999999999999997


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      +..
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>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=99.76  E-value=1.8e-19  Score=140.83  Aligned_cols=78  Identities=36%  Similarity=0.590  Sum_probs=72.2

Q ss_pred             EEeCCCCCCCCHHHHHHHHhcCCCeeEE-EEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccch
Q 012034           31 VFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  108 (472)
Q Consensus        31 l~V~nLp~~~tee~L~~~F~~fG~I~~v-~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~  108 (472)
                      |||+|||.++|+++|+++|++||.|.++ .+++| .+|+++|||||+|.+.++|++|++.||+..+.|+.|.|.++.++.
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 67777 579999999999999999999999999999999999999997654

>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=99.76  E-value=1.2e-18  Score=134.42  Aligned_cols=76  Identities=32%  Similarity=0.537  Sum_probs=74.0

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .|||+|||+++|+++|+++|++||.|.+++|..+++|+++|||||+|.+.++|.+|++.+||..++|++|+|+++.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            4999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.76  E-value=1.3e-18  Score=137.41  Aligned_cols=81  Identities=25%  Similarity=0.477  Sum_probs=76.2

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+++|||+||+.++|+++|+++|+.||.|.+|++.+++ +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|+|+.
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            46789999999999999999999999999999999875 78999999999999999999999999999999999999997


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            64

>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=99.76  E-value=2e-18  Score=134.39  Aligned_cols=78  Identities=35%  Similarity=0.654  Sum_probs=74.2

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ++|||+|||.++++++|+++|++||.|.+|+++++. +|.++|||||+|.+.++|.+|++.|||..+.|++|+|.|+++
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            579999999999999999999999999999999875 678999999999999999999999999999999999999864

>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=99.75  E-value=1.7e-18  Score=133.91  Aligned_cols=76  Identities=32%  Similarity=0.563  Sum_probs=71.7

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      .++|||+|||+++|+++|+++|++||.|.++.+..| .+++++|||||+|.+.|+|.+|++ ++++.|+|+.|.|.+|
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            478999999999999999999999999999999998 578999999999999999999995 8999999999999876

>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=99.75  E-value=1e-18  Score=144.94  Aligned_cols=79  Identities=25%  Similarity=0.342  Sum_probs=73.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|.+..+  ++++|||||+|.+.++|..|++.|||+.|.|+.|.|.++.
T Consensus         5 ~~~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           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34678999999999999999999999999999998764  5679999999999999999999999999999999999986


Q ss_pred             c
Q 012034          106 K  106 (472)
Q Consensus       106 ~  106 (472)
                      .
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.6e-18  Score=134.36  Aligned_cols=77  Identities=38%  Similarity=0.543  Sum_probs=73.9

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      +|||+|||.++|+++|+++|++||.|.+++|++++ +|+++|||||+|.+.++|.+|++.|||..+.|++|+|.|+++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            69999999999999999999999999999999986 589999999999999999999999999999999999999864

>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=99.75  E-value=6.1e-19  Score=143.40  Aligned_cols=81  Identities=31%  Similarity=0.551  Sum_probs=75.5

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .++|||+|||+++|+++|+++|++||+|.++.|.+| .++.++|||||+|.+.++|.+|++ ++++.|.|+.|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            578999999999999999999999999999999998 468899999999999999999996 799999999999999987


Q ss_pred             chh
Q 012034          107 KSE  109 (472)
Q Consensus       107 ~~~  109 (472)
                      +.+
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            643

>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=99.75  E-value=2.1e-18  Score=135.27  Aligned_cols=78  Identities=23%  Similarity=0.323  Sum_probs=73.9

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ..++|||+|||.++|+++|+++|+.||.|.+|.+..+.+|++||||||+|.+.++|.+|++ +++..+.|+.|.|.++.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4678999999999999999999999999999999999999999999999999999999996 79999999999999864

>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=99.74  E-value=2.6e-18  Score=134.68  Aligned_cols=79  Identities=32%  Similarity=0.667  Sum_probs=73.3

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecC--eeEEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVS--KPLYVA  205 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g--k~l~V~  205 (472)
                      ..+++|||+|||.++|+++|+++|++||.|.+++|++++ +|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|+
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            346789999999999999999999999999999999985 68999999999999999999999999999987  569998


Q ss_pred             Ec
Q 012034          206 VA  207 (472)
Q Consensus       206 ~a  207 (472)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=9.8e-20  Score=144.84  Aligned_cols=81  Identities=31%  Similarity=0.430  Sum_probs=75.9

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||+++|+++|+++|++||.|.++.|+.+.+|++||||||+|.+.++|.+||+ ||+..|.|+.|.|.++.
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            45678999999999999999999999999999999888899999999999999999999996 99999999999999987


Q ss_pred             cc
Q 012034          106 KK  107 (472)
Q Consensus       106 ~~  107 (472)
                      .+
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
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=99.74  E-value=9e-19  Score=142.30  Aligned_cols=84  Identities=36%  Similarity=0.561  Sum_probs=78.1

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..+++|||+|||+++++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|..|++.|||..|.|+.|+|.|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            346789999999999999999999999999999998874 7899999999999999999999999999999999999999


Q ss_pred             ccHHH
Q 012034          208 QRKEE  212 (472)
Q Consensus       208 ~~k~~  212 (472)
                      ..+.+
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87753

>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=99.74  E-value=2.2e-18  Score=136.43  Aligned_cols=80  Identities=29%  Similarity=0.473  Sum_probs=75.7

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..+|||+|||+++|+++|+++|+.||.|.+|+|+.++ +|.++|||||+|.+.++|.+|++.+||..++|++|.|.++++
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            3589999999999999999999999999999999886 589999999999999999999999999999999999999976


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        85 ~   85 (89)
T d2cqba1          85 M   85 (89)
T ss_dssp             C
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=99.74  E-value=6.9e-19  Score=138.40  Aligned_cols=80  Identities=26%  Similarity=0.456  Sum_probs=70.5

Q ss_pred             CcceEEeCCCCCCCC-HHHHHHHHhcCCCeeEEEEEEC--CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           27 KFNNVFVKNLDESTT-DEDLKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        27 ~~~~l~V~nLp~~~t-ee~L~~~F~~fG~I~~v~i~~d--~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ..++|||+|||.++| +++|+++|++||.|.+|.|..+  .+++++|||||+|.+.++|.+|++ ||++.+.|+.|.|.+
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            467899999999986 5569999999999999998765  478999999999999999999996 999999999999999


Q ss_pred             cccc
Q 012034          104 AQKK  107 (472)
Q Consensus       104 a~~~  107 (472)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8765

>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=99.74  E-value=3.3e-18  Score=134.11  Aligned_cols=79  Identities=33%  Similarity=0.653  Sum_probs=73.7

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecC--eeEEEE
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVS--KPLYVA  205 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g--k~l~V~  205 (472)
                      ..+++|||+|||.++|+++|+++|++||.|.++++++++ +|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            345789999999999999999999999999999999875 78999999999999999999999999999976  889999


Q ss_pred             Ec
Q 012034          206 VA  207 (472)
Q Consensus       206 ~a  207 (472)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.74  E-value=4.7e-18  Score=135.55  Aligned_cols=81  Identities=23%  Similarity=0.300  Sum_probs=76.0

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+++|||+|||.++|+++|+++|+.||.|.+|.++.+. ++.++|||||+|.+.++|..|++.|||..++|++|+|.|+.
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            45789999999999999999999999999999999875 68899999999999999999999999999999999999986


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      ..
T Consensus        86 ~~   87 (93)
T d1h2vz_          86 GF   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.74  E-value=2.3e-18  Score=138.73  Aligned_cols=83  Identities=27%  Similarity=0.420  Sum_probs=75.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHC------CCccCCcc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALN------GKKFDDRE   98 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~ln------g~~i~g~~   98 (472)
                      ...++|||+|||+++|+++|+++|++||.|.++.++.+ .+++++|||||+|.+.++|.+|++.||      |..+.|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            45678999999999999999999999999999999888 478899999999999999999999987      56689999


Q ss_pred             eeeeccccch
Q 012034           99 WYVGKAQKKS  108 (472)
Q Consensus        99 l~V~~a~~~~  108 (472)
                      |.|.++..+.
T Consensus        86 l~v~~a~~k~   95 (98)
T d1x4ha1          86 LKVDLAVTRD   95 (98)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999998764

>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=99.73  E-value=7.6e-19  Score=134.24  Aligned_cols=74  Identities=23%  Similarity=0.416  Sum_probs=69.2

Q ss_pred             eEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        30 ~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +|||+|||+++|+++|+++|++||.|.+|.|+.| .++++||||||+|++.++|.+|++ .+++.|+|+.|.|..|
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            5999999999999999999999999999999998 579999999999999999999997 4788999999999865

>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=99.73  E-value=3.5e-18  Score=135.49  Aligned_cols=81  Identities=31%  Similarity=0.484  Sum_probs=76.4

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||.++|+++|+++|+.||.|.+++|+.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|+|++
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            34689999999999999999999999999999999985 68899999999999999999999999999999999999998


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      ++
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.73  E-value=3.1e-18  Score=136.62  Aligned_cols=82  Identities=28%  Similarity=0.474  Sum_probs=77.0

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||.++|+++|+++|++||.|.+++|++++ +|.++|||||+|.+.++|.+|++.|||..++|+.|+|.+|.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            44689999999999999999999999999999999885 78999999999999999999999999999999999999997


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .+.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            653

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=1.7e-18  Score=132.34  Aligned_cols=74  Identities=32%  Similarity=0.539  Sum_probs=70.1

Q ss_pred             eEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        30 ~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~-~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      +|||+|||.++||++|+++|++||.|.++.+..+. +++++|||||+|.+.++|.+|++ +|++.|+|+.|.|.+|
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            49999999999999999999999999999998884 68999999999999999999996 9999999999999876

>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=99.73  E-value=1.4e-18  Score=137.51  Aligned_cols=81  Identities=44%  Similarity=0.703  Sum_probs=75.2

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ..+|||+|||.++|+++|+++|+.||.|.+++|+.+.. .++|||||+|.+.++|.+|++.|||..++|+.|.|.+++.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            34799999999999999999999999999999998854 47999999999999999999999999999999999999877


Q ss_pred             HH
Q 012034          211 EE  212 (472)
Q Consensus       211 ~~  212 (472)
                      .+
T Consensus        87 ~~   88 (89)
T d1cvja2          87 KE   88 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.73  E-value=4.3e-18  Score=136.06  Aligned_cols=81  Identities=22%  Similarity=0.488  Sum_probs=75.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC--CCCcccEEEEEcCCHHHHHHHHHHh-CCcEecCeeEEEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEM-NGKMIVSKPLYVAV  206 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~--~g~s~g~afV~f~s~~~A~~Ai~~l-~g~~i~gk~l~V~~  206 (472)
                      ..++|||+|||.++++++|+++|+.||.|.+|+|+++.  +|.++|||||+|.+.++|.+|++.| ||..++|++|.|.|
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            45689999999999999999999999999999998874  6899999999999999999999998 89999999999999


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      |..+
T Consensus        87 A~~~   90 (94)
T d2cpha1          87 ADSE   90 (94)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9865

>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=99.73  E-value=4.2e-18  Score=136.65  Aligned_cols=77  Identities=22%  Similarity=0.389  Sum_probs=72.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|.+|++..|     ||||||+|.+.++|.+|++.||+..|.|+.|+|.|++
T Consensus        16 ~~~~~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          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45678999999999999999999999999999999976     7999999999999999999999999999999999987


Q ss_pred             cc
Q 012034          106 KK  107 (472)
Q Consensus       106 ~~  107 (472)
                      .+
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.73  E-value=5.1e-18  Score=131.74  Aligned_cols=78  Identities=15%  Similarity=0.303  Sum_probs=68.4

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC-CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~-~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ++|||+|||+++|+++|+++|+.||.|..+.++.+ ..|.++|||||+|.+.++|.+|++.|||..++|++|+|+++++
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            68999999999999999999999999988877655 4788999999999999999999999999999999999999864

>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=99.72  E-value=4.1e-18  Score=133.85  Aligned_cols=77  Identities=27%  Similarity=0.454  Sum_probs=71.9

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      ..++|||+|||.++++++|+++|++||+|.+|.+.++     +|||||+|++.++|.+|++.|||..|.|+.|.|.+|..
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            3567999999999999999999999999999999865     78999999999999999999999999999999999976


Q ss_pred             ch
Q 012034          107 KS  108 (472)
Q Consensus       107 ~~  108 (472)
                      +.
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            54

>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=99.72  E-value=1.3e-17  Score=132.93  Aligned_cols=81  Identities=27%  Similarity=0.501  Sum_probs=75.4

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...++|||+|||.++++++|+++|+.||.|.+|+++.+..+ ++|||||+|.+.++|.+|+..|||..++|+.|+|.+|.
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            34568999999999999999999999999999999988654 79999999999999999999999999999999999998


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        88 ~r   89 (93)
T d2cq3a1          88 AR   89 (93)
T ss_dssp             SS
T ss_pred             cC
Confidence            75

>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=99.72  E-value=9.7e-18  Score=135.34  Aligned_cols=81  Identities=31%  Similarity=0.501  Sum_probs=76.3

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .++|||+||++++|+++|+++|++||.|.+++|+.+. ++.++|||||+|.+.++|.+|++.||+..|+|+.|+|.++..
T Consensus         8 ~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~   87 (99)
T d1whwa_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTI   87 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCC
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4579999999999999999999999999999999875 789999999999999999999999999999999999999887


Q ss_pred             HH
Q 012034          210 KE  211 (472)
Q Consensus       210 k~  211 (472)
                      +.
T Consensus        88 ~~   89 (99)
T d1whwa_          88 KK   89 (99)
T ss_dssp             CS
T ss_pred             CC
Confidence            53

>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=99.72  E-value=1.2e-17  Score=130.17  Aligned_cols=75  Identities=27%  Similarity=0.399  Sum_probs=71.0

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  204 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V  204 (472)
                      .+++|||+||+.++|+++|+++|++||.|.+|+|+.++ +|.++|||||+|.+.++|.+|++.|||..|+|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            35689999999999999999999999999999999885 5889999999999999999999999999999999987

>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=99.72  E-value=5.2e-18  Score=137.47  Aligned_cols=84  Identities=30%  Similarity=0.451  Sum_probs=75.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCee--------EEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccC
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTIT--------SAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFD   95 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~--------~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~   95 (472)
                      ....++|||+|||.++|+++|+++|+.||.|.        .+.+..| .+|+++|||||+|.++++|.+|++.|||..|.
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            35678999999999999999999999999884        4555565 46899999999999999999999999999999


Q ss_pred             Ccceeeeccccch
Q 012034           96 DREWYVGKAQKKS  108 (472)
Q Consensus        96 g~~l~V~~a~~~~  108 (472)
                      |+.|.|.++..+.
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999997654

>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=99.71  E-value=2e-18  Score=133.81  Aligned_cols=76  Identities=25%  Similarity=0.466  Sum_probs=69.4

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCC-ccCCcceeeeccccc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK-KFDDREWYVGKAQKK  107 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~-~i~g~~l~V~~a~~~  107 (472)
                      ++|||+|||.++|+++|+++|++||.|.++.+..+     ||||||+|.+.++|.+|++.|||. .+.|+.|.|.++..+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            57999999999999999999999999988777654     799999999999999999999996 599999999999876


Q ss_pred             hh
Q 012034          108 SE  109 (472)
Q Consensus       108 ~~  109 (472)
                      ..
T Consensus        77 ~~   78 (80)
T d2cqha1          77 KL   78 (80)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>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=99.71  E-value=1.2e-18  Score=141.62  Aligned_cols=84  Identities=20%  Similarity=0.322  Sum_probs=78.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|+.||.|.++.++.+ .+|+++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45789999999999999999999999999999998887 57899999999999999999999999999999999999999


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      ..+.+
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87654

>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=99.71  E-value=6.4e-18  Score=132.44  Aligned_cols=78  Identities=29%  Similarity=0.563  Sum_probs=74.3

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .|||+|||+++|+++|+++|+.||.|++++|++|+ +|.++|||||+|.+.++|..|++.|||..+.|++|.|.++...
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            59999999999999999999999999999999985 6899999999999999999999999999999999999998753

>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=5.7e-18  Score=139.65  Aligned_cols=77  Identities=21%  Similarity=0.301  Sum_probs=71.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      +..++|||+|||.++|+++|+++|++||+|.+|.|.     +++|||||+|.+.++|.+|++.|||..|.|+.|+|.|+.
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-----~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-----SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-----ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            456899999999999999999999999999999874     458999999999999999999999999999999999986


Q ss_pred             cc
Q 012034          106 KK  107 (472)
Q Consensus       106 ~~  107 (472)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.71  E-value=9.1e-18  Score=131.56  Aligned_cols=77  Identities=38%  Similarity=0.663  Sum_probs=71.3

Q ss_pred             eeeecCCCCccHHHHHHHHhccCceEEEEEeeCCC----CCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS----GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       134 l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~----g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      |||+|||+++|+++|+++|+.||.|.+++|.++++    +.++|||||+|.+.++|.+|++.+||..++|+.|.|.++++
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            79999999999999999999999999999988753    24799999999999999999999999999999999999865


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.71  E-value=3.8e-18  Score=131.05  Aligned_cols=75  Identities=35%  Similarity=0.571  Sum_probs=71.0

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      |+|||+|||+++|+++|+++|++||.|.+++|++|+ +|+++|||||+|.+.++|.+|++ ++++.++|+.|.|++|
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            579999999999999999999999999999999986 58999999999999999999996 7999999999999976

>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=99.71  E-value=1.1e-17  Score=133.94  Aligned_cols=79  Identities=25%  Similarity=0.404  Sum_probs=72.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|+.||.|..+.+..+  +.++|||||+|++.++|..|++.||++.|.|+.|.|+++.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            45678999999999999999999999999999887554  4568999999999999999999999999999999999986


Q ss_pred             c
Q 012034          106 K  106 (472)
Q Consensus       106 ~  106 (472)
                      .
T Consensus        90 ~   90 (95)
T d1x4aa1          90 S   90 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.71  E-value=1.1e-17  Score=135.37  Aligned_cols=80  Identities=23%  Similarity=0.468  Sum_probs=74.6

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ++|||+||+.++|+++|+++|+.||.|.+|+|+++. +|.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.++..+
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEECCCC
Confidence            479999999999999999999999999999999985 6899999999999999999999 59999999999999998765


Q ss_pred             HH
Q 012034          211 EE  212 (472)
Q Consensus       211 ~~  212 (472)
                      ..
T Consensus        98 ~n   99 (101)
T d2cq4a1          98 KN   99 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.71  E-value=1.9e-17  Score=131.05  Aligned_cols=80  Identities=29%  Similarity=0.429  Sum_probs=73.3

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||+++|+++|+++|+.||.|.+|+|+.|+ +|.++|||||+|.+.++|.+|++.  ...++|+.|.|+++.
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            35689999999999999999999999999999999986 699999999999999999999974  458999999999998


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .++
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            764

>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=9.1e-18  Score=131.87  Aligned_cols=79  Identities=20%  Similarity=0.250  Sum_probs=72.9

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeE-EEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~-v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|+.||.|.. +.+..+.+|+++|||||+|++.++|.+|++.||++.|.|+.|+|..+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999876 56777789999999999999999999999999999999999999764

>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=99.71  E-value=1.1e-17  Score=136.23  Aligned_cols=83  Identities=28%  Similarity=0.534  Sum_probs=77.2

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ++|||+||+.++|+++|+++|+.||.|.+|+|+.++ +|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.++..+
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            479999999999999999999999999999998875 6899999999999999999999999999999999999999876


Q ss_pred             HHHH
Q 012034          211 EERR  214 (472)
Q Consensus       211 ~~~~  214 (472)
                      ..+.
T Consensus        89 ~~~~   92 (104)
T d1p1ta_          89 KNKE   92 (104)
T ss_dssp             THHH
T ss_pred             CCcc
Confidence            5443

>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=5.9e-18  Score=135.82  Aligned_cols=81  Identities=17%  Similarity=0.251  Sum_probs=72.7

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCC-eeEEEEEECC--CCCceeEEEEEeCCHHHHHHHHHHHCCC--ccCCcceeeec
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGT-ITSAVVMRDG--DGKSKCFGFVNFENADDAAKAVEALNGK--KFDDREWYVGK  103 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~-I~~v~i~~d~--~g~skG~aFV~F~~~e~A~~Av~~lng~--~i~g~~l~V~~  103 (472)
                      ++|||+|||.++|+++|+++|++||+ |.++.+++|.  +|+++|||||+|+++++|.+|++.|++.  .+.|+.|.|.|
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            67999999999999999999999996 9999999883  5889999999999999999999998654  45799999999


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      |..+.+
T Consensus        82 A~p~~~   87 (96)
T d2disa1          82 AEPEID   87 (96)
T ss_dssp             SCSSCS
T ss_pred             cCCCCC
Confidence            976554

>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=99.70  E-value=5.9e-18  Score=132.02  Aligned_cols=78  Identities=38%  Similarity=0.718  Sum_probs=72.1

Q ss_pred             eeeecCCCCccHHHHHHHHhccCceEEE-EEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccHH
Q 012034          134 LYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKE  211 (472)
Q Consensus       134 l~V~nL~~~~t~e~L~~~F~~~G~I~~v-~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k~  211 (472)
                      |||+|||.++|+++|+++|++||.|.++ +|+++. +|+++|||||+|.+.++|.+|++.|+|..++|++|+|.++..++
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            7999999999999999999999999765 677774 68899999999999999999999999999999999999998764

>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=99.70  E-value=1.7e-17  Score=126.71  Aligned_cols=74  Identities=26%  Similarity=0.278  Sum_probs=69.0

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      |+|||+|||+++|+++|+++|+.||.|.++.+..+.++. +|||||+|+++++|.+|++ +|++.|+|+.|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            689999999999999999999999999999999997665 5799999999999999995 8999999999999865

>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=1.5e-17  Score=128.48  Aligned_cols=75  Identities=28%  Similarity=0.409  Sum_probs=69.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      .+.++|||+||+  +|+++|+++|++||.|.++.+.++     +|||||+|++.++|.+|+++||+..+.|+.|.|.|+.
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            457899999985  999999999999999999998754     7899999999999999999999999999999999997


Q ss_pred             cc
Q 012034          106 KK  107 (472)
Q Consensus       106 ~~  107 (472)
                      ++
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>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=5.1e-18  Score=128.65  Aligned_cols=70  Identities=34%  Similarity=0.554  Sum_probs=66.6

Q ss_pred             EEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        31 l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      |||+|||.++|+++|+++|++||.|.++.+..+ .+++++|||||+|.+.++|.+|++.|||+.|.|+.|+
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            799999999999999999999999999999988 5789999999999999999999999999999998764

>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=99.70  E-value=6.6e-18  Score=134.14  Aligned_cols=83  Identities=28%  Similarity=0.469  Sum_probs=74.1

Q ss_pred             CcceEEeCCCCCCCCHHHHHH----HHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           27 KFNNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~----~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      ..++|||+|||.++|+++|++    +|++||+|.+|.+..  +++++|||||+|++.++|.+|++.||+..+.|+.|.|.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            468999999999999999875    689999999987754  56789999999999999999999999999999999999


Q ss_pred             ccccchhHH
Q 012034          103 KAQKKSERE  111 (472)
Q Consensus       103 ~a~~~~~~~  111 (472)
                      ||..+++..
T Consensus        80 ~ak~~~~~~   88 (91)
T d1nu4a_          80 YAKTDSDII   88 (91)
T ss_dssp             ECSSCCTHH
T ss_pred             EeCCCchhh
Confidence            998876543

>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=99.70  E-value=4.7e-17  Score=128.87  Aligned_cols=81  Identities=32%  Similarity=0.509  Sum_probs=74.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++..+..+ .+|||||+|.+.++|.+|++.+||..+.|+.|+|.|+..
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            3568999999999999999999999999999999988544 489999999999999999999999999999999999976


Q ss_pred             HH
Q 012034          210 KE  211 (472)
Q Consensus       210 k~  211 (472)
                      +.
T Consensus        86 ~~   87 (90)
T d2cqia1          86 PS   87 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>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=99.69  E-value=1.7e-17  Score=142.45  Aligned_cols=80  Identities=35%  Similarity=0.559  Sum_probs=75.3

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .++|||+|||+++|+++|+++|+.||.|++|+|++++ +|.++|||||+|.+.++|.+|++.|||..|+|++|+|.++..
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~  121 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS  121 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            3579999999999999999999999999999999885 688999999999999999999999999999999999999875


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus       122 ~  122 (139)
T d1u6fa1         122 G  122 (139)
T ss_dssp             C
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=99.69  E-value=2.1e-17  Score=129.79  Aligned_cols=80  Identities=28%  Similarity=0.512  Sum_probs=69.7

Q ss_pred             ccceeeeecCCCCccH-HHHHHHHhccCceEEEEEeeC--CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          130 QGLNLYIKNLGDSIDD-EKLKELFSEFGTITSCKVMRD--PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~-e~L~~~F~~~G~I~~v~i~~~--~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      .+.+|||+|||.++++ ++|+++|++||.|++|+|..+  .++.++|||||+|.+.++|.+|++ +||..++|+.|.|++
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            3568999999998865 569999999999999998764  378899999999999999999994 999999999999999


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      +..+
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8764

>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=99.69  E-value=5e-17  Score=134.59  Aligned_cols=78  Identities=23%  Similarity=0.393  Sum_probs=73.0

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      +++|||+|||.++|+++|+++|+.||.|.+|++..+  +.++|||||+|.+.++|..|++.|||..|+|+.|.|.++..+
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            468999999999999999999999999999999865  678999999999999999999999999999999999998654

>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=99.69  E-value=2e-17  Score=131.02  Aligned_cols=81  Identities=28%  Similarity=0.528  Sum_probs=75.1

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..+|||+|||+++|+++|+++|+.||.|..+.++.+. +|.++|||||.|.+.++|.+|+..|||..++|+.|.|.++.+
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            3479999999999999999999999999999887764 688999999999999999999999999999999999999876


Q ss_pred             HH
Q 012034          210 KE  211 (472)
Q Consensus       210 k~  211 (472)
                      +.
T Consensus        85 ~~   86 (90)
T d1x5sa1          85 SS   86 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.69  E-value=3.1e-17  Score=133.27  Aligned_cols=79  Identities=28%  Similarity=0.421  Sum_probs=73.2

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .++|||+|||+++|+++|+++|+.||.|.+++|+.+. +|+++|||||+|.+.++|.+|++.+|+ .|+|++|.|.++..
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~   88 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYL   88 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTT
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCC
Confidence            3579999999999999999999999999999999886 589999999999999999999998876 79999999999875


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        89 ~   89 (103)
T d2cqda1          89 G   89 (103)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.69  E-value=3.3e-17  Score=127.71  Aligned_cols=77  Identities=23%  Similarity=0.324  Sum_probs=70.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccC-Ccceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD-DREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~-g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++.++++    .+|||||+|.+.++|.+|++.|||..|. |+.|.|.||
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            45789999999999999999999999999999999765    3689999999999999999999999985 689999998


Q ss_pred             cc
Q 012034          105 QK  106 (472)
Q Consensus       105 ~~  106 (472)
                      ++
T Consensus        82 kk   83 (83)
T d2b0ga1          82 KK   83 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            63

>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=99.68  E-value=4.5e-17  Score=128.38  Aligned_cols=78  Identities=17%  Similarity=0.348  Sum_probs=70.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCcc-CCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF-DDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i-~g~~l~V~~a  104 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++.+..+   +++|||||+|++.++|.+|+..|||..+ +|+.|.|.++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            34678999999999999999999999999988877654   4578999999999999999999999988 5899999998


Q ss_pred             cc
Q 012034          105 QK  106 (472)
Q Consensus       105 ~~  106 (472)
                      +.
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.68  E-value=4.3e-17  Score=127.93  Aligned_cols=78  Identities=31%  Similarity=0.415  Sum_probs=71.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++||.|..+.+..     ++|||||+|.+.++|.+|++.||+..|.|+.|.|.|+.
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            3467899999999999999999999999998887754     48999999999999999999999999999999999987


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      ++.
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.68  E-value=8.1e-17  Score=125.70  Aligned_cols=76  Identities=34%  Similarity=0.543  Sum_probs=71.4

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+|||+|||+++|+++|+++|+.||.|.+++|+.|. +|.++|||||+|.+.++|.+|++ ++++.|+|+.|.|+.|.
T Consensus         7 ~~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           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            479999999999999999999999999999999986 59999999999999999999996 69999999999998874

>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=99.68  E-value=3.4e-17  Score=134.47  Aligned_cols=76  Identities=24%  Similarity=0.402  Sum_probs=70.2

Q ss_pred             cceEEeCCCC-CCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecccc
Q 012034           28 FNNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp-~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~  106 (472)
                      .++|||+||+ ..+|+++|+++|++||.|.+|.|++|.    +|||||+|++.++|.+|++.|||..|.|+.|.|.++..
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~~   77 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            5789999995 569999999999999999999999873    78999999999999999999999999999999999864


Q ss_pred             c
Q 012034          107 K  107 (472)
Q Consensus       107 ~  107 (472)
                      .
T Consensus        78 ~   78 (109)
T d2adca1          78 Q   78 (109)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.68  E-value=1.6e-17  Score=131.33  Aligned_cols=76  Identities=24%  Similarity=0.426  Sum_probs=68.3

Q ss_pred             CcceEEeCCCCCCCCHHHH---HHHHhcCCCeeEEEEEECC-CC---CceeEEEEEeCCHHHHHHHHHHHCCCccCCcce
Q 012034           27 KFNNVFVKNLDESTTDEDL---KKIFGEYGTITSAVVMRDG-DG---KSKCFGFVNFENADDAAKAVEALNGKKFDDREW   99 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L---~~~F~~fG~I~~v~i~~d~-~g---~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l   99 (472)
                      ..++|||+|||+++++++|   +++|++||+|.+|.+.+|. ++   ..+|||||+|++.++|.+|++.|||..++|+.|
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            3567999999999999999   7789999999999999984 33   345999999999999999999999999999999


Q ss_pred             eee
Q 012034          100 YVG  102 (472)
Q Consensus       100 ~V~  102 (472)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            874

>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=99.68  E-value=4.2e-18  Score=135.21  Aligned_cols=81  Identities=22%  Similarity=0.352  Sum_probs=75.2

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ....+|||+|||.++|+++|+++|+.||.|.+++|+.+.+|+++|||||+|.+.++|.+|++ +||..++|+.|.|.+++
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            34568999999999999999999999999999999887889999999999999999999995 99999999999999987


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .|
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=99.68  E-value=3e-17  Score=133.13  Aligned_cols=80  Identities=18%  Similarity=0.176  Sum_probs=73.4

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ....+|||+|||+++|+++|+++|+.||. .++.++++.+++++|||||+|++.++|.+|++ +|++.|.||.|.|.++.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            45678999999999999999999999984 57888999899999999999999999999996 89999999999999887


Q ss_pred             cc
Q 012034          106 KK  107 (472)
Q Consensus       106 ~~  107 (472)
                      ..
T Consensus        91 ~~   92 (102)
T d1weza_          91 TA   92 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.68  E-value=2.8e-17  Score=133.79  Aligned_cols=81  Identities=25%  Similarity=0.422  Sum_probs=71.8

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC--CCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d--~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ...++|||+|||+++|+++|+++|+.|| |.++.++.+  .+++++|||||+|.+.++|++|+ .||+..|.|+.|+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            3568999999999999999999999999 677777766  46889999999999999998777 4999999999999999


Q ss_pred             cccch
Q 012034          104 AQKKS  108 (472)
Q Consensus       104 a~~~~  108 (472)
                      +..+.
T Consensus        91 a~~~~   95 (104)
T d1wi8a_          91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.68  E-value=1.8e-17  Score=132.99  Aligned_cols=79  Identities=28%  Similarity=0.418  Sum_probs=72.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      +..++|||+|||.++|+++|+++|++||.|..+.    .+++++|||||+|.+.++|.+|++.||+..|.|+.|.|.|+.
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~   89 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            4578999999999999999999999999887653    367899999999999999999999999999999999999998


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      .+.
T Consensus        90 ~k~   92 (96)
T d1fjca_          90 EKG   92 (96)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

>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=99.68  E-value=3.8e-17  Score=124.79  Aligned_cols=74  Identities=28%  Similarity=0.536  Sum_probs=68.8

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      .|||+|||+++|+++|+++|++||.|.+++|.+++ +|+++|||||+|.+.++|.+|++ +++..|+|+.|.|+.|
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            38999999999999999999999999999999885 68899999999999999999996 7999999999998643

>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=99.67  E-value=2e-17  Score=130.14  Aligned_cols=74  Identities=34%  Similarity=0.371  Sum_probs=68.2

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccch
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  108 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~  108 (472)
                      ++|||+|||+++|+++|+++|++||+|.++.+.+|      |||||+|.+.++|.+||+.|||..|.|+.|.|.++..+.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            46999999999999999999999999999998654      799999999999999999999999999999998876543

>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=99.67  E-value=3.1e-17  Score=133.16  Aligned_cols=80  Identities=34%  Similarity=0.538  Sum_probs=74.0

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ++|||+|||+++|+++|+++|++||.|.++.|.++. ++.++|||||+|.+.++|.+|+ .+++..|+|+.|.|.++..+
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 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHH-TSCSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHH-HhCCCeECCEEEEEEECccc
Confidence            479999999999999999999999999999999886 5789999999999999999999 57999999999999998876


Q ss_pred             HH
Q 012034          211 EE  212 (472)
Q Consensus       211 ~~  212 (472)
                      ++
T Consensus       100 e~  101 (103)
T d1x4ba1         100 EE  101 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.67  E-value=5.7e-17  Score=132.91  Aligned_cols=80  Identities=16%  Similarity=0.280  Sum_probs=72.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCcc--CCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKF--DDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i--~g~~l~V~  102 (472)
                      .....+|||+|||+++|+++|+++|++||.|.++.+..+   +++|||||+|++.++|.+|++.||+..|  .++.|.|.
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~---~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE---TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee---CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            356778999999999999999999999999999999987   4589999999999999999999999998  57788888


Q ss_pred             ccccc
Q 012034          103 KAQKK  107 (472)
Q Consensus       103 ~a~~~  107 (472)
                      ++..+
T Consensus        81 ~s~~~   85 (108)
T d2adba1          81 FSKLT   85 (108)
T ss_dssp             ECSSC
T ss_pred             ecCCc
Confidence            87654

>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=99.67  E-value=3e-17  Score=132.02  Aligned_cols=75  Identities=28%  Similarity=0.463  Sum_probs=68.4

Q ss_pred             CCcceEEeCCCC-CCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp-~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+||+ ..+++++|+++|++||.|.++.|       +||||||+|++.++|++||+.|||+.|.|+.|.|.++
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i-------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE-------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE-------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            445679999997 67889999999999999999988       3789999999999999999999999999999999998


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ..+
T Consensus        86 ~~~   88 (98)
T d1wf2a_          86 AEP   88 (98)
T ss_dssp             TSC
T ss_pred             CCC
Confidence            653

>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=99.67  E-value=7.9e-17  Score=129.05  Aligned_cols=76  Identities=28%  Similarity=0.494  Sum_probs=71.8

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+||+.++++++|+++|+.||.|.+|++.++     +|||||+|.+.++|.+|+..|||..|.|+.|+|.|+++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4568999999999999999999999999999999986     89999999999999999999999999999999999876


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        92 ~   92 (96)
T d1x4ga1          92 S   92 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.67  E-value=2.4e-17  Score=133.51  Aligned_cols=79  Identities=34%  Similarity=0.631  Sum_probs=73.9

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+|||.++|+++|+++|+.||.|.++.+..+.++.++|||||+|.+.++|.+|++.|||..|.|+++.|.+++
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            3468999999999999999999999999999999998889999999999999999999999999999999988887654

>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=99.66  E-value=1.5e-16  Score=124.49  Aligned_cols=77  Identities=23%  Similarity=0.342  Sum_probs=72.7

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .++|||+|||.++|+++|+++|+.||.|.+|++.++.+|.++|||||+|.+.++|.+|+ .+++..+.|+.|.|.+..
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 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHH-TCCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHH-HHCCCEECCEEEEEEEcC
Confidence            34899999999999999999999999999999999989999999999999999999999 579999999999999864

>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=99.66  E-value=2.9e-17  Score=133.50  Aligned_cols=83  Identities=24%  Similarity=0.284  Sum_probs=73.9

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeE-EEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~-v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...++|||+|||+++|+++|+++|+.||.|.. +.+..+.+|+++|||||+|.++++|.+|++ +|++.|.|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            45677999999999999999999999999876 555566899999999999999999999996 8999999999999988


Q ss_pred             ccchh
Q 012034          105 QKKSE  109 (472)
Q Consensus       105 ~~~~~  109 (472)
                      ..+..
T Consensus        85 ~~~~~   89 (103)
T d2cpya1          85 TLEDM   89 (103)
T ss_dssp             CHHHH
T ss_pred             CHHHh
Confidence            65443

>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=99.66  E-value=2.6e-17  Score=125.58  Aligned_cols=74  Identities=20%  Similarity=0.380  Sum_probs=68.7

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      .|||+|||+++|+++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|.+|++ .++..++|+.|.|++|
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            48999999999999999999999999999999885 68999999999999999999995 5778899999999865

>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=99.66  E-value=3.7e-17  Score=128.85  Aligned_cols=77  Identities=18%  Similarity=0.379  Sum_probs=67.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||.++|+++|+++|++|| +..+.+     ++++|||||+|.+.++|.+|++.||++.|.|+.|.|+++.
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~-----~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-----EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-----eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3567899999999999999999999999 233333     3568999999999999999999999999999999999986


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      .+.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.66  E-value=1.9e-16  Score=122.04  Aligned_cols=75  Identities=19%  Similarity=0.426  Sum_probs=69.9

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      .+|||+|||+++|+++|+++|++||.|..+.+..++ ++.++|||||+|.+.++|.+|+ .++|..|+|+.|.|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            479999999999999999999999999999998875 6789999999999999999988 58999999999999876

>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=99.66  E-value=2.1e-16  Score=141.62  Aligned_cols=107  Identities=25%  Similarity=0.440  Sum_probs=92.8

Q ss_pred             ccCeeEEEcCcccchhhhhhhccCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEEC-CCCCceeEEEEEeCCHHH
Q 012034            3 INDKQVFVGHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADD   81 (472)
Q Consensus         3 ~~~k~v~v~~~~~~~~r~~~~~~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d-~~g~skG~aFV~F~~~e~   81 (472)
                      +++..+.+.....+............++|||+|||.++|+++|+++|+.||.|..+.|+.| .+|+++|||||+|.+.++
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~  151 (183)
T d1u1qa_          72 VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS  151 (183)
T ss_dssp             ETTEECEEEECCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHH
T ss_pred             ccccchhhhhhhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHH
Confidence            4566677777766666655555677899999999999999999999999999999999998 468999999999999999


Q ss_pred             HHHHHHHHCCCccCCcceeeeccccchhH
Q 012034           82 AAKAVEALNGKKFDDREWYVGKAQKKSER  110 (472)
Q Consensus        82 A~~Av~~lng~~i~g~~l~V~~a~~~~~~  110 (472)
                      |.+|++ ++++.+.|+.|.|.+|.++.++
T Consensus       152 A~~Al~-~~~~~~~G~~i~V~~A~~k~e~  179 (183)
T d1u1qa_         152 VDKIVI-QKYHTVNGHNCEVRKALSKQEM  179 (183)
T ss_dssp             HHHHHT-SSCEEETTEEEEEEECCCHHHH
T ss_pred             HHHHHH-hCCCeECCEEEEEEecCCcccc
Confidence            999997 7899999999999999877554

>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=99.65  E-value=1.9e-16  Score=127.26  Aligned_cols=82  Identities=30%  Similarity=0.539  Sum_probs=74.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhC------CcEecCeeE
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN------GKMIVSKPL  202 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~------g~~i~gk~l  202 (472)
                      .+++|||+|||+++|+++|+++|++||.|.++.+..+. .+.++|||||+|.+.++|.+|++.+|      |..+.|+.|
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            45789999999999999999999999999999998875 67799999999999999999999886      678899999


Q ss_pred             EEEEcccHH
Q 012034          203 YVAVAQRKE  211 (472)
Q Consensus       203 ~V~~a~~k~  211 (472)
                      .|.++..+.
T Consensus        87 ~v~~a~~k~   95 (98)
T d1x4ha1          87 KVDLAVTRD   95 (98)
T ss_dssp             EEECCCCCC
T ss_pred             EEEECCCCC
Confidence            999987753

>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=99.65  E-value=2.1e-16  Score=126.38  Aligned_cols=79  Identities=20%  Similarity=0.326  Sum_probs=72.5

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..+++|||+|||.++|+++|+++|+.||.|..+.+..+  +.++|||||+|.+.++|.+|++.|||..|.|++|.|.|++
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            34568999999999999999999999999999998665  4578999999999999999999999999999999999987


Q ss_pred             c
Q 012034          209 R  209 (472)
Q Consensus       209 ~  209 (472)
                      .
T Consensus        90 ~   90 (95)
T d1x4aa1          90 S   90 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.65  E-value=1e-16  Score=122.31  Aligned_cols=74  Identities=22%  Similarity=0.384  Sum_probs=69.4

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      .|||+|||.++|+++|+++|+.||.|..+.+..++ ++.++|||||+|.+.++|.+|++ +||+.|+|++|.|++|
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            38999999999999999999999999999988875 67899999999999999999995 9999999999999875

>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=99.65  E-value=1.4e-16  Score=121.53  Aligned_cols=72  Identities=19%  Similarity=0.421  Sum_probs=64.5

Q ss_pred             EEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccccch
Q 012034           31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKS  108 (472)
Q Consensus        31 l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~~~~  108 (472)
                      |||+|||.++|+++|+++|++|| +..+.+     ++++|||||+|.+.++|.+|++.||+..+.|+.|.|+++...+
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            79999999999999999999999 444443     4568999999999999999999999999999999999997643

>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=99.65  E-value=1.3e-16  Score=129.74  Aligned_cols=81  Identities=19%  Similarity=0.242  Sum_probs=72.2

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEE-EECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVV-MRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i-~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ...+.|||+|||+++||++|+++|+.||.|..+.+ +.+.+++++|||||+|.++++|++|++ +|+..|.|+.|.|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            45667999999999999999999999999887544 445789999999999999999999996 8999999999999988


Q ss_pred             ccc
Q 012034          105 QKK  107 (472)
Q Consensus       105 ~~~  107 (472)
                      ..+
T Consensus        92 ~~~   94 (104)
T d1wg5a_          92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
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=99.65  E-value=1.2e-16  Score=125.39  Aligned_cols=75  Identities=28%  Similarity=0.449  Sum_probs=70.8

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .++|||+|||.++++++|+++|+.||.|.+|++.++     +|||||+|.+.++|.+|++.|||..|.|+.|+|+||..+
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            457999999999999999999999999999999876     789999999999999999999999999999999998754

>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=99.64  E-value=1.9e-16  Score=127.10  Aligned_cols=77  Identities=21%  Similarity=0.375  Sum_probs=70.1

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCC--cceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDD--REWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g--~~l~V~~  103 (472)
                      ...++|||+|||.++|+++|+++|++||.|.++.+.++     ++||||+|.+.++|.+|++.||+..|.|  ++|.|.|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            45689999999999999999999999999999998754     7899999999999999999999999987  4799999


Q ss_pred             cccc
Q 012034          104 AQKK  107 (472)
Q Consensus       104 a~~~  107 (472)
                      ++..
T Consensus        90 ak~~   93 (97)
T d1whya_          90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8753

>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=99.64  E-value=2.7e-17  Score=129.71  Aligned_cols=77  Identities=19%  Similarity=0.373  Sum_probs=69.3

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||+++|+++|+++|++||.|.+|.+..    .++|||||+|++.++|++|+.  +++.|+|+.|.|.++.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            4578999999999999999999999999999987653    468999999999999999995  7889999999999987


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      .+.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.64  E-value=1.9e-16  Score=128.03  Aligned_cols=82  Identities=26%  Similarity=0.472  Sum_probs=72.9

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceE--------EEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecC
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTIT--------SCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVS  199 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~--------~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g  199 (472)
                      ...++|||+|||.++|+++|+++|+.||.|.        .+.+..+. +|.++|||||+|.+.++|.+|++.|||..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            3567999999999999999999999999885        34555553 58899999999999999999999999999999


Q ss_pred             eeEEEEEcccH
Q 012034          200 KPLYVAVAQRK  210 (472)
Q Consensus       200 k~l~V~~a~~k  210 (472)
                      +.|+|++++.+
T Consensus        86 r~i~V~~a~~~   96 (101)
T d2cpea1          86 SKLKVSLARKK   96 (101)
T ss_dssp             EECEEECSSCC
T ss_pred             EEEEEEEcCCC
Confidence            99999999765

>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=99.64  E-value=1.2e-16  Score=128.42  Aligned_cols=77  Identities=25%  Similarity=0.268  Sum_probs=70.5

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      ...++|||+|||+++++++|+++|++||+|.++.+..      +|||||+|.+.++|++||+.||+..|.|+.|.|.++.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            4567899999999999999999999999999999864      5899999999999999999999999999999999876


Q ss_pred             cch
Q 012034          106 KKS  108 (472)
Q Consensus       106 ~~~  108 (472)
                      .+.
T Consensus        87 ~~~   89 (98)
T d1wg4a_          87 VYP   89 (98)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            543

>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=99.64  E-value=1.5e-16  Score=122.61  Aligned_cols=74  Identities=30%  Similarity=0.491  Sum_probs=68.7

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .+++|||+|++  +|+++|+++|++||.|.++++.++     +|||||+|.+.++|.+|++.|||..++|++|+|.|+++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            45689999985  899999999999999999999765     78999999999999999999999999999999999975


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        77 ~   77 (79)
T d2bz2a1          77 Q   77 (79)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.63  E-value=3.4e-16  Score=121.85  Aligned_cols=77  Identities=19%  Similarity=0.367  Sum_probs=70.3

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEe-cCeeEEEEEc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI-VSKPLYVAVA  207 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i-~gk~l~V~~a  207 (472)
                      ..+++|||+|||.++|+++|+++|+.||.|.+++++++    .+|||||+|.+.++|..|++.|||..+ +|++|+|.|+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            34678999999999999999999999999999999875    478999999999999999999999988 4689999998


Q ss_pred             cc
Q 012034          208 QR  209 (472)
Q Consensus       208 ~~  209 (472)
                      +.
T Consensus        82 kk   83 (83)
T d2b0ga1          82 KK   83 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            63

>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=99.63  E-value=2.1e-16  Score=123.90  Aligned_cols=78  Identities=18%  Similarity=0.360  Sum_probs=72.0

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEE-EEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITS-CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~-v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..+.|||+|||++++++||+++|+.||.|.. +.+..+.+|.++|+|||+|.+.++|.+|++.||+..+.|++|+|+++
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            3457999999999999999999999999876 56777788999999999999999999999999999999999999975

>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=99.63  E-value=6e-17  Score=125.28  Aligned_cols=74  Identities=27%  Similarity=0.430  Sum_probs=68.4

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCc-EecCeeEEEEEcccHH
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGK-MIVSKPLYVAVAQRKE  211 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~-~i~gk~l~V~~a~~k~  211 (472)
                      +|||+|||.++|+++|+++|++||.|.++++...     +|||||+|.+.++|.+|++.|||. .++|++|+|.|+..+.
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            6999999999999999999999999988777664     899999999999999999999996 6999999999998764

>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=99.63  E-value=1.2e-16  Score=126.82  Aligned_cols=83  Identities=34%  Similarity=0.522  Sum_probs=73.8

Q ss_pred             cceeeeecCCCCccHHHHHH----HHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEE
Q 012034          131 GLNLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV  206 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~----~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~  206 (472)
                      +++|||+|||.++++++|++    +|+.||.|.+|++..  ++.++|||||+|.+.++|.+|++.+||..++|+.|+|.|
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            46899999999999999864    589999999999865  366899999999999999999999999999999999999


Q ss_pred             cccHHHHHH
Q 012034          207 AQRKEERRA  215 (472)
Q Consensus       207 a~~k~~~~~  215 (472)
                      ++.+.+...
T Consensus        81 ak~~~~~~~   89 (91)
T d1nu4a_          81 AKTDSDIIA   89 (91)
T ss_dssp             CSSCCTHHH
T ss_pred             eCCCchhhc
Confidence            988765443

>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=99.63  E-value=2.9e-16  Score=123.85  Aligned_cols=76  Identities=22%  Similarity=0.382  Sum_probs=68.3

Q ss_pred             ccceeeeecCCCCccHHHH---HHHHhccCceEEEEEeeCCC----CCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeE
Q 012034          130 QGLNLYIKNLGDSIDDEKL---KELFSEFGTITSCKVMRDPS----GISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL  202 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L---~~~F~~~G~I~~v~i~~~~~----g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l  202 (472)
                      +..+|||+|||.++++++|   +++|++||.|.+|.|++++.    +..+|||||+|.+.++|.+|++.|||..++|+.|
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            4557999999999999999   67899999999999998852    2345999999999999999999999999999999


Q ss_pred             EEE
Q 012034          203 YVA  205 (472)
Q Consensus       203 ~V~  205 (472)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.63  E-value=2.4e-16  Score=129.70  Aligned_cols=76  Identities=24%  Similarity=0.304  Sum_probs=70.4

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ..++|||+|||.++++++|+++|+.||.|.+|.|..     ++|||||+|.+.++|.+|++.|||..|.|++|+|.|+..
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            346899999999999999999999999999998854     489999999999999999999999999999999999865


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      .
T Consensus        84 ~   84 (111)
T d1whxa_          84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.62  E-value=3.3e-17  Score=132.89  Aligned_cols=83  Identities=27%  Similarity=0.410  Sum_probs=76.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+++|||+|||.++++++|+++|+.||.|..+.+..+. +|.++|||||+|.+.++|.+|++.|||..|.|++|.|.|++
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            35689999999999999999999999999998887764 68899999999999999999999999999999999999998


Q ss_pred             cHHH
Q 012034          209 RKEE  212 (472)
Q Consensus       209 ~k~~  212 (472)
                      .+++
T Consensus        97 ~k~~  100 (102)
T d2cpxa1          97 NKKQ  100 (102)
T ss_dssp             CCSC
T ss_pred             Cccc
Confidence            7653

>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=99.62  E-value=4.4e-16  Score=122.58  Aligned_cols=79  Identities=13%  Similarity=0.263  Sum_probs=71.2

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHH--CCCccCCcceeee
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL--NGKKFDDREWYVG  102 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~l--ng~~i~g~~l~V~  102 (472)
                      ....++|||+|||.++|+++|+++|++||.|.++.+.++     +|||||+|++.++|.+|++.+  ++..+.|+.|+|.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            357889999999999999999999999999999998865     689999999999999999865  5778999999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      +++.+.
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            987553

>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=99.62  E-value=2.7e-16  Score=129.60  Aligned_cols=84  Identities=20%  Similarity=0.237  Sum_probs=74.6

Q ss_pred             cCCcceEEeCCCCCCCCHHHHHHHHhcCCCeeE-EEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeec
Q 012034           25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK  103 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~-v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~  103 (472)
                      ....++|||+|||+++|+++|+++|+.||.|.. +.+..+.+|+++|||||+|.+.++|.+|++ ||+..|+|+.|.|.+
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            345678999999999999999999999999876 455566899999999999999999999996 899999999999998


Q ss_pred             cccchh
Q 012034          104 AQKKSE  109 (472)
Q Consensus       104 a~~~~~  109 (472)
                      +.....
T Consensus        94 ~~~~~~   99 (112)
T d1wela1          94 ITKKGM   99 (112)
T ss_dssp             ECHHHH
T ss_pred             cChHHH
Confidence            876554

>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=99.62  E-value=3.3e-16  Score=128.46  Aligned_cols=74  Identities=22%  Similarity=0.459  Sum_probs=68.9

Q ss_pred             cceeeeecCC-CCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          131 GLNLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       131 ~~~l~V~nL~-~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      +++|||+||+ ..+|+++|+++|+.||.|.+|+|+++    .+|||||+|.+.++|.+|++.|||..|.|+.|.|.|++
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 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT----TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec----ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3589999995 56999999999999999999999987    37899999999999999999999999999999999975

>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=99.61  E-value=4.1e-16  Score=124.86  Aligned_cols=80  Identities=15%  Similarity=0.185  Sum_probs=71.9

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCc-eEEEEEeeCC--CCCcccEEEEEcCCHHHHHHHHHHhCCc--EecCeeEEEEE
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGT-ITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEMNGK--MIVSKPLYVAV  206 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~-I~~v~i~~~~--~g~s~g~afV~f~s~~~A~~Ai~~l~g~--~i~gk~l~V~~  206 (472)
                      |.|||+|||.++|+++|+++|+.||. |.+++++++.  .++++|||||+|.+.++|.+|++.|++.  .+.|++|.|.|
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            67999999999999999999999995 9999998874  5789999999999999999999998754  45799999999


Q ss_pred             cccHH
Q 012034          207 AQRKE  211 (472)
Q Consensus       207 a~~k~  211 (472)
                      |..+.
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            97653

>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=2.9e-16  Score=126.48  Aligned_cols=78  Identities=26%  Similarity=0.318  Sum_probs=70.6

Q ss_pred             CCcceEEeCCCCCC-CCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHH--HHCCCccCCcceeee
Q 012034           26 TKFNNVFVKNLDES-TTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE--ALNGKKFDDREWYVG  102 (472)
Q Consensus        26 ~~~~~l~V~nLp~~-~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~--~lng~~i~g~~l~V~  102 (472)
                      ...++|||+|||.+ +|+++|+++|++||.|.++.++++     +|||||+|++.++|.+|++  .+++..+.|+.|.|.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~   90 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEE
Confidence            55689999999985 899999999999999999999865     6899999999999999998  578889999999999


Q ss_pred             ccccch
Q 012034          103 KAQKKS  108 (472)
Q Consensus       103 ~a~~~~  108 (472)
                      +++++.
T Consensus        91 ~s~~~~   96 (99)
T d1x4fa1          91 LSEKYK   96 (99)
T ss_dssp             EECSCS
T ss_pred             EcCCcc
Confidence            997654

>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=99.61  E-value=1.2e-15  Score=116.29  Aligned_cols=74  Identities=19%  Similarity=0.220  Sum_probs=68.3

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ++|||+|||.++++++|+++|+.||.|.++++..++++. ++||||+|.+.++|.+|+ .+|++.|+|+.|.|+.+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            479999999999999999999999999999999887654 579999999999999998 58999999999999854

>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=99.61  E-value=5.4e-16  Score=124.57  Aligned_cols=73  Identities=29%  Similarity=0.546  Sum_probs=67.2

Q ss_pred             ccceeeeecCC-CCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~-~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..++|||+||+ +.+++++|+++|++||.|.+++|       ++|||||+|.+.++|.+|++.|||..|.|++|+|.|+.
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i-------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   86 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAA   86 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE-------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETT
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE-------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34679999996 67888999999999999999998       37899999999999999999999999999999999986


Q ss_pred             c
Q 012034          209 R  209 (472)
Q Consensus       209 ~  209 (472)
                      .
T Consensus        87 ~   87 (98)
T d1wf2a_          87 E   87 (98)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.61  E-value=6.9e-16  Score=125.20  Aligned_cols=83  Identities=18%  Similarity=0.280  Sum_probs=73.9

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEE-EEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITS-CKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~-v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      .++|||+|||+++|+++|+++|+.||.|.. +.+..+.+|.++|||||+|.+.++|.+|++ +|+..|+|+.|.|.++..
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            457999999999999999999999999876 556666789999999999999999999995 999999999999999876


Q ss_pred             HHHHH
Q 012034          210 KEERR  214 (472)
Q Consensus       210 k~~~~  214 (472)
                      ++.+.
T Consensus        87 ~~~~~   91 (103)
T d2cpya1          87 EDMRE   91 (103)
T ss_dssp             HHHHH
T ss_pred             HHhhh
Confidence            65543

>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=99.61  E-value=1.8e-16  Score=119.91  Aligned_cols=70  Identities=30%  Similarity=0.525  Sum_probs=66.0

Q ss_pred             eeeecCCCCccHHHHHHHHhccCceEEEEEeeCC-CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEE
Q 012034          134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY  203 (472)
Q Consensus       134 l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~-~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~  203 (472)
                      |||+|||.++|+++|+++|+.||.|..+++.+++ ++.++|||||+|.+.++|.+|++.|||..|+|+.|+
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            7999999999999999999999999999998875 688999999999999999999999999999998763

>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=99.60  E-value=1.2e-15  Score=123.90  Aligned_cols=77  Identities=26%  Similarity=0.300  Sum_probs=69.6

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHH--CCCccCCcceeeec
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL--NGKKFDDREWYVGK  103 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~l--ng~~i~g~~l~V~~  103 (472)
                      ...++|||+|||.++||++|+++|++||.|.++.+.++     ||||||+|++.++|++|++.+  ++..+.|+.|+|.+
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~   87 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEE
Confidence            45788999999999999999999999999999998754     789999999999999999987  45678999999999


Q ss_pred             cccc
Q 012034          104 AQKK  107 (472)
Q Consensus       104 a~~~  107 (472)
                      +..+
T Consensus        88 s~~~   91 (104)
T d1wexa_          88 STSK   91 (104)
T ss_dssp             CSSS
T ss_pred             cCCC
Confidence            8654

>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=99.60  E-value=1.3e-15  Score=119.23  Aligned_cols=75  Identities=28%  Similarity=0.408  Sum_probs=69.3

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ..+|||+|||.++|+++|+++|+.||.|..+.+..     ++|||||+|.+.++|.+|+..|||..|.|+.|.|.|++++
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            35799999999999999999999999998888754     4899999999999999999999999999999999998754

>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=99.60  E-value=1.1e-15  Score=120.30  Aligned_cols=77  Identities=22%  Similarity=0.323  Sum_probs=69.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEe-cCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI-VSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i-~gk~l~V~~a~  208 (472)
                      .+++|||+|||.++|+++|+++|+.||.|.++.+..+   .++|||||+|.+.++|.+|+..|||..+ +|++|+|+|++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            3568999999999999999999999999988877654   4578999999999999999999999988 58999999987


Q ss_pred             c
Q 012034          209 R  209 (472)
Q Consensus       209 ~  209 (472)
                      .
T Consensus        86 ~   86 (88)
T d2adca2          86 S   86 (88)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.59  E-value=1.1e-15  Score=120.34  Aligned_cols=74  Identities=20%  Similarity=0.350  Sum_probs=65.4

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .++|||+|||.+++++||+++|++|| +..+.+.     .++|||||+|.+.++|.+|++.||+..+.|++|.|+++..+
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            35899999999999999999999999 3334443     35899999999999999999999999999999999998654

>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=99.59  E-value=5.3e-17  Score=131.93  Aligned_cols=78  Identities=19%  Similarity=0.232  Sum_probs=73.9

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      ..++++|+++..+++|++|+++|++||+|.+|.|.++.+|+++|||||+|++.++|.+|++.|||+.++|+.|.|+++
T Consensus        26 ~~~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          26 AVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             ccchHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            346799999999999999999999999999999998899999999999999999999999999999999999999875

>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=99.59  E-value=8.8e-16  Score=122.90  Aligned_cols=77  Identities=27%  Similarity=0.402  Sum_probs=70.4

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .++|||+||+.++|+++|+++|+.||.|..++.    ++.++|||||+|.+.++|.+|++.|||..|+|++|+|.|+..+
T Consensus        16 ~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k   91 (96)
T d1fjca_          16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             GGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            468999999999999999999999998876653    4678999999999999999999999999999999999999876


Q ss_pred             H
Q 012034          211 E  211 (472)
Q Consensus       211 ~  211 (472)
                      .
T Consensus        92 ~   92 (96)
T d1fjca_          92 G   92 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.59  E-value=1.4e-15  Score=123.56  Aligned_cols=79  Identities=25%  Similarity=0.450  Sum_probs=70.4

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC--CCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~--~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      ..++|||+|||+++|+++|+++|+.|| |.+++++.+.  ++.++|||||+|.+.++|.+|+ .+|+..|.|+.|+|.++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEEC
Confidence            457899999999999999999999999 7788777654  6789999999999999998666 69999999999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        92 ~~~   94 (104)
T d1wi8a_          92 DQA   94 (104)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.58  E-value=3.1e-15  Score=113.91  Aligned_cols=71  Identities=21%  Similarity=0.429  Sum_probs=64.4

Q ss_pred             eeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       134 l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      |||+|||.++++++|+++|++|| +..+.+.     +++|||||+|.+.++|.+|++.|||..++|++|.|+|+..+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 5555543     46899999999999999999999999999999999998754

>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=99.58  E-value=7e-16  Score=121.41  Aligned_cols=74  Identities=16%  Similarity=0.354  Sum_probs=67.5

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .++|||+|||+++|+++|+++|++||.|.+|++..+    ++|||||+|.+.++|.+|+.  ++..|+|++|.|.++..+
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k   78 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCC
Confidence            468999999999999999999999999999987654    68999999999999999985  788999999999998654

>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=99.57  E-value=1.1e-15  Score=123.65  Aligned_cols=80  Identities=18%  Similarity=0.245  Sum_probs=72.6

Q ss_pred             cccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       129 ~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ..+.+|||+|||+++|+++|+++|+.|| +.++.++.+.++.++|||||+|.+.++|.+|++ +|+..|+|+.|.|.++.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            3456899999999999999999999997 557888888889999999999999999999985 89999999999999877


Q ss_pred             cH
Q 012034          209 RK  210 (472)
Q Consensus       209 ~k  210 (472)
                      .+
T Consensus        91 ~~   92 (102)
T d1weza_          91 TA   92 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.57  E-value=1.6e-15  Score=119.48  Aligned_cols=78  Identities=15%  Similarity=0.209  Sum_probs=69.9

Q ss_pred             cCCcceEEeCCCCCC-CCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHH--CCCccCCcceee
Q 012034           25 KTKFNNVFVKNLDES-TTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL--NGKKFDDREWYV  101 (472)
Q Consensus        25 ~~~~~~l~V~nLp~~-~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~l--ng~~i~g~~l~V  101 (472)
                      ....++|||+|||.. +|+++|.++|++||.|.++.+..+     ++||||+|++.++|..|++.|  ++..+.|+.|.|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            356888999999986 789999999999999999999865     679999999999999999966  677899999999


Q ss_pred             eccccc
Q 012034          102 GKAQKK  107 (472)
Q Consensus       102 ~~a~~~  107 (472)
                      .++++.
T Consensus        80 ~~s~~~   85 (89)
T d1x4da1          80 HLSQKY   85 (89)
T ss_dssp             EEECCC
T ss_pred             EECCCc
Confidence            998754

>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=99.56  E-value=5.5e-15  Score=116.18  Aligned_cols=79  Identities=20%  Similarity=0.333  Sum_probs=71.0

Q ss_pred             ccccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHh--CCcEecCeeEEEE
Q 012034          128 KFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM--NGKMIVSKPLYVA  205 (472)
Q Consensus       128 ~~~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l--~g~~i~gk~l~V~  205 (472)
                      ...+++|||+|||.++++++|+++|+.||.|.++++.++     ++||||+|.+.++|.+|++.+  ++..+.|++|+|.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            345678999999999999999999999999999999865     689999999999999999865  5778999999999


Q ss_pred             EcccHH
Q 012034          206 VAQRKE  211 (472)
Q Consensus       206 ~a~~k~  211 (472)
                      |++.++
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            997653

>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=99.56  E-value=1.9e-15  Score=123.61  Aligned_cols=76  Identities=20%  Similarity=0.354  Sum_probs=69.6

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEe--cCeeEEEEEccc
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI--VSKPLYVAVAQR  209 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i--~gk~l~V~~a~~  209 (472)
                      .+|||+||++++|+++|+++|++||.|.+|.++.++   ++|||||+|.+.++|.+|+..|||..|  .+++|.|.+++.
T Consensus         8 ~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~   84 (108)
T d2adba1           8 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL   84 (108)
T ss_dssp             EEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCC
Confidence            479999999999999999999999999999998863   589999999999999999999999998  578899988865


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        85 ~   85 (108)
T d2adba1          85 T   85 (108)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.56  E-value=1e-15  Score=120.14  Aligned_cols=72  Identities=25%  Similarity=0.317  Sum_probs=66.9

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      .|||+|||.++|+++|+++|++||.|.++++..+      |||||+|.+.++|.+|++.|||..|.|+.|.|.++..+
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            5999999999999999999999999999998753      79999999999999999999999999999998877544

>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=99.56  E-value=4.1e-15  Score=119.16  Aligned_cols=76  Identities=21%  Similarity=0.358  Sum_probs=69.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecC--eeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVS--KPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g--k~l~V~~a  207 (472)
                      ..++|||+||+.++++++|+++|++||.|+.+++.++     ++||||+|.+.++|.+|++.||+..|.|  ++|+|.|+
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~a   90 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeC
Confidence            3468999999999999999999999999999999875     7899999999999999999999999976  58999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      +..
T Consensus        91 k~~   93 (97)
T d1whya_          91 KSG   93 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>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=99.56  E-value=8e-17  Score=127.50  Aligned_cols=77  Identities=17%  Similarity=0.344  Sum_probs=67.8

Q ss_pred             ceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEE------ECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeee
Q 012034           29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVM------RDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVG  102 (472)
Q Consensus        29 ~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~------~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~  102 (472)
                      ++|||+|||.++||++|+++|+.||.|.++.+.      ...+++++|||||+|.+.|+|.+|++ |||..+.|+.|.|.
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            679999999999999999999999988766543      23467899999999999999999995 99999999999998


Q ss_pred             cccc
Q 012034          103 KAQK  106 (472)
Q Consensus       103 ~a~~  106 (472)
                      ++..
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            7643

>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=99.55  E-value=3.8e-15  Score=119.53  Aligned_cols=75  Identities=19%  Similarity=0.242  Sum_probs=69.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEccc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR  209 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~~  209 (472)
                      ...+|||+|||+++++++|+++|+.||.|++++|.+      +|||||+|.+.++|.+||+.|||..+.|+.|.|.+++.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~   87 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEec
Confidence            345799999999999999999999999999999864      58999999999999999999999999999999999865


Q ss_pred             H
Q 012034          210 K  210 (472)
Q Consensus       210 k  210 (472)
                      +
T Consensus        88 ~   88 (98)
T d1wg4a_          88 Y   88 (98)
T ss_dssp             E
T ss_pred             C
Confidence            4

>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=99.55  E-value=4.1e-15  Score=120.71  Aligned_cols=81  Identities=22%  Similarity=0.292  Sum_probs=71.8

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEE-EEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v-~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      ...+|||+|||+++|+++|+++|+.||.|..+ .+..+.++.++|||||+|.+.++|.+|+ .+|+..|.|+.|.|.++.
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 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHH-TTTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHH-hhCCCEEcceEEEEEECC
Confidence            44579999999999999999999999988874 5555668899999999999999999999 499999999999999887


Q ss_pred             cHH
Q 012034          209 RKE  211 (472)
Q Consensus       209 ~k~  211 (472)
                      .++
T Consensus        93 ~~~   95 (104)
T d1wg5a_          93 RAE   95 (104)
T ss_dssp             TTT
T ss_pred             HHH
Confidence            653

>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=99.55  E-value=9e-16  Score=124.52  Aligned_cols=75  Identities=17%  Similarity=0.358  Sum_probs=72.1

Q ss_pred             eeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       133 ~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      +++|+++.+++++++|+++|++||.|++|+|+++.+|+++|||||+|.+.++|.+|++.|||+.++|++|.|+|+
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 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            588899999999999999999999999999999889999999999999999999999999999999999999985

>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=99.54  E-value=1.1e-15  Score=124.08  Aligned_cols=78  Identities=19%  Similarity=0.164  Sum_probs=69.7

Q ss_pred             CCcceEEeCCCCCCC-CH----HHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCccee
Q 012034           26 TKFNNVFVKNLDEST-TD----EDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY  100 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~-te----e~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~  100 (472)
                      ...++|||+||+.++ ++    ++|+++|+.||.|.++.+++     ++|||||+|++.++|.+|++.|||..|.|+.|.
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            467899999999886 33    56999999999999999984     478999999999999999999999999999999


Q ss_pred             eeccccch
Q 012034          101 VGKAQKKS  108 (472)
Q Consensus       101 V~~a~~~~  108 (472)
                      |.|++...
T Consensus        78 v~~a~~~~   85 (104)
T d1weya_          78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EeecccCC
Confidence            99997554

>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=99.54  E-value=9.4e-15  Score=120.37  Aligned_cols=89  Identities=22%  Similarity=0.214  Sum_probs=75.7

Q ss_pred             CCcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCH-HHHHHHHHHHCCCccCCcceeeecc
Q 012034           26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENA-DDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        26 ~~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~-e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      .....+||+|||.++|+++|+++|++||+|.+|.|+++     +|||||.|++. ++|..|+..+++..+.++.+.|.++
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            34566799999999999999999999999999999865     79999999985 7899999999999999998888888


Q ss_pred             ccchhHHHHHHHHHH
Q 012034          105 QKKSEREQELKGQFE  119 (472)
Q Consensus       105 ~~~~~~~~~~~~~~~  119 (472)
                      ..+.+.+.+...+..
T Consensus        84 ~~~~~~e~~~~~k~~   98 (113)
T d1owxa_          84 VLEGEVEKEALKKII   98 (113)
T ss_dssp             ECCHHHHHHHHHHHH
T ss_pred             eccchhhHHHHHHHH
Confidence            777666655444433

>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=99.52  E-value=6.2e-15  Score=118.48  Aligned_cols=76  Identities=20%  Similarity=0.293  Sum_probs=69.2

Q ss_pred             ccceeeeecCCC-CccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHH--HhCCcEecCeeEEEEE
Q 012034          130 QGLNLYIKNLGD-SIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA--EMNGKMIVSKPLYVAV  206 (472)
Q Consensus       130 ~~~~l~V~nL~~-~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~--~l~g~~i~gk~l~V~~  206 (472)
                      .+++|||+|||. .+|+++|+++|+.||.|.++.++++     +|||||+|.+.++|.+|++  .+++..++|+.|+|.|
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~   91 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL   91 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEE
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEE
Confidence            456899999997 4899999999999999999999875     7899999999999999998  5788899999999999


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      ++++
T Consensus        92 s~~~   95 (99)
T d1x4fa1          92 SEKY   95 (99)
T ss_dssp             ECSC
T ss_pred             cCCc
Confidence            9765

>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=99.51  E-value=2.2e-14  Score=116.31  Aligned_cols=76  Identities=20%  Similarity=0.263  Sum_probs=69.1

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHh--CCcEecCeeEEEEEc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM--NGKMIVSKPLYVAVA  207 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l--~g~~i~gk~l~V~~a  207 (472)
                      .+.+|||+|||..+|+++|+++|+.||.|+++++.++     +++|||+|.+.++|..|++.+  ++..+.|++|+|.|+
T Consensus        14 ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s   88 (104)
T d1wexa_          14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEc
Confidence            4568999999999999999999999999999999865     789999999999999999987  456788999999998


Q ss_pred             ccH
Q 012034          208 QRK  210 (472)
Q Consensus       208 ~~k  210 (472)
                      ..+
T Consensus        89 ~~~   91 (104)
T d1wexa_          89 TSK   91 (104)
T ss_dssp             SSS
T ss_pred             CCC
Confidence            765

>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=99.49  E-value=1.3e-14  Score=119.32  Aligned_cols=84  Identities=19%  Similarity=0.368  Sum_probs=74.5

Q ss_pred             ccceeeeecCCCCccHHHHHHHHhccCceEEE-EEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v-~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      .+.+|||+|||+++|+++|+++|+.||.|..+ .+..+.+|.++|||||+|.+.++|.+|+ .+||..|+|+.|.|..+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al-~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHH-TSCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHH-HcCCCcCCCEEEEEEEcC
Confidence            45689999999999999999999999998764 4556678999999999999999999999 599999999999999998


Q ss_pred             cHHHHH
Q 012034          209 RKEERR  214 (472)
Q Consensus       209 ~k~~~~  214 (472)
                      .++...
T Consensus        96 ~~~~~~  101 (112)
T d1wela1          96 KKGMLE  101 (112)
T ss_dssp             HHHHHH
T ss_pred             hHHHHH
Confidence            776543

>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=99.49  E-value=9.7e-15  Score=118.31  Aligned_cols=76  Identities=20%  Similarity=0.207  Sum_probs=67.9

Q ss_pred             ccceeeeecCCCCccH-----HHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEE
Q 012034          130 QGLNLYIKNLGDSIDD-----EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV  204 (472)
Q Consensus       130 ~~~~l~V~nL~~~~t~-----e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V  204 (472)
                      ..++|||+||+.++..     ++|+++|+.||.|.++++++     +++||||+|.+.++|.+|++.|||..|+|++|+|
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v   78 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEE
Confidence            3468999999988733     56899999999999999986     4889999999999999999999999999999999


Q ss_pred             EEcccH
Q 012034          205 AVAQRK  210 (472)
Q Consensus       205 ~~a~~k  210 (472)
                      .|++.+
T Consensus        79 ~~a~~~   84 (104)
T d1weya_          79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             eecccC
Confidence            998644

>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=99.49  E-value=3.3e-14  Score=111.77  Aligned_cols=76  Identities=20%  Similarity=0.312  Sum_probs=68.2

Q ss_pred             ccceeeeecCCCC-ccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHh--CCcEecCeeEEEEE
Q 012034          130 QGLNLYIKNLGDS-IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM--NGKMIVSKPLYVAV  206 (472)
Q Consensus       130 ~~~~l~V~nL~~~-~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l--~g~~i~gk~l~V~~  206 (472)
                      .+.+|||+||+.. +|++||+++|+.||.|.++.++.+     +++|||+|++.++|..|++.+  ++..+.|++|+|.|
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~   81 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   81 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEE
Confidence            3457999999985 889999999999999999999876     679999999999999999965  67889999999999


Q ss_pred             cccH
Q 012034          207 AQRK  210 (472)
Q Consensus       207 a~~k  210 (472)
                      +++.
T Consensus        82 s~~~   85 (89)
T d1x4da1          82 SQKY   85 (89)
T ss_dssp             ECCC
T ss_pred             CCCc
Confidence            8753

>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=99.46  E-value=2.2e-14  Score=115.51  Aligned_cols=66  Identities=18%  Similarity=0.383  Sum_probs=59.6

Q ss_pred             cCCcceEEeCC--CCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccC
Q 012034           25 KTKFNNVFVKN--LDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD   95 (472)
Q Consensus        25 ~~~~~~l~V~n--Lp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~   95 (472)
                      ....++|||.|  ||.++|+++|+++|++||.|.++.+..+     +|||||+|++.++|.+|+++|||+.+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            45678899955  9999999999999999999999988765     789999999999999999999999873

>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=99.41  E-value=1.8e-13  Score=112.53  Aligned_cols=74  Identities=23%  Similarity=0.254  Sum_probs=65.1

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCH-HHHHHHHHHhCCcEecCeeEEEEEcccH
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTP-EEASRALAEMNGKMIVSKPLYVAVAQRK  210 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~-~~A~~Ai~~l~g~~i~gk~l~V~~a~~k  210 (472)
                      ..+||+||++++|+++|+++|++||.|.+|.|+++     +|||||+|.+. ++|..|+..+++..+.++.+.|.++..+
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence            34599999999999999999999999999999875     89999999985 7899999999999888777777766544

>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=99.36  E-value=5.4e-15  Score=116.75  Aligned_cols=73  Identities=18%  Similarity=0.338  Sum_probs=64.5

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeC------CCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEE
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD------PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA  205 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~------~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~  205 (472)
                      ..|||+|||.++|+++|+++|+.||.|..+.+...      ..+.++|||||+|.+.++|.+|+ .|||..+.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            36999999999999999999999998877665432      35678999999999999999998 599999999999996

>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=99.36  E-value=3.1e-13  Score=108.30  Aligned_cols=81  Identities=19%  Similarity=0.320  Sum_probs=69.3

Q ss_pred             cCCcceEEeCCC--CCCCC---------HHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCc
Q 012034           25 KTKFNNVFVKNL--DESTT---------DEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKK   93 (472)
Q Consensus        25 ~~~~~~l~V~nL--p~~~t---------ee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~   93 (472)
                      .+..++|+|+|+  |.++.         +++|++.|++||.|.+|.+..+   +.+|||||+|++.++|.+|++.|||..
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            356788999998  55432         3689999999999999988665   457999999999999999999999999


Q ss_pred             cCCcceeeeccccch
Q 012034           94 FDDREWYVGKAQKKS  108 (472)
Q Consensus        94 i~g~~l~V~~a~~~~  108 (472)
                      ++|+.|.|.++..+.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999886554

>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=99.36  E-value=5.7e-13  Score=107.08  Aligned_cols=64  Identities=27%  Similarity=0.464  Sum_probs=58.0

Q ss_pred             ccceeeeec--CCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec
Q 012034          130 QGLNLYIKN--LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV  198 (472)
Q Consensus       130 ~~~~l~V~n--L~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~  198 (472)
                      ...+|||.|  |+.++|+++|+++|++||.|+++.+..+     ++||||+|.+.++|.+|+..|||+.+.
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            345788865  9999999999999999999999998875     789999999999999999999999873

>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=99.34  E-value=4.8e-13  Score=102.86  Aligned_cols=74  Identities=20%  Similarity=0.244  Sum_probs=63.1

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcc-eeeecccc
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDRE-WYVGKAQK  106 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~-l~V~~a~~  106 (472)
                      .+.|+|.+||.+++++.| +.|++||+|.++.+.     +++|||||+|.+.++|++||+ +||..|+|+. |.|..+..
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~-----~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS-----NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC-----SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec-----CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            466999999999987655 579999999998764     457999999999999999996 8999999985 67888876


Q ss_pred             ch
Q 012034          107 KS  108 (472)
Q Consensus       107 ~~  108 (472)
                      +.
T Consensus        77 k~   78 (81)
T d1wwha1          77 KN   78 (81)
T ss_dssp             HH
T ss_pred             hh
Confidence            54

>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=99.30  E-value=3e-12  Score=102.44  Aligned_cols=78  Identities=22%  Similarity=0.311  Sum_probs=67.1

Q ss_pred             ccceeeeecC--CCCc---------cHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEec
Q 012034          130 QGLNLYIKNL--GDSI---------DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV  198 (472)
Q Consensus       130 ~~~~l~V~nL--~~~~---------t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~  198 (472)
                      .+.+|+|+|+  +.++         .++||++.|++||.|..+++..+   ..+|||||+|.+.++|.+|+..|||+.++
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            3458999998  4432         23789999999999999998765   46899999999999999999999999999


Q ss_pred             CeeEEEEEcccH
Q 012034          199 SKPLYVAVAQRK  210 (472)
Q Consensus       199 gk~l~V~~a~~k  210 (472)
                      |++|.|.++..+
T Consensus        84 gr~i~v~~~~g~   95 (99)
T d2dita1          84 GRQITAQAWDGT   95 (99)
T ss_dssp             TEECEEEECCSC
T ss_pred             CEEEEEEEeCCc
Confidence            999999998654

>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=99.24  E-value=1.1e-11  Score=95.09  Aligned_cols=75  Identities=13%  Similarity=0.150  Sum_probs=64.0

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCee-EEEEEccc
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKP-LYVAVAQR  209 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~-l~V~~a~~  209 (472)
                      .+-|+|.++|.+.+++.| ++|++||.|.++++.++     +|||||+|.+.++|.+|+ .+||..++|+. |.|..+..
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~-----~~~~fV~f~~~~~A~~Al-~~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS-----SSEEEEEESSHHHHHHHH-TTTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC-----CCEEEEEEcccHHHHHHH-hcCCCeECCcEEEEEEeCCC
Confidence            346999999999987655 57999999999988653     799999999999999999 59999999974 67888877


Q ss_pred             HHH
Q 012034          210 KEE  212 (472)
Q Consensus       210 k~~  212 (472)
                      |..
T Consensus        77 k~~   79 (81)
T d1wwha1          77 KNV   79 (81)
T ss_dssp             HHH
T ss_pred             hhh
Confidence            653

>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=99.23  E-value=3.6e-12  Score=102.94  Aligned_cols=80  Identities=25%  Similarity=0.295  Sum_probs=68.4

Q ss_pred             CcceEEeCCC--CCCCC--------HHHHHHHHhcCCCeeEEEEEECCC---CCceeEEEEEeCCHHHHHHHHHHHCCCc
Q 012034           27 KFNNVFVKNL--DESTT--------DEDLKKIFGEYGTITSAVVMRDGD---GKSKCFGFVNFENADDAAKAVEALNGKK   93 (472)
Q Consensus        27 ~~~~l~V~nL--p~~~t--------ee~L~~~F~~fG~I~~v~i~~d~~---g~skG~aFV~F~~~e~A~~Av~~lng~~   93 (472)
                      ..+.|.|+|+  +.++.        .++|++.|++||.|.+|.|.++..   ..++|++||+|.+.++|.+|++.|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4677999999  55543        357899999999999999988643   3457999999999999999999999999


Q ss_pred             cCCcceeeecccc
Q 012034           94 FDDREWYVGKAQK  106 (472)
Q Consensus        94 i~g~~l~V~~a~~  106 (472)
                      ++||.|.|.+...
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999864

>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=99.23  E-value=7.1e-12  Score=101.14  Aligned_cols=81  Identities=17%  Similarity=0.316  Sum_probs=68.6

Q ss_pred             cceeeeecC--CCCc--------cHHHHHHHHhccCceEEEEEeeCCCC---CcccEEEEEcCCHHHHHHHHHHhCCcEe
Q 012034          131 GLNLYIKNL--GDSI--------DDEKLKELFSEFGTITSCKVMRDPSG---ISKGSGFVAFSTPEEASRALAEMNGKMI  197 (472)
Q Consensus       131 ~~~l~V~nL--~~~~--------t~e~L~~~F~~~G~I~~v~i~~~~~g---~s~g~afV~f~s~~~A~~Ai~~l~g~~i  197 (472)
                      +..|.|.|+  +.++        ..+||++.|++||.|++|.|.++.++   ...|++||.|.+.++|.+|+..|||+.+
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f   83 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   83 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCS
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEE
Confidence            457888998  4443        23689999999999999999887543   3568999999999999999999999999


Q ss_pred             cCeeEEEEEcccHH
Q 012034          198 VSKPLYVAVAQRKE  211 (472)
Q Consensus       198 ~gk~l~V~~a~~k~  211 (472)
                      +||.|.|.++....
T Consensus        84 ~gR~v~v~f~~~~~   97 (104)
T d1o0pa_          84 ANRVVVTKYCDPDS   97 (104)
T ss_dssp             SSSCCEEEEECHHH
T ss_pred             CCeEEEEEEcCHHH
Confidence            99999999987543

>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=97.65  E-value=0.00014  Score=51.73  Aligned_cols=61  Identities=21%  Similarity=0.276  Sum_probs=54.3

Q ss_pred             HHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEcc
Q 012034          146 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ  208 (472)
Q Consensus       146 e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a~  208 (472)
                      +.|.+.|+++|.|.++.+....+|..  .|-|...+.++|.-|+..||.+.|++|+|.|+++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            45667899999999999988766665  48999999999999999999999999999999874

>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=97.28  E-value=0.00049  Score=52.15  Aligned_cols=69  Identities=17%  Similarity=0.259  Sum_probs=57.9

Q ss_pred             cceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCC--C-CceeEEEEEeCCHHHHHHHHHHHCCCccCC
Q 012034           28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD--G-KSKCFGFVNFENADDAAKAVEALNGKKFDD   96 (472)
Q Consensus        28 ~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~--g-~skG~aFV~F~~~e~A~~Av~~lng~~i~g   96 (472)
                      .|+|.|++||..+||+++.+.++..|++........+.  + ..-.-|||.|.+.++.....+.++|+.+-+
T Consensus         1 ~tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           1 LSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CCEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             CceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            37899999999999999999999999988777776531  2 123579999999999999999999998754

>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=97.05  E-value=0.0007  Score=48.05  Aligned_cols=60  Identities=27%  Similarity=0.296  Sum_probs=52.3

Q ss_pred             HHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeeccc
Q 012034           44 DLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQ  105 (472)
Q Consensus        44 ~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a~  105 (472)
                      .|.+.|+++|.|.++.+..-.+|..  .|-|...+.++|..|+..|+...|++++|.|..+.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4456899999999999987666654  68899999999999999999999999999998764

>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=96.87  E-value=0.00058  Score=50.99  Aligned_cols=54  Identities=22%  Similarity=0.415  Sum_probs=48.1

Q ss_pred             HHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHCCCccCCcceeeecc
Q 012034           43 EDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKA  104 (472)
Q Consensus        43 e~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~lng~~i~g~~l~V~~a  104 (472)
                      .+|.+.|+.||+|.-|++..|       -..|+|.+-++|.+|++ +++..+.|+.|.|.-.
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            467788999999999999877       68999999999999996 8999999999998753

>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=96.79  E-value=0.0011  Score=49.44  Aligned_cols=54  Identities=17%  Similarity=0.372  Sum_probs=48.6

Q ss_pred             HHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhCCcEecCeeEEEEEc
Q 012034          146 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVA  207 (472)
Q Consensus       146 e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~g~~i~gk~l~V~~a  207 (472)
                      .+|.+.|+.||+|.=+++..+       -.+|+|.+-++|-+|+ .++|..+.|+.|.|+..
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al-~l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVL-DVDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHH-HGGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHh-ccCCeEEcceEEEEecC
Confidence            577889999999999999876       6899999999999998 79999999999999853

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.48  E-value=0.0052  Score=46.28  Aligned_cols=68  Identities=12%  Similarity=0.201  Sum_probs=56.6

Q ss_pred             ceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCC--CC-CcccEEEEEcCCHHHHHHHHHHhCCcEecC
Q 012034          132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP--SG-ISKGSGFVAFSTPEEASRALAEMNGKMIVS  199 (472)
Q Consensus       132 ~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~--~g-~s~g~afV~f~s~~~A~~Ai~~l~g~~i~g  199 (472)
                      ++|.|++||..+|++++.+.++..|.+........+  .+ ..-.-|+|.|.+.++.....+..+|+.+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            468999999999999999999999999887766543  11 223569999999999999999999998743

>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=95.03  E-value=0.023  Score=42.80  Aligned_cols=57  Identities=21%  Similarity=0.372  Sum_probs=47.5

Q ss_pred             CcceEEeCCCCCCCCHHHHHHHHhcCCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHHC
Q 012034           27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN   90 (472)
Q Consensus        27 ~~~~l~V~nLp~~~tee~L~~~F~~fG~I~~v~i~~d~~g~skG~aFV~F~~~e~A~~Av~~ln   90 (472)
                      .-..||.-.+|+.|...||.++|+.||.|.--+| .| +     -|||...+.|+|+.++..++
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd-T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD-T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET-T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC-c-----eEEEEecCHHHHHHHHHHhc
Confidence            3455999999999999999999999999875555 43 2     69999999999999987643

>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=89.02  E-value=0.54  Score=35.09  Aligned_cols=56  Identities=27%  Similarity=0.380  Sum_probs=44.8

Q ss_pred             cceeeeecCCCCccHHHHHHHHhccCceEEEEEeeCCCCCcccEEEEEcCCHHHHHHHHHHhC
Q 012034          131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN  193 (472)
Q Consensus       131 ~~~l~V~nL~~~~t~e~L~~~F~~~G~I~~v~i~~~~~g~s~g~afV~f~s~~~A~~Ai~~l~  193 (472)
                      ...+|.-..|..+...||.++|+.||.|.---| .|      --|||...+.++|..++..++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC------ceEEEEecCHHHHHHHHHHhc
Confidence            346899999999999999999999998753333 33      169999999999888876544